This episode features Prof. Emad El-Omar MD FRCP from the University of New South Wales in Sydney, Australia, speaking about a recent paper exploring the healthy microbiome concept, as well as the latest research on how the gut microbiome contributes to the pathophysiology of several diseases. Prof. El-Omar talked about research on H. pylori-induced disease in the stomach; it’s known that these bacteria decrease acid secretion, which shifts the gastric microbiology in a way that drives progression to cancer. Prof. El-Omar recently co-authored a review paper in Gut that addressed the definition of a healthy gut microbiome. Although a definition has not yet been established, progress is being made by studying healthy people such as centenarians around the world. The best approach may be to define a core microbiome signature that’s present across healthy phenotypes. The core is likely defined by the gut microbiome’s function, so diverse compositions may be able to support health. The paper authors emphasize that pursuing knowledge about what makes a healthy microbiome is a worthwhile pursuit, and they outline what research is necessary to make continued progress in this area. Validation and reproducibility are critical for moving toward clinical applications.

Episode abbreviations and links:

• Review article on the healthy microbiome concept, co-authored by Prof. El-Omar: What defines a healthy gut microbiome?

About Prof. Emad El-Omar MD FRCP:

Professor El-Omar graduated in Medicine from Glasgow University, Scotland, and trained as a gastroenterologist. He worked as a Visiting Scholar/Scientist at Vanderbilt University, TN, and National Cancer Institute, MD, USA, and was Professor of Gastroenterology at Aberdeen University, Scotland, for 16 years before taking up the Chair of Medicine at St George & Sutherland Clinical School, University of New South Wales, Sydney, Australia. He is the Editor in Chief of the journal Gut. His research interests include all aspects of the microbiome, inflammation driven GI cancer and IBD. He is the Director of the Microbiome Research Centre at UNSW/St George Hospital, Sydney.

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This episode features computational microbiologist Dr. Tarini Ghosh PhD from  Indraprastha Institute of Information Technology (Delhi, India) speaking about his recently published paper that proposes a novel Health-Associated Core Keystone (HACK) index for measuring a healthy microbiome. To create the index, the group used a huge volume of sequence data – over 201 terabytes – from more than 45,000 individuals with and without disease across different geographies. The ultimate aim is to create a universal measure for a health-associated microbiome. The HACK index is based on taxa in the gut microbiome, and consists of 3 components:  (1) prevalence and connectedness in the gut microbiome of healthy individuals, (2) longitudinal stability, and (3) association with disease. Keystone taxa were generally more prevalent / abundant in the gut microbiome but not always. The group is now working to connect the identified taxa to specific functions. In the future, this index may be used as a diagnostic tool, possibly to predict a positive response in clinical trials.

Episode abbreviations and links:

• Paper outlining the HACK index: Toward a health-associated core keystone index for the human gut microbiome.
• Review on defining normal microbiome references for global populations: Normal Gut Microbiomes in Diverse Populations: Clinical Implications

About Dr. Tarini Ghosh PhD:

Dr. Tarini Shankar Ghosh leads the Microbiome Informatics group at the Department of Computational Biology at the Indraprastha Institute of Information Technology – Delhi, India. His research focuses on mining global microbiome datasets using advanced statistical methods, machine learning, and deep learning to develop predictive models and indexes that can  facilitate formulation of novel microbiome-derived clinical end-points along with the development of generic and population-specific microbiome-derived diagnostics/therapeutics. His research includes identifying the global and cohort-specific markers of microbiome-resilience and disease, investigating the microbiome taxa associated with response to different therapies and cross-body-site microbiome associations.

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This episode features Dr. Céline Druart PhD of Pharmabiotic Research Institute (PRI) speaking about the role of regulatory science in the development of microbiome biomarkers. First, PRI’s Communication and Membership Manager Camille Bello briefly describes the work of the PRI in supporting the development of therapeutic and diagnostic products derived from microbiome science. Regulation is important to protect consumers and reward innovation, and the development of biomarkers that predict response to treatment, for example, can help move toward personalized medicine. Dr. Druart notes many potential microbiome-based biomarkers have emerged but none have been successfully validated to date. Regulation always follows innovation, and regulatory science is important because it helps regulatory frameworks evolve. A recent Delphi consensus paper co-authored by Dr. Druart acknowledges that biomarker development is a complex process and that a particular challenge is the lack of validation of analytical methods for measuring the microbiome. However, it’s important to remember that techniques can continue to improve even after they’ve been validated. Dr. Druart argues that biomarker validation needs public-private collaborations to design and execute the large clinical studies that are necessary.

Episode abbreviations and links:

• Recent paper co-authored by Dr. Druart: State of the art and the future of microbiome-based biomarkers: a multidisciplinary Delphi consensus
• PRI website: https://pharmabiotic.org/
• PRI LinkedIn page: https://www.linkedin.com/company/pharmabiotic-research-institute-pri
• PRI conference, February 3–5, 2026: https://www.pharmabioticsevent.com/

About Dr. Céline Druart PhD:

Céline Druart obtained her PhD in Biomedical and Pharmaceutical Sciences from UCLouvain (Belgium) in 2014. Following a 3-year project in Patrice Cani’s research group focused on developing the potential beneficial effects of a human gut commensal Akkermansia muciniphila, she worked for 3 years at A-Mansia Biotech (now known as The Akkermansia Company), responsible for clinical programs, regulatory affairs and IP dossiers, as the Scientific and Business Project Manager. Céline joined the PRI in July 2021 as Microbiome Project Manager, managing the Regulatory Science activities of the Association, coordinating Task Group work, and supporting PRI Industry Members in their development planning. She became the PRI’s Executive Director in January 2024.

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This episode features Raphaela Joos from University College Cork in Ireland, speaking about efforts by the Human Microbiome Action Consortium to create an expert-led consensus around the concept of a healthy human microbiome. Ms. Joos, a PhD student who was first author of the resulting paper, notes that a healthy human microbiome can be defined at many different levels. Some parameters such as diversity and resilience are good for a microbial community, and other parameters such as antimicrobial resistance are good for the microbial community but not necessarily good for the host. Another challenge with the definition was how to define health. The group decided that the definition of healthy microbiome needed to be more inclusive than just the microbiome of a healthy person with no disease diagnoses. At present, causality is not clear so we don’t know whether disease-associated microbiomes are adaptive or are driving the disease. The main consensus that emerged from this expert discussion was that more data are needed, tracking large cohorts of people over time in many geographical areas. Only in this way will it be possible to overcome individual variability and truly identify the robust features of a healthy microbiome. Different microbiome compositions can have similar functional capacities, so possibly a functional signature will emerge.

Episode abbreviations and links:

• Perspective paper by Human Microbiome Action Consortium, first authored by Joos: Examining the healthy human microbiome concept

About Raphaela Joos:

Born and bred in Germany, I obtained my BSc in Psychology with a focus on biological neuropsychology, nutrition and statistics at Leiden University and the University of Melbourne. Fascinated by nutritional science and its impact on mental health, I then pursued a MSc on the topic of Microbiome in Health and Disease at King’s College London, delving into microbiology, bioinformatics and microbiome science. After the masters I moved to Cork for a research assistant position investigating the structure and infection mechanisms of bacteriophages involved in cheese fermentation using the protein-folding software AlphaFold. Before starting my PhD, I worked as a project manager under Prof Paul Ross and Prof Aonghus Lavelle on the Human Microbiome Project, organising a workshop featuring international leaders in microbiome research to establish a roadmap to define a healthy microbiome. My PhD now focuses on investigating the role of the infant microbiome in development, applying statistical modelling strategies to integrate functional microbiome data with clinical data.

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This episode features Dr. Gianluca Ianiro MD PhD, a gastroenterologist from the Fondazione A. Gemelli IRCCS and Università Cattolica del Sacro Cuore in Rome (Italy), speaking about how to advance gut microbiome testing for use in medicine. His interest in the gut microbiome began with the clinical observation that fecal microbiota transplantation (FMT) was remarkably successful at curing recurrent C. difficile infection – and from there, he began a program of research on FMT. Current gut microbiome tests are widely variable and don’t provide any clinically relevant information, but some people do them out of curiosity. Over the years it’s become increasingly clear that gut microbiome testing must be standardized to move toward clinical utility. Dr. Ianiro co-authored a recent consensus paper on the challenges of gut microbiome testing and how to move toward standardization. He describes several initiatives that aim to standardize and validate gut microbiome testing, from sample collection to analysis. Dr. Ianiro says promising data exist for gut microbiome testing to predict colorectal cancer, to predict the response to some cancer treatments, and to diagnose inflammatory bowel disease. The field is moving toward some important factors that define a microbiome as “healthy”, but these need to be associated with a clear health outcome if they’re eventually to be used in clinical practice.

Episode abbreviations and links:

• Consensus paper on microbiome testing, co-authored by Dr. Ianiro: International consensus statement on microbiome testing in clinical practice
• “Healthy microbiome” consensus paper by Human Microbiome Action: Examining the healthy human microbiome concept
• Article by Liping Zhao on microbial guild-based analysis of the gut microbiome: Guild-based analysis for understanding gut microbiome in human health and diseases
• Paper from Zitvogel lab on gut microbiome to predict cancer treatment response: Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors
• Two papers on gut microbiome testing for identifying colorectal cancer: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation, Association of distinct microbial signatures with premalignant colorectal adenomas
• Paper on gut microbiome testing for identifying inflammatory bowel disease: Noninvasive, microbiome-based diagnosis of inflammatory bowel disease

About Dr. Gianluca Ianiro MD PhD:

Gianluca Ianiro is a gastroenterologist at the Digestive Disease Center of the Fondazione A. Gemelli IRCCS and adjunct professor in gastroenterology at the Università Cattolica del Sacro Cuore in Rome, Italy.

He has since gone on to establish himself as a key clinical and translational investigator focusing mainly in the field of intestinal microbiota, and has received several research grants in support of his innovative research. His current research is focused mainly on disentangling the rules of donor microbiome engraftment, on investigating microbiome diagnostics and therapeutics in noncommunicable disorders (including cancer), and on bringing microbiome into clinical practice.

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In this episode, the ISAPP hosts discuss human milk and the infant gut with Dr. Simone Renwick PhD from Mother-Milk-Infant Center of Research Excellence (MOMI CORE) at UC San Diego, USA. Dr. Renwick talks about her work investigating how communities of microbes versus individual microbes in the infant gut metabolize human milk oligosaccharide (HMO) structures, and what we know about the origin and functions of the microbes contained in human milk.

Key topics from this episode:

• Dr. Renwick studies how components of human milk foster the development of the infant gut microbiota. These components include HMOs (special sugars found in human milk) and the milk microbiota.
• HMOs cannot be metabolized by the human body, but when microbes in the infant gut break them down, it has health benefits for the infant (because infants who receive no human milk are predisposed to a range of diseases).
• Dr. Renwick used in vitro models to mimic infant microbiota communities, and found that these communities rapidly degraded the HMOs. This metabolism increased microbes associated with health and suppressed potentially pathogenic microbes. 
• Although most research on HMOs focuses on bifidobacteria that are specially equipped to break them down, she looked at individual strains within the infant gut community and found approximately 100 species capable of directly degrading HMOs.
• Once breastfeeding ceases, some microbes in the infant gut adapt to different sources of sugars, but others greatly decrease in abundance.
• Microbes act differently in a community than on their own. Within a complex community, microbes that are better equipped to degrade the HMOs will act quickly, producing byproducts that are then are available to other members.
• All of the different in vitro models have their advantages and disadvantages. The spatial relationships of the human body are often missing in in vitro models.
• Humans appear to have the highest concentration of milk oligosaccharides of any mammal.
• The milk microbiota is another active area of investigation. Live microbes are present in the mammary gland, but their source is still unknown. They tend to resemble the composition of the microbiota on the skin as well as the infant oral cavity, but curiously, anaerobic bacteria are also found in the milk microbiota. Somehow these microbes may move from the mother’s gut to the milk. These microbes may not directly metabolize HMOs. (See this paper.)
• Formula companies are beginning to put HMO structures into their products – mainly 2′-Fucosyllactose.

Episode links:

• Human milk oligosaccharides — Prebiotics in a class of their own? ISAPP webinar.
• The many functions of human milk oligosaccharides: A Q&A with Prof. Ardythe Morrow. ISAPP blog.
• Bifidobacteria in the infant gut use human milk oligosaccharides: how does this lead to health benefits? ISAPP blog.

About Dr. Simone Renwick PhD:

Dr. Simone Renwick is the Milk & Microbes postdoctoral fellow at the Mother-Milk-Infant Center of Research Excellence (MOMI CORE) at the University of California, San Diego, USA. Her research focuses on understanding the role of human milk components, such as the human milk oligosaccharides (HMOs) and milk microbiota, in fostering the developing infant gut microbiota. She is also interested in the potential therapeutic applications of milk components in diseases that affect adults. Currently, Simone is supervised by Drs. Lars Bode, Rob Knight, Pieter Dorrestein, and Jack Gilbert. Prior to her postdoc, Simone completed her PhD in Molecular and Cellular Biology (MCB) at the University of Guelph, Canada, under the supervision of Dr. Emma Allen-Vercoe.

She was the recipient of the Students and Fellows Association poster prize at the ISAPP 2023 meeting in Sitges, Spain.

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This episode features Dr. Anissa Armet PhD RD from the University of Alberta in Canada, speaking about the impact of diet on both the gut microbiota and overall health. Dr. Armet, a registered dietitian and researcher, says the Western diet along with the associated gut microbiome changes have played a role (amongst other things) in the rise of autoimmune diseases in industrialized societies. Dr. Armet describes a recent dietary study she and her collaborators published, for which they created a very high fiber diet called the Non-Industrialized Microbiome restore (NiMe, pronounced “nee mee”) diet. They created recipes and meal plans based on what some non-industrialized populations in the world typically consume, which included 45 grams of dietary fiber per day, and only small portions of animal proteins and dairy products. The participants in this controlled feeding trial saw substantial cardiometabolic benefits as well as certain changes in the gut microbiota after three weeks on the diet. Interestingly, the diet initially reduced the diversity of participants’ gut microbiota, likely because of increased pH in the gut, but diversity rebounded toward the end of the trial. The researchers also introduced a strain of L. reuteri isolated from the gut microbiota of people in a non-industrialized society, to observe whether it would engraft since the diet was known to contain growth substrates for the bacteria. Although the strain did not engraft in the gut microbiota (except in one participant), the health benefits of the diet overall were still observed. The researchers concluded that the NiMe diet can be used to target the gut microbiome and change community characteristics that are relevant for health.

Episode abbreviations and links:

• Dr. Armet’s Instagram account
• Published study on the NiMe diet (called the “restore diet” in the publication): Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation
• Previous research in Papua New Guinea, which informed the NiMe diet: The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes
• Review on how the gut microbiome informs knowledge about healthy dietary patterns: Rethinking healthy eating in light of the gut microbiome
• New publication from another research group, which complements the NiMe study findings: Immune and metabolic effects of African heritage diets versus Western diets in men: a randomized controlled trial
• Downloadable NiMe diet book: The NiMe Diet: Scientific Principles and Recipes

About Dr. Anissa Armet PhD RD:

Dr. Anissa Armet is a Registered Dietitian and postdoctoral researcher at the University of Alberta. Anissa completed her PhD in Nutrition and Metabolism in March 2024, then transitioned into her postdoc to research the effects of microbiome-targeted dietary interventions in inflammatory bowel diseases. She uses machine learning to determine if the gut microbiome predicts clinical responses in the context of precision nutrition. Anissa has authored several peer-reviewed publications, including a review on healthy eating in light of the gut microbiome and a dietary intervention trial on microbiome restoration. Being equally passionate about knowledge translation, Anissa co-authored an award-winning, open-access, high-protein cookbook designed to support muscle health, is currently developing a plant-based version, and recently co-authored an open-access ebook, The NiMe Diet: Scientific Principles and Recipes.

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This episode features Prof. Yves Desjardins PhD from Laval University in Canada. Prof. Desjardins, an agrologist by training, explains that polyphenols are metabolites synthesized by plants and present in the plant foods we consume. When humans consume polyphenols, we absorb a small fraction (around 5%) of them in the upper gastrointestinal tract, but most of them reach the colon and interact in various ways with the gut microbiota. They have two main effects in the gut, which appear somewhat contradictory: antibacterial effects and a prebiotic-like effect. In the latter case, polyphenols interact with the host epithelium to induce mucin production, creating a niche for certain bacteria to grow. Typical bacteria that increase under these circumstances are bifidobacteria and Akkermansia muciniphila. In these ways, polyphenols have an impact on certain microorganisms and on the microbiome as a whole. In the future, supplements with polyphenols and fiber may be designed to help manipulate the microbiome in a certain way. Currently there are many health benefits associated with polyphenols. The primary benefit is for cardiometabolic health, and some studies also show benefits for cognition.

Episode abbreviations and links:

• Paper proposing the term duplibiotic: Polyphenol-Mediated Gut Microbiota Modulation: Toward Prebiotics and Further
• COSMOS trial on cocoa polyphenols for preventing cardiovascular events and mortality: Effect of cocoa flavanol supplementation for the prevention of cardiovascular disease events: the COcoa Supplement and Multivitamin Outcomes Study (COSMOS) randomized clinical trial
• Study from Desjardins lab on how cranberry polyphenols protect mice against an obesogenic diet: A polyphenol-rich cranberry extract protects from diet-induced obesity, insulin resistance and intestinal inflammation in association with increased Akkermansia spp. population in the gut microbiota of mice
• 2025 paper on how polyphenols are mechanistically connected to metabolic health: Therapeutic Potential of Cranberry Proanthocyanidins in Addressing the Pathophysiology of Metabolic Syndrome: A Scrutiny of Select Mechanisms of Action
• Study on how polyphenols can influence host infections: UPEC Colonic-Virulence and Urovirulence Are Blunted by Proanthocyanidins-Rich Cranberry Extract Microbial Metabolites in a Gut Model and a 3D Tissue-Engineered Urothelium
• Study on how berry polyphenols can improve cognition in people with mild cognitive impairment: Effects of a polyphenol-rich grape and blueberry extract (Memophenol™) on cognitive function in older adults with mild cognitive impairment: A randomized, double-blind, placebo-controlled study

About Prof. Yves Desjardins PhD:

Yves Desjardins is a full professor at the Institute of Nutrition and Functional Foods, Laval University, Québec, Canada. He holds the NSERC/Symrise Partnership Chair on the prebiotic effects of polyphenols (PhenoBio+). Trained in plant physiology, his research focuses on the phytochemistry and functionality of plant bioactives. He has led numerous preclinical and clinical studies on type-2 diabetes, cognitive decline, inflammation, and infections. His current work explores the impact of tannins on gut microbiota, mucosal immunity, and gut barrier function. He has collaborated with the food industry to validate the health benefits of horticultural products (e.g., Urophenol, Glucophenol, Neurophenol). Recognized for his innovative research on fruit polyphenols, he chaired the first International Symposium on Health Effects of Fruits and Vegetables (FAVHEALTH 2005), the OECD Symposium in Lisbon (2010), and organized the 2017 International Congress on Polyphenols and Health in Québec City.

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This episode features Dr. Vanessa Leone PhD from the University of Wisconsin – Madison on how gut microbes and eating patterns impact the host circadian system and overall health. In mouse models, Dr. Leone has found that in a 24-hour period, minor changes occur in the composition of the gut microbiota, while more important changes occur in gut microbiota function (that is, metabolite production). However, these changes depend on the type of diet and the timing of meal consumption. Metabolic health is also affected by this interplay. In humans, obesity is correlated with loss of microbiota rhythmicity, although causality remains unclear. One study by Dirk Haller found that a loss of rhythmicity helped predict which people with prediabetes would progress to diabetes. Constantly shifting timezones (or shifting between day and night shifts) appears to be more detrimental to metabolic health than maintaining a constant schedule, and research is ongoing about what might mitigate these effects. In this field of research it’s important to consider people’s chronotype: their tendency to rise early versus stay up late. In the future, Dr. Leone hopes to untangle more about how different factors affect metabolic health: diet, gut microbiota, and the circadian system.

Episode abbreviations and links:

• Paper from the lab of Dirk Haller showing that 13 OTUs lost rhythms in those with prediabetes, predicting who might develop diabetes: Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes
• Review paper: Daily Eating Patterns and Their Impact on Health and Disease
• Paper on the importance of timing in microbiome sample collection: Time of sample collection is critical for the replicability of microbiome analyses
• University of Wisconsin – Madison Leone Lab webpage

About Dr. Vanessa Leone PhD:

Vanessa A. Leone, Ph.D. is an Assistant Professor in the Department of Animal & Dairy Sciences at the University of Wisconsin-Madison, where she also obtained a Ph.D. She performed postdoctoral studies and was an Instructor of Medicine at the University of Chicago in the Section of Gastroenterology, Hepatology, & Nutrition where she examined how the gut microbiome impacts complex metabolic  diseases. Dr. Leone currently studies how day vs. night oscillatory patterns of gut microbes influence the body’s internal clock and metabolism. She hopes to mechanistically define what constitutes a microbial oscillator versus a non-oscillator, examine how host factors impact the broader diurnal structure and functional outputs of the gut microbiome, and to determine how microbial oscillations impact host metabolism. These findings will likely pave the way to identify how timed delivery of pre-, pro-, or postbiotics can be leveraged to promote a balanced gut microbiota and improve host health.

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This episode features Prof. William Chen from Nanyang Technological University in Singapore, speaking with the ISAPP hosts about precision fermentation. In Singapore, enhancing national food security is of interest and one of the technologies used to achieve this is precision fermentation. Prof. Chen describes the differences between traditional fermentation, biomass fermentation, and precision fermentation. In precision fermentation, food scientists use genetically modified microorganisms to produce a food ingredient of interest. In some cases the product is secreted out of the cell, and in other cases it must be extracted from the cell. The approach has great potential to bypass the need for a large amount of land to produce food, and may reduce costs associated with food production. As this approach continues to develop, education and transparency with consumers is key. Regulatory frameworks and approval processes differ from country to country, and this is an area that will continue to evolve in the years ahead as more food ingredients or other useful products are generated.

Episode abbreviations and links:

• Review: Precision fermentation to advance fungal food fermentations

About Prof. William Chen PhD:

William Chen is the Michael Fam Endowed Professor and Director of Food Science & Technology Programme at Nanyang Technological University Singapore. He is concurrently Director of Singapore Future Ready Food Safety Hub (FRESH). He is also Director of Singapore Agri-food Innovation Lab.

Professor Chen is active in securing and leading large competitive research grants from major government agencies as well as leading international food companies. His food technology innovations have been extensively attracting global attention. His views on food tech innovations, food safety and food security have been regularly covered by major local and international media outlets. He is also advisor/consultant to overseas universities, Singapore government agencies, food industry, and international organizations (ADB, FAO, WHO among others).

In this second special episode about ISAPP’s annual meeting, held in Banff (Canada) in July 2025, Executive Director Marla Cunningham introduces the four highest-scoring posters from the poster session. Four speakers, all members of the ISAPP Students and Fellows association (SFA), join the podcast to describe the work they presented via poster at the meeting:

• Benjamin Levine (University of Illinois Urbana-Champaign, USA): Individual intestinal motility responses to acute whole-grain prebiotic ingestion mediates post-prandial nutrient metabolism: a single-blind randomized controlled clinical trial
• Caroline Dricot (University of Antwerp, Belgium): Isala citizen-science study: navigating the vaginal microbiome’s metabolic landscape
• Ceylon Simon (University College Cork and APC Microbiome Ireland; fellow in the Marie Skłodowska-Curie Actions “Cell Envelope Anti-Bacterials”, or CLEAR, Doctoral Network): Targeted microbiome editing using a novel bacteriophage-derived endolysin with lytic activity against C. difficile 
• Dr. Qinnan Yang, PhD (University of Michigan, USA): Synergistic interaction of Akkermansia muciniphila and mucin-degrading Bacteroides in Inflammatory bowel diseases

Episode abbreviations and links:

• The ISAPP Annual Meeting Program Guide, with abstracts for each poster presentation

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This episode features Dr. Abigail (Abbey) Thiel PhD, who works remotely (from the US) with Wageningen University to manage a project focused on developing animal-free milk proteins using precision fermentation. Dr. Thiel explains that the motivation for the project is to find alternatives to animal-produced foods using microorganisms to produce key components of dairy products. Her project focuses on producing the protein casein, which is found in milk (and contributes to its structure and stability), to eventually produce a milk substitute or a protein powder that could be used as a food ingredient. A specific yeast is used to produce the casein: the scientists insert directions for making the protein into the yeast, then put it in a bioreactor to produce the protein. After that, they figure out how to purify the protein so it can be used in various applications. The final step is upscaling the process to produce abundant and cost-effective casein. The group has also started initial digestion studies to see how the purified casein is digested. Meanwhile, Dr. Thiel is passionate about food science communication and has a YouTube channel called Abbey the Food Scientist, where she strives to build awareness of food science as a career and also to address myths about food science.

Episode abbreviations and links:

• Book co-edited by Dr. Thiel: Careers in Food Science
• Abbey the Food Scientist YouTube channel

About Dr. Abigail Thiel PhD:

Abigail (Abbey) Thiel is a food scientist, educator, and project manager of research focused on producing milk proteins using yeast. She earned her PhD in Food Science from the University of Wisconsin-Madison and later worked as a postdoctoral researcher at Wageningen University & Research in the Netherlands. Abbey is passionate about making the science behind food accessible to all. She runs a successful YouTube channel with over 1.4 million views, breaking down food science concepts for everyday audiences, and created an online course, Food Science for Beginners. In addition, she develops high school curriculum and educational resources to help students explore food science as a career path.

Continuing in the series on the latest fermented food science, we are highlighting Episode 9 from our archives. In this episode, the ISAPP hosts talk about fermented foods and non-human primates with Katie Amato of Northwestern University, USA. Amato describes what she has learned from studying the gut microbiota of non-human primates and how it relates to our understanding of human and gut microbial co-evolution over time. She also talks about non-human primate behaviors around fermented foods and what they might tell us about the need for human fermented food consumption.

Key topics from this episode:

• A list of species categorized as non-human primates.
• Changes in the gut microbiota of primates depend on habitats and available food across different seasons.
• Primates in captivity have a different gut microbiota from wild ones – for example, animals kept in the zoo have a lower gut microbiota diversity.
• Fermentation as a process to improve access to nutritional components of food; knowledge about primates’ use of fermentation and their gut microbes can tell us something about early human evolution.
• Primates may derive benefits from using fermented foods. Consumption of fermented foods (overripe fruits) by primates is linked to certain habitats and climate factors; some non-human primates appear to intentionally leave fruits to ferment before returning to consume them.
• There are benefits to translating the knowledge obtained from studying gut microbiota of primates to humans. 

Episode abbreviations and links:

Dissertation study: The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra)

Study: Fermented food consumption in wild nonhuman primates and its ecological drivers

Mentors mentioned: Kathy Cottingham, Matt Ayres, David Peart, John Gilbert, Mark McPeek, Craig Layne, Rob McClung.
Steve Ross, Alejandro Estrada, Paul Garber, Angela Kent, Rod Mackie, Steve Leigh, Rob Knight.

Additional resources:

Research on the microbiome and health benefits of fermented foods – a 40 year perspective. ISAPP blog
New ISAPP-led paper calls for investigation of evidence for links between live dietary microbes and health. ISAPP blog

About Assoc. Prof. Katie Amato:

Dr. Amato is a biological anthropologist at Northwestern University studying the influence of gut microbes on host ecology and evolution. Her research examines how changes in the gut microbiota impact host nutrition, energetics, and health. She uses non-human primates as models for studying host-gut microbe interactions in selective environments and for providing comparative insight into the evolution of the human gut microbiota. Her main foci are understanding how the gut microbiome may buffer hosts during periods of nutritional stress and how the gut microbiome programs normal inter-specific differences in host metabolism. Dr. Amato is the President of the Midwest Primate Interest Group, an Associate Editor at Microbiome, an Editorial Board member at Folia Primatologica, and a Fellow for the Canadian Institute of Advanced Research’s ‘Humans and the Microbiome’ Program.

This episode features Dr. Paul Cotter PhD of TEAGASC in Ireland, talking about the creation of fermented foods and how they can lead to health benefits. A huge array of foods can be fermented, and historically fermentation was used to extend the shelf life of a food that people had an abundance of. Dr. Cotter’s work in the field originally started with a bacteria-killing bacteriocin that had been isolated from kefir, and later moved toward the microbes in fermented foods. Currently he’s interested in comparing the artisanal approach to fermented foods, which leads to somewhat unpredictable results in the final products, with the industrial approach, which leads to more consistent results. In different artisanal fermented foods, which strains are common and which are unique? Potentially some of the strains can be used to confer a health benefit, and even a benefit that’s personalized to an individual. Dr. Cotter sees the role of fermented foods as possibly targeting pre-disease rather than disease if their ability to confer health benefits can be unravelled further.

Episode abbreviations and links:

• Paper in Cell showing huge microbial diversity in foods: Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome
• DOMINO research project website

Additional resources:

ISAPP infographic: Fermented foods

About Dr. Paul Cotter PhD:

Prof Paul Cotter is the Head of Food Biosciences at Teagasc (the Irish Agriculture and Food Development Authority), is a Principal Investigator with the large Irish Research Centres, APC Microbiome Ireland, VistaMilk and Food for Health Ireland and head of microbiology/co-founder of SeqBiome, a microbiome sequencing and bioinformatics service provider. He is a molecular microbiologist, with a particular focus on the microbiology of foods (especially fermented foods), the food systems and of humans, as well as probiotics and postbiotics. Prof Cotter is the author of >400 peer-reviewed, was included in the Clarivate list of highly cited researchers for 2018-2024, received an honorary doctorate from the University of Antwerp in 2024 and is the Field Chief Editor of Frontiers in Microbiology.

In this episode, Prof. Christophe Courtin PhD from KU Leuven in Belgium discusses the potential of fermented foods to provide health benefits and create more sustainable food systems. His work focuses in particular on fermenting cereal grains as a way to create products with better properties or enhanced health impact. Fermentation is a form of food processing that can introduce benefits beyond the raw materials used. Prof. Courtin leads HealthFerm, a European project with the aim of generating research on fermentation that supports a transition to more plant-based products in the diet, using wheat, oats, fava bean, and yellow pea. Fermentation can be scaled up both in industrialized countries and in developing countries. More intervention studies are needed to find out the health-promoting components of fermented foods and their mechanisms – although scientists know a fair amount about yogurt and other fermented dairy products, evidence is needed for other types of fermented foods. This episode is part of our series on the latest fermented food science.

Episode abbreviations and links:

• Review on sourdough bread fermentation: Wheat Sourdough Breadmaking: A Scoping Review
• HealthFerm project website
• Paper establishing a link between live dietary microbes and health benefits: Positive Health Outcomes Associated with Live Microbe Intake from Foods, Including Fermented Foods, Assessed using the NHANES Database

Additional resources:

ISAPP blog post: Food of the future: Fermented and sustainable

About Prof. Christophe Courtin PhD:

Prof. Christophe Courtin is a full professor at the Laboratory of Food Chemistry and Biochemistry at KU Leuven, Belgium. His research focuses on cereal constituents, the enzymes that degrade them and microorganisms in cereal processing. The emphasis is on a basic understanding of the structure and properties of these constituents as well as on their technological and health functionality in cereal-based processes and products. Expertise and an extensive network in this area have been built up through over 40 supervised PhDs, projects and national and international collaborations. He coordinates HealthFerm, a 23 partner Horizon Europe project. He is author of 350 peer-reviewed papers (WoS h-index: 69) and inventor on 12 patent families. Recent awards are the Harald Perten Prize (ICC, 2021) and the Belfort Lecture Award (Whistler Centre for Carbohydrate Research, Purdue University, 2023).

Continuing in the series on the latest fermented food science, we are highlighting Episode 3 from our archives. The hosts continue their discussion of fermented foods with Prof. Bob Hutkins, University of Nebraska – Lincoln. Prof. Hutkins elaborates on how the microbes associated with fermented foods may confer health benefits, as well as how food scientists choose strains for fermentation. He emphasizes how the live microbes in fermented foods differ from probiotics. Before listening to this episode, it’s recommended that you check out The science of fermented foods, Part 1. 

Key topics from this episode:

• Why working in the field of fermented foods is exciting and rewarding
• The challenges for scientists, especially when it comes to designing clinical studies with various fermented foods
• The benefits of fermented foods – from being safe as well as nutritious, to the health benefits that live microbes present in the foods can provide
• How microbes are selected for fermentation; companies focus on strain performance – i.e., good growth and survival to preserve the food and provide a desired flavor and texture
• The activities of live microbes present in fermented foods, from initiating the fermentation process to benefiting human health
• The differences between probiotics and live microbes in fermented foods
• How live microbes in fermented foods might affect your gut microbiota and why some scientists believe that fermented foods are important for getting regular doses of live microbes

Episode links:

• Microbiology and Technology of Fermented Foods, 2nd Ed., by Robert W. Hutkins
• The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods
• The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic
• Gut-microbiota-targeted diets modulate human immune status, study by Stanford researchers

Additional resources:

• Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics.
• Postbiotics. ISAPP infographic
• Fermented foods. ISAPP infographic
• What are fermented foods? ISAPP video
• Do fermented foods contain probiotics? ISAPP blog post
• How are probiotic foods and fermented foods different? ISAPP infographic
• Are fermented foods probiotics? Webinar by Mary Ellen Sanders, PhD

About Prof. Bob Hutkins:

Bob Hutkins is the Khem Shahani Professor of Food Microbiology at the University of Nebraska. He received his Ph.D. from the University of Minnesota and was a postdoctoral fellow at Boston University School of Medicine. Prior to joining the University of Nebraska, he was a research scientist at Sanofi Bio Ingredients.

The Hutkins Lab studies bacteria important in human health and in fermented foods. His group is particularly interested in understanding factors affecting persistence and colonization of probiotic bacteria in the gastrointestinal tract and how prebiotics shift the intestinal microbiota and metabolic activities. The lab also conducts clinical studies using combinations of pro- and prebiotics (synbiotics) to enhance health outcomes. More recently we have developed metagenome-based models that can be used in personalized nutrition.

Professor Hutkins has published widely on probiotics, prebiotics, and fermented foods and is the author of the recently published 2nd edition of Microbiology and Technology of Fermented Foods.

Welcome to the first episode of our new series on the latest fermented food science. We are highlighting Episode 1 from our archives with guest Prof. Bob Hutkins, University of Nebraska – Lincoln. Prof. Hutkins wrote a popular textbook on fermented foods and has had a 40-year career in fermentation science. He shares why he ended up in fermentation science, as well as how fermented foods are made and how important live microbes are for their health benefits.

Key topics from this episode:

• What fermented foods are
• The scientific consensus definition published by ISAPP
• Fermentation processes and practices used in early times and still used today
• The benefits and safety of fermented foods, as well as the difference between fermentation and food spoilage
• The live microbes present in fermented foods, how many are present, and their potential health benefits
• Why some fermented foods have live microbes and others do not; and how even when live microbes are absent due to heat treatment, for example, these products may still be classified as fermented 
• The differences between fermented foods, probiotics, and probiotic fermented foods

Episode links:

• Microbiology and Technology of Fermented Foods, 2nd Ed., by Robert W. Hutkins
• The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods
• The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic
• Synbiotics: Definitions, Characterization, and Assessment – ISAPP webinar featuring Prof. Bob Hutkins and Prof. Kelly Swanson

Additional resources:

• Fermented foods. ISAPP infographic
• What are fermented foods? ISAPP video
• Do fermented foods contain probiotics? ISAPP blog post
• How are probiotic foods and fermented foods different? ISAPP infographic
• Are fermented foods probiotics? Webinar by Mary Ellen Sanders, PhD

About Prof. Bob Hutkins:

Bob Hutkins is the Khem Shahani Professor of Food Microbiology at the University of Nebraska. He received his Ph.D. from the University of Minnesota and was a postdoctoral fellow at Boston University School of Medicine. Prior to joining the University of Nebraska, he was a research scientist at Sanofi Bio Ingredients.

The Hutkins Lab studies bacteria important in human health and in fermented foods. His group is particularly interested in understanding factors affecting persistence and colonization of probiotic bacteria in the gastrointestinal tract and how prebiotics shift the intestinal microbiota and metabolic activities. The lab also conducts clinical studies using combinations of pro- and prebiotics (synbiotics) to enhance health outcomes. More recently we have developed metagenome-based models that can be used in personalized nutrition.

Professor Hutkins has published widely on probiotics, prebiotics, and fermented foods and is the author of the recently published 2nd edition of Microbiology and Technology of Fermented Foods.

In this episode, ISAPP’s current President Prof. Maria Marco PhD and past President Prof. Dan Merenstein join the podcast hosts for a conversation about highlights in biotic science from the past year. Prof. Marco points out a paper published in Nature Microbiology, the result of an ISAPP discussion group exploring whether diet may be a confounder of biotic effects in clinical studies. The group concluded that scientists should work with dietitians to include data on participants’ habitual diet in future studies on biotics – particularly with on prebiotics. These efforts will help scientists establish causality and understand the basis of individual responses to a biotic intervention. Prof. Merenstein highlighted conversations in 2024 around the role of probiotics in the neonatal intensive care unit (NICU), including ISAPP’s panel on this topic at the annual meeting in Cork, Ireland. Although US regulators have recently warned against the use of probiotics for preterm infants in the NICU setting, the data overwhelmingly points to benefits and this may eventually drive regulatory change. Prof. Marco added that a take-away from ISAPP’s panel was that parents of preterm infants should be included in the decision-making around whether to use probiotics. The guests talked about Prof. Merenstein’s recent appointment to the National Academy of Medicine and his rigorous approach to primary care research. Further highlights in the science this year were ISAPP’s papers exploring evidence for probiotics restoring an antibiotic-disrupted microbiota, and evidence for the benefits of probiotics in healthy individuals – both of which found a lack of conclusive evidence to answer these questions. Many gaps exist in the knowledge around biotics, gut microbiota, and health – for example, another paper this year found that the abundance of microorganisms in a fecal sample is a confounder of microbiome-disease associations. And finally, beyond the scientific advancements, conveying the scientific concepts to the general public requires careful consideration and dedicated effort.

Episode abbreviations and links:

• ISAPP paper calling for dietary data to be included in clinical trials on biotics: Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome
• Blog article on ISAPP’s panel on the use of probiotics for preterm infants: Expert Panel at ISAPP Annual Meeting Addresses Probiotic Use for Premature Infants
• Blog article on Prof. Merenstein’s appointment to the National Academy of Medicine: ISAPP Board Member Prof. Dan Merenstein MD Elected to National Academy of Medicine
• Explanation of ISAPP’s paper exploring whether probiotics restore an antibiotic-disrupted microbiota: ISAPP panel concludes that more evidence is needed to determine whether probiotics help restore an antibiotic-disrupted microbiota
• Paper showing fecal microbial load may confound microbiome-disease associations: Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

About Prof. Maria Marco PhD

Dr. Maria Marco, PhD, is a Professor in the Department of Food Science and Technology at the University of California, Davis. She earned her bachelor’s degree in microbiology at The Pennsylvania State University and her PhD in microbiology at the University of California, Berkeley. As a postdoc at NIZO food research in The Netherlands, she developed a love for lactic acid bacteria and the importance of these microorganisms in our foods and the digestive tract. Her postdoctoral studies led to the discovery that probiotics are metabolically active in the intestine and responsive to dietary intake. Dr. Marco started her lactic acid bacteria and gut health laboratory at UC Davis in 2008 and has built an internationally-recognized, NIH, USDA, and NSF funded research program on probiotics, fermented foods, and dietary modulation of the gut microbiome. Dr. Marco also consults with and has received funding from international foundations and companies to investigate how certain microbes in foods or supplements may benefit health. She is active with science communication activities such as the EATLAC project and is the instructor for two food microbiology courses. Dr. Marco received the American Society for Microbiology Distinguished Lecturer award in 2012. Recently, she founded the ongoing Gordon Research Conference series on Lactic Acid Bacteria. Dr. Marco attended her first ISAPP meeting as a postdoc and participated as an invited expert before joining the ISAPP Board of Directors in 2019.

About Prof. Dan Merenstein

Dr. Daniel Merenstein, MD, is a Professor with tenure of Family Medicine at Georgetown University, where he also directs Family Medicine research. Dr. Merenstein has a secondary appointment in the undergraduate Department of Human Science, in the School of Health. Dr. Merenstein teaches two undergraduate classes, a research capstone and a seminar class on evaluating evidence based medical decisions. He has been funded by PCORI, NIH, USDA, foundations and industry. The primary goal of Dr. Merenstein’s research is to provide answers to common clinical questions that lack evidence and improve patient care. Dr. Merenstein is a clinical trialist who has recruited over 2,000 participants for 10 probiotic trials since 2006. He is an expert on probiotics, on antibiotic stewardship in outpatient settings, and also conducts HIV research in a large women’s cohort. He sees patients in clinic one day a week. Dan lives in Maryland with his wife and 4 boys.

This episode features Prof. Malú Tansey PhD and colleague Dr. Andrea Merchak PhD from the University of Florida, USA, discussing neuroinflammation and the role of gut microbes in Parkinson’s disease (PD) and other neurodegenerative diseases. “Inflammaging” tends to occur as aging progresses, but the links that have been made between the gut and the brain in PD have led their group to the hypothesis that PD may be an age-acquired autoimmune condition. Genetic factors are relevant, although not everyone with PD has the predisposing genes. Those with a certain genetic mutation have a different immune phenotype from normal. Furthermore, the gut microbiota influences the immune system and the inflammatory environment within the body, with some metabolites known to cross the blood-brain barrier and influence the immune cells of the brain. Currently the group is focusing on using the gut microbiome, blood, and colonic biopsies to gain insights into the brain. A combination of diet and probiotics is promising as an intervention to prevent neurodegeneration as people age.

Episode abbreviations and links:

• Review on the fundamental role of neuroinflammation in Parkinson’s disease: Inflammation and immune dysfunction in Parkinson disease
• Post on bioRxiv showing immune similarities in people with PD and people with IBD: Peripheral Blood Immune Cells from Individuals with Parkinson’s Disease or Inflammatory Bowel Disease Share Deficits in Iron Storage and Transport that are Modulated by Non-Steroidal AntiInflammatory Drugs
• Review on the gut dysfunction in PD and whether it precedes brain pathology, with links to dysregulated immune activity: The gut-brain axis: is intestinal inflammation a silent driver of Parkinson’s disease pathogenesis?

About Prof. Malú Tansey PhD:

Malú Gámez Tansey, Ph.D. is the Norman and Susan Fixel Chair in Neuroscience and Neurology and former Director of the Center for Translational Research in Neurodegenerative Disease at the University of Florida. Her lab focuses on the role of inflammation and immune system responses in brain health and neurodegenerative disease, with particular focus on central-peripheral neuroimmune crosstalk and the gut-brain axis, with the long-term goal of developing better therapies to prevent and/or delay these diseases.

Dr. Tansey obtained her B.S/M.S in Biological Sciences from Stanford University and her Ph.D. in Cell Regulation from UT Southwestern followed by post-doctoral work in neuroscience at Washington University. As head of Chemical Genetics at Xencor, she co-invented novel soluble TNF inhibitors that have now advanced to clinical trials in Alzheimer’s disease. She returned to academia as an Assistant Professor of Physiology at UT Southwestern in 2002 and was recruited to Emory University School of Medicine as a tenured Associate Professor in 2009. After 10 year at Emory and rising to the rank of Full Professor where she earned several mentoring awards

from students and faculty for her efforts in championing early-stage investigators, women and other under-represented groups in STEM, she was recruited to the Department of Neuroscience in the College of Medicine at the University of Florida, where she served on the

executive committees for the McKnight Brain Institute and the Fixel Institute for Neurological Diseases. She will be moving to the Stark Neuroscience Research Institute at Indiana University in Indianapolis in January of 2025 as the first Director of Neuroimmunology Research and Executive Associate Director of Education at the Stark NRI.

About Dr. Andrea Merchak PhD:

Andrea Merchak, Ph.D. is a Gator Neuroscholar Postdoctoral Associate at the University of Florida. She obtained her B.S. at Centre College with a focus on behavioral neuroscience and her Ph.D. from the University of Virginia. There, her thesis work explored the link between the gut microbiota and the brain in mood disorders and multiple sclerosis. Her current work explores the relationship between gut health and genetic predispositions for neurodegeneration. She has received recognition for her work through the Young Scientist Award from the International Prebiotics, Probiotics, and Gut Microbiome Conference, the

Outstanding Graduate Student Award from the University of Virginia, as well as a track record of funding from the NIH. She will be moving to the Stark Neuroscience Research Institute at Indiana University in Indianapolis in March of 2025 as an Assistant Professor of Neurology.

This episode features Prof. Kerensa Broersen PhD from University of Twente in the Netherlands, speaking about using an innovative model of the microbiota-gut-brain axis to learn about neurodegenerative diseases such as Parkinson’s disease. Prof. Broersen says that while clinical studies are applicable to human health and animal models have great physiological complexity, her lab focuses on a model that’s more flexible and that allows manipulation of specific signalling events – a microbiota-gut-brain axis on a microfluidic chip. To make the brain component, they use stem cells from healthy people (from bone marrow, blood, or urine), which can differentiate into different types of cells depending on the factors they’re exposed to. They create cells that represent different areas of the brain, and can keep them alive and functional for at least 100 days. They can also represent disease processes in the model. It’s known that the gut microbiota is involved in neurological disease and may be either a cause or consequence of the brain pathology; so in this model, the scientists culture gut microbes in one microfluidic device and the brain in another microfluidic device, then connect the two. This allows them to make changes in one compartment and see how it affects the other. In this way, Prof. Broersen is aiming to understand some of the very basic mechanisms of neurodegenerative disease development and progression.

Episode abbreviations and links:

• Study on how proteins found in food may influence the mechanisms of neurodegenerative disease pathology: Cross-seeding of alpha-synuclein aggregation by amyloid fibrils of food proteins 
• Lab website, Applied Stem Cell Technologies 

About Prof. Kerensa Broersen PhD:

Kerensa Broersen obtained a PhD in food chemistry from Wageningen University and Research, the Netherlands, in 2005, followed by two postdoctoral positions at the Medical Research Council in Cambridge, UK and the Free University of Brussels in Belgium, both focussing on protein aggregation in neurodegenerative disorders. She then joined the University of Twente at a tenure track assistant professor position to further investigate neurodegenerative disorders making use of neuronal cell types. Following a sabbatical at the University of California – Berkeley, in the group of Randy Schekman, Kerensa Broersen moved into the field of gut-brain communication studying the fundamentals of signaling pathways driving the intricate interaction between the intestinal microbiome, the gut and the brain. For this, she is making use of the differentiation potential of stem cells to create mini-versions of the organs involved cultured onto microfluidic devices.

This episode features Dr. Alex Parker PhD from Université de Montréal talking about models for studying neurodegenerative diseases. His lab makes use of the worm C. elegans, a common model organism for studying disease and aging as it has many genes in common with humans. Focusing on amyotrophic lateral sclerosis (ALS), Dr. Parker makes models that reflect some aspect of the disease – in this case, genes that are directly linked to ALS are directly expressed in the nervous systems of the worms. Then the lab screens different small molecules from drug collections to see what seems to protect the worms from neurodegeneration. In human ALS, the microbiome is a potential factor that could influence the development of disease if a genetic predisposition is present. Dr. Parker’s lab screened a collection of microorganisms and found one strain that protected the worms from progression of neurodegeneration. Simultaneously, they saw that genes involved in lipid metabolism were being altered. Their work indicates a signaling mechanism from the intestine to the nervous system turns on a protective pathway in the worms – and interestingly, feeding the worms fatty acids directly was not as effective, possibly indicating that the live microorganism is working through multiple pathways. Currently the group is testing the probiotic in mouse models and in an upcoming clinical trial examining how the lipid profile of ALS patients changes as the disease progresses.

Episode abbreviations and links:

• Paper on the probiotic strain that suppresses neurodegeneration in C. elegans: Fatty acids derived from the probiotic Lacticaseibacillus rhamnosus HA-114 suppress age-dependent neurodegeneration
• The  Université de Montréal’s CRCHUM research centre website

About Dr. Alex Parker PhD:

Alex Parker obtained a PhD in Medical Genetics at the University of British Columbia with Dr. Ann Rose using the model organism C. elegans to study Huntington’s disease. From there he did postdoctoral training with Dr. Christian Neri at INSERM, (Paris, France) to develop drug discovery methods for trinucleotide repeat disorders. He is now a professor in the department of neuroscience at the Universite de Montreal, and a researcher at the CRCHUM. His research focuses on developing genetic models for a wide range neurodegenerative diseases with a special focus on amyotrophic lateral sclerosis to find new therapeutic strategies with translation to clinical settings. Recently his team discovered a probiotic that protects against neurodegeneration in animal models and is now part of a clinical trial for ALS.

In this special episode, ISAPP’s Executive Director Marla Cunningham highlights ISAPP’s annual meeting, held in Banff, Canada in July 2025. Four speakers join the podcast to describe their talks from the meeting:

• Dr. Carolina Tropini PhD (University of British Columbia): Leveraging the gut environment for functional biosensor microbes
• Prof. André Marette PhD (Université Laval): Next generation probiotics for metabolic and liver health
• Dr. Peijun Tian PhD (Jiangnan University): Psychobiotics: unveiling the molecular basis of host mood regulation
• Josiane Kenfack (University of Yaounde I): The Leke project: Mapping the vaginal microbiome and benefits of vaginal lactobacilli in Cameroon

Episode abbreviations and links:

• Earlier biosensor work from Tropini lab showing the electrogenic properties of B. subtilis: Electrogenic dynamics of biofilm formation: Correlation between genetic expression and electrochemical activity in Bacillus subtilis
• Paper led by Marette lab on the mechanisms of how yogurt benefits metabolic health: Gut microbiota and fermentation-derived branched chain hydroxy acids mediate health benefits of yogurt consumption in obese mice
• Mouse study with work by Dr. Tian showing the antidepressant effects of a probiotic strain: Towards a psychobiotic therapy for depression: Bifidobacterium breve CCFM1025 reverses chronic stress-induced depressive symptoms and gut microbial abnormalities in mice
• Review on differences in the vaginal microbiota globally, co-authored by Josiane Kenfack: Diversity in women and their vaginal microbiota

About our speakers:

Carolina Tropini, University of British Columbia, Canada

Dr. Carolina Tropini is an Assistant Professor at the University of British Columbia in the Department of Microbiology and Immunology and the School of Biomedical Engineering, and a Canada Tier 2 Research Chair in Quantitative Microbiota Biology for Health Applications. In 2020 she was nominated a Paul Allen Distinguished Investigator, and she was the first Canadian to be awarded the Johnson & Johnson Women in STEM2D Scholar, which was granted in the field of Engineering. She is the inaugural Alan Bernstein Canadian Institute for Advanced Research (CIFAR) Fellow in the Humans & the Microbiome Program and a Michael Smith Foundation for Health Research Scholar. In 2019, she was nominated as a CIFAR Azrieli Global Scholar.

The Tropini lab is investigating how a disrupted physical environment due to altered nutrition or concurrent with intestinal diseases affects the microbiota and host at a multi-scale level. They are a cross-disciplinary group that incorporates techniques from microbiology, bioengineering and biophysics to create highly parallel assays and study how bacteria and microbial communities function, with the goal of translating the knowledge gained to improve human health.

Dr. Tropini conducted her Ph.D. in Biophysics at Stanford University. Her studies in the laboratory of Dr. KC Huang combined computational and experimental techniques to investigate bacterial mechanics and morphogenesis. In 2014 she received the James S. McDonnell Foundation Postdoctoral Fellowship Award, and she joined the laboratory of Dr. Justin Sonnenburg at Stanford. During her post-doc, Dr. Tropini applied her background in biophysics to study the impact of physical perturbations on host-associated microbial communities living in the gut.

André Marette, Université Laval, Canada

Dr. André Marette is a Professor of Medicine and researcher at the Heart and Lung Institute Hospital Center (IUCPQ), and at the Institute of Nutrition and Functional Foods (INAF) at Laval University. He holds a Valbiotis Research Chair in plant bioactives and metabolic liver diseases and a Pfizer Research Fund in the pathogenesis of insulin resistance and cardiovascular complications.

Dr. Marette is an international renowned expert on how nutrition and the microbiome modulate immunometabolic pathways involved in obesity and cardiometabolic diseases (CMD). He is investigating the metabolic impact of nutritional interventions and microbiome-based therapeutics (probiotics, prebiotics) using both clinical and pre-clinical studies, and uses various cellular models and molecular tools to discover novel disease biomarkers and mechanistic targets. Dr. Marette’s research work has been published in over 330 papers, reviews and book chapters and also authored two books.

He has received several awards for his work including the prestigious Charles Best Award and Lectureship from the University of Toronto for his overall contribution to the advancement of scientific knowledge in the field of diabetes.

Peijun Tian, Jiangnan University, P. R. China

Peijun Tian is an Associate Professor and Master’s supervisor at the School of Food Science and Technology, Jiangnan University. He earned his Ph.D. in Food Science from Jiangnan University (January 2021) and was a visiting scholar at the APC Microbiome Institute, Ireland (September 2019–October 2020). He completed postdoctoral research at Jiangnan University, supported by the prestigious “National Postdoctoral Program for Innovative Talent” (top 1% in China). His research focuses on elucidating the interactions between gut microbiota and brain function, exploring the application of probiotics to mitigate stress, support neurodevelopment, and address neurodegenerative disorders. He has authored over 30 peer-reviewed articles, including three ESI Highly Cited Papers, with an H-index of 23 (Google Scholar, March 2025). In 2025, he was honored with the Glenn Gibson Early Career Researcher Award by the International Scientific Association for Probiotics and Prebiotics (ISAPP).

Josiane Kenfack, University of Yaounde I, Cameroon

Josiane Kenfack is a PhD student passionate about scientific research aimed at improving women’s health through the advancement of studies of the vaginal microbiome and probiotics. Josiane is co-coordinator of a citizen science project in Cameroon, the LEKE project. This project was inspired by the Isala project (https://isala.be/en/) which aims to better understand the female microbiome while raising awareness about vaginal health and breaking taboos. Through the LEKE project, Josiane and colleagues have conducted field activities to explore vaginal and menstrual health and promote good practices with women and men in rural and urban areas. In her ongoing research, she is investigating beneficial lactobacilli that could serve as biotherapeutics or probiotics development to combat conditions such as bacterial vaginosis, HIV, and sexually transmitted infections which are still prevalent in Africa. while she co-coordinates in Cameroon the IMVAHA project which aims to determine the impact of different menstrual products on the vaginal microbiome.

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Continuing our series on the microbiota-gut-brain axis, we are highlighting Episode 34 from our archives. In this episode, the ISAPP hosts discuss a new study on how the gut virome affects the host during stress, with Nathaniel (Nate) Ritz from the Institute for Systems Biology in Seattle, USA and Thomaz Bastiaanssen from APC Microbiome Ireland. The guests give an overview of the microbiota-gut-brain axis, then delve into a new study they led on the virome and its effects on stress responses in mice.

Key topics from this episode:

• The gut and the brain communicate in various ways, and the microbiota play a role in some of these modes of communication. Various studies use animal models to look at mechanisms that might be applicable to humans.
• Why would the microbiota affect the human brain? Because we evolved with a ‘background’ of microbes and have relied on them as we evolved. For example, gut microbes produce metabolites the human body is unable to produce by itself.
• The newly published paper is titled “The gut virome is associated with stress-induced changes in behaviour and immune responses in mice”.
• Most microbiota-gut-brain axis research to date has looked at the bacterial component of the microbiome, but this misses the bigger context. The virome is the collection of viruses in the gut, mostly consisting of bacteriophages (which infect bacteria in the gut). This study focused on the virome and how it influenced the gut bacteriome as well as host behavior.
• Bioinformatics challenges exist when working with the virome for several reasons. For one, distinguishing the biology of a bacteriophage from its host can be challenging.
• The study used a fecal virome transplant: taking a fecal sample, removing the cellular organisms and small particulates so that the bacteriophages were left over, and then concentrating them and administering them. The researchers took this entire virome from a mouse, then transferred it back to the same individual mouse while it was undergoing stress.
• After stress, differences were seen in the mouse gut bacteriome and virome. The mice had higher anxiety- and depression-like behaviour, plus changes in their immune systems. But after the fecal virome transplant, some of their behaviours were improved.
• Do the viruses impact the host nervous system directly, or do they only affect the host by way of the bacteriome? This is not fully known, but there appears to be very little interaction of the bacteriophages with the host. 
• Analysis of the gut bacteriome or virome must respect the compositional nature of the data. The types of measurements used to analyze the microbiome and virome are confounded by compositional effects, and in the field this is not respected as much as it should be.
• The next step after this study is to explore the changes in microbiome function in the mice, perhaps pinpointing which bacterial groups need to be changed to normalize the mouse behaviours.

Episode links:

• Study showing how bacteriophages in the gut are associated with inflammation: Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis
• The idea of gut microbiota volatility: Volatility as a Concept to Understand the Impact of Stress on the Microbiome
• Two-part microbiome bioinformatics analysis guidebook by Thomaz Bastiaanssen (See supplementary data for an in-depth, reproducible tutorial in R): Part 1, Part 2
• Information on John Aitchison’s work on compositional analysis: Aitchison’s Compositional Data Analysis 40 Years on: A Reappraisal

About Nathaniel Ritz:

Dr. Nathaniel Ritz completed his PhD in Prof. John Cryan’s lab at APC Microbiome Ireland where he studied the role of the bacteriome and the virome in social and stress-related disorders. His interests lie in elucidating microbiota-host interactions and establishing microbiota causality within the microbiota-gut-brain axis. Nathaniel has recently moved to Seattle, Washington, USA, to join the lab of Dr. Sid Venkatesh as a postdoctoral fellow at the Institute for Systems Biology to further unravel the mechanisms underpinning microbe-host interaction. Outside of the lab, Nathaniel is an avid rock climber, dog walker, and partner to fellow scientist Dr. Minke Nota. More details and current position can be found at https://venkatesh.isbscience.org/

About Thomaz Bastiaanssen:

Dr. Thomaz Bastiaanssen is the lead bioinformatician in Prof. John F. Cryan’s microbiota-gut-brain axis group in Cork, Ireland. He is interested in the ecological dynamics governing host-microbe communication and how this complex interplay can impact human well-being. He will soon transition to a new role at Amsterdam UMC, the Netherlands, where he will continue to study the microbiome gut-brain axis. Besides working on multi-omics analyses, he enjoys horror stories, tabletop games and spending time with his wife, son, and corgi. His website can be found at: https://thomazbastiaanssen.github.io/

Continuing our series on the microbiota-gut-brain axis, we are highlighting Episode 26 from our archives. In this episode, ISAPP podcast host Prof. Dan Tancredi PhD welcomes guest Prof. Emeran Mayer MD, a gastroenterologist and researcher at University of California Los Angeles. They talk about the microbiota-gut-brain axis, covering its evolutionary origins and how this complex system works in the human body to support overall health.

Key topics from this episode:

• Microbiota-gut-brain communication has a long evolutionary history: microbes have been around for billions of years and they stored a lot of information in their genes. At some point in evolution microbes got inside the digestive tube of a primitive marine animal called hydra and it proved advantageous for this animal.
• The hydra shows the origin of the human enteric nervous system (ENS): microbes live inside this tube and transfer genes to the nerve cells of this digestive tube, showing the origin of neurotransmitters.
• Today in humans the neurotransmitters influence gene expression of microbes and change the microbial behaviors; the metabolites produced feed back to the brain.
• Prof. Mayer’s initial interest as a gastroenterologist was the ENS and how it regulates motility. Subsequently the ENS was found to regulate many gut functions. The gut also houses a large part of the immune system and a complex hormonal system, and all these systems are connected with each other and communicate with the brain.
• There is an increasing understanding that many chronic diseases relate to Inappropriate engagement of the immune system, starting in the gut.
• When Prof. Mayer started in the field, the term “gut health” did not exist. Now it’s a ubiquitous term which has associations with wellbeing, acknowledging the gut has influence on many other body systems.
• The associations between gut (microbiota) and brain health started with provocative animal experiments from Cork, Ireland, in which researchers manipulated the gut microbiome and found changes in emotion-like behaviors of animals. However, it has been difficult to translate to human interventions.
• How do microbiome-targeted dietary interventions affect the brain? We do know the “Standard American Diet” (deficient in fiber) has changed the gut microbes in a way that compromises the production and maintenance of the gut barrier. 
• There are many misconceptions about “leaky gut”, but basically contact between beneficial microbes and immune system sensors stimulate the immune system of the gut to low-grade inflammation. This can alter the tight junctions, making the gut more permeable, and ultimately this can affect the brain. Diet can affect the role of microbes in maintaining an effective gut barrier.
• Prof. Mayer describes how he ended up studying the microbiota-gut-brain axis – he would not have predicted how important and popular this field would become.
• In the future, there will be more sophisticated and personalized interventions. He sees a paradigm shift happening from reductionist approaches in medicine to systems biological approaches. This field is making us acknowledge that diet will play a major role.

Episode links:

• Prof. Mayer’s first academic book, Basic and Clinical Aspects of Chronic Abdominal Pain (Pain Research and Clinical Management) 
• Prof. Mayer’s first book for the general public, The Mind-Gut Connection
• Review on microbiota-gut-brain axis: The Microbiota-Gut-Brain Axis: From Motility to Mood 
• Review on the impact of diet on intestinal permeability: Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia
• Review on microbiota-dependent interactions between diet and the immune system: Human nutrition, the gut microbiome, and immune system: envisioning the future

About Prof. Emeran Mayer MD:

Emeran A Mayer is a Gastroenterologist, Neuroscientist and Distinguished Research Professor in the Department of Medicine at the David Geffen School of Medicine at UCLA, the Executive Director of the G. Oppenheimer Center for Neurobiology of Stress & Resilience and Founding Director of the Goodman Luskin Microbiome Center at UCLA. He is one of the pioneers and leading researchers in the bidirectional communication within the brain gut microbiome system with wide-ranging applications in intestinal and brain disorders. He has published 415 scientific papers, co edited 3 books and has an h-index of 125. He published the best selling books The Mind Gut Connection in 2016, the Gut Immune Connection in June 2021, and the recipe book Interconnected Plates in 2023. He is currently working on a MasterClass and a PBS documentary about the mind gut immune connection. He is the recipient of numerous awards, including the 2016 David McLean award from the American Psychosomatic Society and the 2017 Ismar Boas Medal from the German Society of Gastroenterology and Metabolic Disease.

This episode features Dr. Eldin Jašarević PhD from University of Pittsburgh discussing research that investigates how maternal signals influence the general development and neurodevelopment of the offspring. Dr. Jašarević’s particular interest in this field stems from his family’s journey as refugees from Bosnia who found their way to the US. His lab studies how maternal stress or diet signals the developing brain to facilitate a lasting change, focusing on the role of the gut and vaginal microbiomes. His work in mouse models has shown that even mild stressors early in pregnancy trigger a gut microbiome change that lasts, but the challenge is to figure out whether the microbiome is responsible for the lasting effect. More human intervention studies are needed to understand how these findings may benefit pregnant women and the eventual development of their children. Regarding brain development, germ-free mice have brains that grow and develop differently from mice with an intact microbiome: for example, microbial metabolites are involved in key epigenetic processes for the brain. In general, the field may be moving toward understanding host-microbial interactions and dispersal of microbial-derived metabolites in pre-conception health and fertility, to eventually enable earlier intervention.

Episode abbreviations and links:

• Mouse study using a c-section model to show how, with maternal stress, the vaginal microbiome signals to the offspring’s brain and gut: The maternal vaginal microbiome partially mediates the effects of prenatal stress on offspring gut and hypothalamus
• Review describing two overlapping processes by which the maternal (gut and vaginal) microbiota affects offspring development and health: Prenatal and postnatal contributions of the maternal microbiome on offspring programming
• Preprint accounting for why germ-free mice have a shortened reproductive lifespan: The microbiota extends the reproductive lifespan by safeguarding the ovarian reserve

About Dr. Eldin Jašarević PhD:

Eldin Jašarević is an Assistant Professor in the Departments of Obstetrics, Gynecology and Reproductive Sciences and Computational and Systems Biology at the University of Pittsburgh, and a Principal Investigator at Magee-Womens Research Institute. He received his Ph.D. in Neuroscience from the University of Missouri, where he worked at the Thompson Center for Autism and Neurodevelopmental Disorders. His predoctoral research focused on the role of maternal lifetime experiences on brain development. During his postdoctoral fellowship with Dr. Tracy Bale at the University of Pennsylvania, Eldin defined mechanisms by which disease susceptibility can be transferred across generations via the microbiome. His current research focuses on understanding how microbial-derived signals act as regulators of development, with particular emphasis on the germline. His contributions to the field have been recognized through his selection as a Kavli Fellow of the National Academy of Sciences, a Burroughs Wellcome Fellow, and through research funding from NIMH, NICHD, and NIDDK.

This episode features Dr. Boushra Dalile PhD from KU Leuven in Belgium – ISAPP’s 2024 Glenn Gibson Early Career Researcher Award winner – discussing the protective role of fiber and prebiotics on cognitive health. Dr. Dalile is trained in psychology, and in her current work she undertakes human intervention studies to examine the effects of interventions using fibers, prebiotic fibers, and / or short-chain fatty acids on human stress- and anxiety- related processes. Fermentable fibers in the diet are known to result in the production of short-chain fatty acids (SCFAs), and she has been involved in studies in which participants receive the SCFAs directly. Interestingly, sufficient SCFAs circulating in the blood are required for protection against a stressor, regardless of any intervention. Dr. Dalile explains that cognitive deterioration may start 20 to 30 years before the first symptoms occur in later life, so that prevention (or “cognitive resilience”) is the most promising strategy. So far, the best recommendation is to maintain a fiber-rich diet throughout adulthood, although various research groups are working to find out whether a specific intervention could be effective for protecting cognition. This episode is the first of a series on the microbiota-gut-brain axis.

Episode abbreviations and links:

• Review on the role of short-chain fatty acids: The role of short-chain fatty acids in microbiota–gut–brain communication
• Human study on how short-chain fatty acids change stress response: Colon-delivered short-chain fatty acids attenuate the cortisol response to psychosocial stress in healthy men: a randomized, placebo-controlled trial
• Human study on the effects of wheat bran on reactions to stress and fear: Extruded Wheat Bran Consumption Increases Serum Short-Chain Fatty Acids but Does Not Modulate Psychobiological Functions in Healthy Men: A Randomized, Placebo-Controlled Trial
• Human study on how short-chain fatty acids modulate fear and stress responses: Colonic butyrate administration modulates fear memory but not the acute stress response in men: A randomized, triple-blind, placebo-controlled trial
• Expert perspective on evidence for prebiotics to promote cognitive functioning: Targeting cognitive resilience through prebiotics: A focused perspective

Additional resources:

ISAPP blog post: Can we estimate prebiotic effects from short-chain fatty acid production?

About Dr. Boushra Dalile PhD:

Dr. Boushra Dalile PhD is a Postdoctoral Researcher at the Laboratory of Biological Psychology at KU Leuven, Belgium. She was trained in psychology (Swinburne University of Technology, Australia) and cognitive neuroscience (University of Skövde, Sweden; The Max Planck Institute for Human Cognitive and Brain Sciences, Germany), before being awarded a PhD in Biomedical Sciences in 2021 at the Translational Research Center for Gastrointestinal Disorders at KU Leuven under supervision of Prof. Kristin Verbeke. Since her PhD, she investigates the effects of dietary fiber and the role of short-chain fatty acids (SCFAs) on stress and anxiety, and is currently mapping out their putative mechanisms of action in humans. Her latest research seeks to harness butyrate’s neuro-psychopharmacological potential in modulating learning and memory to advance translational research on anxiety and help shape treatment options and dietary recommendations. Her work was published in Nature Reviews Gastroenterology & Hepatology, The Lancet Planetary Health, Neuropsychopharmacology, and Psychoneuroendocrinology.

Completing our series on the role of biotics in animal health, we are highlighting Episode 22 from our archives. In this episode, Prof. Kelly Swanson PhD from University of Illinois at Urbana-Champaign discusses the role of biotics in animal and human nutrition. He reviews the criteria for prebiotics and synbiotics, then discusses how we gain knowledge about nutrition and the role of biotics in animals compared to humans.

Key topics from this episode:

• A good argument can be made that biotics are essential for our diet; they are beneficial even if efficacy is sometimes difficult to prove.
• Nutrients have an impact on the host’s health and simultaneously on the host-associated microbes.
• Health benefits are essential to the FDA definition of fiber.
• Antibiotics’ effect on the microbiota: short-term effects may be minor, but we still don’t know the long-term effects.
• The synbiotics definition, criteria for products to meet this definition, and the health outcomes from using these biotic substances.
• The difference between complementary and synergistic synbiotics.
• When studying biotics in companion animals (cats and dogs), can results from one host be extrapolated to another host? Final studies should be in the target host.
• Biotics are important in veterinary medicine and a popular topic of study.
• Predictions about the future of nutrition science as informed by the microbiome.

Episode links:

• US FDA: United States Food and Drug Administration
• Randomized, controlled trial from Swanson lab on a potential prebiotic: 454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber.
• Prebiotic definition: Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics.
• Synbiotic definition: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics.
• Review on antibiotic use in agriculture: Antibiotics Overuse in Animal Agriculture: A Call to Action for Health Care Providers.

Additional resources:

• Synbiotics. ISAPP infographic.
• New synbiotic definition lays the groundwork for continued scientific progress. ISAPP blog post.
• Synbiotics: Definitions, Characterization, and Assessment. ISAPP webinar.

About Prof. Kelly Swanson:

Kelly Swanson is the Kraft Heinz Company Endowed Professor in Human Nutrition at the University of Illinois at Urbana-Champaign. His laboratory studies the effects of nutritional interventions, identifying how diet impacts host physiology and gut microbiota. His lab’s primary emphasis is on gastrointestinal health and obesity in dogs, cats, and humans. Much of his work has focused on dietary fibers and ‘biotics’. Kelly has trained over 40 graduate students and postdocs, published over 235 peer-reviewed manuscripts, and given over 150 invited lectures at scientific conferences. He is an active instructor, teaching 3-4 nutrition courses annually, and has been named to the university’s ‘List of Teachers Ranked as Excellent by Their Students’ 30 times. He serves on advisory boards for many companies in the human and pet food industries and non-profit organizations, including the Institute for the Advancement of Food and Nutrition Sciences and International Scientific Association for Probiotics and Prebiotics.

This episode features Prof. Naowarat (Ann) Cheeptham, a cave microbiologist from Thompson Rivers University (Canada), speaking about a fungal infection in bats that causes white nose syndrome. She and her collaborators are looking at the microbiomes of the bats and their environments for possible ways to prevent this serious infection. White nose syndrome is caused by Pseudogymnoascus destructans infecting bats in hibernation and causing them to act in unnatural ways. The condition has caused massive death of bats in North America, although not in other regions of the world with the same fungus. Dr. Cheeptham and colleagues are looking for strategies to prevent white nose syndrome. Initially they screened environmental bacteria with activity against the fungus, but had difficulty knowing how to apply these bacteria to the bats. Their current approach is to take four bacterial strains isolated from healthy bats and apply them in bat boxes so they may become established on the vulnerable bats to prevent white nose syndrome. The preventative actions of the bacteria are still under investigation, but the collaborators believe the mechanism is related to metabolite production. This episode is part of a series on the role of biotics in animal health.

Episode abbreviations and links:

• Paper on bat wing microbiomes: DNA Metabarcoding Analyses Reveal Fine-Scale Microbiome Structures on Western Canadian Bat Wings
• Paper on bat wing bacteria with inhibitory action against Pseudogymnoascus destructans: Microbial Isolates with Anti-Pseudogymnoascus destructans Activities from Western Canadian Bat Wings

About Prof. Ann Cheeptham PhD:

Dr. Cheeptham is a professor at the Department of Biological Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada. Her research interests include cave microbiomes/new drug discovery, white-nose syndrome in bats, alternative treatment tools against multidrug-resistant infections, and geomicrobiology.  Her work has fortunately been featured in the New York Times, WIRED, Bloomberg TV network’s Spark series, Al Jazeera TV, the CBC’s Nature of Things (The Antibiotic Hunters episode), Global TV (Global 16×9 and Global Health), Knowledge Network, CBC radio (Daybreak) and in several International and Canadian magazines.  Besides her passion for cave microbiology and research, she is also drawn to pedagogical issues in microbiology education. Recently, she has been the recipient of the 2022 3M National Teaching Fellowship from the Society for Teaching and Learning in Higher Education (STLHE) and 3M, the 2020 TRU Faculty Excellence Award, and the 2020 D2L Innovation Award in Teaching and Learning STLHE and D2L (Desire2Learn).

This episode features Prof. Alex Hristov PhD from Penn State University (USA) talking about the microbiota of ruminants and how it can be targeted for reduced methane production. The rumen (pre-stomach area) of cows and other animals contains microorganisms that digest the feed before it enters the rest of the gastrointestinal tract. Hydrogen is produced to inhibit further fermentation of the feed, and this hydrogen is rapidly converted to enteric methane, which is emitted by the animal – accounting for a large proportion of methane emissions that contribute to global warming. Several approaches exist for targeting the rumen microbiota with the aim of reducing methane emissions. Some feed additives, including one recently approved by regulators in the US, can reduce enteric methane by around 30% and appear safe for the animal. Vaccines against the methane-producing archaea in the rumen are another potential approach suitable for grazing livestock. Direct microbials have also been advanced. Many other sources of methane emissions exist besides livestock, but significantly reducing the methane production in the livestock industry could have a major positive impact on global warming. Feed additives for now are the leading strategy, and adoption of existing solutions in multiple places is critical. This episode is part of a series on the role of biotics in animal health.

Episode abbreviations and links:

• Paper on feed additive for reducing methane emissions: An inhibitor persistently decreased enteric methane emission from dairy cows with no negative effect on milk production
• Review paper on reducing methane emissions via feed additives: Advances in nutrition and feed additives to mitigate enteric methane emissions
• Announcement of FDA approval of feed additive: Elanco Announces FDA Has Completed Review of Bovaer®, First-in-Class Methane-Reducing Feed Ingredient, for U.S. Dairy Industry
• Study showing microorganisms transferred from the rumen of one animal to another: Successful transfer of DHP-degrading bacteria from Hawaiian goats to Australian ruminants to overcome the toxicity of Leucaena
• Estimation of methane emissions from bison versus agricultural animals: Historic, pre-European settlement, and present-day contribution of wild ruminants to enteric methane emissions in the United States

About Prof. Alex Hristov PhD:

Dr. Alexander N. Hristov is a Distinguished Professor of Dairy Nutrition in the Department of Animal Science at The Pennsylvania State University. He has a Ph.D. in Animal Nutrition from his native Bulgaria. Hristov has worked at the USDA-ARS Dairy Forage Research Center in Madison, WI, the Ag Canada Research Center in Lethbridge, AB, was on the faculty at the Department of Animal and Veterinary Science, University of Idaho from 1999 to 2008 and is at Penn State since 2008. Hristov’s main research interests are in the areas of mitigation of nutrient losses and gaseous emissions from dairy operations and protein and amino acid nutrition of dairy cattle. He has published over 220 peer-reviewed journal papers, books, and book chapters.

Continuing our series on the role of biotics in animal health, we are highlighting Episode 5 from our archives. This episode features a former ISAPP board member, Prof. George Fahey, giving an overview of animal prebiotic research and describing future opportunities for prebiotics in animal nutrition. Prof. George Fahey is a prominent animal nutrition scientist who is currently Professor Emeritus at University of Illinois. Fahey explains how animal nutrition research relates to human nutrition research, and the changes in the field he has seen over the course of his long career. He describes the research on prebiotics for animal nutrition, covering both livestock and companion animals.

Key topics from this episode:

• A short history of animal prebiotics research as well as future opportunities in animal nutrition.
• Pro- and prebiotics are being explored as an alternative to antibiotic treatment in production animals. Antibiotics are overused, leading to an increase in antibiotic resistance; the “biotics” therefore have great potential in animal nutrition.
• Probiotics can potentially be used instead of antibiotics to inhibit pathogens and support the gut microbiota in animals.
• Prebiotics possibly have high nutritional value and beneficial effects in animals, especially in poultry and pigs.
• There are limitations to using prebiotics in the animal industry, especially for some animals such as horses and ruminants.
• There has been increased use of prebiotics for companion animals (pets) in the past few years. Now many pet foods contain prebiotics.
• Benefits of using prebiotics in companion animals:
  •  Support digestive health
  •  Improve stool quality
  • Support the gut microbiota, which also translates to good stool quality
• A short overview of how companion animals’ food is produced, and the timing of adding prebiotics.
• Wild animals’ diet has low nutrition with limited to no prebiotic intake, resulting in a shorter lifespan in comparison with companion animals
• Some take-home points from animal models and animal nutrition research.

Episode links:

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics
The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

About Prof. George Fahey:

George C. Fahey, Jr. is Professor Emeritus of Animal Sciences and Nutritional Sciences at the University of Illinois at Urbana-Champaign. He served on the faculty since 1976 and held research, teaching, and administrative appointments. His research was in the area of carbohydrate nutrition of animals and humans. He published numerous books, book chapters, journal articles, and research abstracts.

He currently serves on two editorial boards, numerous GRAS expert panels, and is scientific advisor to both industry and governmental organizations. He retired from the University in 2010 but continues to serve on graduate student committees and departmental search committees. He owns Fahey Nutrition Consulting, Inc. that provides services to the human and pet food industries.

This episode features Prof. Jan Suchodolski DACVM PhD from Texas A&M University, discussing the gut microbiome in dogs and other companion animals as part of our series on the role of biotics in animal health. Prof. Suchodolski’s lab focuses on understanding gastrointestinal (GI) diseases in pets and developing diagnostic tests for research and clinical practice. His lab works on building a model of what’s happening with animal health, combining microbiome measures with measures of host health. For example, they found that severe gut microbiome dysbiosis in dogs reflected a greater extent of mucosal damage, contributing to the big picture of GI disease. Certain microbiome features when combined with metabolites are promising biomarkers of GI disease in pets. Test reproducibility is highly important, and treatment tends to be multi-modal. Prof. Suchodolski cautions against direct-to-consumer pet microbiome tests, noting that unvalidated assays are very common.

Episode abbreviations and links:

• Study showing dysbiosis with antibiotic administration in dogs: Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs
• Study showing microbiome and metabolite features of dogs with inflammatory bowel disease: Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease
• Purina Institute Microbiome Forum Virtual Event 2024

About Prof. Jan Suchodolski DACVM PhD:

Jan S. Suchodolski is a professor, Purina PetCare Endowed Chair for Microbiome Research, associate director and head of microbiome sciences at the Gastrointestinal Laboratory at Texas A&M University. He received his DrVetMed from the University Vienna, Austria and his PhD in veterinary microbiology from Texas A&M University. He is board certified in immunology by the American College of Veterinary Microbiologists (ACVM). His research is focused on developing biomarkers for gastrointestinal disease and therapeutic approaches for the modulation of the intestinal microbiota. He has authored or co-authored more than 400 peer-reviewed articles in the area of veterinary gastroenterology and microbiome research. In 2024, he received the AVMA career achievement in canine research award.

This episode, part of a series on the role of biotics in animal health, is a broad-ranging conversation on biotics for agricultural animals, with Prof. Steve Ricke PhD from University of Wisconsin-Madison. Prof. Ricke explains some of the different applications of biotics for poultry as well as swine and ruminants: rapid growth, efficient use of feed, and reducing inflammation. Biotics may also have a role in food safety as it relates to agricultural animals, with research showing how microbiome diversity shapes the impact of pathogens. Animal genetics, diet, and microbiome interactions are extremely complex and fortunately the tools to study these interactions have improved in the past several decades. Prof. Ricke urges scientists to take into account the microbial ecology surrounding the animal – and not to forget the potential impact of the animal on its environment.

Episode abbreviations and links:

• USDA/ARS: United States Department of Agriculture / Agricultural Research Service
• Article on approaches to poultry food safety: Strategies to improve poultry food safety, a landscape review.
• Article on method for early interventions in chickens: Applications of in ovo technique for the optimal development of the gastrointestinal tract and the potential influence on the establishment of its microbiome in poultry.

About Prof. Steve Ricke PhD:

Prof. Steven C. Ricke received his B.S. and M.S. from the Univ. of Illinois, Champaign-Urbana, IL. and Ph.D. from the Univ. of Wisconsin, Madison, WI. Prof. Ricke was a USDA-ARS postdoctorate in the Microbiology Department at North Carolina State Univ. then joined Texas A&M Univ. as a professor in the Poultry Science Dept.  In 2005, he became the first holder of the new Donald “Buddy” Wray Endowed Chair in Food Safety and Director of the Center for Food Safety at the University of Arkansas (UA) and was a faculty member of the Dept. of Food Science and Cellular/ Molecular Graduate program. In 2020 he became the Director of the Meat Science and Animal Biologics Discovery Program in the Animal and Dairy Sciences Dept. at the University of Wisconsin-Madison. Prof. Ricke’s lab conducts studies on the growth, survival, and pathogenesis of pathogens in the poultry gut and their interactions with gut microbiota.

This episode features Dr. Thomas Greiner PhD from the University of Gothenburg (Sweden), speaking about the various functions of GLP-1 in the gut, and the role of gut microbes in GLP-1 production, with ultimate effects on host health. He noted that GLP-1 is produced by enteroendocrine cells called L-cells, both in the small intestine and the colon. These cells respond to nutrients and microbially-produced short-chain fatty acids, but responses differ between the small intestine and colon, leading Dr. Greiner to investigate the different functions of GLP-1 at these two sites. Using germ-free mice and other models, Dr. Greiner has developed a hypothesis that the function of GLP-1 in the small intestine is to improve insulin secretion postprandially, whereas the functions of GLP-1 in the colon are to allow for increased energy intake (in a situation of energy deficiency), dampen inflammation, and protect local tissues. He and his colleagues are taking two different approaches in aiming to improve metabolic health in humans: finding inhibitors of bacterial enzymes to decrease production of a harmful molecule produced by bacteria; and a probiotic approach of administering butyrate-producing bacteria. With the latter approach, the sensitivity of the bacteria to oxygen is a problem to overcome, but their group has evolved a bacterial strain to tolerate some oxygen, with the idea of testing it as a probiotic.

Episode abbreviations and links:

• Paper exploring the role of the gut microbiota in GLP-1 signaling: GLP-1R signaling modulates colonic energy metabolism, goblet cell number and survival in the absence of gut microbiota
• Study on the functions of GLP-1 in the colon: Microbial Modulation of Energy Availability in the Colon Regulates Intestinal Transit
• Bäckhed Lab Instagram account: @backhed_lab

About Dr. Thomas Greiner PhD:

Thomas Greiner is a medical scientist at the Wallenberg Laboratory, University of Gothenburg, with over 15 years of experience in functional genetics and metabolic research. His work focuses on the intricate interplay between gut microbiota, intestinal hormones such as GLP-1, and host metabolism. He has explored how microbial and hormonal signals influence energy balance, intestinal function, and the development of metabolic diseases. His research primarily uses molecular approaches in mouse models to investigate the role of microbial signals in metabolic disease and to uncover new functions of gut hormones in regulating intestinal physiology.

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The ISAPP hosts discuss microbes, mucus, and milk with Dr. Clara Belzer PhD from Wageningen University in the Netherlands in this episode. Dr. Belzer, a molecular geneticist, specializes in studying the microorganisms that are equipped to break down the glycans in mucus and human milk within the host environment.

Key topics from this episode:

• Dr. Belzer’s research focuses on the microbes living in the host that survive on glycans (chains of sugars) produced by the host: milk oligosaccharides and mucus. The host is not good at digesting these sugars, but can use them when they’re separated into smaller components. These long chains of sugars end up in the large intestine, where certain microbes begin to digest them.
• There seems to be an evolutionary adaptation that sustains the symbiotic relationship between human milk and bacteria in the infant gut; many immune molecules in the human milk suppress pathogens, so the human milk oligosaccharides (HMOs) are available to the bacteria in the infant gut that can break them down. The bacteria are not suppressed by the acidic environment in the infant gut.
• Human milk is the best food for infants, but innovations in infant formula may make it more similar to human milk.
• Akkermansia is a genus of bacteria mostly found in adults, but also sometimes in infants, which grows in the mucosal layer of the intestines. (It doesn’t survive on dietary glycans.) Dr. Belzer’s hypothesis is that the environment created by human milk in the infant gut also fosters bacteria that can grow on mucus, creating a succession of host-benefitting bacteria. They found that HMOs, in addition to mucus, can support the growth and survival of Akkermansia, potentially helping it build a microbial network.
• There’s a genetic component to the HMOs contained in human milk; similarly, the sugar content in the mucosal glycans is related to host genetics.
• Lean individuals have a higher abundance of Akkermansia; these bacteria improve metabolism (for example, increasing insulin sensitivity) and have effects on the immune system, which both contribute to a lean phenotype. The root of these effects may be the strengthening of the gut barrier, which dampens signals from the lumen.
• Dr. Belzer has used both omics and culture-based approaches in her research. As part of her research she tries to make microbial synthetic communities, growing them in the lab and stimulating them with different glycans. This technique yields insights about the functions and microbial ecology in the gut.
• Killed Akkermansia are still able to bring health benefits to the host. Dr. Belzer had the idea that the pili structures on the bacteria were what communicated with the host, and sure enough, this was borne out in a study that showed the proteins in the pili (Amuc_1100) remained intact in the pasteurized bacteria and could stimulate the host immune system. This is a valuable finding because Akkermansia are difficult to culture.
• When Akkermansia fails to occupy the niche in the mucus layer, Bacteroides species may occupy the niche instead, forming a different microbial community in the mucus. Research is ongoing about the effects of different microbes carrying out similar functions for the host. Furthermore, scientists have many more microbial functions to discover.

Episode abbreviations and links:

• Paper showing the growth of Akkermansia on HMOs: Akkermansia muciniphila uses human milk oligosaccharides to thrive in the early life conditions in vitro
• Study showing attenuation of diet-induced obesity in mice with Akkermansia: Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
• Study showing the Amuc_1100 protein mechanism for Akkermansia: A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice

About Dr. Clara Belzer PhD:

Dr. Clara Belzer is Associate Professor Microbiology at the Laboratory of Microbiology of Wageningen University. The Belzer group is called ‘Microbes Mucus and Milk’ and the research is focused on the interaction of the gut microbiome with host mucus and milk. After obtaining her PhD at the Erasmus Medical Center Dr. Belzer did a postdoc at Harvard medical school. By now Dr. Belzer has years of experience on gut microbiome studies on anaerobes, including synthetic communities and different biotic concepts, with a special interest for the Akkermansia muciniphila. The group of Dr. Belzer works on several microbiome HMO and mucus related topics funded by national and international grants, some also in collaboration with medical centers and industry.

The ISAPP hosts discuss the microbiome in inflammatory bowel disease (IBD) with leading expert Prof. Harry Sokol MD PhD, who is Professor of Gastroenterology at Saint Antoine Hospital and has positions with Sorbonne University and the Micalis Institute, INRAE in Paris, France. Sokol talks about the specific gut bacteria that seem to be important in IBD, as well as the challenge of targeting the gut microbiome for therapeutic effects.

Key topics from this episode:

• Dr. Sokol says that while more and more gastroenterologists see the gut microbiome as relevant to disease diagnosis, prognosis, and treatment, the microbiome is not yet an important part of clinical practice. Fecal microbiota transplantation is widely used for recurrent C. difficile infection, but its utility in chronic disease is not established.
• Earlier in his research career, he started with the ‘global description’ strategy of surveying the gut microbiome of patients with IBD using the available scientific tools. More recently, Dr. Sokol has focused on ‘candidate microorganisms’ to target such as Faecalibacterium prausnitzii, or F. prau.
• How do scientists know F. prau is important for IBD? First, those with IBD have less of these bacteria. And patients with Crohn’s disease who have the lowest amounts in their gut microbiomes have the highest chance of disease relapse. Furthermore, these bacteria are human-specific and are found at a very high prevalence in healthy individuals – it makes up between 5 and 10% of the average person’s gut microbiome. A recent prospective study (GEM) also found that F. prau was one of the bacterial species that decreased even before the onset of inflammation and disease. Now Dr. Sokol and others are exploring the therapeutic uses of these bacteria.
• The ultimate goal with IBD is to use treatments that target the microbiome alongside treatments that target the host.
• A decrease in F. prau within the gut microbiome is not specific to IBD; it’s also seen in people with IBS and diarrhea. These bacteria may have multiple effects in the body.
• Dr. Sokol’s group worked on CARD9, an IBD susceptibility gene. The gene’s effect on phenotype occurs through the microbiome, because in mice, fecal microbiota transplantation (FMT) was enough to transfer the susceptibility to colitis. The microbiota also transferred an immune defect in IL-22 production, related to an alteration in tryptophan metabolism in the microbiome. Normally some bacteria in the microbiota use tryptophan to produce indoles, which lead to the production of IL-22, but this process was altered in the mice that received the FMT.
• This tryptophan metabolism in the microbiome is altered in IBD as well as other diseases. It’s one of the major functions of the gut microbiome, similar to short-chain fatty acid production and bile acid metabolism.
• As for F. prau, challenges remain with growing and scaling up production for industrial use, but currently Dr. Sokol and collaborators have a method that works. Perhaps eventually they will zone in on the molecules produced by the bacteria, but then again the bacteria may be more effective because it may address different mechanisms of action and different targets simultaneously.

Episode abbreviations and links:

• Dr. Sokol mentions two scientists who initially got him interested in the gut microbiome: Prof. Philippe Marteau MD PhD and Prof. Joël Doré PhD
• Recent work on CARD9 & the gut microbiota in colitis: Dissecting the respective roles of microbiota and host genetics in the susceptibility of Card9-/- mice to colitis
• Review on the potential therapeutic applications of F. prau: Faecalibacterium: a bacterial genus with promising human health applications

About Prof. Harry Sokol MD PhD:

Harry Sokol is Professor in the Gastroenterology department of Saint-Antoine Hospital (APHP, Sorbonne Université, Paris, France). the co-director of the Microbiota, Gut & Inflammation team (INSERM CRSA UMRS 938, Sorbonne Université, Paris), group leader in Micalis institute (INRAE) and coordinator of the “Paris Center for Microbiome Medicine” (www.fhu-pacemm.fr/). He is an internationally recognized expert in the inflammatory bowel disease (IBD) and gut microbiota fields, in which he has published more than 330 papers in major journals. He is the current president of the French group of Fecal Microbiota Transplantation, and the head of the APHP Fecal Microbiota Transplantation Center. His work on the role of gut microbiota in IBD pathogenesis led to landmark papers, including the identification of the pivotal role of the commensal bacteria Faecalibacterium prausnitzii in gut homeostasis and IBD. Currently, his work focuses on deciphering gut microbiota–host interactions in health and disease to better understand their role in pathogenesis and develop innovative treatments. Harry received two grants from the European Research Council (ERC) in 2016 and 2022, and he is a member of the International Organization for the Study of IBD (IOIBD). Since 2020, he is recognized as a Highly Cited Researcher (Clarivate, Web of Science). Harry Sokol is currently Associate Editor for Gastroenterology. Harry Sokol co-founded Exeliom biosciences (https://www.exeliombio.com/).

Find Harry on X/Twitter: @h_sokol

This episode features Dr. Jee-Yon Lee MD PhD, assistant project scientist at the University of California Davis, USA, speaking about a recent paper on the mechanisms of sorbitol intolerance and the contributions of the gut microbiota. Dr. Lee explains how gut microbes in the large intestine can drive sorbitol intolerance, and how their research group designed a probiotic intervention to ameliorate it in a mouse model.

Key topics from this episode:

• Dr. Lee joined Baumler lab in 2017 to study how ecological causes such as diet or chronic disease can change host cell metabolism, thereby changing the gut microbiota, and also the effect of the gut microbiota on chronic diseases.
• Sorbitol is a sugar alcohol used as an artificial sweetener. It cannot be absorbed or catabolized in the small intestine so it reaches the large intestine and draws water into the lumen through osmosis. Large amounts cause diarrhea, but normally small amounts do not. 
• Some people are sensitive to small amounts of sorbitol and are said to have sorbitol intolerance. Where does the intolerance originate? Possibly the inability of bacteria in the large intestine to catabolize sorbitol using enzymes.
• Sorbitol intolerance (causing diarrhea) can be transient, such as after taking antibiotics. 
• What is happening in sustained sorbitol intolerance? Clinically, a recent history of taking antibiotics plus a high-fat diet is associated with diarrhea as well as low-grade inflammation. A mouse model showed that a high-fat diet plus antibiotics led to low-grade inflammation, which may be at the root of sorbitol intolerance.
• Clostridia are the main bacteria catabolizing sorbitol in the gut. Overall, a high-fat diet plus antibiotics together drive the gut ‘dysbiosis’, and contribute to the chronic depletion of mitochondrial function in the colonic epithelium. This makes the colonic environment less hypoxic, sustains the depletion of Clostridia, and thereby induces sorbitol intolerance.
• From this, Dr. Lee helped design a probiotic intervention. They selected 3 strains of bacteria and tested them with the high-fat diet and antibiotics mouse model. All of them protected the host from sorbitol intolerance in slightly different ways.
• Decreased sorbitol dehydrogenase activity may be a biomarker of sorbitol intolerance; currently there’s no way to diagnose this intolerance clinically, so patients typically cut out the substance to discover their intolerance.

Episode abbreviations and links:

• Paper on sorbitol intolerance discussed in the podcast: High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota
• Review: The microbiome and gut homeostasis

About Dr. Jee-Yon Lee MD PhD:

Dr. Jee-Yon Lee is an Assistant Project Scientist in Dr. Andreas Baumler’s lab at UC Davis, focusing on studying host-microbial interactions and their impact on human health and non-communicable diseases. She earned her MD and PhD from Yonsei University College of Medicine and served as a family medicine physician in South Korea until 2017. She joined Dr. Andreas Baumler’s lab in 2017 as a visiting scholar and completed her postdoctoral research there. Dr. Lee’s long-term research goal is to elucidate the ecological causes of dysbiosis, its consequences on the development of human diseases, and to find potential therapeutics targeting the microbiome.

In this episode, the ISAPP hosts discuss the gut microbiome’s role in chronic diseases with Dr. Purna Kashyap MBBS, from Mayo Clinic in Rochester, Minnesota, USA. Dr. Kashyap talks about how to discover the complex factors that trigger and perpetuate chronic diseases such as inflammatory bowel disease, zeroing in on the gut microbiome as a contributor to different aspects of gastrointestinal (GI) tract physiology.

Key topics from this episode:

• Dr. Kashyap became interested in some of the initial studies linking the gut microbiome to chronic diseases around 2007-2008, and subsequently began to study the molecular mechanisms that underlie changes in GI tract physiology.
• How can scientists figure out causality in chronic diseases and the role of gut microbes? Dr. Kashyap sees causality as an ongoing cascade of events in the GI tract, with no single causal factor. Both the initial triggers and the perpetuating factors can be considered part of what causes these diseases.
• Microbes can help perpetuate a certain state in the host because once they establish themselves they serve to make the environment more conducive to their survival. In chronic diseases, the factor that triggers the microbial community configuration may not be as important as the factor(s) that perpetuate it on an ongoing basis.
• The gut microbiome is changeable but not easy to change. Scientists need to know how the microbial community sustains itself and intervene there to change the community.
• Even small microbiome studies can be informative if you look at who responds to the intervention and why. This information can be valuable for informing which treatments might work for which subgroups of people.
• Dr. Kashyap encourages combining three types of research: large-scale studies on microbial metabolites and potential drug targets; clinical studies on the metabolites present in various subgroups; preclinical models studying the effects of individual metabolites.
• Diet, microbes, and host uptake all contribute to the physiological effects of different metabolites. And for example, if a metabolite is low, knowing which microbes are present is not enough information to explain why it’s low.
• In gastroenterology, clinicians primarily care about the gut microbiome in relation to the new treatments it makes possible. Now that FDA-approved treatments exist (standardized fecal microbiota transplants for recurrent C. difficile), clinicians may start paying more attention.
• Does Dr. Kashyap recommend interventions to patients based on their gut microbiomes? A high-fiber diet is good for the gut microbiome and also for overall health, so he advises patients to adhere to dietary recommendations for their daily fiber intake.

Episode abbreviations and links:

• Article on the microbiome in irritable bowel syndrome: Multi-omics for biomarker approaches in the diagnostic evaluation and management of abdominal pain and irritable bowel syndrome: what lies ahead
• Study comparing the effects of gut microbiota from people in the US vs. rural Thailand: Industrialized human gut microbiota increases CD8+ T cells and mucus thickness in humanized mouse gut
• Study on the effects of the metabolite tryptamine: Gut Microbiota-Produced Tryptamine Activates an Epithelial G-Protein-Coupled Receptor to Increase Colonic Secretion
• GWAS: Genome-wide association studies

About Dr. Purna Kashyap:

Dr. Purna Kashyap is practicing gastroenterologist and Professor of Medicine and Physiology, the Bernard and Edith Waterman Director of the Microbiome program, and Director of the germ-free mouse facility in the Center for Individualized Medicine at Mayo Clinic, Rochester, MN. The NIH funded Gut Microbiome laboratory led by Dr. Kashyap is focused on delineating the complex interactions between diet, gut microbiome, and host gastrointestinal physiology.  The laboratory uses germ-free mouse models in conjunction with measures of gastrointestinal physiology in vitro and in vivo to investigate effects of gut microbial products on host gastrointestinal function. In parallel, they use a systems approach incorporating multi-omics, patient metadata, and physiologic tissue responses in human studies, to aid in discovery of novel microbial drivers of disease. The overall goal of the program is to develop novel microbiota-targeted therapies. Dr. Kashyap has published nearly 100 peer reviewed articles including journals like Cell, Cell Host Microbe, Science Translational Medicine, Nature Communications, and Gastroenterology. He was inducted to American Society of Clinical Investigation in 2021. He has previously served on the scientific advisory board of American Gastroenterology Association Gut Microbiome Center, and on the council of American Neurogastroenterology and Motility Society. He now serves on the council and the research committee of AGA, in an editorial role for Gut Microbes and as an ad hoc reviewer on NIH study sections.

In this episode, the ISAPP hosts discuss a new study on how the gut virome affects the host during stress, with Nathaniel (Nate) Ritz from the Institute for Systems Biology in Seattle, USA and Thomaz Bastiaanssen from APC Microbiome Ireland. The guests give an overview of the microbiota-gut-brain axis, then delve into a new study they led on the virome and its effects on stress responses in mice.

Key topics from this episode:

• The gut and the brain communicate in various ways, and the microbiota play a role in some of these modes of communication. Various studies use animal models to look at mechanisms that might be applicable to humans.
• Why would the microbiota affect the human brain? Because we evolved with a ‘background’ of microbes and have relied on them as we evolved. For example, gut microbes produce metabolites the human body is unable to produce by itself.
• The newly published paper is titled “The gut virome is associated with stress-induced changes in behaviour and immune responses in mice”.
• Most microbiota-gut-brain axis research to date has looked at the bacterial component of the microbiome, but this misses the bigger context. The virome is the collection of viruses in the gut, mostly consisting of bacteriophages (which infect bacteria in the gut). This study focused on the virome and how it influenced the gut bacteriome as well as host behavior.
• Bioinformatics challenges exist when working with the virome for several reasons. For one, distinguishing the biology of a bacteriophage from its host can be challenging.
• The study used a fecal virome transplant: taking a fecal sample, removing the cellular organisms and small particulates so that the bacteriophages were left over, and then concentrating them and administering them. The researchers took this entire virome from a mouse, then transferred it back to the same individual mouse while it was undergoing stress.
• After stress, differences were seen in the mouse gut bacteriome and virome. The mice had higher anxiety- and depression-like behaviour, plus changes in their immune systems. But after the fecal virome transplant, some of their behaviours were improved.
• Do the viruses impact the host nervous system directly, or do they only affect the host by way of the bacteriome? This is not fully known, but there appears to be very little interaction of the bacteriophages with the host. 
• Analysis of the gut bacteriome or virome must respect the compositional nature of the data. The types of measurements used to analyze the microbiome and virome are confounded by compositional effects, and in the field this is not respected as much as it should be.
• The next step after this study is to explore the changes in microbiome function in the mice, perhaps pinpointing which bacterial groups need to be changed to normalize the mouse behaviours.

Episode links:

• Study showing how bacteriophages in the gut are associated with inflammation: Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis
• The idea of gut microbiota volatility: Volatility as a Concept to Understand the Impact of Stress on the Microbiome
• Two-part microbiome bioinformatics analysis guidebook by Thomaz Bastiaanssen (See supplementary data for an in-depth, reproducible tutorial in R): Part 1, Part 2
• Information on John Aitchison’s work on compositional analysis: Aitchison’s Compositional Data Analysis 40 Years on: A Reappraisal

About Nathaniel Ritz PhD:

Dr. Nathaniel Ritz completed his PhD in Prof. John Cryan’s lab at APC Microbiome Ireland where he studied the role of the bacteriome and the virome in social and stress-related disorders. His interests lie in elucidating microbiota-host interactions and establishing microbiota causality within the microbiota-gut-brain axis. Nathaniel has recently moved to Seattle, Washington, USA, to join the lab of Dr. Sid Venkatesh as a postdoctoral fellow at the Institute for Systems Biology to further unravel the mechanisms underpinning microbe-host interaction. Outside of the lab, Nathaniel is an avid rock climber, dog walker, and partner to fellow scientist Dr. Minke Nota. More details and current position can be found at https://venkatesh.isbscience.org/

About Dr. Thomaz Bastiaanssen PhD:

Dr. Thomaz Bastiaanssen is the lead bioinformatician in Prof. John F. Cryan’s microbiota-gut-brain axis group in Cork, Ireland. He is interested in the ecological dynamics governing host-microbe communication and how this complex interplay can impact human well-being. He will soon transition to a new role at Amsterdam UMC, the Netherlands, where he will continue to study the microbiome gut-brain axis. Besides working on multi-omics analyses, he enjoys horror stories, tabletop games and spending time with his wife, son, and corgi. His website can be found at: https://thomazbastiaanssen.github.io/

This episode, we discuss how to advance from probiotic mechanisms to human applications, with Prof. Graciela Lorca PhD at the University of Florida in Gainesville, USA. Prof. Lorca talks about her experiences seeking out the mechanisms of action of a probiotic – including which molecules from bacteria may have beneficial effects – and bringing a probiotic through drug trials for use in Type 1 diabetes. They also discuss probiotic responders versus nonresponders and how dietary intake may provide clues about who will respond to an intervention.

Key topics from this episode:

• Prof. Lorca’s lab is primarily concerned with discovering the mechanisms of action of specific probiotics, including the molecules they produce that can have beneficial effects on a host.
• Knowing how a probiotic works allows scientists to select strains that are likely to be effective for a certain application.
• Prof. Lorca’s lab found that L. johnsonii produces extracellular vesicles (EVs) and that a few proteins carried in these EVs may be important markers of where and how they affect the host. She triggered antibodies against these proteins, allowing them to be tracked in the host.
• EVs are small protrusions from the bacterial membrane, and only some bacteria produce them. Evs have complex cargo, which mostly represents the metabolic state of the cell.
• Prof. Lorca studied bacteria that appeared to affect autoimmunity in animal models. In humans, administering these bacteria changed immune markers; this intervention is now in a Phase II trial with humans who have Type 1 diabetes. The bacteria may be acting in the small intestine, but they don’t colonize permanently.
• Extensive data on safety were required to advance the probiotic through to a Phase II trial. Although administering EVs could be an even safer approach, they are difficult to purify from bacteria. Prof. Lorca continues to investigate the bioactive components of these EVs to perhaps administer only those components.
• Prof. Lorca is also interested in responders versus nonresponders to a probiotic intervention. One of her clinical trials showed that people had either high lactic acid bacteria (LAB) or low LAB at baseline. For those with high levels of LAB, the levels didn’t change much over time. But for those with initially low levels of LAB, the levels increased over time. The latter responded better to treatment. Furthermore, people with high LAB were shown to consume a diet with more long-chain fatty acids, which LAB can utilize. Overall, dietary intake may be a key part of uncovering responders and nonresponders.
• Over the next ten years in this field, Prof. Lorca believes we will be able to increasingly personalize probiotics according to someone’s genetics and dietary intake. Regulatory aspects are complicated but continue to evolve.

Episode links:

• Article on how bacterial EVs may have effects on type 1 diabetes: Internalization of extracellular vesicles from Lactobacillus johnsonii N6.2 elicit an RNA sensory response in human pancreatic cell lines
• Tracking bacterial EVs in the host: Identification of Biomarkers for Systemic Distribution of Nanovesicles From Lactobacillus johnsonii N6.2
• Clinical trial showing feasibility of using a probiotic strain in applications related to type 1 diabetes: Lactobacillus johnsonii N6.2 Modulates the Host Immune Responses: A Double-Blind, Randomized Trial in Healthy Adults
• Using diet to predict levels of bacteria in the gut: Identification of food and nutrient components as predictors of Lactobacillus colonization
• Master of Science degree at University of Florida: Microbiome in Health and Disease

About Prof. Graciela Lorca PhD:

Dr. Graciela Lorca is currently a Professor in the Department of Microbiology and Cell Science at the University of Florida. She completed her Licentiate in Genetics studies at the National University of Misiones and later received her doctoral degree in Food Technology at the National University of Tucuman in Argentina. She completed her postdoctoral studies at the University of California San Diego in Molecular Microbiology and at the University of Toronto in Structural Biology and Gene Regulation. Since joining the Department of Microbiology and Cell Science at the University of Florida in 2007, Dr. Lorca has focused on the identification of environmental signals that modulate host-microbe interactions. Using multiomic approaches, her laboratory is investigating the bacterial components such as extracellular vesicles that target host pathways involved on those beneficial interactions in vitro and in vivo. Furthermore, Dr. Lorca’s laboratory is currently conducting human trials to evaluate the use of Lactobacillus johnsonii Type 1 Diabetes patients. Dr. Lorca currently teaches a graduate and undergraduate level Probiotics course. She is also in charge of the new concentration on Microbiome in health and disease within the Online Master program at Department of Microbiology and Cell Science.

How microbes and mucus interact in the gut, With Dr. Mindy Engevik PhD

Episode summary:

In this episode, the ISAPP hosts discuss mucus-microbe interactions in the digestive tract with Dr. Mindy Engevik PhD from the Medical University of South Carolina, USA. They discuss how mucus in the gut is produced and degraded, and different ways that pathogens and commensal microbes interact with the mucus layer. Dr. Engevik describes some different ways that commensal bacteria make use of mucus, as well as dietary influences on gut mucus production.

Key topics from this episode:

• The gut epithelium has special cells called goblet cells that actively secrete mucus. In the small intestine, mucus forms a light barrier but in the colon, it forms a thicker barrier with two layers: an inner layer free of microbes, and an outer layer where mucus and microbes coexist.
• Bacteria in the gut make use of mucus in different ways. Many microbes have the capacity to degrade mucus, and it can provide a carbon source for bacteria to survive. Even bacterial quorum sensing can be influenced by mucus.
• Bifidobacteria increase mucus production. Akkermansia are good at degrading mucus and also increasing mucus production. Pathogens, however, degrade the mucus and cause inflammation so mucus production is suppressed.
• Several human diseases involve a dysfunctional gut mucus layer – for example, inflammatory bowel disease.
• Various models are used for studying mucus – for example, traditional cell lines and human intestinal organoids.
• Dr. Engevik’s work has found interactions between Clostridioides difficile and Fusobacterium nucleatum in the gut: these bacteria can interact to form biofilms that are more antibiotic-resistant than normal.
• Individual differences exist in gut microbes as well as glycan structure in the gut, so the best insights will likely come from understanding the entire network of microorganisms, metabolites, and mucus. 
• Dietary components influence the gut microbiota, which influences mucus production in the gut. High dietary fiber increases the amount of mucus produced by the goblet cells. Some bacteria degrade dietary substrates, then switch over to mucus when they don’t get what they need from the diet.
• Dr. Engvik is an avid science communicator and advocates for scientists being present on social media. She has found science communication a great way to engage with the public as well as fostering scientific collaborations. The Instagram account showing microscopy images from her lab is @the_engevik_labs

Episode links:

• Bifidobacterium dentium Fortifies the Intestinal Mucus Layer via Autophagy and Calcium Signaling Pathways
• Characterizing the mucin-degrading capacity of the human gut microbiota
• Mucin-Degrading Microbes Release Monosaccharides That Chemoattract Clostridioides difficile and Facilitate Colonization of the Human Intestinal Mucus Layer
• Fusobacterium nucleatum Secretes Outer Membrane Vesicles and Promotes Intestinal Inflammation

About Dr. Mindy Engevik PhD:

Mindy Engevik is an Assistant Professor at the Medical University of South Carolina. She has Ph.D. in Systems Biology & Physiology and an interest in microbe-epithelial interactions in the gastrointestinal tract. Her lab focuses on how commensal friendly bacteria in the human gut interact with intestinal mucus and she tries to leverage this information to treat intestinal disorders. You can follow her on Twitter at @micromindy.

Microbial species and strains: What’s in a name? with Dr. Jordan Bisanz PhD

Episode summary:

In this episode, the ISAPP podcast hosts speak with Dr. Jordan Bisanz PhD, Assistant Professor of Biochemistry and Molecular Biology at Penn State University in State College, USA. They discuss how to define a bacterial strain, the diversity of strains within a species, and how genetic differences correspond with functional differences. They also talk about manipulating microbial communities for insights about health and disease.

Key topics from this episode:

• Dr. Bisanz says just because strains within a species are genetically related doesn’t mean they do the same things. Bacteria gain and lose genes rapidly, but we don’t yet know what a lot of those genes do.
• Natural variation in strains can be used as a tool to find out the functions of genes. 
• Metagenomics illuminates strain-level differences, but that assumes we know what makes a strain. There’s no single accepted definition of a strain.
• Knowing the mechanisms behind the effects of a strain on a host is important for predicting if closely related strains will have the same effect.
• Moving forward, it could be useful to have functional information to go along with strains and their taxonomic descriptors.
• Dr. Bisanz’s lab tests experimentally how microbial genes are gained and lost in vivo, both through wetlab experiments and computational approaches.
• Experiments on strains are essential – for example, two strains with differences in 1000 SNPs might be functionally the same, while differences in 2-3 key SNPs might make a big difference.
• When testing probiotic effects, you may be testing something derived from the original microbial genome but not identical. How can this be managed in industry? Understanding the mechanisms is important, strains that function similarly can qualify as the same strain.
• A microbiome involves multiple microbes working together, acting differently from all the strains in isolation.
• Dr. Bisanz studies tractable microbial communities: find the microorganisms that are different in a disease state compared to a healthy state, and create a synthetic community of the microbes that are absent. What are the functions of this community?
• The challenge is that microbiologists need to be able to manipulate the microbes but cannot do this in a whole human fecal sample.
• Is gut microbiome sequencing useful? At the level of individual, it may not provide value. But putting the data all together, in the future it may provide interesting information. The challenge with interpretation is that the microbiome is driving, but also responding to, dietary inputs.
• In the microbiome field, gnotobiotic models (using humanized mice) need to be taken a step further than they currently go – specifying not only which microbes established in the host, but also how they could plausibly affect the mechanism.

Episode abbreviations and links:

• Review on strain diversity co-authored by Dr. Bisanz: Challenges and opportunities of strain diversity in gut microbiome research
• Computational and experimental resources for mapping phenotypes to genes: A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria
• Example of mechanistic insights: Human gut bacteria produce ΤΗ17-modulating bile acid metabolites
• Research highlight on complex synthetic microbial communities: Making gut microbiomes from scratch
• Description of a defined complex microbial community: Design, construction, and in vivo augmentation of a complex gut microbiome

About Dr. Jordan Bisanz PhD:

Jordan Bisanz is an assistant professor of Biochemistry and Molecular Biology at the Pennsylvania State University and the One Health Microbiome Center. The Bisanz lab combines computational analyses and wet lab experimentation to understand how gut microbes interact with each other and their host. The lab specializes in coupling human intervention studies with multi ‘omics approaches and gnotobiotic models to understand how host-microbe interactions shape health generating both mechanistic insights and translational targets.

A systems biology perspective on the gut microbiome, with Dr. Sean Gibbons PhD

Episode summary:

In this episode, the ISAPP hosts discuss the microbiome and systems biology with Dr. Sean Gibbons PhD, Associate Professor at the Institute for Systems Biology in Seattle, USA. Prof. Gibbons talks about exploring and manipulating the complex ecology of the microbiome with the aim of engineering outputs of this system. He describes the utility of artificial intelligence in microbiome science and how the microbiome will play a role in personalized medicine in the future, including in the delivery of probiotics and prebiotics.

Key topics from this episode:

• Dr. Gibbons’ lab primarily focuses on designing bioinformatic tools for exploring and manipulating the complex ecology of the microbiome, and trying to shape the outputs of the system. He emphasizes the need for computational tools alongside traditional microbiological techniques, which are needed to validate computational findings.
• From the work so far, he says probiotics appear to be efficacious but context-specific, so the effects may appear dampened in trials with heterogeneous participants.
• He underlines that artificial intelligence (AI) is needed to integrate complexity and predict emergent outputs of a biological system that includes a microbiome. Reductionist approaches are somewhat limited because each component of a complex system may behave differently on its own.
• Diet is a key way to deliberately manipulate the gut microbiome. Researchers are working on how to push the system in a predictable direction. One approach is to create orthogonal niches for organisms: for example, an item in the diet (such as seaweed) that could support an organism that wouldn’t otherwise be there. His lab is working on tools that predict the likelihood of engraftment of a particular organism in a complex community.
• Reliable tools are needed to map taxonomic composition onto functional outputs.
• Two branches existed in the history of AI: (1) extracting new knowledge using approaches such as neural nets, and (2) A symbolic AI family of modelling, in which you already have knowledge and you can use it to make predictions about a system (making use of knowledge graphs).
• Dr. Gibbons says microbiome measurements will likely be a part of clinical medicine in the future, because the microbiome accounts for individuals’ personalized responses to some interventions that cannot be explained by any other known factor.
• In the future, we will be able to develop tools for precision prebiotic, probiotic, and dietary interventions through metabolic modelling work. 
• Many probiotics have great efficacy in a particular context – so one challenge ahead is to find a rational way to deploy these organisms and to prove they work well. We will need to address the regulatory challenges inherent in personalized approaches as well.

Episode links:

• DGGE: Denaturing Gradient Gel Electrophoresis
• Paper on correlation analyses: Use and abuse of correlation analyses in microbial ecology
• Comment on a new approach to clinical trials required for precision medicine: Personalized medicine: Time for one-person trials
• Paper on the gut microbiome and statin response: Heterogeneity in statin responses explained by variation in the human gut microbiome
• Paper on developing niches in a microbial ecosystem: Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal
• Paper on horizontal gene transfer in the gut microbiome: Elevated rates of horizontal gene transfer in the industrialized human microbiome

About Dr. Sean Gibbons PhD:

Sean Gibbons earned his PhD in biophysics from the University of Chicago in 2015. He completed his postdoctoral work at MIT in 2018. Sean is now an associate professor at the Institute for Systems Biology, in Seattle. His lab studies the ecology and evolution of microbial communities. In particular, Sean is interested in how host-associated bacterial communities influence the health and wellness of the host organism. His group designs computational and wet-lab tools for studying these complex systems. Ultimately, the Gibbons Lab aims to develop strategies for engineering the ecology of the gut microbiome to improve human health.

Human milk oligosaccharides in the infant gut, with Dr. Simone Renwick PhD Episode summary:

In this episode, the ISAPP hosts discuss human milk and the infant gut with Dr. Simone Renwick PhD from Mother-Milk-Infant Center of Research Excellence (MOMI CORE) at UC San Diego, USA. Dr. Renwick talks about her work investigating how communities of microbes versus individual microbes in the infant gut metabolize human milk oligosaccharide (HMO) structures, and what we know about the origin and functions of the microbes contained in human milk.

Key topics from this episode:

• Dr. Renwick studies how components of human milk foster the development of the infant gut microbiota. These components include HMOs (special sugars found in human milk) and the milk microbiota.
• HMOs cannot be metabolized by the human body, but when microbes in the infant gut break them down, it has health benefits for the infant (because infants who receive no human milk are predisposed to a range of diseases).
• Dr. Renwick used in vitro models to mimic infant microbiota communities, and found that these communities rapidly degraded the HMOs. This metabolism increased microbes associated with health and suppressed potentially pathogenic microbes. 
• Although most research on HMOs focuses on bifidobacteria that are specially equipped to break them down, she looked at individual strains within the infant gut community and found approximately 100 species capable of directly degrading HMOs.
• Once breastfeeding ceases, some microbes in the infant gut adapt to different sources of sugars, but others greatly decrease in abundance.
• Microbes act differently in a community than on their own. Within a complex community, microbes that are better equipped to degrade the HMOs will act quickly, producing byproducts that are then are available to other members.
• All of the different in vitro models have their advantages and disadvantages. The spatial relationships of the human body are often missing in in vitro models.
• Humans appear to have the highest concentration of milk oligosaccharides of any mammal.
• The milk microbiota is another active area of investigation. Live microbes are present in the mammary gland, but their source is still unknown. They tend to resemble the composition of the microbiota on the skin as well as the infant oral cavity, but curiously, anaerobic bacteria are also found in the milk microbiota. Somehow these microbes may move from the mother’s gut to the milk. These microbes may not directly metabolize HMOs. (See this paper.)
• Formula companies are beginning to put HMO structures into their products – mainly 2′-Fucosyllactose.

Episode links:

• Human milk oligosaccharides — Prebiotics in a class of their own? ISAPP webinar.
• The many functions of human milk oligosaccharides: A Q&A with Prof. Ardythe Morrow. ISAPP blog.
• Bifidobacteria in the infant gut use human milk oligosaccharides: how does this lead to health benefits? ISAPP blog.

About Dr. Simone Renwick PhD:

Dr. Simone Renwick is the Milk & Microbes postdoctoral fellow at the Mother-Milk-Infant Center of Research Excellence (MOMI CORE) at the University of California, San Diego, USA. Her research focuses on understanding the role of human milk components, such as the human milk oligosaccharides (HMOs) and milk microbiota, in fostering the developing infant gut microbiota. She is also interested in the potential therapeutic applications of milk components in diseases that affect adults. Currently, Simone is supervised by Drs. Lars Bode, Rob Knight, Pieter Dorrestein, and Jack Gilbert. Prior to her postdoc, Simone completed her PhD in Molecular and Cellular Biology (MCB) at the University of Guelph, Canada, under the supervision of Dr. Emma Allen-Vercoe.

She was the recipient of the Students and Fellows Association poster prize at the ISAPP 2023 meeting in Sitges, Spain.

We discuss microbes, mucus, and milk with Dr. Clara Belzer PhD from Wageningen University in the Netherlands in this episode. Dr. Belzer, a molecular geneticist, specializes in studying the microorganisms that are equipped to break down the glycans in mucus and human milk within the host environment.

Key topics from this episode:

• Dr. Belzer’s research focuses on the microbes living in the host that survive on glycans (chains of sugars) produced by the host: milk oligosaccharides and mucus. The host is not good at digesting these sugars, but can use them when they’re separated into smaller components. These long chains of sugars end up in the large intestine, where certain microbes begin to digest them.
• There seems to be an evolutionary adaptation that sustains the symbiotic relationship between human milk and bacteria in the infant gut; many immune molecules in the human milk suppress pathogens, so the human milk oligosaccharides (HMOs) are available to the bacteria in the infant gut that can break them down. The bacteria are not suppressed by the acidic environment in the infant gut.
• Human milk is the best food for infants, but innovations in infant formula may make it more similar to human milk.
• Akkermansia is a genus of bacteria mostly found in adults, but also sometimes in infants, which grows in the mucosal layer of the intestines. (It doesn’t survive on dietary glycans.) Dr. Belzer’s hypothesis is that the environment created by human milk in the infant gut also fosters bacteria that can grow on mucus, creating a succession of host-benefitting bacteria. They found that HMOs, in addition to mucus, can support the growth and survival of Akkermansia, potentially helping it build a microbial network.
• There’s a genetic component to the HMOs contained in human milk; similarly, the sugar content in the mucosal glycans is related to host genetics.
• Lean individuals have a higher abundance of Akkermansia; these bacteria improve metabolism (for example, increasing insulin sensitivity) and have effects on the immune system, which both contribute to a lean phenotype. The root of these effects may be the strengthening of the gut barrier, which dampens signals from the lumen.
• Dr. Belzer has used both omics and culture-based approaches in her research. As part of her research she tries to make microbial synthetic communities, growing them in the lab and stimulating them with different glycans. This technique yields insights about the functions and microbial ecology in the gut.
• Killed Akkermansia are still able to bring health benefits to the host. Dr. Belzer had the idea that the pili structures on the bacteria were what communicated with the host, and sure enough, this was borne out in a study that showed the proteins in the pili (Amuc_1100) remained intact in the pasteurized bacteria and could stimulate the host immune system. This is a valuable finding because Akkermansia are difficult to culture.
• When Akkermansia fails to occupy the niche in the mucus layer, Bacteroides species may occupy the niche instead, forming a different microbial community in the mucus. Research is ongoing about the effects of different microbes carrying out similar functions for the host. Furthermore, scientists have many more microbial functions to discover.

Episode abbreviations and links:

• Paper showing the growth of Akkermansia on HMOs: Akkermansia muciniphila uses human milk oligosaccharides to thrive in the early life conditions in vitro
• Study showing attenuation of diet-induced obesity in mice with Akkermansia: Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
• Study showing the Amuc_1100 protein mechanism for Akkermansia: A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice

About Dr. Clara Belzer PhD:

Dr. Clara Belzer is Associate Professor Microbiology at the Laboratory of Microbiology of Wageningen University. The Belzer group is called ‘Microbes Mucus and Milk’ and the research is focused on the interaction of the gut microbiome with host mucus and milk. After obtaining her PhD at the Erasmus Medical Center Dr. Belzer did a postdoc at Harvard medical school. By now Dr. Belzer has years of experience on gut microbiome studies on anaerobes, including synthetic communities and different biotic concepts, with a special interest for the Akkermansia muciniphila. The group of Dr. Belzer works on several microbiome HMO and mucus related topics funded by national and international grants, some also in collaboration with medical centers and industry.

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Lactobacilli in the microbiomes of the gut, skin, reproductive tract and more, with Prof. Kingsley Anukam PhD Episode summary:

In this episode, the ISAPP podcast hosts cover a range of topics related to lactobacilli and health with Prof. Kingsley Anukam PhD from Nnamdi Azikiwe University in Nigeria. Prof. Anukam has a special interest in lactobacilli, and studies lactobacilli in microbiomes across many different contexts: fermented foods, skin, gut, and reproductive tract sites. He talks about the wide range of research he has led in Nigeria using diverse sources of funding.

Key topics from this episode:

• Prof. Anukam describes his collaboration with Prof. Gregor Reid PhD early in his career, prompted by a paper claiming that African women did not have vaginal microbiomes dominated by lactobacilli. Subsequent work showed this was not the case – confounding factors contributed to the initial result.
• He cautions researchers against making conclusions about race or ethnicity when geographical variations or other factors could better account for the differences between groups. In studies it’s important to specify the geography as well as the other factors (dietary, cultural) that may impact the gut microbiome in these populations.
• There is a long history of fermented foods in Africa but not a lot of research has been done on them. In a 2009 paper with Prof. Reid, Prof. Anukam reported isolated lactic acid species from a fermented food called okpeye produced in Eastern Nigeria. The isolates showed potential for industrial applications.
• Most of his research studies are funded from outside Nigeria, with different sources of funding.
• ‘Parachute’ science is common in Africa, where researchers come into an African country, obtain samples and leave. He encourages researchers to involve local scientists to build capacity and allow them to do the analysis.
• Prof. Anukam describes a clinical trial he led on the skin microbiome and malodor in Nigerian youth. He found the skin microbiome in the armpit was altered if individuals used deodorants and antiperspirants; and these individuals kept having the same malodor issues. Individuals with less odor were found to have more lactobacilli on the skin, with differences in composition between men and women. They developed a topical cream to use as an intervention for 14 days, and found that lactobacilli on the skin increased and less odor was reported.
• The microbiome(s) of the male reproductive organs have not been studied very much. Semen has a microbiome, and this is shown by both culture and non-culture methods. It is dominated by lactobacilli, and this corresponds with semen quality. The evidence is mixed on the existence of testes and prostate microbiomes. A gut-testes connection may exist, however, as shown in mouse studies.
• Prof. Anukam says in a study of subjects seeking reproductive healthcare, different microbiomes were observed both in males and females having difficulty conceiving.
• The semen microbiome could play a significant role in reproduction – for example, it may produce metabolites that could affect the female reproductive tract and influence the environment for conception to take place. When doing in vitro fertilization, evidence has shown that if the samples are contaminated by pathogens, it can be difficult to achieve conception.

Episode links:

• Paper from 2009 on fermented foods: African traditional fermented foods and probiotics
• Paper from 2021 on skin malodor: Topical cream containing live lactobacilli decreases malodor-producing bacteria and downregulates genes encoding PLP-dependent enzymes on the axillary skin microbiome of healthy adult Nigerians
• Paper from 2021 on reproductive microbiomes: Microbiome Compositions From Infertile Couples Seeking In Vitro Fertilization, Using 16S rRNA Gene Sequencing Methods: Any Correlation to Clinical Outcomes?

About Prof. Kingsley Anukam PhD:

Kingsley C Anukam is a research scientist in human microbiome and biotherapeutics with over 20 years experience. He shares his time between Canada and Nigeria as an adjunct professor at Nnamdi Azikiwe University where he assists in the training and supervision of post graduate students working in the area of probiotics, fermented foods, human microbiome, infectious diseases, laboratory diagnostics, human genomics and forensic DNA analysis. He had his graduate education in Nigeria and post doctorate training in Dr. Gregor Reid’s Lab at Lawson Health Research Institute and Department of Microbiology and Immunology, Western University, Canada. He is the first from Africa to show that vaginal microbiome of healthy Nigerian women is similar to women from other populations irrespective of geographical location. He has sequenced and annotated the full genome of over 10 Lactobacillus species of African origin mainly from the reproductive tract and African fermented foods in collaboration with Prof. Sarah Lebeer. He played a significant role in the formation of the DORA project, an ISALA-inspired citizen science for vaginal health in Nigeria. He has over 80 scientific research publications in peer-reviewed journals and listed among first 10 most cited researcher at Nnamdi Azikiwe University by Google Scholar. He is currently the Chief Editor, Journal of Medical Laboratory Science, and a peer-reviewer of several international journals.

In this episode, the ISAPP podcast hosts themselves are the experts: Prof. Colin Hill PhD from APC Microbiome Ireland / University College Cork and Prof. Dan Tancredi PhD from University of California – Davis talk about their recent work investigating the health benefits from consuming higher quantities of live dietary microbes – and not just microbes that meet the probiotic criteria.

Key topics from this episode:

• Profs. Hill and Tancredi were involved with others in a recent series investigations & 3 published papers on whether there should be a recommended daily intake of live microbes.
• Prof. Hill started by writing a blog, prompted by the finding that meta-analyses on probiotics tended to show some general benefits for health. Would this apply to any safe, live microbes – even those that do not meet the probiotic criteria?
• Various hypotheses (hygiene hypothesis, old friends hypothesis, missing microbes hypothesis) posit that a lack of microbes is associated with poorer health.
• Clean water and clean food have reduced the burden of infectious disease. But at the same time, across populations there has been an increase in chronic diseases. Could a lack of live dietary microbes be contributing to this increase in chronic disease, because the immune system lacks adequate inputs? Or in other words, could there be a general health benefit for healthy people in consuming high quantities of live microbes?
• To address the hypothesis scientifically: they investigated the health status of people who eat large vs. small numbers of safe live microbes in their diets. Starting with NHANES data in the US, the researchers classified foods into categories of high / medium / low numbers of live microbes.
• Note that not all fermented foods contain live microbes, but some contain high numbers of live microbes. A possible confounding factor in the analysis was that high microbe foods tend to be healthier foods.
• The researchers published a series of 3 papers. The 3rd paper showed an association between intake of live microbes and various (positive) measurements of health. Consistent, modest improvements were seen across a range of health outcomes.
• This is an association, but statistically the team did use regression analysis to statistically adjust for effects on health that could be due to other factors besides the live microbial intake.
• The take-home is not to eat unsafe or rotten food, but rather to eat more high-microbe or fermented foods, and in general eat a healthy diet.

Episode links:

• Prof. Hill’s blog: Recommended daily allowance (RDA) for microbes?
• Paper 1: Should There Be a Recommended Daily Intake of Microbes?
• Paper 2: A Classification System for Defining and Estimating Dietary Intake of Live Microbes in US Adults and Children
• Paper 3: Positive health outcomes associated with live microbe intake from foods, including fermented foods, assessed using NHANES database

About Prof. Colin Hill PhD:
Colin Hill has a Ph.D in molecular microbiology and is a Professor in the School of Microbiology at University College Cork, Ireland. He is also a founding Principal Investigator in APC Microbiome Ireland, a large research centre devoted to the study of the role of the gut microbiota in health and disease. His main interests lie in the role of the microbiome in human and animal health. He is particularly interested in the effects of probiotics, bacteriocins, and bacteriophage. In 2005 Prof. Hill was awarded a D.Sc by the National University of Ireland in recognition of his contributions to research. In 2009 he was elected to the Royal Irish Academy and in 2010 he received the Metchnikoff Prize in Microbiology and was elected to the American Academy of Microbiology. He has published more than 600 papers and holds 25 patents. More than 80 PhD students have been trained in his laboratory. He was president of ISAPP from 2012-2015.

About Prof. Dan Tancredi PhD:
Daniel J. Tancredi, PhD, is Professor in Residence of Pediatrics in the University of California, Davis School of Medicine. He has over 25 years of experience and over 300 peer-reviewed publications as a statistician collaborating on a variety of health-related research. A frequent collaborator on probiotic and prebiotic research, he has attended all but one ISAPP annual meeting since 2009 as an invited expert. In 2020, he joined the ISAPP Board of Directors. Colin Hill and Daniel co-host the ISAPP Podcast Series “Science, Microbes, and Health”. On research teams, he develops and helps implement effective study designs and statistical analysis plans, especially in settings with clusters of longitudinal or otherwise correlated measurements, including cluster-randomized trials, surveys that use complex probability sampling techniques, and epidemiological research. He teaches statistics and critical appraisal of evidence to resident physicians; graduate students in biostatistics, epidemiology, and nursing; and professional scientists. Dan grew up in the American Midwest, in Kansas City, Missouri, and holds a bachelor’s degree in behavioral science from the University of Chicago and masters and doctoral degrees in mathematics from the University of Illinois at Chicago. He lives in the small Northern California city of Davis, with his wife Laurel Beckett (UC Davis Distinguished Professor Emerita), their Samoyed dogs Simka and Milka, and near their two grandkids.

The role of microbes in gut-brain communication, with Prof. Emeran Mayer MD Episode summary:

In this episode, ISAPP podcast host Prof. Dan Tancredi PhD welcomes guest Prof. Emeran Mayer MD, a gastroenterologist and researcher at University of California Los Angeles. They talk about the microbiota-gut-brain axis, covering its evolutionary origins and how this complex system works in the human body to support overall health.

Key topics from this episode:

• Microbiota-gut-brain communication has a long evolutionary history: microbes have been around for billions of years and they stored a lot of information in their genes. At some point in evolution microbes got inside the digestive tube of a primitive marine animal called hydra and it proved advantageous for this animal.
• The hydra shows the origin of the human enteric nervous system (ENS): microbes live inside this tube and transfer genes to the nerve cells of this digestive tube, showing the origin of neurotransmitters.
• Today in humans the neurotransmitters influence gene expression of microbes and change the microbial behaviors; the metabolites produced feed back to the brain.
• Prof. Mayer’s initial interest as a gastroenterologist was the ENS and how it regulates motility. Subsequently the ENS was found to regulate many gut functions. The gut also houses a large part of the immune system and a complex hormonal system, and all these systems are connected with each other and communicate with the brain.
• There is an increasing understanding that many chronic diseases relate to Inappropriate engagement of the immune system, starting in the gut.
• When Prof. Mayer started in the field, the term “gut health” did not exist. Now it’s a ubiquitous term which has associations with wellbeing, acknowledging the gut has influence on many other body systems.
• The associations between gut (microbiota) and brain health started with provocative animal experiments from Cork, Ireland, in which researchers manipulated the gut microbiome and found changes in emotion-like behaviors of animals. However, it has been difficult to translate to human interventions.
• How do microbiome-targeted dietary interventions affect the brain? We do know the “Standard American Diet” (deficient in fiber) has changed the gut microbes in a way that compromises the production and maintenance of the gut barrier. 
• There are many misconceptions about “leaky gut”, but basically contact between beneficial microbes and immune system sensors stimulate the immune system of the gut to low-grade inflammation. This can alter the tight junctions, making the gut more permeable, and ultimately this can affect the brain. Diet can affect the role of microbes in maintaining an effective gut barrier.
• Prof. Mayer describes how he ended up studying the microbiota-gut-brain axis – he would not have predicted how important and popular this field would become.
• In the future, there will be more sophisticated and personalized interventions. He sees a paradigm shift happening from reductionist approaches in medicine to systems biological approaches. This field is making us acknowledge that diet will play a major role.

Episode links:

• Prof. Mayer’s first academic book, Basic and Clinical Aspects of Chronic Abdominal Pain (Pain Research and Clinical Management) 
• Prof. Mayer’s first book for the general public, The Mind-Gut Connection
• Review on microbiota-gut-brain axis: The Microbiota-Gut-Brain Axis: From Motility to Mood 
• Review on the impact of diet on intestinal permeability: Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia
• Review on microbiota-dependent interactions between diet and the immune system: Human nutrition, the gut microbiome, and immune system: envisioning the future

About Prof. Emeran Mayer MD:

Emeran A Mayer is a Gastroenterologist, Neuroscientist and Distinguished Research Professor in the Department of Medicine at the David Geffen School of Medicine at UCLA, the Executive Director of the G. Oppenheimer Center for Neurobiology of Stress & Resilience and Founding Director of the Goodman Luskin Microbiome Center at UCLA. He is one of the pioneers and leading researchers in the bidirectional communication within the brain gut microbiome system with wide-ranging applications in intestinal and brain disorders. He has published 415 scientific papers, co edited 3 books and has an h-index of 125. He published the best selling books The Mind Gut Connection in 2016, the Gut Immune Connection in June 2021, and the recipe book Interconnected Plates in 2023. He is currently working on a MasterClass and a PBS documentary about the mind gut immune connection. He is the recipient of numerous awards, including the 2016 David McLean award from the American Psychosomatic Society and the 2017 Ismar Boas Medal from the German Society of Gastroenterology and Metabolic Disease.

The effects of metabolites in the colon, with Prof. Kristin Verbeke PhD

Episode summary:

In this episode, the ISAPP podcast hosts talk about colonic metabolites with Prof. Kristin Verbeke PhD, from KU Leuven, Belgium. She talks about characterizing microbial metabolism in the colon and the consequences of producing various metabolites, both beneficial ones (such as short-chain fatty acids) and potentially detrimental ones.

Key topics from this episode:

• Prof. Verbeke is a pharmacist by training, and now leads hospital breath testing and carries out research on microbial metabolites in the gastrointestinal tract, including how prebiotics and probiotics can change bacterial metabolism.
• The majority of protein in the diet is digested in the small intestine, but about 5% of animal protein and 10-15% of plant protein reaches the large intestine to be fermented by the microbiota. This produces metabolites, which are shown in vitro to be toxic. However, in vivo there is less evidence of toxicity; the negative effects of these metabolites may be reduced by the interactions of different compounds in the colon.
• Short-chain fatty acids (SCFAs) are produced when the body digests dietary fiber, and Prof. Verbeke’s group and others are investigating whether they are responsible for the benefits of eating fiber.
• Most SCFAs are quickly absorbed in the large intestine, and they serve as an energy source for the cells. They then travel to the liver via portal circulation, where they have additional functions. What’s left over reaches systemic circulation.
• The difficulty is knowing how many SCFAs are produced in the colon, and how many reach systemic circulation. In one experiment, they labeled the SCFAs that were administered to the colon via capsule; 36% ended up in systemic circulation. Further, when SCFAs were administered at physiological doses the subjects receiving them (compared to placebo) showed a lower cortisol response to stress.
• SCFAs also affect fat oxidation and fat synthesis in the liver. Their relevance to non-alcoholic fatty liver disease are being investigated.
• It’s important to eat fiber, and lots of different types. After fiber consumption, SCFAs increase in a sustained manner and take about 8h to get back to baseline. But with SCFA delivery via capsule they spike quickly and then disappear.
• As for coatings to deliver to the colon, some coatings are time-dependent, pH dependent, etc. and this is an area for further exploration.

Episode links:

• Study on protein fermentation: Modulation of protein fermentation does not affect fecal water toxicity: a randomized cross-over study in healthy subjects
• Study on SCFAs: Systemic availability and metabolism of colonic-derived short-chain fatty acids in healthy subjects: a stable isotope study
• Review: Coated dosage forms for colon-specific drug delivery

About Prof. Kristin Verbeke PhD:

Kristin Verbeke graduated from the KU Leuven, Belgium as a pharmacist in 1991. She obtained a PhD in Pharmaceutical Sciences at the Laboratory of Radiopharmaceutical Chemistry in 1995 and subsequently spend a postdoctoral period in developing radioactively labelled compounds. In 2002, she was appointed at the department of gastroenterology of the Medical Faculty of the Leuven University where she got involved in the use of stable isotope labelled compounds to evaluate gastrointestinal functions. Within the University Hospitals Leuven, she is responsible for the clinical application of diagnostic 13C- and H2-breath tests. Her current research interest specifically addresses the microbial bacterial metabolism in the human colon. Her team has developed several analytical techniques based on mass spectrometry and stable isotope or radioisotope technologies to evaluate several aspects of intestinal metabolism and function in humans (transit time, intestinal permeability, carbohydrate fermentation, protein fermentation, metabolome analysis). Collaborative research has allowed showing an aberrant bacterial metabolism in patient groups with end stage renal failure, inflammatory bowel diseases, irritable bowel disorders and alcohol abuse. These collaborations all have resulted in high quality peer-reviewed papers. In addition, she showed the impact of dietary interventions (modulation of macronutrient composition, pre- or probiotic interventions) on the microbial metabolism and its impact on health. As a PI, she acquired grant support from the university and different funding bodies and successfully completed these projects. Similarly, she supervised several PhD projects that all resulted in the achievement of a PhD degree. Her research resulted in over 200 full research papers. Together with colleague Prof. J. Delcour, she was the beneficiary of the W.K. Kellogg Chair in Cereal Sciences and Nutrition (2010-2020). She is the president of the Belgian Nutrition Society, the vice-chair of the Leuven Food Science and Nutrition Center, and the co-chair of the Prebiotic task force at ILSI Europe. Furthermore, Kristin Verbeke is the editor of the journal Gut Microbiome and member of the editorial board of Gastrointestinal Disorders. Kristin joined the ISAPP Board of Directors in 2023.

In this episode, the ISAPP podcast hosts talk about how the probiotic field has evolved over the past 20 years with Dr. Mary Ellen Sanders PhD, ISAPP’s outgoing executive director. She describes how ISAPP is a unique organization advancing the science in the field, highlights what she has enjoyed about being a part of the ISAPP community, and looks ahead to the future of the field.

Key topics from this episode:

• Sanders describes her career path and how it led to her role with ISAPP. 
• Both ISAPP and Sanders’ role have changed over time, but she always appreciated two things: great scientific discussions, and interacting with an excellent board of directors.
• ISAPP has always been dedicated to following the science, highlighting where the evidence is but also the shortcomings of the evidence.
• The development of microbiome science changed the field of probiotics but it remains important to focus on what probiotics can do for health, rather than what they can do for the microbiome.
• Mechanisms are important to elucidate, but the most important thing is whether a product impacts health.
• Sanders says regulations are needed and in the future she hopes regulators will reach out to the expert scientists more frequently and be clear about the standards they expect for a claim.
• ISAPP meetings are unique–both scientifically enlightening and a lot of fun. Longtime ISAPP board member Prof. Gregor Reid PhD MBA had the initial idea for the successful ‘discussion groups’ held every year. 
• In the future, Sanders thinks probiotics will be used more precisely, like medicines. But also the concept of live dietary microbes may become more popular, with quantities of safe microorganisms being consumed for health benefits.

Episode links:

• Read about Todd Klaenhammer, a well-known food microbiologist who supervised Sanders as a graduate student.
• Early paper by Mary Ellen Sanders (1993): Effect of Consumption of Lactic Cultures on Human Health
• An overview of ISAPP activities is found here.
• The ISAPP-linked scientific papers on live dietary microbes:
• Should There Be a Recommended Daily Intake of Microbes?
• A Classification System for Defining and Estimating Dietary Intake of Live Microbes in US Adults and Children
• Positive Health Outcomes Associated with Live Microbe Intake from Foods, Including Fermented Foods, Assessed using the NHANES Database

About Dr. Mary Ellen Sanders PhD:

Mary Ellen Sanders, PhD has served in several roles within ISAPP. She was the founding president, executive science officer and executive director and has retired from ISAPP as of June 30, 2023. She is also a consultant in the area of probiotic microbiology. She works internationally with food and supplement companies to develop new probiotic products and offers perspective on paths to scientific substantiation of probiotic product label claims. She is the current chair of the United States Pharmacopeia’s Probiotics Expert Panel, was a member of the working group convened by the FAO/WHO that developed guidelines for probiotics and serves on the World Gastroenterology Organisation Guidelines Committee preparing practice guidelines for the use of probiotics and prebiotics for gastroenterologists.

Studying microbial ecosystems and how they support health, with Prof. Emma Allen-Vercoe PhD

Episode summary:

In this episode, the ISAPP podcast hosts talk about microbial ecosystems with Prof. Emma Allen-Vercoe PhD from the University of Guelph in Canada. Prof. Allen-Vercoe describes how her lab brings together information from microbial sequencing and culturing to learn about the human gut microbiome and how it supports health. She discusses what we know about the industrialized gut microbiome and possible ways to improve health by manipulating it.

Key topics from this episode:

• What the microbiome is and the suite of tools that are typically used to study it.
• Allen-Vercoe does both sequencing and culturing in her lab as well as metabolomics, proteomics, and transcriptomics to discover on a molecular level at what the microbes are doing. They have a model system called “Robogut” to study microbial ecosystems.
• Culturing is still crucial and it’s important for trainees in microbiology to gain experience culturing organisms that are less straightforward to grow. The late Sydney Finegold inspired others to try culturing more challenging microorganisms.
• The challenge of culturing is matching the techniques in the lab to what happens in nature when it grows. Her lab builds metagenome-associated genomes to be able to predict the particular substrates that a certain microbe needs to grow.
• The “missing microbes” hypothesis is that the human microbiome has been depleted over a few generations in people from industrialized societies, and this correlates with an increase in chronic diseases.
• The Yanomami people from South America have very diverse gut microbiomes and they share certain species with other non-industrialized societies very distant from them around the world, which are not found in industrialized populations. People in industrialized societies are never exposed to these microbes, but even if they were, the microbes might not stick around because the substrates needed to sustain them  (e.g. through the diet) are absent. 
• The industrialized microbiome is not necessarily ‘bad’ but we do have to find out more about whether the lack of certain microbes has health effects. This is possible through the Robogut system, which can perturb microbial ecosystems and look at their behavior without affecting people’s health.
• Fecal transplants have limitations, so they’ve started to work on therapeutic ecosystems. These are “clean” or defined ecosystems that can be administered therapeutically.

Episode links:

• Paper on the Robogut system: The Robogut: A Bioreactor Model of the Human Colon for Evaluation of Gut Microbial Community Ecology and Function
• Allen-Vercoe mentioned the work of Sydney (Sid) Finegold in tackling difficult-to-culture microorganisms.
• 2009 review by Blaser and Falkow: What are the consequences of the disappearing human microbiota? 
• Book by Martin Blaser: Missing Microbes – How the Overuse of Antibiotics Is Fueling Our Modern Plagues
• Paper on Yanomami gut microbiomes: Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter-Gatherer Group
• Paper from Allen-Vercoe lab: Culturing Human Gut Microbiomes in the Laboratory

About Prof. Emma Allen-Vercoe PhD:

Emma obtained her BSc (Hons) in Biochemistry from the University of London, and her PhD in Molecular Microbiology through an industrial partnership with Public Health England. Emma started her faculty career at the University of Calgary in 2005, with a Fellow-to-Faculty transition award through CAG/AstraZeneca and CIHR, to study the normal microbes of the human gut. In particular, she was among the few that focused on trying to culture these ‘unculturable’ microbes in order to better understand their biology. To do this, she developed a model gut system to emulate the conditions of the human gut and allow communities of microbes to grow together, as they do naturally. Emma moved her lab to the University of Guelph in late 2007, and has been a recipient of several Canadian Foundation for Innovation Awards that has allowed her to develop her specialist anaerobic fermentation laboratory further. This has been recently boosted by the award of a Tier 1 Canada Research Chair in Human Gut Microbiome Function and Host Interactions. In 2013, Emma co-founded NuBiyota, a research spin-off company that aims to create therapeutic ecosystems as biologic drugs, on a commercial scale. The research enterprise for this company is also based in Guelph.