Data from: Stability of the gorilla microbiome despite simian immunodeficiency virus infection

Simian immunodeficiency viruses (SIVs) have been discovered in over 45
primate species; however, the pathogenic potential of most SIV strains
remains unknown due to difficulties inherent in observing wild
populations. Because those SIV infections that are pathogenic have been
shown to induce changes in the host's gut microbiome, monitoring the
microbiota present in faecal samples can provide a noninvasive means for
studying the effects of SIV infection on the health of wild-living
primates. Here, we examine the effects of SIVgor, a close relative of
SIVcpz of chimpanzees and HIV-1 of humans, on the gut bacterial
communities residing within wild gorillas, revealing that gorilla gut
microbiomes are exceptionally robust to SIV infection. In contrast to the
microbiomes of HIV-1-infected humans and SIVcpz-infected chimpanzees,
SIVgor-infected gorilla microbiomes exhibit neither rises in the
frequencies of opportunistic pathogens nor elevated rates of microbial
turnover within individual hosts. Regardless of SIV infection status,
gorilla microbiomes assort into enterotypes, one of which is
compositionally analogous to those identified in humans and chimpanzees.
The other gorilla enterotype appears specialized for a leaf-based diet and
is enriched in environmentally derived bacterial genera. We hypothesize
that the acquisition of this gorilla-specific enterotype was enabled by
lowered immune system control over the composition of the microbiome. Our
results indicate differences between the pathology of SIVgor and
SIVcpz/HIV-1 infections, demonstrating the utility of investigating host
microbial ecology as a means for studying disease in wild primates of high
conservation priority.