Species-level, food-specific associations predicted in a cohort of 10,068 people may guide personalized nutrition
While diet is a major determinant of the human gut microbiome, little is known about diet-microbiome associations at species-level resolution. New findings from the Human Phenotype Project found species-level, food-specific associations validated at population scale that might guide personalized nutrition
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Diet and nutrition are major determinants of the composition and function of the human gut microbiome. Despite major advances in the field, scientists have yet to figure out how to personalize nutrition based on an individual’s gut microbiome and identify diet-microbiome associations that can guide personalized dietary advice
A new study found species-level, food-specific associations validated in a cohort of 10,068 people, which could help guide personalized nutrition
The researchers analyzed diet-microbiome associations in 10,068 predominantly healthy Israeli adults from the Human Phenotype Project, the world’s largest, deepest phenotype multi-omic study, using app-based dietary logs and shotgun metagenomics. Data from 7,998 participants were analyzed at baseline and 2,070 participants were included in the test set. Of those, 1,654 participants were followed up at 2 years and 1,412 participants at 4 years. For external validation, the researchers analyzed data from two independent cohorts (Australia, n = 118; Israel, n = 188).
Associations between specific foods, whole diet patterns, and the gut microbiome were quantified. Diet predicted 92% of gut species(669 of 724 species tested)and 98% of microbial pathways(313 of 320 pathways) when age, sex, body mass index, and comorbidities were included as covariates. Minimally processed, nutrient-rich intake was the strongest positive predictor of microbial alpha diversity. However, ultra-processed foods were the strongest negative predictor of microbial diversity. It turned out that food processing was a stronger driver of microbial diversity than whether the diet was primarily animal or plant-based.
Distinct specific food-microbe associations were identified, including positive correlations of coffee with butyrate-producing Lawsonibacter asaccharolyticus, yogurt with Streptococcus thermophilus, and dairy and bread with Bifidobacterium longumand B. adolescentis. The abundance of specific species from the Lachnospiraceaeand Clostridiumfamilies was strongly predicted by nut and banana consumption. Longitudinal analyses showed that some diet-microbiome associations persisted over 4 years
The researchers also built an exploratory framework to simulate personalized dietary interventions based on predicted shifts in the microbiome. For example, Akkermansia muciniphila and Faecalibacterium prausnitzii were among the gut bacteria most often predicted to change with dietary changes that included one or two food changes (e.g., decreasing white bread and increasing nuts) and were independently associated with cardiometabolic markers
In conclusion, these findings highlight the potential of personalized nutrition strategies based on an individual’s gut microbiome. This means that if the clinician knows which taxa are dysregulated in a patient and which foods and dietary patterns modulate those taxa, then it would be possible to personalize dietary advice rather than giving generic lifestyle advice. To move from observation to prescription, personalized nutrition needs randomized trials that measure changes in the gut microbiome in response to microbiome-targeted diets.
Reference:
Segev T, Barak D, Zahavi L, et al. Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition. Nat Med. 2026; 32(5):1884-1894. doi: 10.1038/s41591-026-04312-x
July 6th, 2026
By Andreu Prados
Categories: Diet, Digestive Health, Food & Ingredients, Gut Microbiota, Gut Microbiota Composition, Nutrition, Research & Practice
Andreu Prados
Andreu Prados is a science and medical writer specializing in making trusted evidence of gut microbiome-related treatments understandable, engaging and ready for use for a range of audiences. He holds bachelor’s degrees in Pharmacy and Human Nutrition and Dietetics and a PhD in nutrition communication. Follow Andreu on Twitter @andreuprados
