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      A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy

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          Abstract

          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.

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          Most cited references28

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          UniFrac: a new phylogenetic method for comparing microbial communities.

          We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.
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            Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.

            The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community beta diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.
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              Accurate determination of microbial diversity from 454 pyrosequencing data.

              We present an algorithm, PyroNoise, that clusters the flowgrams of 454 pyrosequencing reads using a distance measure that models sequencing noise. This infers the true sequences in a collection of amplicons. We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2012
                13 June 2012
                : 7
                : 6
                : e36466
                Affiliations
                [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
                Columbia University, United States of America
                Author notes

                Conceived and designed the experiments: KA JV. Performed the experiments: KA JP JV. Analyzed the data: KA KR JM NS TM CC S. Raza AM DG CH JV. Contributed reagents/materials/analysis tools: KA KR JM NS AM CH JV. Wrote the paper: KA KR JM CC DG CH JV. Critical review of the manuscript: IVdV. Clinical recruitment of subjects: S. Rosenbaum.

                Article
                PONE-D-11-24996
                10.1371/journal.pone.0036466
                3374618
                22719832
                bbe9648b-ebfc-4b8f-b669-d56be75c6b54
                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.
                History
                : 2 December 2011
                : 6 April 2012
                Page count
                Pages: 15
                Categories
                Research Article
                Biology
                Computational Biology
                Genomics
                Metagenomics
                Genomics
                Metagenomics
                Microbiology
                Applied Microbiology
                Medical Microbiology
                Microbial Pathogens
                Medicine
                Infectious Diseases
                Gynecologic Infections
                Infectious Disease Modeling
                Obstetrics and Gynecology
                Pregnancy
                Pregnancy Complications
                Preterm Labor
                Female Genital Diseases
                Genitourinary Infections

                Uncategorized
                Uncategorized

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