This episode features Prof. Kevin Foster PhD from University of Oxford (UK), speaking about his lab’s ecological approach to the gut microbiome and efforts to understand and predict dynamics of different species in the microbiome. They also focus on how these ecological dynamics map onto health outcomes, and how they inform interventions. In a 2023 paper, they explored the concept of colonization resistance in the gut, and why certain bacteria or combinations of bacteria are particularly good at preventing pathogens from thriving. Both diversity and composition are important for determining the extent to which a community resists a pathogen. But a microbiome may equally resist a probiotic that’s introduced because the probiotic microorganism doesn’t have access to a unique nutrient. How bacteria interact with each other can help determine resiliency or stability of the microbiome overall. While it’s true that hundreds of species of bacteria exist in the gut, the scale at which the microbes interact locally is much more limited (on the scale of tens of species). Episode abbreviations and links: 2023 paper examining colonization resistance against 2 pathogens: Microbiome diversity protects against pathogens by nutrient blocking.  About Prof. Kevin Foster PhD: Professor Kevin Foster FRS is the Chair of Microbiology at the Dunn School of Pathology, University of Oxford. Prior to this, he was Professor of Evolutionary Biology in the departments of Biology and Biochemistry at Oxford. Before Oxford, he had a lab at Harvard as a Bauer Fellow in the FAS Center for Systems Biology. He did his undergrad at Cambridge in Natural Sciences and his Ph.D. at the University of Sheffield in evolutionary biology. Professor Foster’s research integrates the traditional fields of ecology and evolution with the latest methods in computation, microbiology, molecular genetics, and the study of the mammalian microbiome. The lab focuses on how bacteria compete and succeed in their communities and seeks to use this to manipulate gut communities for better health.

This episode features Dr. Joao Xavier PhD, a systems biologist from Memorial Sloan Kettering Cancer Center, speaking about the application of ecological principles and tools to individuals being treated for cancer. His lab combines multi-omics profiling with ecological models to generate insights on how microbes interact with each other, for application to clinical risk prediction and microbiota-focused interventions. He has studied individuals receiving bone marrow transplantation, who take antibiotics to prepare for treatment; the antibiotics cause significant gut microbiota shifts and the risk of bloodstream infections increases, so his lab is looking at whether the gut microbiota could mitigate this risk. Currently microbiome monitoring is not being used clinically in patients receiving cancer treatments, but a path exists for gaining the evidence needed to make this feasible and useful. Potentially, microbiome monitoring could allow physicians to move from reactive treatment with antibiotics to proactive intervention that prevents serious infections. Or the clinician could simulate potential treatment scenarios and figure out which one is the most beneficial. Probiotics could be administered to shape the microbiome – but rather than adding microorganisms that may simply be missing, these probiotics would be developed by thinking about the microbiome outcome and how to pressure the ecosystem in a certain direction. Episode abbreviations and links: Review in Nature Reviews Clinical Oncology, arguing for the relevance of microbiota management guided by ecological principles in cancer care: making the case for Ecological management of the microbiota in patients with cancer Mouse study investigating what may drive an increase in oral bacteria within the fecal microbiota and how it may link to patient outcomes: Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes About Dr. Joao Xavier PhD: Joao B. Xavier, PhD, is a faculty member in the Program for Computational and Systems Biology at Memorial Sloan Kettering Cancer Center in New York. His lab combines experiments, computational modeling, and clinical data to study how the human microbiota influences cancer treatment outcomes. Dr. Xavier’s work has uncovered links between gut bacteria, immune recovery, and infection risk in patients undergoing intensive therapies such as allogeneic hematopoietic stem cell transplantation. He recently authored a Nature Reviews Clinical Oncology article (2025) proposing “ecological management” of the microbiota in oncology. This approach applies principles of ecosystem management to preserve beneficial microbes, minimize treatment-related damage, and guide precision interventions. He was awarded the 2026 ASM Microbiome Data Prize by the American Society for Microbiology in recognition of these contributions. His group collaborates broadly across clinical and basic sciences to develop microbiota-informed strategies that could improve responses to chemotherapy, immunotherapy, and infection control.

This episode features Prof. Jens Walter PhD, a microbial ecologist from University College Cork / APC Microbiome Ireland, explaining how he applies ecological and evolutionary frameworks for the purposes of understanding and modulating microbiomes. Although there appears to be a high amount of stochasticity (or randomness) in microbiomes, stochastic and deterministic elements work together to determine outcomes. Priority effects (based on arrival order of a bacterium or other microorganism) are important, with communities likely taking shape through a combination of priority effects and adaptation to the niche. The potential to modulate the microbiome is high in early life, as there are many ecological possibilities. For established microbiomes (for example, in adults), Prof. Walter’s group has found that diet (for example, the “NiMe” diet they developed)  is a possible way to modulate the microbial community, although the effect on the overall ecosystem is small. Nevertheless, dietary modulation may have positive and important effects on host health. Episode abbreviations and links: Paper showing how fiber precisely modulates the gut microbiome: Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production About Prof. Jens Walter PhD: Jens Walter serves as the Professor of Ecology, Food, and the Microbiome at University College Cork and the APC Microbiome Ireland. His expertise lies at the interface of evolutionary ecology of the gut microbiome and human nutrition. His research focuses on the evolutionary and ecological processes that have shaped host-microbiome symbiosis and the translation of basic microbiome science into therapeutic and nutritional strategies. Dr. Walter and his collaborators have pioneered the application of ecological theory to elucidate ecological and nutritional factors that shape gut microbiomes and have achieved targeted modulations of microbiomes via dietary strategies and live microbes. Prof. Walter has published >140 peer-reviewed publications (google scholar H-index 69, >23,000 citations) and is a ‘highly cited researcher’ according to the Web of Science group.

This episode features Dr. Marjon de Vos PhD from the University of Groningen (the Netherlands) speaking about microbial ecology and evolution, and in particular how these affect antimicrobial resistance. She studies the urobiome as well as the factors that contribute to urinary tract infections and successful treatment of these infections with antibiotics. Her lab combines molecular biology techniques with phenotypic and growth measurements, as well as computational modeling. She has found evidence of microbial interactions mediating evolutionary potential of microorganisms – for example, in vitro experiments showed that in the presence of Enterococcus, E. coli speeds up its rate of developing antimicrobial resistance. Thus, interactions within the bacterial ecosystem may affect pathogens’ sensitivity to antimicrobials. Prebiotics are a potential intervention: if bacteria that make a pathogen more susceptible to antimicrobials are already present in the urobiome, their numbers could be enhanced. Probiotics are another possibility. From a One Health perspective, such approaches are important to explore because they support antimicrobial stewardship and help maintain control of antimicrobials in the environment overall. Episode abbreviations and links: Preprint describing pathogens’ differing rates and evolutionary trajectories towards antibiotic resistance based on other microbes present: Microbial interactions affect the tempo and mode of antibiotic resistance evolution Paper describing ecological interactions between different bacterial species in urinary tract infections: Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections Research showing how 5 different bacteria affect the conjugation efficiency of E. coli: Community context influences the conjugation efficiency of Escherichia coli  About Dr. Marjon de Vos PhD: We investigate ecological and evolutionary processes in microbial communities, with a focus on infectious contexts. Our goal is to unravel the genotype–phenotype–fitness relationships within (evolving) communities and to identify the ecological factors that drive microbial evolution. To achieve this, we combine molecular biology techniques with phenotypic and growth measurements, as well as computational modeling. Our research places special emphasis on the urobiome and urinary tract infections in postmenopausal women, as well as on sepsis. By uncovering the fundamental ecological and evolutionary dynamics of microbial communities in infectious diseases, we aim to contribute to the development of strategies that alleviate infections and help curb the emergence and spread of antibiotic resistance.

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 Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

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. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

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. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

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. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

This episode features Dr. Amir Zarrinpar, MD PhD, from UC San Diego (USA) speaking about his work on circadian biology and host metabolism, and what’s currently known about microbial mechanisms. Dr. Zarrinpar explains that in mouse models, restricting feeding to the nocturnal (awake) period is important for their metabolic and overall health. When mice eat during the nocturnal period, the microbiome is very dynamic and essential for maintaining normal circadian rhythm. On a high-fat diet, they change their feeding timing and sleeping behavior simultaneously, and the microbiome fluctuations are disrupted. However, when mice experience time-restricted feeding they are protected from the deleterious consequences of the high-fat diet. The hypothesis is that the time-restricted feeding restores the normal circadian fluctuations of the microbiome. Even though the composition doesn’t change much, the microbes may be changing what they’re doing. Dr. Zarrinpar has used metatranscriptomics to find out what the microbes are actually doing (what genes they’re using), and saw patterns that correlated with time-restricted feeding, indicating that the microbiome may play a key role in the beneficial metabolic effects of time-restricted feeding. Overall, the host may be trying to interpret what’s happening in the environment through microbial signals. The key question to answer going forward is why certain microbe-derived signals prompt the host to alter its metabolic response. Episode abbreviations and links: Paper on using metatranscriptomics to capture microbiome shifts related to circadian rhythms: Metatranscriptomics uncovers diurnal functional shifts in bacterial transgenes with profound metabolic effects Zarrinpar Lab website About Dr. Amir Zarrinpar, MD PhD: Dr. Amir Zarrinpar is an Associate Professor in the Division of Gastroenterology at UC San Diego. Dr. Zarrinpar is a renowned expert in the field of microbiome research and its applications to human health and disease. His work focuses on understanding the complex relationships between the gut microbiome, circadian rhythms, and host metabolism, with the goal of developing novel therapeutic strategies for diseases such as obesity, diabetes, and liver disease. Dr. Zarrinpar has published numerous papers in top-tier journals and has received several awards for his research, including the Litwin IBD Pioneer Award and the American Gastroenterological Association’s Microbiome Junior Investigator Research Award. He is also a dedicated mentor and educator, having supervised numerous students, fellows, and junior faculty members in his laboratory. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

This episode features Prof. Dirk Haller from Technical University of Munich (Germany) speaking about his work in the field of nutritional immunology, trying to unravel how immunity and gut microbiota interact with metabolism, ultimately impacting the emergence of chronic diseases. He focuses on how microbe-host interactions in the gut impact inflammatory or tumorigenic responses – essentially, the microbiota adapts and this drives disease progression. He sees the gut microbiota as a new dimension in nutrition science, with nutrients shown to trigger metabolic changes and impact the microbial environment in the gut. Interestingly, circadian rhythms (which also impact metabolism) seem to establish within the first year of life; and when a relevant microbial community is removed from the host for a week or two, it still shows diurnal oscillations. Lots of uncertainty still exists within the field, however. Prof. Haller recommends that gut microbiome studies report the timing of fecal sample collection, as it can be a major confounder. The metabolic output of microorganisms doesn’t correlate directly with the metabolic health of the host, so much more research needs to be done. Episode abbreviations and links: Paper on circadian rhythms in infant fecal samples: Diurnal rhythmicity of infant fecal microbiota and metabolites: A randomized controlled interventional trial with infant formula Paper on nutrition-microbiota interactions in pediatric Crohn’s disease: Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn’s disease About Prof. Dirk Haller PhD: Prof. Dirk pioneered the field of nutrition and microbiome research, and over the past two decades, he developed highly innovative and truly interdisciplinary research at the borders of different scientific fields. He finished two study programs emphasizing human nutrition and microbiology, before becoming engaged with the fascinating world of commensal microbes in the digestive tract and their impact on human health and diseases. He holds the Chair of Nutrition and Immunology at the Technical University of Munich and chronic intestinal inflammation became his prime research paradigm. In more than 250 publications, he developed ground-breaking and novel concepts to the question of how the non-infectious community of commensal bacteria contributes to the pathogenesis of chronic pathologies in the digestive tract. He developed Priority and Collaborative Research Programs thereby building microbiome research in Germany. Receiving the Main Award of the German Society of Medical Microbiology in 2015, the distinguished Research Award of the United European Gastroenterology Association in 2021, and the recognition as Highly Cited Scientist in 2024 highlights his global scientific reputation across disciplines. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

This episode features Prof. Ben Willing PhD from the University of Alberta, Canada, speaking about his work investigating fermented foods such as kefir for potential cardiometabolic health benefits. The microorganisms associated with fermented foods are not standardized – for example, traditional kefirs have some microorganisms in common, but other microorganisms that are present sporadically. Moreover, kefir at the supermarket is created by taking microbial isolates (not necessarily associated with traditional kefir) and introducing them into the product. Several yeast species are present in traditional kefir but not in supermarket kefir. Prof. Willing studied the health benefits associated with traditional fermented kefir. His group found that specific kefir grains that could lower cholesterol in a mouse model and lower immune markers associated with cardiovascular disease; however, not all traditional kefirs had the same effect and supermarket kefirs were not effective. They isolated a set of 9 microorganisms to make the kefir in the lab, which were sufficient to replicate the effect. The ultimate goal is to produce a product that could be used at a commercial scale and is effective for human health. In initial human studies, the product showed a positive effect. Interestingly, a Canadian public survey about fermented foods found that consumers often expect a health benefit from fermented foods; this is an important area for future scientific and regulatory progress. Episode abbreviations and links: Paper showing benefits of traditional kefir in a mouse model: Traditional kefir reduces weight gain and improves plasma and liver lipid profiles more successfully than a commercial equivalent in a mouse model of obesity Study showing the impact of kefir-associated microorganisms: Kefir microbial composition is a deciding factor in the physiological impact of kefir in a mouse model of obesity Human study: Consumption of kefir made with traditional microorganisms resulted in greater improvements in LDL cholesterol and plasma markers of inflammation in males when compared to a commercial kefir: a randomized pilot study About Prof. Ben Willing PhD: Prof. Willing is a Professor of Gut Microbiology and former Canada Research Chair (Tier 2) in Microbiology of Nutrigenomics in the Department of Agricultural, Food and Nutritional Science at the University of Alberta. He completed his PhD at the University of Saskatchewan studying the role of the microbiota in intestinal development in gnotobiotic pigs. His postdoctoral training was at the Swedish Agricultural University in Uppsala Sweden with Prof. Janet Jansson where he studied the relationship between the microbiome and inflammatory bowel diseases in a twin cohort, and at the University of British Columbia with Prof. Brett Finlay where he studied the impact of antibiotics and faecal transplantation on infection resistance and asthma. His research group is working to understand both fundamental and applied questions in gut microbiology, with a particular focus on how it interacts with diet and antibiotic exposures. Fundamental research includes identifying mechanisms through which specific core members of the microbiome regulate host physiology using gnotobiotic piglet and mouse models to understand their impact on infection resistance, metabolic disease and multiple sclerosis. Applied questions include developing and testing the impact of fermented foods on human health using clinical trials. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

This episode features Dr. Karen Corbin PhD RD from AdventHealth Translational Research Institute (USA), speaking about how the triad of diet, gut microbiome, and host characteristics contribute to energy balance as well as metabolic diseases. From the perspective of host physiology, she explores how to use diet to remodel the gut microbiome to impact energy balance in healthy individuals and those with obesity. Energy balance relates to many different diseases: metabolic diseases and even brain-related conditions. Her center is equipped to measure energy metabolism very precisely and deeply, controlling participants’ energy intake and measuring the resulting oxygen consumption and carbon dioxide production. Diets that feed the gut microbiome lead to more fecal energy loss and higher microbial biomass, indicating that some of the dietary energy is not absorbed by the host, but rather is used for biomass growth. Diet is a must-have in gut microbiome studies because researchers need to know what substrates the microbes are seeing from the host diet. Overall, the field needs to balance highly controlled studies with real-world studies and interpret the results together. Metabolite analysis is a quickly evolving area; some metabolites are associated with leanness or obesity. Other metabolites are promising for revealing a participant’s dietary intake (as Gibbons lab work has shown). Dr. Corbin is exploring the concept that possibly some people – because of genetics, microbiome, or other factors – reabsorb more of the energy substrates produced in the colon. An oversupply of energy to the host is detrimental for metabolic-related diseases, so in the future perhaps a precision intervention could be developed that prevents the gut microbiome from allowing the host to absorb an excess amount of energy. Episode abbreviations and links: 2023 diet study on energy balance led by Dr. Corbin: Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial Review exploring the “thrifty microbiome” concept: New Evidence for a Thrifty Microbiome in Humans Work from Gibbons lab showing evidence of dietary intake through fecal metabolites: Metagenomic estimation of dietary intake from human stool Geeks That Speak website About Dr. Karen Corbin PhD RD: Karen Corbin, PhD, RD, is an Associate Investigator at the AdventHealth Translational Research Institute and the Founder and Chief Geek of Geeks That Speak. Dr. Corbin’s scientific career is focused on human nutrition and metabolism. She explores the mechanisms, including the gut microbiome, that drive individual susceptibility to metabolic diseases such as and obesity, diabetes and liver disease. Her overall goal is to advance clinically relevant research that is poised to transform patient care. Dr. Corbin is also an expert in scientific storytelling. She founded Geeks That Speak to help scientists and other “geeks” to deliver complex scientific information in a way that is impactful, relevant and inspires action. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

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. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

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. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

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. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

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. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

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 […]

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, […]

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. Sign up for our monthly newsletter Follow us on LinkedIn, Bluesky, X, Facebook, Instagram, Threads

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 […]