Diarrheal disease results in microbiome stunting in infant macaques and is linked to a diverse set of known and uncultured Campylobacter species.

16s and shotgun sequences that help characterize the infant rhesus macaque microbiome during cases of diarrheal disease.Diarrheal diseases remain one of the leading causes of death for children under 5 globally, a trend that disproportionally impacts those living in low- and middle-income countries (LMIC). Campylobacter spp., a zoonotic pathogen that is found in the flora of many different animal species, is one of the leading causes of food-borne infection in humans. Moreover, recent molecular surveillance studies have shown that the total burden of Campylobacter spp. is greater than what can be attributed to known/culturable species suggesting that unknown/unculturable Campylobacter could play a significant role in this complex etiology. In this study, we performed longitudinal microbiome profiling and metagenomic genome assembly on samples collected from over 100 infant rhesus macaques across 5 time-points and at any time they presented with clinical diarrhea during their first year of life. Diarrhea was associated with taxonomic and functional changes of the infant gut microbiome that was in part associated with an increased relative abundance of Campylobacter. Indeed, we constructed 36 Campylobacter metagenomic assembled genomes (MAGs), 15 of which belong to uncultured species. Comparative genomics classified the 15 uncultured MAGs into 4 metagenomic groups and revealed similarities with Campylobacter MAGs identified in human fecal samples predominately from LMIC, suggesting that these microbes also colonize the gut of humans most impacted by diarrheal diseases. These data will aid in the efforts aimed at understanding the mechanisms by which unculturable Campylobacter sp. impact human health.