A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy
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1 Department of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, United States of America, 2 Department of Pathology & Immunology, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, United States of America, 3 Bioinformatics Research Laboratory, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, United States of America, 4 Harvard School of Public Health, Harvard University, Cambridge, Massachusetts, United States of America, 5 Broad Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America, 6 Department of Molecular Virology and Microbiology, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, United States of America
Abstract Top
While current major national research efforts (i.e., the NIH Human Microbiome Project) will enable comprehensive metagenomic characterization of the adult human microbiota, how and when these diverse microbial communities take up residence in the host and during reproductive life are unexplored at a population level. Because microbial abundance and diversity might differ in pregnancy, we sought to generate comparative metagenomic signatures across gestational age strata. DNA was isolated from the vagina (introitus, posterior fornix, midvagina) and the V5V3 region of bacterial 16S rRNA genes were sequenced (454FLX Titanium platform). Sixty-eight samples from 24 healthy gravidae (18 to 40 confirmed weeks) were compared with 301 non-pregnant controls (60 subjects). Generated sequence data were quality filtered, taxonomically binned, normalized, and organized by phylogeny and into operational taxonomic units (OTU); principal coordinates analysis (PCoA) of the resultant beta diversity measures were used for visualization and analysis in association with sample clinical metadata. Altogether, 1.4 gigabytes of data containing >2.5 million reads (averaging 6,837 sequences/sample of 493 nt in length) were generated for computational analyses. Although gravidae were not excluded by virtue of a posterior fornix pH >4.5 at the time of screening, unique vaginal microbiome signature encompassing several specific OTUs and higher-level clades was nevertheless observed and confirmed using a combination of phylogenetic, non-phylogenetic, supervised, and unsupervised approaches. Both overall diversity and richness were reduced in pregnancy, with dominance of Lactobacillus species (L. iners crispatus, jensenii and johnsonii, and the orders Lactobacillales (and Lactobacillaceae family), Clostridiales, Bacteroidales, and Actinomycetales. This intergroup comparison using rigorous standardized sampling protocols and analytical methodologies provides robust initial evidence that the vaginal microbial 16S rRNA gene catalogue uniquely differs in pregnancy, with variance of taxa across vaginal subsite and gestational age.Citation: Aagaard K, Riehle K, Ma J, Segata N, Mistretta T-A, et al. (2012) A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy. PLoS ONE 7(6): e36466. doi:10.1371/journal.pone.0036466
Editor: Adam J. Ratner, Columbia University, United States of America
Received: December 2, 2011; Accepted: April 6, 2012; Published: June 13, 2012
Copyright: © 2012 Aagaard et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was funded by the National Institutes of Health (NIH Director New Innovator Award (DP2120OD001500-01 K.A.), NICHD/NIDDK #R01DK080558-01 (K.A.), UH3 DK083990l (J.V.), NIH 1R01HG005969 (C.H.), and the NIH Common Fund Human Microbiome-HMP (K.A., J.V., J.P., C.H., (NIHU54HG004969 D.G.)), and the Burroughs Welcome Fund (Burroughs Welcome Fund Preterm Birth Initiative (K.A. and J.V.)). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: aagaardt@bcm.edu
Editor: Adam J. Ratner, Columbia University, United States of America
Received: December 2, 2011; Accepted: April 6, 2012; Published: June 13, 2012
Copyright: © 2012 Aagaard et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was funded by the National Institutes of Health (NIH Director New Innovator Award (DP2120OD001500-01 K.A.), NICHD/NIDDK #R01DK080558-01 (K.A.), UH3 DK083990l (J.V.), NIH 1R01HG005969 (C.H.), and the NIH Common Fund Human Microbiome-HMP (K.A., J.V., J.P., C.H., (NIHU54HG004969 D.G.)), and the Burroughs Welcome Fund (Burroughs Welcome Fund Preterm Birth Initiative (K.A. and J.V.)). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: aagaardt@bcm.edu
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