Microbial function and genital inflammation in young South African women at high risk of HIV infection

Abstract

Background Female genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activities has not been established. Since proteins are key elements representing actual microbial functions, this study utilized metaproteomics to evaluate the relationship between FGT microbial function and inflammation in 113 young and adolescent South African women at high risk of HIV infection. Women were grouped as having low, medium, or high FGT inflammation by K-means clustering according to pro-inflammatory cytokine concentrations. Results A total of 3186 microbial and human proteins were identified in lateral vaginal wall swabs using liquid chromatography-tandem mass spectrometry, while 94 microbial taxa were included in the taxonomic analysis. Both metaproteomics and 16S rRNA gene sequencing analyses showed increased non-optimal bacteria and decreased lactobacilli in women with FGT inflammatory profiles. However, differences in the predicted relative abundance of most bacteria were observed between 16S rRNA gene sequencing and metaproteomics analyses. Bacterial protein functional annotations (gene ontology) predicted inflammatory cytokine profiles more accurately than bacterial relative abundance determined by 16S rRNA gene sequence analysis, as well as functional predictions based on 16S rRNA gene sequence data (p < 0.0001). The majority of microbial biological processes were underrepresented in women with high inflammation compared to those with low inflammation, including a Lactobacillus-associated signature of reduced cell wall organization and peptidoglycan biosynthesis. This signature remained associated with high FGT inflammation in a subset of 74 women 9 weeks later, was upheld after adjusting for Lactobacillus relative abundance, and was associated with in vitro inflammatory cytokine responses to Lactobacillus isolates from the same women. Reduced cell wall organization and peptidoglycan biosynthesis were also associated with high FGT inflammation in an independent sample of ten women. Conclusions Both the presence of specific microbial taxa in the FGT and their properties and activities are critical determinants of FGT inflammation. Our findings support those of previous studies suggesting that peptidoglycan is directly immunosuppressive, and identify a possible avenue for biotherapeutic development to reduce inflammation in the FGT. To facilitate further investigations of microbial activities, we have developed the FGT-DB application that is available at http://fgtdb.org/.

Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression

“…The protonated form of LA predominates at a pH below its acid dissociation constant ( pKa 3.86) and possesses virucidal and anti-inflammatory activity, in contrast to the lactate anion that predominates at pH > 3.86 [ 38 , 41 , 42 ]. These data, and others [ 29 , 44 , 45 ], indicate that metabolites produced by optimal FRT microbiota species are likely key mediators of the health benefits associated with Lactobacillus -dominant microbiota.…”

“…Lateral vaginal wall swabs were collected by the study nurse by rotating Dacron swabs 360° on the lateral vaginal wall before being placed in 1 ml phosphate-buffered saline (PBS), transported to the laboratory at 4° C and stored at −80 °C. Samples were computational randomised and the eluted material subjected to metaproteomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a Q-Exactive quadrupole-Orbitrap MS (Thermo Fisher Scientific, MA, USA) coupled with a Dionex UltiMate 3000 nano-UPLC system (120 min per sample) [ 45 ]. Proteomic data were used to infer vaginal microbiome composition and host secretome as described previously [ 45 ].…”

“…Samples were computational randomised and the eluted material subjected to metaproteomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a Q-Exactive quadrupole-Orbitrap MS (Thermo Fisher Scientific, MA, USA) coupled with a Dionex UltiMate 3000 nano-UPLC system (120 min per sample) [ 45 ]. Proteomic data were used to infer vaginal microbiome composition and host secretome as described previously [ 45 ]. Briefly, proteins were identified using two different databases: (i) UniProt database restricted to human and microbial entries (73,910,451, release August 2017) and filtered using the MetaNovo pipeline [ 48 ] and (ii) human proteins combined with a vaginal metagenome-based database obtained from the study of Afiuni-Zadeh et al [ 49 ].…”

Vaginal Dysbiotic Microbiome in Women With No Symptoms of Genital Infections

“…The predicted key functional pathways in the normal microbiota were peptidoglycan biosynthesis, phosphatidylglycerol biosynthesis I and II, peptidoglycan biosynthesis IV and pyrimidine nucleotide salvage pathways. Increased cell wall organization and peptidoglycan biosynthesis in Lactobacillus dominated microbiomes have been associated with reduced FGT inflammation ( Alisoltani et al., 2020 ) and in modulating the immune system ( Song et al., 2018 ). Peptidoglycan biosynthesis IV and pyrimidine nucleotide salvage pathways have been further described during the proliferative phase of menstrual cycle and associated with increased bacterial proliferation ( Chen et al., 2017 ).…”

Correction to: Microbial function and genital inflammation in young South African women at high risk of HIV infection

“…The author reported that Additional file 2 for this article [1] is a draft copy of Additional file 1. The correct additional file 2 should have been an excel file.…”