Host immunogenetic variation and metagenomically-derived gut microbiome functionality in a wild vertebrate population

Background: The gut microbiome (GM) is important for host health and survival, and is partially shaped by host immunogenetics. To date, no study has investigated the influence of host Major Histocompatibility Complex (MHC) genes on the metagenomically derived gut microbiome functionality in a wild population. We used a natural population of the Seychelles warbler (Acrocephalus sechellensis) to assess the effects of MHC genes on GM taxonomy and functionality using shotgun metagenomics.

Results: Our results show that MHC-II diversity and the presence of one specific MHC-I allele (Ase-ua 7) are associated with taxonomic GM composition in both 16S and metagenomic analysis. Lactococcus lactisdecreased and Staphylococcus lloydii increased with increasing MHC-II diversity. MHC-I allele Ase-ua 7 was linked to reduced Enterococcus casselifavus and Gordonia sp OPL2 but increased Escherichia coliand Vulcaniibacterium thermophilum. Additionally, MHC-I diversity was associated with an increased prevalence of microbial host defence and reduced prevalence in microbial metabolism.

Conclusion: These results suggest that MHC-I diversity may induce microbial host defence and metabolism trade-offs. In addition, MHC-I (not MHC-II) is important in shaping the GM and explains some interindividual variation in the Seychelles warbler. Overall, we highlight the importance of host immunogenetics in shaping the gut microbiome, both taxonomically and functionally.