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To test how SIVcpz infection affects the contents and stability of the gut microbiome, we followed the gut microbial communities of individual chimpanzees from Gombe National Park, Tanzania. Gombe chimpanzees represent the only habituated, wild-living ape population naturally infected by SIVcpz, and they have been monitored noninvasively for SIVcpz?infection and AIDS-like symptoms for the past 13 years through the collection of fecal samples (Rudicell et?al., Selleckchem PF2341066 2010, Santiago et?al., 2003?and?Terio et?al., 2011). We identified six individuals who became infected during the observation period,?two of which developed AIDS-like symptoms 3.5 and 4.5 years postinfection, while the others remained asymptomatic (Keele et?al., 2009, Rudicell et?al., 2010?and?Terio et?al., 2011). We were thus able to track the composition of the gut microbiota in individuals who progressed from uninfected to SIVcpz positive, as well as from asymptomatic SIVcpz infection to AIDS. We sequenced bacterial 16S ribosomal RNA (rRNA) libraries prepared from 49 fecal samples collected over 9 years from 6 chimpanzees, yielding, per sample, an average of 11,260 high-quality sequences, which were binned into operational taxonomic units (OTUs) and assigned taxonomic classifications. The timings of fecal samples AZ191 and SIVcpz infections across individuals are presented in Figure?1. Complete sample information is presented in Table S1 (available online). To determine whether SIVcpz infection altered the composition of the gut microbiota, we tested if samples obtained INCB018424 datasheet after infection differed from those recovered before infection in terms of the relative abundances of bacterial phylotypes. Based on Euclidean distances, which are well suited to detect changes in the frequencies of dominant community constituents, gut communities recovered from individuals postinfection differed significantly in composition from those present preinfection, and gut communities recovered from SIVcpz-infected individuals were significantly more variable in terms of community composition than were gut communities recovered from uninfected individuals (p?