2-months Longitunidal healthy human gut microbiome

The effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has not been robustly investigated. Here we first compared two approaches to study the fungal community (Internal-Transcribed-Spacer and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis, and correlated dietary data with both bacterial and fungal communities. We found that shotgun DNA sequencing after an adapted enrichment fungal protocol provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal communities in fecal samples. The mycobiome was significantly more dynamic than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study highlights a competitive inter-kingdom interaction between bacteria and fungi for food foraging.