Cutting-edge research and practical applications of microbiome-based nutritional therapies
The satellite symposium “Diet, nutrition, and gut microbiome” that preceded the 13th annual GMFH World Summit focused on the role of nutrition in shaping health outcomes by impacting the gut microbiome. Janelle Smith, registered dietitian (RD), updated how disordered eating may affect the gut microbiome through impacting neuroinflammation and gut permeability, antibodies to appetite hormones, and metabolism-altering microbes. While introducing food slowly to minimize uncomfortable digestive symptoms and including diverse dietary sources of prebiotics and resistant starch is key, Smith acknowledged the importance of addressing the potential adverse psychosocial effects of controlling diet during eating disorders recovery.
Impact of gut microbes in eating disorders.
Source: Smith’s presentation at the GMFH World Summit 2025.
Diet is the main factor driving gut microbiome composition, but only partly explains gut microbiome adaptations. However, available dietary assessment tools designed for use in research (i.e., food frequency questionnaires, food record tools, and 24-hour dietary recall tools) ignore dietary “dark matter,” including nutrients such as phytochemicals that impact the microbiome but are not quantified in food labels. Abigail Johnson, RD, acknowledged that microbiome nutrition studies should collect information about food ingredients (e.g., emulsifiers, colors), type of cooking, probiotic content of foods, how foods are grown (e.g., organic/conventional), foods unique to different cultural eating traditions, and how foods are packaged as all of them are potential confounders explaining authentic microbiome-health relationships. Last, Tamara Freuman, Master of Science (MS) degree, RD, Certified Dietitian-Nutritionist (CDN), shared practical strategies and insights for healthcare professionals to guide patients in translating dietary recommendations into sustainable, long-term behavior changes that support digestive health.
Current dietary assessment tools designed for research ignore the impact of numerous nutrients and non-nutritive compounds on the microbiome.
Source: Johnson’s presentation at the GMFH World Summit 2025.
Emulsifiers, fermented foods, prebiotics, and digestive and metabolic health
Research must adopt a systems approach focused on microbiome-host interactions in connected ecosystems to understand microbiome impacts better and leverage microbial functions. Karine Clément, MD PhD, full professor of nutrition at Pitié Salpêtrière hospital and Sorbonne Université in Paris, updated the crosstalk between microbiome alterations and derived metabolites found in obesity based on a systems approach. New unpublished findings from the Nutriomics study found that predicting weight loss response with GLP1 analogues and physical exercise is possible when stratifying participants by microbiome gene richness, which opens the potential role of incorporating gut microbiome information for disease stratification, biomarkers, or add-on therapy.
Diet-driven effects on the microbiome may partly explain the current rise in obesity and related metabolic conditions. Food additives ubiquitous in modern diets are in the spotlight due to their potential involvement in the onset and development of non-communicable diseases. However, the extent of food additives’ impact varies among individuals. Benoit Chassaing, PhD, from Institut Pasteur, presented in vitro findings showing that the sensitivity to dietary emulsifier carboxymethylcellulose of fecal samples can be predicted by specific metagenomic signatures. For instance, bacteria including Adlercreutzia equolifaciens and Frisingicoccus caecimuris correlated positively with intestinal inflammation. Further research is needed to probe the potential of the fecal microbiome to predict dietary emulsifier sensitivity in the context of healthy individuals and those with gastrointestinal conditions. Chassaing also presented the first clinical trial to show that a low emulsifier diet is a safe and effective intervention for mild-to-moderately active Crohn’s disease, reducing clinical symptoms and fecal calprotectin.
The ADDapt trial showed that emulsifier dietary restriction reduces symptoms and inflammation in patients with active CD.
Source: Chassaing’s presentation at the GMFH World Summit 2025.
Maria Marco, PhD, from the University of California Davis, updated new findings on the mechanisms of action of dairy- and vegetable-origin fermented foods that have been widely used as food staples for centuries. Human studies (mainly on fermented dairy) indicate that fermented foods can improve digestive health. Marco presented new findings that fermented cabbage can affect intestinal barrier function, and these effects may vary based on fermentation time, the presence of a probiotic inoculant, and homemade versus commercial process methodology.
Fermented foods that have been tested in human trials.
Source: Marco’s presentation at the GMFH World Summit 2025.
Not all prebiotic fibers impact the gut microbiome and host similarly. Andrew Gewirtz, PhD, MD, from Georgia State University, presented findings in mice showing that the benefits of fiber-rich foods are not recapitulated by supplemental fiber. Prebiotic fibers, such as inulin, can nourish gut bacteria and may provide benefits similar to dietary fiber. Still, they are not without risk, as inulin-enriched diets induced hepatocellular carcinoma in 10% of mice. Other fibers, such as psyllium and wheat bran, have shown benefits in mice in restoring the colonic microbiota depleted by a low-fiber diet and reducing the severity of diet-induced obesity, respectively.
Not all prebiotic fibers work the same in the gut microenvironment.
Source: Gewirtz’s presentation at the GMFH World Summit 2025.
Non-bacterial clues to gastrointestinal and liver diseases
Although less studied than bacteria, other key microorganisms are present in the gut, including viruses, phages, yeast, and fungi. These microorganisms, which shape host physiology and the activity of the gut microbes, are the focus of emerging research and may be as important as bacteria. Robert Schooley, MD, PhD, from the University of California, San Diego, covered the role of bacteriophages as a promising approach to the treatment of multidrug-resistant bacterial pathogens, including reducing Escherichia coli load that may cause fatal bloodstream infections in hematological cancer patients and reducing mortality in patients with alcoholic hepatitis, among others. These findings are significant considering that no fundamentally new antibiotics have been discovered for 20 years. Limitations of phages include the narrow host range of phages, uncertain predictive value of in vitro phage susceptibility testing, the acid lability of most phages requiring strategies to mitigate inactivation by gastric acid, development of phage resistance during therapy, major knowledge gaps related to phage pharmacology, and development of adaptive immune responses to phages during therapy.
Potential niches for therapeutic use of phages.
Source: Schooley’s presentation at the GMFH World Summit 2025.
Kyla Ost, PhD, from the University of Colorado Anschutz Medical Campus, focused on virulence factors of yeast and fungi in the gut that make up 1-2% of the microbiome biomass. Beneficial and pathogenic yeast and fungi species are the same, so it is not a good idea to simplify their classification into “good” and “bad”. For instance, Candida species dominate and are immunomodulatory. Some Candida species stimulate adaptive and innate immune responses during homeostasis that promote metabolic health and boost immune surveillance. It is known that early-life colonization with Candida dubliniensis promotes metabolic health. In contrast, host extrinsic (e.g., diet, antibiotics) and intrinsic (e.g, age, anti-microbial peptides such as peptide YY) factors may boost fungal dysbiosis associated with decreased bacterial diversity and intestinal inflammation. Therefore, immune interactions regulate Candida morphology (hyphae-associated effectors from Candida exacerbate pathogenic inflammation) and virulence factor expression in the gut (pathogenic potential varies between Candida strains).
Fungi and yeasts are not “good” or “bad” because their virulence depends on morphology and virulence factors driven by host immunity.
Source: Ost’s presentation at the GMFH World Summit 2025.
Extra-intestinal implications of gut microbiome manipulation
Diet is an overlooked intervention for cancer prevention and treatment outcomes, shaping the gut microbiome. Carrie Daniel-MacDougall, PhD, MPH, from the MD Anderson Cancer Center at the University of Texas, presented ongoing and published clinical trials on the role of diet in shaping cancer treatment outcomes through supporting the gut microbiome. The Be GONE Trial found adding ½ cup of cooked, canned navy beans to the usual diet over a 2-week ramp-up period, followed by 1 cup per day for an additional 6 weeks, was a safe, scalable dietary strategy to favorably modulate the gut microbiome of patients with obesity and a history of colorectal cancer and/or polyps. Unpublished data from the Diet and Immune Effects Trial (DIET) and Prebiotic Food Enriched Diet (PreFED) trials showed that a high fiber (30-50 g/d) versus a control fiber diet (20 g/d) is associated with a favourable immune checkpoint blockade response in patients with metastatic melanoma on immunotherapy.
Adding navy beans to one’s usual diet may enhance gut microbiome and regulate host markers linked to obesity and colorectal cancer.
Source: Daniel-MacDougall’s presentation at the GMFH World Summit 2025.
Jonathan Peled, MD, explored associations with foods and fecal microbiome diversity in immunotherapy patients. Microbiome diversity declines in a regimen-specific fashion in adults undergoing allogeneic hematopoietic cell transplantation (allo-HCT), and some diet components are associated with the outcome of fecal microbiome diversity. Unpublished data showed that low fecal diversity was most strongly associated with foods rich in simple sugars in the prior two days, and the effect was additive to antibiotics. Of note, dietary sucrose exacerbated antibiotic-induced Enterococcus expansion, an effect that was not explained simply by a reduction in fiber intake. These findings suggest that avoiding sugar intake while on antibiotics is a possible way to mitigate antibiotic-induced dysbiosis. Peled shared that rationally designed probiotics (e.g., SER-155, an oral investigational cultivated microbiome therapeutic comprised of 16 bacterial Firmicutes strains) are probably better than commercially available probiotics in improving microbial (e.g., gut domination by pathobionts) and health outcomes (e.g., bloodstream infections) in adults undergoing allo-HCT.
Investigational microbiome therapeutic SER-155 in adults undergoing allo-HCT.
Source: Peled’s presentation at the GMFH World Summit 2025.
Cynthia Sears, MD, at the Johns Hopkins University School of Medicine, updated novel mechanisms for colon carcinogenesis involving the role of polymicrobial bacterial biofilms. What is interesting to note is that Clostridioides difficile toxins have been shown to promote biofilm invasion deep into colonic crypts in mice and humans, highlighting a potential way to tackle early onset colorectal cancer. Enterotoxigenic Bacteroides fragilis (ETBF) has been linked to inflammatory bowel disease and colon cancer and it turned out that its pro-inflammatory and tumorigenic functions are driven by the B. fragilis toxin gene it possesses. While not everyone with ETBF on their colon will develop cancerous lesions, preliminary findings suggest that stress and antibiotic use may disrupt the gut microbiome and make ETBF more likely to induce inflammation.
Last, Andrea Merchak, PhD, from the University of Florida (USA), gave an overview of the mechanisms of gut-brain communication. Preliminary clinical work suggests the role of bile acid metabolism in multiple sclerosis and gut inflammation in dementia. However, there are limited microbiome-based interventions ready to use for tackling brain inflammation and neurodegeneration in the clinical setting.
Therapeutic applications of microbiota-gut-brain axis in neurodegenerative diseases.
Source: Merchak’s presentation at the GMFH World Summit 2025.
Personalized nutrition, best practices in microbiome research, and microbiome-based interventions in vulnerable populations
Beyond plenary sessions, four parallel workshop sessions took place during the GMFH World Summit. They covered tailoring recommendations based on microbiome status, non-traditional model systems in microbiome research, to fiber or not to fiber in gastrointestinal conditions, and probiotic supplementation and the infant microbiota.
Attendees can access on-demand content for the GMFH World Summit 2025 keynote, plenary, and workshops recordings. The 14th GMFH World Summit will take place in 2026 in Porto (Portugal).
