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标题：In silico trio-biomarkers for bacterial vaginosis revealed by species dominance network analysis
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作者：Zhanshan Sam Ma ; Aaron M. Ellison
期刊名称：Computational and Structural Biotechnology Journal
印刷版ISSN：2001-0370
出版年度：2021
卷号：19
页码：2979-2989
DOI：10.1016/j.csbj.2021.05.020
出版社：Computational and Structural Biotechnology Journal
摘要：BV (bacterial vaginosis) influences 20%–40% of women but its etiology is still poorly understood. An open question about the BV is which of the hundreds of bacteria found in the human vaginal microbiome (HVM) are the major force driving the vaginal microbiota dysbiosis. Here, we recast the question of microbial causality of BV by asking if there are any prevalent ‘signatures’ (network motifs) in the vaginal microbiome networks associated with it? We apply a new framework [species dominance network analysis by Ma & Ellison (2019): Ecological Monographs ) to detect critical structures in HVM networks associated with BV risks and etiology. We reanalyzed the 16 s-rRNA gene sequencing datasets of a mixed-cohort of 25 BV patients and healthy women. In these datasets, we detected 15 trio-motifs that occurred exclusively in BV patients. We failed to find any of these 15 trio-motifs in three additional cohorts of 1535 healthy women. Most member-species of the 15 trio motifs are BV-associated anaerobic bacteria (BVAB), Ravel’s community-state type indicators, or the most dominant species; virtually all species interactions in these trios are high-salience skeletons, suggesting that those trios are strongly connected ‘cults’ associated with the occurrence of BV. The presence of the trio motifs unique to BV may act as indicators for its personalized diagnosis and could help elucidate a more mechanistic interpretation of its risks and etiology. We caution that scarcity of large longitudinal datasets of HVM also limited further verifications of our findings, and these findings require further clinical tests to launch their applications.
关键词：BV (Bacterial vaginosis) ; BV-associated anaerobic bacteria (BVAB) ; Community dominance ; Core/periphery network (CPN) ; Diversity-stability relationship (DSR) ; High-salience skeleton networks (HSN) ; Species dominance ; Species dominance network (SDN)