Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri

The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this lemur’s virtually unexplored gut microbiome will deepen our understanding of the species’ health determinants and inform conservation efforts. Through metagenomic assembly and integration into an updated reference database, we found the I. indri fecal microbiome remains largely uncultivated (cultivated species representing <0.1% relative abundance) and is largely specific to this primate species. After reconstructing 342 metagenome-assembled genomes encompassing 48 candidate species from a total of 22 samples (18 of which newly sequenced), we substantially improved microbiome mappability to 85% on average and found evidence for a proportionally large core microbiome. Social group membership emerged as the main determinant of both their taxonomic and functional gut microbiome composition. Using strain-level profiling, we detected extensive microbiome transmission within social groups,suggesting physical interaction is key in promoting microbiome acquisition.Strain sharing rates were highest b etween mothers and their offspring. Intergroup strain sharing was minimal and inversely correlated with geographical distance, aligning with the rare intergroupinteractionsandstableterritoryoccupancycoupledwithongoinghabitatfragmentation.Noevidenceofmicrobiomeacquisition throughgeophagywasdetected.Thesefindingsunderscoretheprofoundinfluenceofsocialstructureonmicrobiometransmission and composition in I. indri, and highlight the importance of considering social dynamics into research and conservation strategies