A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy
Autor: | Kjersti Aagaard, Cristian Coarfa, Nicola Segata, Sean Rosenbaum, Toni-Ann Mistretta, Kevin Riehle, Dirk Gevers, James Versalovic, Sabeen Raza, Joseph F. Petrosino, Ignatia B. Van den Veyver, Jun Ma, Aleksandar Milosavljevic, Curtis Huttenhower |
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Rok vydání: | 2012 |
Předmět: |
Adult
DNA Bacterial Applied Microbiology Gynecologic Infections lcsh:Medicine Genomics Microbiology 03 medical and health sciences Pregnancy Phylogenetics Humans Microbiome lcsh:Science Biology Microbial Pathogens 030304 developmental biology 0303 health sciences Multidisciplinary Bacteria biology Phylogenetic tree Preterm Labor Genitourinary Infections 030306 microbiology lcsh:R Human microbiome Computational Biology Obstetrics and Gynecology biology.organism_classification Bacteroidales Pregnancy Complications Infectious Diseases Female Genital Diseases Medical Microbiology Metagenomics Evolutionary biology Vagina Medicine Metagenome Female lcsh:Q Infectious Disease Modeling Research Article Human Microbiome Project |
Zdroj: | PLoS ONE, Vol 7, Iss 6, p e36466 (2012) PLoS ONE |
ISSN: | 1932-6203 |
Popis: | 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. |
Databáze: | OpenAIRE |
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