By Marla Cunningham, ISAPP Executive Director
I’m sure you’ve read the results of trials similar to these (fictional) conclusions:
‘Our findings showed an increase in Faecalibacterium and Enterococcus, two groups associated with reduced inflammation, and a decrease in Clostridium spp, which have been associated in previous studies with metabolic risk. These results suggest a beneficial modulation of the microbiome by intervention X, possibly contributing to the observed health benefits in this study.’
In biotic (and other) intervention trials, it is commonplace to see the practice of hypothesising beneficial mechanistic roles for taxonomic changes based on literature review associations. Yet despite the apparent logic of this approach, such findings are only suggestive and require confirmation in rigorous experimental studies before we can have confidence that the microbiome is indeed moving to a healthier state.
A problem that persists in the microbiome field is that confounding factors make the interpretation of microbiota changes and their implications for health challenging. Two of the key challenges are causation (both attribution and directionality) and the interindividual nature of microbiome responses:
- Cause or consequence. Changes in microbiome features during an intervention trial may be a direct result of the intervention, a result of other exposures, like dietary or lifestyle changes, or a consequence of the change in host health status. Microbiota, host and diet influence each other in an interrelated triad – change any, and the others can respond in turn (except diet doesn’t respond – or does it? Food cravings might be linked to the microbiome). While the impact of the microbiome on host health is often highlighted, the environment within the gut also influences the microbiome – with host changes in inflammatory tone, immune status and gut barrier function impacting the functions and numbers of the microbes within. Thus, the causal contribution of any microbiota change is rarely easy to disentangle.
- Interindividual responses. Microbiota composition differs widely between individuals and populations. If putatively beneficial changes are demonstrated in one population, such results may be difficult to extrapolate to other populations, limiting external validity of study findings. Further, within studies, heterogenous responses across study participants are averaged into mean group response rates, obscuring unique causes and consequences to be found within individual outcomes.
In the face of these and other challenges, what progress have we made in recent years in interpreting gut microbiome changes, and where does the science stand now on the application and interpretation of microbiome endpoints in clinical trials? Below are six areas of developing insights and continued progress in this area.
These and related questions are the subject of ISAPP’s most recent podcast series on the implementation of microbiome science in biotic science and practice. Listen here to episodes throughout May and June where ISAPP experts interview scientists on key new publications on this topic. Links and notes included below for further listening and reading.
Shift from composition to function
Through one lens, gut microbes can be seen as metabolic factories – consuming substrates and producing metabolites, orchestrated by their genetic machinery and modulated by environmental exposures. A huge amount of functional redundancy exists in any given microbiome, with shared genes and functions present across a broad range of taxa. In one individual, butyrate production may be carried out by a different set of microbes than in another – and the loss of any one taxon may be well compensated by another taking over the same niche and performing similar metabolic functions. As this understanding has grown, and shotgun sequencing prices have decreased, metagenomic data has been increasingly used for not just better taxonomic resolution, but also for readouts of functional potential based on gene abundance. Providing a readout of the butyrate-production capacity of a microbiome provides a useful tool to compare across microbiomes, and make inferences and comparisons about the host-relevant outputs produced.
However, despite recent emphasis on the promise of functional rather than compositional readouts, as well as the difficulties of interindividual and population level variability, Ghosh and colleagues recently developed a species-based health-associated core keystone (HACK) index with significant promise. Utilising a dataset of 45,000 gut microbiomes across six continents, they identified and ranked a list of 201 consistently health-associated taxa, with positive predictive value to differentiate healthy and diseased cohorts as well as responses to health-associated interventions such as the Mediterranean diet. (Listen to Prof Tarini Ghosh explain the HACK index in this episode.)
Expression rather than potential
While gene analysis provides an indication of metabolic potential, metabolomics provides direct measurement of the chemical milieu created by microbial and host interactions. A snapshot summation of the outputs of microbial activity can be taken from blood, urine, stool and other samples. Interpretation of such findings can be challenging, however, with analyses separated by various degrees of removal from microbial production – due to degradation of molecules, cross feeding metabolism, and duplicate host production. An important example is SCFA measurement. While SCFAs are understood as a key mediator of microbe:host interactions, the utility of their measurement in faeces has proved disappointing, with a lack of correlation to colonic production (in large part, because SCFA transporters are upregulated for greater utilisation when production is increased). However, plasma SCFAs can be reliable postprandial markers, providing temporally relevant information about the microbiota response to interventions (read key takeaways on SCFA measurement here). Joos and colleagues (listen to Raphaela Joos here on outputs from the Human Microbiome Action Consortium) recommend metabolomic methods as adjuncts to metagenomic sequencing approaches as key to better understanding the functional impacts of interventions.
Where to measure?
Whether culturing, gene sequencing or profiling molecules, the wealth of microbiome analysis and interpretation in the literature is limited to the most common sample type – faeces. If we were solely interested in correlations of the microbiome with rectal health, faeces would be a good sample choice – spatially and temporally relevant (albeit reflecting the luminal microbiota more than the adherent mucosal populations). However, interactions of biotic substances with the microbiota occur throughout the small and large intestine, with local microbiome profiles that differ significantly from the faecal microbiome. These discrepancies may significantly cloud our ability to accurately identify relevant causal relationships between interventions, microbial markers and health status. While sampling in more proximal locations has long been a challenge due to its invasive nature, advances have been made in ingestible sampling devices to provide data on other gastrointestinal sites, and capture changes which may be occurring in different spatial and temporal dimensions than those in faeces. The field awaits more insights from trials such as these, to reveal the potential of these new windows into biotic:microbiota:host interactions.
Who is the healthy control?
The majority of microbiota associations with health and disease have been deduced through case:control studies, where the healthy group is defined through variable inclusion/exclusion criteria, such as absence of known disease and lifestyle risk factors. The key operative factor, and challenge in this approach is that the risk factors and health status must be ‘known’ in advance. Further, in the absence of any existing host genetic or environmental risk, the microbiota of any currently healthy individual may be the latent risk factor itself, predisposing to future disease. To address this challenge, Joos and colleagues (more here) proposed large inclusive longitudinal cohorts where the definition of health emerges over time, reducing misleading conclusions because of miscategorising ‘healthy’ control groups.
Awareness of these challenges within the body of literature when interpreting microbiome readouts, and preferencing longitudinal comparison groups, may go some way towards reducing erroneous conclusions about the significance of microbiota changes.
Considering population-specific definitions of microbiome improvement
Consider two patients. One is in remission from inflammatory bowel disease, with their most important treatment goal being to prevent recurrence. Another patient has a family history of early death from cardiovascular disease, and wants to reduce their long term cardiometabolic risk. Conceivably, in each of these situations, there may be a different set of microbiota functions to optimise (and minimise), in order to promote the specific host:microbiome interactions relevant to their health goals. Could a microbiome that is well-suited to protect against one type of disease in one type of host and dietary context be ill-suited to protect against a different type of disease in a different host and context?
This possibility that a ‘health-promoting microbiome’ may look different for different patient populations, or even between individuals, may be a path forward for future research and application of biotic therapies. While ‘personalisation’ and ‘precision nutrition’ are current buzzwords in the field, this often amounts to assessing an individual’s position in comparison to an ‘optimal’ microbiota, and aiming to personalise interventions to move individuals from their respective baselines towards this healthier (microbially-defined) position. Beyond this, we might need to consider the possibility that the ideal microbiota of each population may differ, as a function of their health status, exposures and healthcare needs – creating population-specific metrics against which to assess progress.
Is microbiome analysis relevant?
While biotics are often thought of as being microbiome-modulating strategies, all of the biotics family are known to have direct interactions with the host, e.g. via epithelial, endocrine and immune receptor interactions – with or without any contribution from the commensal microbiota. Further, excessive focus on the study of microbiota impacts may detract from the ultimate goal of any health-related intervention – to improve health – demonstrated by meaningful improvements in clinical endpoints.
Sanders and Hill reflect on some of the challenges with microbiome measures in their recent perspective article (here), and highlight key considerations for each biotic substance with regards to the relevance and utility of microbiome endpoints. For example, since prebiotics are by definition targeted at commensal microbes, measuring microbiota outcomes may be of higher relevance in prebiotic studies. Contrast this with postbiotics, which likely mediate much of their activity though proximal interactions of bioactive cellular components with host receptors, where microbiome endpoints may be exploratory at best, or other host-related mechanisms may be of greater priority to explore.
While best practice in this field remains far from clearcut, ongoing research, debate, and expert thinking continues to move us forward with important considerations and insights for a more nuanced application and interpretation of microbiome data in biotic studies.
Highlighted Talks from the 2025 ISAPP Annual Meeting
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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:
Episode abbreviations and links:
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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ISAPP welcomes two new scientists to its board of directors
/in News /by KCThe ISAPP board of directors is pleased to welcome two prominent scientists and frequent ISAPP collaborators to its ranks: Prof. Hannah Holscher, PhD, RD from the University of Illinois Urbana-Champaign (USA), and Prof. Jens Walter PhD from University College Cork (Ireland). The appointment of these board members was announced at the recent ISAPP annual meeting in Banff, Canada.
The two new members of the board of directors were selected to complement the expertise of the other 12 academic board members, expanding ISAPP’s capacity for effective collaboration and leadership within the field of probiotics, prebiotics, synbiotics, postbiotics, and fermented foods.
Prof. Holscher is a registered dietitian and nutrition scientist whose research integrates clinical nutrition, microbiome science, and computational biology to investigate how diet influences human health. Using clinical and computational approaches, she has contributed foundational studies and translational research that have advanced the emerging field of nutritional microbiology. Prof. Holscher was recently honored as an inaugural Excellence in Nutrition Fellow by the American Society for Nutrition (ASN), awarded for significant impact in the field of nutrition.
Prof. Walter is a microbiologist whose work focuses on the evolutionary ecology of the gut microbiome and its relationship with human nutrition. His research explores how ecological and evolutionary processes shape host-microbe interactions, aiming to translate microbiome science into therapeutic and dietary strategies. His team has led numerous human trials examining how fiber, prebiotics, whole diets, and live microbes influence the gut microbiota and health. He has authored over 180 peer-reviewed publications and is recognized as a Highly Cited Researcher by Clarivate.
In addition to their research leadership, Profs. Holscher and Walter both actively promote science in the field through outreach activities such as webinars, YouTube videos, and media articles.
“Hannah and Jens bring unique expertise in nutrition and intestinal microbiology to the board of directors and are both leaders in their fields,” says ISAPP President Prof. Maria Marco. “We’re happy to have them join our mission and look forward to working with them to sustain and grow ISAPP’s reach.”
ISAPP’s Executive Director Marla Cunningham says, “We are thrilled to welcome Hannah and Jens to our board of directors. Both have leading research programs and have been valuable ISAPP collaborators over the years. We welcome their expertise on the board and look forward to their contributions to help ISAPP carry out its mission of advancing biotic science.”
ISAPP is governed by an academic, volunteer group of board members which steers the activities of the organization, leading discussion groups, publications, outreach initiatives, and more.
Unraveling the functions of GLP-1 in the gut, with Dr. Thomas Greiner PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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.
Episode abbreviations and links:
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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Archive Highlight: Microbes that break down mucus and milk to benefit the host, with Dr. Clara Belzer PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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.
Key topics from this episode:
Episode abbreviations and links:
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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Investigating the microbial mechanisms contributing to host metabolism, with Dr. Amir Zarrinpar, MD PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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.
Episode abbreviations and links:
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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Microbiome endpoints in clinical trials for biotics – where do we stand and what have we learnt?
/in ISAPP Science Blog /by KCBy Marla Cunningham, ISAPP Executive Director
I’m sure you’ve read the results of trials similar to these (fictional) conclusions:
‘Our findings showed an increase in Faecalibacterium and Enterococcus, two groups associated with reduced inflammation, and a decrease in Clostridium spp, which have been associated in previous studies with metabolic risk. These results suggest a beneficial modulation of the microbiome by intervention X, possibly contributing to the observed health benefits in this study.’
In biotic (and other) intervention trials, it is commonplace to see the practice of hypothesising beneficial mechanistic roles for taxonomic changes based on literature review associations. Yet despite the apparent logic of this approach, such findings are only suggestive and require confirmation in rigorous experimental studies before we can have confidence that the microbiome is indeed moving to a healthier state.
A problem that persists in the microbiome field is that confounding factors make the interpretation of microbiota changes and their implications for health challenging. Two of the key challenges are causation (both attribution and directionality) and the interindividual nature of microbiome responses:
In the face of these and other challenges, what progress have we made in recent years in interpreting gut microbiome changes, and where does the science stand now on the application and interpretation of microbiome endpoints in clinical trials? Below are six areas of developing insights and continued progress in this area.
Shift from composition to function
Through one lens, gut microbes can be seen as metabolic factories – consuming substrates and producing metabolites, orchestrated by their genetic machinery and modulated by environmental exposures. A huge amount of functional redundancy exists in any given microbiome, with shared genes and functions present across a broad range of taxa. In one individual, butyrate production may be carried out by a different set of microbes than in another – and the loss of any one taxon may be well compensated by another taking over the same niche and performing similar metabolic functions. As this understanding has grown, and shotgun sequencing prices have decreased, metagenomic data has been increasingly used for not just better taxonomic resolution, but also for readouts of functional potential based on gene abundance. Providing a readout of the butyrate-production capacity of a microbiome provides a useful tool to compare across microbiomes, and make inferences and comparisons about the host-relevant outputs produced.
However, despite recent emphasis on the promise of functional rather than compositional readouts, as well as the difficulties of interindividual and population level variability, Ghosh and colleagues recently developed a species-based health-associated core keystone (HACK) index with significant promise. Utilising a dataset of 45,000 gut microbiomes across six continents, they identified and ranked a list of 201 consistently health-associated taxa, with positive predictive value to differentiate healthy and diseased cohorts as well as responses to health-associated interventions such as the Mediterranean diet. (Listen to Prof Tarini Ghosh explain the HACK index in this episode.)
Expression rather than potential
While gene analysis provides an indication of metabolic potential, metabolomics provides direct measurement of the chemical milieu created by microbial and host interactions. A snapshot summation of the outputs of microbial activity can be taken from blood, urine, stool and other samples. Interpretation of such findings can be challenging, however, with analyses separated by various degrees of removal from microbial production – due to degradation of molecules, cross feeding metabolism, and duplicate host production. An important example is SCFA measurement. While SCFAs are understood as a key mediator of microbe:host interactions, the utility of their measurement in faeces has proved disappointing, with a lack of correlation to colonic production (in large part, because SCFA transporters are upregulated for greater utilisation when production is increased). However, plasma SCFAs can be reliable postprandial markers, providing temporally relevant information about the microbiota response to interventions (read key takeaways on SCFA measurement here). Joos and colleagues (listen to Raphaela Joos here on outputs from the Human Microbiome Action Consortium) recommend metabolomic methods as adjuncts to metagenomic sequencing approaches as key to better understanding the functional impacts of interventions.
Where to measure?
Whether culturing, gene sequencing or profiling molecules, the wealth of microbiome analysis and interpretation in the literature is limited to the most common sample type – faeces. If we were solely interested in correlations of the microbiome with rectal health, faeces would be a good sample choice – spatially and temporally relevant (albeit reflecting the luminal microbiota more than the adherent mucosal populations). However, interactions of biotic substances with the microbiota occur throughout the small and large intestine, with local microbiome profiles that differ significantly from the faecal microbiome. These discrepancies may significantly cloud our ability to accurately identify relevant causal relationships between interventions, microbial markers and health status. While sampling in more proximal locations has long been a challenge due to its invasive nature, advances have been made in ingestible sampling devices to provide data on other gastrointestinal sites, and capture changes which may be occurring in different spatial and temporal dimensions than those in faeces. The field awaits more insights from trials such as these, to reveal the potential of these new windows into biotic:microbiota:host interactions.
Who is the healthy control?
The majority of microbiota associations with health and disease have been deduced through case:control studies, where the healthy group is defined through variable inclusion/exclusion criteria, such as absence of known disease and lifestyle risk factors. The key operative factor, and challenge in this approach is that the risk factors and health status must be ‘known’ in advance. Further, in the absence of any existing host genetic or environmental risk, the microbiota of any currently healthy individual may be the latent risk factor itself, predisposing to future disease. To address this challenge, Joos and colleagues (more here) proposed large inclusive longitudinal cohorts where the definition of health emerges over time, reducing misleading conclusions because of miscategorising ‘healthy’ control groups.
Awareness of these challenges within the body of literature when interpreting microbiome readouts, and preferencing longitudinal comparison groups, may go some way towards reducing erroneous conclusions about the significance of microbiota changes.
Considering population-specific definitions of microbiome improvement
Consider two patients. One is in remission from inflammatory bowel disease, with their most important treatment goal being to prevent recurrence. Another patient has a family history of early death from cardiovascular disease, and wants to reduce their long term cardiometabolic risk. Conceivably, in each of these situations, there may be a different set of microbiota functions to optimise (and minimise), in order to promote the specific host:microbiome interactions relevant to their health goals. Could a microbiome that is well-suited to protect against one type of disease in one type of host and dietary context be ill-suited to protect against a different type of disease in a different host and context?
This possibility that a ‘health-promoting microbiome’ may look different for different patient populations, or even between individuals, may be a path forward for future research and application of biotic therapies. While ‘personalisation’ and ‘precision nutrition’ are current buzzwords in the field, this often amounts to assessing an individual’s position in comparison to an ‘optimal’ microbiota, and aiming to personalise interventions to move individuals from their respective baselines towards this healthier (microbially-defined) position. Beyond this, we might need to consider the possibility that the ideal microbiota of each population may differ, as a function of their health status, exposures and healthcare needs – creating population-specific metrics against which to assess progress.
Is microbiome analysis relevant?
While biotics are often thought of as being microbiome-modulating strategies, all of the biotics family are known to have direct interactions with the host, e.g. via epithelial, endocrine and immune receptor interactions – with or without any contribution from the commensal microbiota. Further, excessive focus on the study of microbiota impacts may detract from the ultimate goal of any health-related intervention – to improve health – demonstrated by meaningful improvements in clinical endpoints.
Sanders and Hill reflect on some of the challenges with microbiome measures in their recent perspective article (here), and highlight key considerations for each biotic substance with regards to the relevance and utility of microbiome endpoints. For example, since prebiotics are by definition targeted at commensal microbes, measuring microbiota outcomes may be of higher relevance in prebiotic studies. Contrast this with postbiotics, which likely mediate much of their activity though proximal interactions of bioactive cellular components with host receptors, where microbiome endpoints may be exploratory at best, or other host-related mechanisms may be of greater priority to explore.
While best practice in this field remains far from clearcut, ongoing research, debate, and expert thinking continues to move us forward with important considerations and insights for a more nuanced application and interpretation of microbiome data in biotic studies.
Interactions between immunity, gut microbiota, and metabolism, with Prof. Dirk Haller PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
Subscribe: Apple Podcasts | Spotify | RSS
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:
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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Examining fermented foods for potential cardiometabolic health benefits, with Prof. Ben Willing PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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:
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.
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Diet and gut microbiome contributions to host energy balance, with Dr. Karen Corbin PhD RD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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:
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.
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Progress in understanding the gut microbiome’s role in health and disease states, with Prof. Emad El-Omar MD FRCP
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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.
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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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Five points to know about biotics for animals, from an ISAPP-led paper
/in Uncategorized /by KCBiotics, including probiotics and prebiotics, are well known for their human health benefits. But a growing number of studies have focused on biotic use in both agricultural and companion animals. Biotics have been employed in animals to achieve a variety of health benefits as well as improvements in growth and production efficiency.
A group of animal health experts, comprising academic and industry member scientists convening at the 2023 ISAPP annual meeting, reviewed the evidence on biotics for animals, outlining what’s known to date and the likely future directions in this scientific field. Led by Prof. Kelly Swanson PhD and Emeritus Prof. George Fahey PhD, the group recently published a review in Journal of Animal Science that summarizes their discussion.
Here are five main points from their paper:
Biotic effects are likely specific to each type of animal and its living conditions
The authors caution that a biotics study on one type of animal doesn’t necessarily translate to another type of animal. They write, “Knowledge of the host species of interest is important, as differences in anatomy, physiology and microbiota populations, dietary requirements, environmental exposures, and disease susceptibility dictate biotic type and dosage.”
In addition, many studies even within the same animal species find that biotics can be variable in effectiveness. The authors note that biotics may work differently depending on the diet of the animal, its gut microbiome, or living environment, and studies should be planned with relevant applications in mind.
More work is needed to find out the most effective probiotics for companion animals
In companion animals such as dogs and cats, prebiotics are commonly used and effective whereas probiotics studied so far are less effective for addressing gastrointestinal symptoms. The primary aims of using probiotics in companion animals are to maintain overall health and improve longevity, and while some probiotic strains have shown promise for outcomes related to immunity, stress management, and metabolic health, for example, more work is needed to identify the appropriate strains and doses. The paper authors say host-adapted strains that work more effectively within the gastrointestinal tract of the animal may be identified in the future and result in better outcomes.
Probiotics have potential to greatly reduce the use of antimicrobials in agricultural animals
Traditionally, antimicrobials have been used in agricultural animals such as poultry and ruminants to prevent or treat infections, and to a lesser extent to promote growth. However, concerns about antimicrobial resistance are bringing increased attention to antimicrobial alternatives. Studies exist that show the potential of probiotics to reduce antimicrobial use in swine, poultry, and ruminants as well as aquaculture.
Co-author Shalome Bassett says, “Probiotics, as well as prebiotics, have been shown to be particularly effective in ruminants, not only through improved immunity but also increased productivity and food quality. And, importantly, there’s no evidence of residue issues with their use so dairy or meat products remain safe and nutritious.”
Shaping the animal gut microbiota in early life appears important for health
In animals as in humans, early life is an important time for establishing a gut microbiota that supports health throughout the remainder of the lifespan. Studies in multiple animal species have shown the importance of the gut microbiota for shaping early immune responses, indicating that richer microbial exposures in early life may lead to better resistance against pathogens and better overall health later in the animal’s life.
Biotic use in animals may impact human health, too
The authors say that using biotics in animals can help address challenges beyond health of the animals themselves. Using probiotics and other biotics in animals also has potential to impact human health as well. Although biotics may not have the same magnitude of effects as antimicrobials, administering probiotics to agricultural animals, for example, may be able to improve food safety by reducing zoonotic infections and antimicrobial resistance overall.
The benefits of biotic use in animals are becoming increasingly clear, both for animals and for humans who share their environment. However, each animal is unique, and the most effective biotic solutions will likely be specific to each species. As knowledge of biotic use in animals continues to expand, scientists will continue to zero in on the most effective biotic types and doses for each application.
The HACK index for measuring a health-associated gut microbiome, with Dr. Tarini Ghosh PhD
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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.
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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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Regulatory science and the development of microbiome biomarkers, with Dr. Céline Druart PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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:
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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Identifying features of a healthy microbiome, with Raphaela Joos
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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:
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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Advancing gut microbiome testing for use in clinical practice, with Dr. Gianluca Ianiro MD PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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:
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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Archive Highlight: Human milk oligosaccharides in the infant gut, with Dr. Simone Renwick PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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:
Episode links:
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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ISAPP Board Scientist Honored by American Society for Nutrition as Inaugural Fellow
/in News /by KCProf. Kelly Swanson PhD from the University of Illinois Urbana-Champaign, a nutrition scientist from the ISAPP board of directors, has been named among 55 inaugural Excellence in Nutrition Fellows by the American Society for Nutrition (ASN).
The Excellence in Nutrition recognition program was established this year to honor major contributions in advancing nutrition science and practice, along with dedication to high standards within the nutrition profession. Each new Fellow, ten or more years past their terminal degree, was selected based on significant impact in the field of nutrition as well as active leadership and participation in ASN activities. Prof. Swanson received this honor in March.
Prof. Swanson is a leading researcher in the field of human and animal nutrition, with over 275 peer-reviewed publications. He is currently the Director of the Division of Nutritional Sciences, Kraft Heinz Company Endowed Professor in Human Nutrition, a professor in the Department of Animal Sciences and Division of Nutritional Sciences, and an adjunct professor in the Department of Veterinary Clinical Medicine.
At the University of Illinois, his lab research focuses on gastrointestinal health and obesity in dogs, cats, and humans. To this end, the lab studies the effects of dietary interventions (dietary fibers, biotics, and other functional ingredients) on health outcomes and the gut microbiota, develops strategies to maintain a healthy body weight in obese pets, and evaluates the quality and digestibility of different protein sources for pet and human foods. Prof. Swanson has also been a valued mentor to many early career researchers.
“I am honored to have been selected as an inaugural excellence in nutrition fellow. Being a member of ASN for nearly 3 decades, I have benefited in many ways both professionally and personally.,” said Prof. Swanson. “Within the field of nutrition, biotics are a particularly promising strategy for supporting the health of humans and companion animals as well as the efficient production of agricultural animals for food. I look forward to continuing to contribute to this research area by evaluating how biotics affect the gastrointestinal, immune, and oral health of dogs, cats, and humans.”
Prof. Swanson has played a prominent role in ISAPP’s Board of Directors since 2020, providing perspectives on the use of biotics in both agricultural and companion animals, and contributing significantly to the organization’s scientific direction and outreach.
ISAPP’s executive director Marla Cunningham says, “Kelly has been instrumental in leading a variety of ISAPP activities for biotics and nutrition in both human and animal health – including our 2020 ISAPP consensus statement definition for synbiotics. Kelly is a strong contributor in the nutrition community and is a frequent speaker at conferences, supporting knowledge exchange and collaboration in the field. We’re delighted to see him achieve this recognition for his efforts.”
Exploring resources to inform probiotic recommendations: New UK Probiotic Guide Released
/in ISAPP Science Blog /by KCWell-informed healthcare professionals know the importance of recommending evidence-based probiotic products to their patients to achieve specific health benefits. But finding the available evidence and matching it with specific products available on the market can be challenging. Moreover, not all of the studies on probiotic products are high-quality, making the evidence difficult to assess.
Clinical guidelines are often the first source of reliable information for clinicians looking for guidance in practice. Typically, probiotic guidelines released by relevant clinical associations are the result of a rigorous evaluation of the evidence and are one of the most valuable sources of information for clinicians. Such guidelines are usually developed through transparent criteria on the levels of evidence supporting each probiotic strain or formulation.
While guidelines by clinical associations typically provide recommendations for scientifically supported strains or formulations, product names are not provided. Clinicians who wish to recommend products by name need to further match the strain recommendations to finished products in market. Sometimes relevant commercial products are not available in their country.
Linking evidence to specific products is the focus of an organization called AEProbio (Alliance for Education on Probiotics). Last month AEProbio launched a new Guide to Probiotic Products Available in the United Kingdom, following their popular versions for Canada (introduced in 2008) and the United States (2014). The authors of the UK guide were dietitian Sarah Danaher and pharmacist Dragana Skokovic-Sunjic, and the new guide was funded by the University of Reading’s academic-industry partnership called INFORM Hub. The content and recommendations of the guide were reviewed and approved by the 11 independent academic experts on the UK Expert Review Board (listed at the end of this article) before publishing.
Sarah Danaher emphasized the new resource was motivated by the need of clinicians to understand the evidence around specific probiotic products. She says, “While healthcare professionals generally have a positive attitude towards probiotics, many do not routinely recommend them to patients and are hesitant to do so (Fei et al. 2023).”
Danaher says, “Several key barriers contribute to this reluctance including lack of probiotic knowledge, uncertainty about the strength of clinical evidence, insufficient training in probiotics during professional education, and lack of product regulation. Pharmacists were found to be the most knowledgeable about probiotics. Among doctors, probiotic recommendations were more common among gastroenterologists than GPs, reflecting a greater awareness of the gut-related clinical applications of probiotics. Despite positive attitudes, few HCPs consistently advise on probiotics for patients as there is such uncertainty about which products to recommend or when it is appropriate to do so (Fei et al. 2023).”
AEProbio produced the guides to support the selection of probiotic products for both healthcare professionals and consumers, including the names of relevant products in market. In each country, the authors of the guide aim to include as many products as possible that have probiotic strains (or strain combinations) supported by evidence.
To be included in the latest UK guide, products had to meet minimum criteria for adequate information on the label, as well as recognition of strain safety. Danaher says, “Many products fail to disclose essential information, such as the specific probiotic strain(s) used (just stating the genus and species) or the colony-forming units (CFUs) at the end of shelf life.” For more information on what clinicians should look for on a product label, see ISAPP recommendations here (European version, US version).
Dragana Skokovic-Sunjic authored the initial version of the Clinical Guide to Probiotic Products Available in Canada as a supplement to a series of live continuing medical education modules. What was originally meant to be a one-time resource, however, soon became an ongoing project. She says, “The fast-changing market and growing research over the following few months highlighted the need for regular updates. The initial team of Expert Reviewers was then formed, comprising gastroenterologists, epidemiologists, and pharmacists. Ever since that initial publication, the content of the Guide has been updated annually. All changes are reviewed and approved by the Expert Review Board.”
Skokovic-Sunjic notes, “Evidence is reviewed for the guide if it is from human populations, published in peer-reviewed journals, and addresses clinically relevant outcomes: that is, reducing symptoms, resolving a condition, or enhancing prevention.”
In the guides, different types of evidence are classified into Levels of Recommendation (see here). In brief, Level 1 recommendations are based on RCT evidence regarded as suitable quality by the expert review panel, Level 2 is based on lower quality RCT evidence and other intervention studies, and Level 3 includes professional opinions and reports. It is important to highlight that the committee does not use a recognized recommendation protocol but comes to an agreement based on the panel’s evaluation.
“In categorizing evidence, the Expert Review Board uses its discretion to assign different Levels based on a variety of reasons, such as the small number of study subjects, the impact of the proposed indication, the vulnerability of the intended population (e.g. pediatrics, chronic diseases)”, explains Skokovic-Sunjic. “In case we can’t all agree on higher level of recommendation, then the lower level is assigned until additional studies are completed.”
ISAPP recommends clinicians using the guides focus only on products with Level 1 recommendation. Level 2 and 3 recommendations alone, while of interest, are generally not considered sufficient to guide practice. Since clearly defined criteria (beyond expert panel agreement) are not applied for classifying Level 1 recommendations in the guide, combining use of the guide with recommendations from clinical societies (see resources below) may provide a stronger rationale for clinicians to guide their practice.
Whenever scientific evidence is applied to practice, clinicians are encouraged to review supporting evidence for products and indications of interest to ensure study design, population and clinical effects observed are relevant to their own clinical practice and patients.
With the constant emergence of new evidence on probiotic safety and efficacy as well as the dynamic selection of probiotic brands and products on the market in each country, the task of recommending appropriate probiotics is often a challenge for clinicians. But with knowledge of the strengths and limitations of various resources and an understanding of how they may be used, clinicians can gain more confidence in their recommendations and ensure better patient outcomes overall.
UK Probiotic Guide Authors
Sarah Danaher RD, Dragana Skokovic-Sunjic RPh MSCP
UK Probiotic Guide Expert Review Board
Dr. Gemma Walton PhD
Prof. Glenn Gibson PhD
Prof. Kieran Tuohy PhD UNIMRI
Dr. Anthony Buckley PhD
Lorraine Bailey RD
Fiona Lee HNC
Prof. Kevin Whelan PhD RD
Dr. Eirini Dimidi PhD RD
Prof. Janet Cade PhD RNutr FafN
Dr. James Kennedy BMBCh MRCP(UK) DTM&H
Dr. Andrea Monteagudo-Mera PhD
Additional resources for clinicians
How a non-industrialized diet affects gut microbes and health, with Dr. Anissa Armet PhD RD
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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:
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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Interactions of polyphenols in the gut, with Prof. Yves Desjardins PhD
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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:
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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The interplay between gut microbiota, diet, and circadian rhythms, with Dr. Vanessa Leone PhD
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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:
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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New paper summarizes current findings from global research on the vaginal microbiota
/in ISAPP Science Blog /by KCKnowledge about the vaginal microbiota is important for women’s health worldwide, but the majority of the research to date has centered around women of European descent, with limited data from across different genetic, cultural, environmental, and health conditions.
A new paper led by ISAPP board member Prof. Sarah Lebeer PhD, published in Trends in Microbiology, provides an overview of what’s currently known about the diversity of the vaginal microbiota in women globally. The paper highlights several research gaps that are being addressed in the years ahead with more inclusive research strategies.
Prof. Lebeer is at the center of a network of researchers that aim to build capacity and expand knowledge on the vaginal microbiota globally. What started as a small citizen science project from Prof. Lebeer’s lab in 2020 has grown into a worldwide research alliance called the “Isala Sisterhood”, working to improve women’s health by gaining information about vaginal microbes. The group currently has local citizen science projects underway in Peru, Switzerland, Cameroon, Nigeria, Spain, USA & Hawaii, France, Argentina, and Poland, with more than a dozen additional projects planned. She says, “Only by embracing a diverse, global view of microbiome research can we ensure that our findings and conclusions are truly representative and relevant to all women, regardless of their background or geographical location.”
Prof. Lebeer answers some questions about the new paper, summarizing the research findings in this area to date and her hopes for the future of the Isala Sisterhood.
How do you know a healthy vaginal microbiota is important for women’s health overall?
Prof. Lebeer points to studies showing that irregularities in the vaginal microbiota are associated with a higher risk of bacterial vaginosis, vaginal Candida infections, urinary tract infections, and sexually transmitted diseases. Additionally, vaginal microbiota changes appear to increase the likelihood of HPV-mediated cervical cancer, preterm birth, and vaginal atrophy during menopause. She says, “The exact risk levels vary by geographical location, but these conditions carry substantial morbidity and mortality for women.”
What do scientists already know about a healthy vaginal microbiota?
Although most studies to date have focused on women’s diseases, the Isala Sisterhood first aims to understand the vaginal microbiome in a state of health.
Prof. Lebeer says, “A healthy vaginal microbiota plays a crucial role in protecting the vagina—and the entire female body—from infections and disease while supporting normal physiological function. We know that Lactobacillus species are particularly effective in keeping pathogens at bay, not only by producing lactic acid to maintain a low pH, but also through other genes and molecules that keep the microbiota in a steady state.”
She says these pathogen-protective functions may be served by different bacteria in different populations of women around the world, so a global perspective is necessary for finding out the true criteria for a healthy vaginal microbiota. For example, lactobacilli are often found to be lower in women of African and Latin American descent compared with women of European and Asian descent, but the implications of these differences for health and disease risk are still being unravelled.
What are some of the factors that affect the vaginal microbiota?
Prof. Lebeer explains, “The vaginal microbiota changes over time. Shifts occur in the vaginal microbiota during puberty, pregnancy, and menopause, which influence a woman’s susceptibility to infections, pregnancy outcomes, and overall vaginal health. Understanding these changes can help guide strategies for maintaining a balanced microbiome at different life stages.”
She adds, “It’s also influenced by factors such as hormones, menstruation, pregnancy, menopause, sexual activity, hygiene practices, and even antibiotics or probiotics. With the Isala Sisterhood, we aim to map the relative importance of each of these factors.”
Why is citizen science key to the success of the Isala Sisterhood’s research efforts?
“By implementing citizen science, we have a strong societal component aimed at raising awareness about the vaginal microbiome among scientists and people living in remote areas,” says Prof. Lebeer. “Our goal is to break the taboos surrounding this crucial organ, which not only impacts women’s health but also affects the health of their partners and children.”
Through this global collaboration, what gaps in knowledge do you hope to address?
Prof. Lebeer identifies three knowledge gaps that are a priority to address: “One is that we still don’t have a clear understanding of what the average composition of the vaginal microbiome looks like across women worldwide. A second key gap is our limited understanding of the functions of the vaginal microbiome. While we know that lactobacilli produce lactic acid to inhibit pathogens, we still have little insight into the broader roles played by other genes and molecules in the vaginal microbiome and how they contribute to vaginal health. And a third gap is our incomplete understanding of how the vaginal microbiome impacts a wide range of diseases. While we have a good grasp of its connection to vaginal infections, we are just beginning to uncover how it might influence more systemic conditions.”
“In addition, we cannot ignore potential disparities in health outcomes. If conditions such as bacterial vaginosis are more prevalent in certain populations, this is something we need to investigate and understand better,” she says.
How to respond to the question “Should I take a probiotic?”
/in Consumer Blog /by KCBy Dr. Mary Ellen Sanders PhD and Prof. Daniel Merenstein MD
A Washington Post article published March 11, 2025 by a gastroenterologist addressed a question posed by a reader: “I’ve heard about the benefits of probiotics for years. Should I start taking them?”
We both get this question frequently, and over the years have answered it differently than this journalist. Here’s what we would say.
We would first ask if there are symptoms that are motivating the question. If yes, then we would look to see if any probiotics have been studied to address the issue. Places to check for any evidence include the World Gastroenterological Organisation Guidelines and the Clinical Guide to Probiotic Products* Available in USA, Canada or UK. A 2018 review article addressed the question of how physicians might choose a probiotic for their patients. These resources are compiled after review of evidence by physicians and scientists.**
These resources show that there are many randomized controlled trials of probiotics for a variety of conditions. These studies have found that probiotic strains can impact health or mitigate some conditions, including reducing crying time in colicky babies, improving some mental health endpoints such as anxiety and depressive symptoms, and reducing diarrhea from antibiotics So, if these endpoints are of interest, there may be a probiotic to try.
If no symptoms are being targeted, we would explain that there is not highest level evidence – i.e., systematic review of (homogeneous) randomized controlled trials or individual randomized controlled trials (Level A evidence) – that probiotics are beneficial for generally healthy people (Merenstein et al 2024). But context is needed here: there is not Level A evidence for almost any interventions for healthy people, with the exception of some, not most, cancer screening tests, and some, not all, vaccines. Even with diet and exercise it is difficult to find Level A evidence for healthy people.
We would stress that not all probiotics are the same, and it’s important to choose a specific probiotic to match your goals. Because traditional probiotic strains have a very good safety record, the major downside to trying one is economic. It’s reasonable to try a probiotic for 30 days and if it does help, great. If it doesn’t help, quit. This can be especially useful for GI conditions without good options, such as IBS, which is multifactorial and difficult to treat; also, available medicines are expensive, and have a limited scope. Remember that different people will respond differently to a probiotic (this is also true for drugs).
We would provide advice on how to navigate the probiotic marketplace.
We might share that we undertook a survey of both probiotic dietary supplements and refrigerated probiotic foods at the retail level and found that about 35% of the supplements and 49% of the foods could be traced to published evidence. In general, products listing strain designations also had evidence for some health benefit.
We would warn about wild claims made on the internet and in social media – for any product. Be skeptical.
We would say that contrary to popular belief, even among GI docs, the evidence that fiber and live dietary microbes (such as in some fermented foods) can improve your gut microbiome is limited. In spite of all the research to date, scientists cannot define a healthy microbiome composition, so how can we know how to improve it? However, we know that fiber improves some parameters of gut health and reduces risk of some chronic diseases, but most of us do not eat the recommended daily allowance of fiber. So, increasing dietary fiber from fruits, vegetables and whole grains is a sound recommendation.
But for traditional fermented foods such as kimchi, kombucha and kefir, few randomized controlled trials have documented meaningful health benefits. Some interesting associations have been discovered between increasing live microbes in the diet and health biomarkers (Hill et al. 2024), but these observations need to be confirmed in controlled trials. Still, traditional fermented foods can be nutritious additions to your diet even though most lack convincing evidence about their health benefits beyond nutrition. This fact is often overlooked by many ‘experts’, who, without evidence, recommend consumption of traditional fermented foods to improve gut health while criticizing limitations in probiotic research.
Finally, we would not criticize probiotics because the industry is profitable (if that were the benchmark, where does that leave the pharmaceutical industry?), because probiotic studies are heterogeneous (studies on many categories, including fiber, are as well), because they are not ‘personalized’ (precious few intervention in nutrition OR medicine are personalized – see here) or because many YouTube videos on probiotics are not scientifically accurate (we think it’s safe to say this is not a problem unique to probiotics. For reliable videos on probiotics, see here).
* If using the Clinical Guides, it is best to focus on products with Level I evidence, defined as “Evidence obtained from at least one appropriately designed trial, (e.g., randomization, blinding, appropriate population comparisons)”. Level II or III evidence is worth reviewing but is not high-level evidence.
**As the Washington Post article referenced above indicated, the American Gastroenterological Association thoroughly reviewed evidence for probiotics for a range of GI disorders. They conditionally recommended certain probiotics for prevention of C. difficile and prevention of necrotizing enterocolitis in preterm infants. They did not review information on a well-studied probiotic GI endpoint, antibiotic-associated diarrhea (Cochrane reviews recommend probiotics for adults and children taking antibiotics), nor on any non-GI endpoints.
An overview of precision fermentation, with Prof. William Chen PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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:
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).
Precision fermentation for animal-free milk, with Dr. Abigail Thiel PhD
/in Podcast, Season Four /by LauraPodcast: Play in new window | Download
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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:
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.