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).

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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.

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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.

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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.

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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:

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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:

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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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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.

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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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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.

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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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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.

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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.

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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.

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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.

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