Anatomic Site of Sampling and the Rectal Mucosal Microbiota in HIV Negative Men Who Have Sex with Men Engaging in Condomless Receptive Anal Intercourse

Rectal transmission accounts for the majority of HIV transmissions among men who have sex with men (MSM). We previously demonstrated a distinct rectal mucosal immune environment in MSM engaging in condomless receptive anal intercourse (CRAI) compared with men who do not engage in anal intercourse, including enrichment of the microbiota for the Prevotellaceae family as compared with Bacteroidaceae. Here, we expand upon these previous findings to determine differences by anatomic site of collection (anal vs. rectal mucosa) and examine associations of the predominant taxa with other genera. We analyzed 16SrRNA gene sequences of the V1-V2 region generated on an Illumina MiSeq (R) from 35 MSM engaging in CRAI and 20 male controls. Observation by principal coordinates analysis and analysis of similarities test showed differing composition of the microbiota by anatomic site of collection. When analyzing the top 10 abundant genera from each anatomic site by generalized linear models, the predominant genera (Prevotella enrichment among MSM engaging in CRAI vs. Bacteroides among controls) were consistent; however, the two sites shared only four common genera. In addition, associations between the relative abundance of Prevotella and Bacteroides with other prevalent genera, by Spearman's rank correlations, were inconsistent when stratifying by study group. Prevotella versus Bacteroides predominant microbiota may not define a consistent underlying microbial community, and our data underline the importance of anatomic sampling site. Understanding the rectal mucosal immune environment, of which the microbiota is a critical component, will enable a better understanding of rectal HIV transmission.