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Cervicovaginal Microbiome and Urine Metabolome Paired Analysis Reveals Niche Partitioning of the Microbiota in Patients with Human Papilloma Virus Infections

1
Department of Biochemistry, UPR School of Medicine, San Juan 00936, Puerto Rico
2
PR-INBRE Metabolomics Research Core, UPR School of Medicine, San Juan 00936, Puerto Rico
3
Department of Ob-Gyn, UPR School of Medicine, San Juan 00936, Puerto Rico
4
Department of Microbiology & Medical Zoology, UPR School of Medicine, San Juan 00936, Puerto Rico
*
Authors to whom correspondence should be addressed.
Metabolites 2020, 10(1), 36; https://doi.org/10.3390/metabo10010036
Received: 13 November 2019 / Revised: 11 January 2020 / Accepted: 13 January 2020 / Published: 15 January 2020
(This article belongs to the Special Issue Metabolomics and Multi-Omics Integration)
In this study, we evaluate the association between vaginal and cervical human papillomavirus infections high-risk types (HPV+H), negative controls (HPV−), the bacterial biota, and urinary metabolites via integration of metagenomics, metabolomics, and bioinformatics analysis. We recently proposed that testing urine as a biofluid could be a non-invasive method for the detection of cervical HPV+H infections by evaluating the association between cervical HPV types and a total of 24 urinary metabolites identified in the samples. As a follow-up study, we expanded the analysis by pairing the urine metabolome data with vaginal and cervical microbiota in selected samples from 19 Puerto Rican women diagnosed with HPV+H infections and HPV− controls, using a novel comprehensive framework, Model-based Integration of Metabolite Observations and Species Abundances 2 (MIMOSA2). This approach enabled us to estimate the functional activities of the cervicovaginal microbiome associated with HPV+H infections. Our results suggest that HPV+H infections could induce changes in physicochemical properties of the genital tract through which niche partitioning may occur. As a result, Lactobacillus sp. enrichment coincided with the depletion of L. iners and Shuttleworthia, which dominate under normal physiological conditions. Changes in the diversity of microbial species in HPV+H groups influence the capacity of new community members to produce or consume metabolites. In particular, the functionalities of four metabolic enzymes were predicted to be associated with the microbiota, including acylphosphatase, prolyl aminopeptidase, prolyl-tRNA synthetase, and threonyl-tRNA synthetase. Such metabolic changes may influence systemic health effects in women at risk of developing cervical cancer. Overall, even assuming the limitation of the power due to the small sample number, our study adds to current knowledge by suggesting how microbial taxonomic and metabolic shifts induced by HPV infections may influence the maintenance of microbial homeostasis and indicate that HPV+H infections may alter the ecological balance of the cervicovaginal microbiota, resulting in higher bacterial diversity. View Full-Text
Keywords: cervicovaginal HPV infections; urine; microbiota; multi-omic integrated analyses cervicovaginal HPV infections; urine; microbiota; multi-omic integrated analyses
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MDPI and ACS Style

Chorna, N.; Romaguera, J.; Godoy-Vitorino, F. Cervicovaginal Microbiome and Urine Metabolome Paired Analysis Reveals Niche Partitioning of the Microbiota in Patients with Human Papilloma Virus Infections. Metabolites 2020, 10, 36.

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