Gut microbial diversity and strain sharing in the Indri indri

By reconstructing 342 near-complete genomes representing 48 potential new species from 22 indri fecal samples (mostly newly sequenced), we increased Indri indri gut microbiome mappability by 85%, and identified a substantial core set of shared microbes. The primary factor shaping both the types and functions of these gut bacteria was the indri's social group. Strain-level analysis revealed extensive microbial transmission within social units, highlighting the importance of physical interactions in microbiome acquisition, particularly between mothers and their young. Conversely, intergroup strain sharing was rare and inversely related to geographical distance, mirroring the limited contact and stable territories within a fragmented landscape.