Lay, C. | bioRxiv Science

bioRxiv2026

Taxon-in-context reveals ecological individuality in the human gut microbiome

Ecological theory holds that a microbe's role depends on its surrounding community. Yet abundance profiles and fixed ecological groupings leave its individual context implicit. We introduce taxon-in-context, a reproducible representation of each microbe's context within an individual's microbiome. Across 7,700 metagenomes, we show that common gut species occupy different contexts in different people. This flexibility peaked in early life and declined through adulthood, a pattern reproduced in a larger genus-level compendium. For selected species, context within each person's microbiome revealed age associations beyond species abundance and the person's context mixture. In an independent longitudinal urinary tract infection cohort, microbes switched contexts within individuals. Taxon-in-context enabled recurrence prediction where an abundance-based model performed near chance. Taxon-in-context and these findings expose a measurable, dynamic and individualized layer of microbiome organization, providing a basis for investigating why the same microbe or intervention may have different biological consequences across people.

systems biology↗

bioRxiv2024

A three-country analysis of the gut microbiome indicates taxon associations with diet vary by location and strain

Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. While significant efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research lacks representation from low- and middle-income countries such as Mexico. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,291 individuals across three countries, we examine two bacterial genera prevalent in the human gut, Prevotella and Faecalibacterium, which have gained significant attention due to their potential roles in human health. We find that they show significant associations with many aspects of diet, but that these associations vary in scale and direction, depending on the level of metagenomic resolution and the contextual population. These results highlight the growing importance of assembling metagenomic datasets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome.

microbiology↗