Homo sapiens Raw sequence reads
This is 16s sequencing data from the human rectal microbiome. Rectal mucosal secretions were collected via swab from healthy adult (age 18-59) male human participants without HIV (25 total; 19 were men who have sex with men who had receptive anal intercourse at least 3 times in the prior month, and 6 were control men who never have receptive anal intercourse). DNA was extracted, and 16s microbiome sequencing was conducted.There were five study visits. The first was a screening visit. At the second visit (day 0), a proctoscope was placed in the rectum, and baseline mucosal secretions were collected on swabs for microbiome and cytokine analysis. A small (3mm) experimental injury was then induced in the rectal mucosa with biopsy forceps, and a picture of the injury site was taken with a camera attachment so that the baseline surface area could be measured. Participants returned for three more study visits (days 2, 5, and 8). At each of these visits, the proctoscope was placed again, the injury site was located, a follow-up image of the injury site was collected for surface area measurement to see how quickly the wound was healing, and follow-up mucosal secretion swabs were collected at the border of the injury site for microbiome and cytokine analysis.Study Abstract:Mucosal injury is common during consensual intercourse and induces an inflammatory response that could contribute to transmission of infectious pathogens including HIV. Here, we compared mucosal immune and microbiome responses to experimentally induced mucosal injury between men who have sex with men engaging in receptive anal intercourse (MSM-RAI) and men who do not engage in RAI (controls), all without HIV. Rectal mucosal secretions were collected from adult MSM-RAI (n=19) and controls (n=6) via anoscopy before and up to eight days after experimentally induced injury. Mucosal healing was evaluated by repeated measures of the area of the injury with digital images. MSM-RAI demonstrated overall higher concentrations of pro-inflammatory cytokines, marginally faster wound healing, and a distinct rectal microbiome compared with controls. Different patterns of cytokine response to injury were observed between MSM-RAI and controls; however, IL-6 and IP-10 were important mediators in both groups. Microbial guilds, particularly those belonging to the Lachnospiraceae and Prevotellaceae families, were associated with rectal mucosal inflammation. This work is the first experimental study of rectal mucosal injury and the immune environment in healthy humans and provides a more nuanced understanding of rectal mucosal inflammation after injury, which can inform our understanding of HIV transmission.