The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis

TLDR

The vertebrate gut hosts a diverse bacterial community shaped by the immune system, and disruptions of host‑bacterial interactions are linked to gastrointestinal diseases, yet comprehensive studies are scarce. The study used rhesus macaques to examine how gut bacterial communities are shaped and how they change in disease, comparing healthy animals to those with colitis and undergoing antibiotic therapy. Researchers performed DNA barcoding and pyrosequencing of 141,000 16S rRNA sequences from 100 uncultured GI samples, enabling quantitative community analysis and comparison of colonic contents from healthy versus colitis‑affected animals. Macaque gut communities differ from those of mice and humans, vary by tissue, individual, time, and sex, and show significant compositional differences between healthy and colitis animals, offering comprehensive data and improved methods for studying commensal microbiota in macaque GI disease models and informing large‑scale human gut microbiome screening.

Abstract

The vertebrate gut harbors a vast community of bacterial mutualists, the composition of which is modulated by the host immune system. Many gastrointestinal (GI) diseases are expected to be associated with disruptions of host-bacterial interactions, but relatively few comprehensive studies have been reported. We have used the rhesus macaque model to investigate forces shaping GI bacterial communities. We used DNA bar coding and pyrosequencing to characterize 141,000 sequences of 16S rRNA genes obtained from 100 uncultured GI bacterial samples, allowing quantitative analysis of community composition in health and disease. Microbial communities of macaques were distinct from those of mice and humans in both abundance and types of taxa present. The macaque communities differed among samples from intestinal mucosa, colonic contents, and stool, paralleling studies of humans. Communities also differed among animals, over time within individual animals, and between males and females. To investigate changes associated with disease, samples of colonic contents taken at necropsy were compared between healthy animals and animals with colitis and undergoing antibiotic therapy. Communities from diseased and healthy animals also differed significantly in composition. This work provides comprehensive data and improved methods for studying the role of commensal microbiota in macaque models of GI diseases and provides a model for the large-scale screening of the human gut microbiome.