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Woods Hole Oceanographic Institution

Marco Coolen

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Publications
»Bioavailability of soil organic matter and microbial community dynamics upon permafrost thaw
»7000 years of virus-host molecular dynamics in the Black Sea
»Preservation potential of ancient DNA in Pleistocene marine sediments: Implications for paleoenvironmental reconstructions
»Source-specific variability in post-depositional DNA preservation with potential implications for DNA-based paleecological records
»Exploring preserved ancient dinoflagellalte and haptophyte DNA signatures to infer ecological and environmental conditions during sapropel S1 formation in the eastern Mediterranean
»Ancient DNA in lake sediment records
»Vertical distribution of metabolically active eukaryotes in the water column and sediments of the Black Sea
»DNA and lipid molecular stratigraphic records of haptophyte succession in the Black Sea during the Holocene
»Diversity of Archaea and potential for crenarchaeotal nitrification of group 1.1a in the rivers Rhine and TĂȘt
»Holocene sources of fossil BHPs
»An unusual 17[α],21[β](H)-bacteriohopanetetrol in Holocene sediments from Ace Lake (Antarctica)
»Holocene sources of organic matter in Antarctic fjord
»Variations in spatial and temporal distribution of Archaea in the North Sea
»Archaeal nitrifiers in the Black Sea
»Pleistocene Mediterranean sapropel DNA
»Rapid sulfurisation of highly branched isoprenoid (HBI) alkenes in sulfidic Holocene sediments
»Aerobic and anaerobic methanotrophs in the Black Sea water column
»Fossil DNA in Cretaceous Black Shales: Myth or Reality?
»Sulfur and methane cycling during the Holocene in Ace Lake (Antarctica)
»Ancient algal DNA in the Black Sea
»Archaeal nitrification in the ocean
»Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes
»Biomarker and 16S rDNA evidence for anaerobic oxidation of methane and related carbonate precipitation in deep-sea mud volcanoes of the Sorokin Trough, Black Sea
»Temperature-dependent variation in the distribution of tetraether membrane lipids of marine Crenarchaeota: Implications for TEX86 paleothermometry
»Paleoecology of algae in Ace Lake
»Evolution of the methane cycle in Ace Lake (Antarctica) during the Holocene: Response of methanogens and methanotrophs to environmental change
»Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes.
»Microbial communities in the chemocline of a hypersaline deep-sea basin (Urania basin, Mediterranean Sea)
»Functional exoenzymes as indicators of metabolically active bacteria in 124,000-year-old sapropel layers of the Eastern Mediterranean Sea
»Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments
»Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment
»Effects of nitrate availability and the presence of Glyceria maxima the composition and activity of the dissimilatory nitrate-reducing bacterial community
»Microbial activities and populations in upper sediment and sapropel layers


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Coolen, M. J. L., E. Post, C. C. Davis and L. J. Forney, Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes, Appl. Environ. Microbiol., 71(12), 8729-8737, 2005

To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the human vagina were used to construct model communities that were subsequently used to develop efficient means for the isolation of genomic DNA and an optimal strategy for T-RFLP analyses. The various genera in the model community could best be resolved by digesting amplicons made using bacterial primers 8f and 926r with HaeIII; fewer strains could be resolved using other primer-enzyme combinations, and no combination successfully distinguished certain species of the same genus. To demonstrate the utility of the approach, samples from five women that had been collected over a 2-month period were analyzed. Differences and similarities among the vaginal microbial communities of the women were readily apparent. The T-RFLP data suggest that the communities of three women were dominated by a single phylotype, most likely species of Lactobacillus. In contrast, the communities of two other women included numerically abundant populations that differed from Lactobacillus strains whose 16S rRNA genes had been previously determined. The T-RFLP profiles of samples from all the women were largely invariant over time, indicating that the kinds and abundances of the numerically dominant populations were relatively stable throughout two menstrual cycles. These findings show that T-RFLP of 16S rRNA genes can be used to compare vaginal microbial communities and gain information about the numerically dominant populations that are present. Full text of article can be viewed here.

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