Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome

Abstract

The human cervical-vaginal area contains proteins derived from microorganisms that may prevent or predispose women to gynecological conditions. The liquid Pap test fixative is an unexplored resource for analysis of microbial communities and the microbe-host interaction. Previously, we showed that the residual cell-free fixative from discarded Pap tests of healthy women could be used for mass spectrometry (MS) based proteomic identification of cervical-vaginal proteins. In this study, we reprocessed these MS raw data files for metaproteomic analysis to characterize the microbial community composition and function of microbial proteins in the cervical-vaginal region. This was accomplished by developing a customized protein sequence database encompassing microbes likely present in the vagina. High-mass accuracy data were searched against the protein FASTA database using a two-step search method within the Galaxy for proteomics platform. Data was analyzed by MEGAN6 (MetaGenomeAnalyzer) for phylogenetic and functional characterization. We identified over 300 unique peptides from a variety of bacterial phyla and Candida. Peptides corresponding to proteins involved in carbohydrate metabolism, oxidation-reduction, and transport were identified. By identifying microbial peptides in Pap test supernatants it may be possible to acquire a functional signature of these microbes, as well as detect specific proteins associated with cervical health and disease.

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

“…Due to the important role of database in metaproteomic analysis, we compared two different databases to identify proteins in our dataset: (i) UniProt database restricted to human and microbial entries (73,910,451, release August 2017) and filtered using the MetaNovo pipeline [ 34 ] and (ii) vaginal metagenome-based database with human proteins obtained from the study of Afiuni-Zadeh et al [ 35 ]. The raw data were processed using MaxQuant version 1.5.7.4 against each database, separately.…”

The Role of the Cervicovaginal Microbiome on the Genesis and as a Biomarker of Premalignant Cervical Intraepithelial Neoplasia and Invasive Cervical Cancer

“…Proteomic studies have been performed on cervicovaginal fluid to analyze and understand the role of the microbiota on the cervical region metabolism [87][88][89]. A study using proteomic data showed that dysbiosis causes cervicovaginal inflammation and detrimental changes within the mucosal barrier [90].…”

“…A study using proteomic data showed that dysbiosis causes cervicovaginal inflammation and detrimental changes within the mucosal barrier [90]. Another recent study shows that cervicovaginal microbiome proteomic analysis may be conducted using the residual Papanicolaou test supernatants for community composition and functional microbiota characterization [87]. Proteomic analysis can be used in research to understand the cervicovaginal microbiome and its contribution to women's health and disease in the metabolic context.…”

Association between Cervical Microbiota and HPV: Could This Be the Key to Complete Cervical Cancer Eradication?

“…Since common medium- or large-scale VM analyses employed this technique, the role of non-bacterial constituents of the VM in HPV infection and disease has not yet been described. Therefore, proteomic analysis could be key to a more complete understanding of the VM and its influence on disease in the metabolic context [ 142 , 143 ]. Only after the pathogenic mechanisms of interaction between microbiota and HPV have been fully understood will it be possible to identify the most effective therapeutic strategy.…”