Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients

BackgroundThe accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis using a comprehensive in-house fungal database, and correlated dietary data with both bacterial and fungal communities.ResultsWe found that shotgun DNA sequencing after a new enrichment protocol combined with the most comprehensive and novel fungal databases provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal community analyses in fecal samples. The mycobiome was significantly more variable 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 indicates a potential competitive inter-kingdom interaction between bacteria and fungi for food foraging.ConclusionTogether, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome.1fa3y2hSmo38JAQk6TMPiwVideo AbstractConclusionTogether, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome.1fa3y2hSmo38JAQk6TMPiwVideo Abstract

Automated summary

The study demonstrates that shotgun DNA sequencing combined with a new enrichment protocol and a comprehensive fungal database provides a cost-effective approach to analyze the gut mycobiome at the species level and integrate bacterial and fungal community analyses in fecal samples. The mycobiome is more variable than the bacterial community in terms of composition and functions. Microbial diversity, composition, and functions are associated with habitual diet composition rather than global dietary changes.