The semen microbiome and its relationship with local immunology and viral load in HIV infection.

Semen is a major vector for HIV transmission, but the semen HIV RNA viral load (VL) only correlates moderately with the blood VL. Viral shedding can be enhanced by genital infections and associated inflammation, but it can also occur in the absence of classical pathogens. Thus, we hypothesized that a dysregulated semen microbiome correlates with local HIV shedding. We analyzed semen samples from 49 men who have sex with men (MSM), including 22 HIV-uninfected and 27 HIV-infected men, at baseline and after starting antiretroviral therapy (ART) using 16S rRNA gene-based pyrosequencing and quantitative PCR. We studied the relationship of semen bacteria with HIV infection, semen cytokine levels, and semen VL by linear regression, non-metric multidimensional scaling, and goodness-of-fit test. Streptococcus, Corynebacterium, and Staphylococcus were common semen bacteria, irrespective of HIV status. While Ureaplasma was the more abundant Mollicutes in HIV-uninfected men, Mycoplasma dominated after HIV infection. HIV infection was associated with decreased semen microbiome diversity and richness, which were restored after six months of ART. In HIV-infected men, semen bacterial load correlated with seven pro-inflammatory semen cytokines, including IL-6 (p = 0.024), TNF-α (p = 0.009), and IL-1b (p = 0.002). IL-1b in particular was associated with semen VL (r(2)  = 0.18, p = 0.02). Semen bacterial load was also directly linked to the semen HIV VL (r(2) = 0.15, p = 0.02). HIV infection reshapes the relationship between semen bacteria and pro-inflammatory cytokines, and both are linked to semen VL, which supports a role of the semen microbiome in HIV sexual transmission.

Medical therapy reduces microbiota diversity and evenness in surgically recalcitrant chronic rhinosinusitis.

BACKGROUND: Chronic rhinosinusitis (CRS) is a highly prevalent and heterogeneous condition frequently treated with antibiotics and corticosteroid therapy. However, the effect of medical therapy on sinus microbiota remains unknown. METHODS: We enrolled CRS patients (n = 6) with patent maxillary antrostomies and active mucosal inflammation, who had not received antibiotics or corticosteroids in the previous 8 weeks. A pretreatment and posttreatment maxillary sinus swab was collected, from which DNA was extracted, pyrosequenced, and analyzed using a naïve Bayesian classifier and ecological analyses. RESULTS: Four patients showed significant improvement in endoscopic appearance. The shifts in microbiota in response to therapy were highly individualized. There was no single common microbiota profile among patients with similar clinical outcomes, but overall there was significant decrease in microbiota diversity (t(5) = 2.05, p = 0.10) and evenness (t(5) = 2.28, p = 0.07) after treatment. CONCLUSION: Our findings strongly correlate with earlier studies that examined the impact of antibiotics on human microbiota. We observed that posttreatment, patients frequently became colonized by taxa that are less susceptible to the prescribed antibiotics. Our findings highlight the challenge in seeking generalizable diagnostic and therapeutic options in CRS, particularly regarding microbiological response and outcomes.

Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria.

UNLABELLED: Male circumcision reduces female-to-male HIV transmission. Hypothesized mechanisms for this protective effect include decreased HIV target cell recruitment and activation due to changes in the penis microbiome. We compared the coronal sulcus microbiota of men from a group of uncircumcised controls (n = 77) and from a circumcised intervention group (n = 79) at enrollment and year 1 follow-up in a randomized circumcision trial in Rakai, Uganda. We characterized microbiota using16S rRNA gene-based quantitative PCR (qPCR) and pyrosequencing, log response ratio (LRR), Bayesian classification, nonmetric multidimensional scaling (nMDS), and permutational multivariate analysis of variance (PerMANOVA). At baseline, men in both study arms had comparable coronal sulcus microbiota; however, by year 1, circumcision decreased the total bacterial load and reduced microbiota biodiversity. Specifically, the prevalence and absolute abundance of 12 anaerobic bacterial taxa decreased significantly in the circumcised men. While aerobic bacterial taxa also increased postcircumcision, these gains were minor. The reduction in anaerobes may partly account for the effects of circumcision on reduced HIV acquisition. IMPORTANCE: The bacterial changes identified in this study may play an important role in the HIV risk reduction conferred by male circumcision. Decreasing the load of specific anaerobes could reduce HIV target cell recruitment to the foreskin. Understanding the mechanisms that underlie the benefits of male circumcision could help to identify new intervention strategies for decreasing HIV transmission, applicable to populations with high HIV prevalence where male circumcision is culturally less acceptable.

The otologic microbiome: a study of the bacterial microbiota in a pediatric patient with chronic serous otitis media using 16SrRNA gene-based pyrosequencing.

OBJECTIVE: To characterize bacterial microbiota in middle ear, adenoid, and tonsil specimens using 16SrRNA gene-based pyrosequencing analysis. DESIGN: Cross-sectional study of bacterial microbiota in middle ear, adenoid, and tonsil specimens from a pediatric patient with chronic serous otitis media. Middle ear, adenoid, and tonsil specimens from a pediatric patient were collected and underwent cell lysis and DNA isolation. Pyrosequencing was performed on the 454 Life Sciences GS FLX platform (Roche Diagnostics Corp, Branford, Connecticut). Pyrosequencing data were processed, quality-checked, and taxonomically classified to generate an abundance-based matrix. Ecological analyses were performed. SETTING: Academic, tertiary referral center. MAIN OUTCOME MEASURES: Comparative microbiome analysis. RESULTS: We detected a total of 17 unique bacterial families, with 9, 9, and 12 bacterial families from the middle ear, tonsil, and adenoid specimens, respectively. Pseudomonadaceae dominated the middle ear microbiota at 82.7% relative abundance, whereas Streptococcaceae dominated the tonsil microbiota at 69.2%. Multiple bacteria, including Pseudomonadaceae, Streptococcaceae, Fusobacteriaceae, and Pasteurellaceae, dominated the adenoid microbiota. Overlap between the middle ear and the tonsil microbiota was minimal. In contrast, the adenoid microbiota encompassed bacteria detected from middle ear and tonsil. CONCLUSIONS: Bacterial community analysis using pyrosequencing analysis revealed diverse, previously unknown bacterial communities in a set of pediatric middle ear, tonsil, and adenoid specimens. Our findings suggest that the adenoid may be a source site for both the middle ear and tonsil microbiota. An ecological framework is appropriate in comparative analysis of microbiota from nonsterile body sites.