“Learning about Who We Are,”

Nature (Impact Factor: 41.46). 06/2012; 486(7402):194-5. DOI: 10.1038/486194a
Source: PubMed


Microbial inhabitants outnumber our body's own cells by about ten to
one. These residents have become the subject of intensive research,
which is beginning to elucidate their roles in health and disease. See
Articles p.207 & p.215

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Available from: David A Relman, May 04, 2014
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    • "Trichomonas vaginalis infection [46-48] and bacterial vaginosis [28,41,43,49-67] are risk factors for spontaneous preterm labor and delivery; yet, identification of the patient with either of these conditions who will subsequently have a preterm delivery has proven difficult [60]. Characterization of the microbial composition of ecological niches in the human body [68-77], including the vagina, using culture-independent techniques, is now possible [78-96]. We previously reported a survey of the microbial communities of the vagina using sequencing of the 16S ribosomal RNA (rRNA) gene in normal pregnancy [97]. "
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    ABSTRACT: Background This study was undertaken to determine whether the vaginal microbiota of pregnant women who subsequently had a spontaneous preterm delivery is different from that of women who had a term delivery. Results This was a nested case–control study of pregnant women who had a term delivery (controls) and those who had a spontaneous preterm delivery before 34 weeks of gestation (cases). Samples of vaginal fluid were collected longitudinally and stored at −70°C until assayed. A microbial survey using pyrosequencing of V1-V3 regions of 16S rRNA genes was performed. We tested the hypothesis of whether the relative abundance of individual microbial species (phylotypes) was different between women who had a term versus preterm delivery. A suite of bioinformatic and statistical tools, including linear mixed effects models and generalized estimating equations, was used. We show that: 1) the composition of the vaginal microbiota during normal pregnancy changed as a function of gestational age, with an increase in the relative abundance of four Lactobacillus spp., and decreased in anaerobe or strict-anaerobe microbial species as pregnancy progressed; 2) no bacterial taxa differed in relative abundance between women who had a spontaneous preterm delivery and those who delivered at term; and 3) no differences in the frequency of the vaginal community state types (CST I, III, IV-B) between women who delivered at term and those who delivered preterm were detected. Conclusions The bacterial taxa composition and abundance of vaginal microbial communities, characterized with 16S rRNA gene sequence-based techniques, were not different in pregnant women who subsequently delivered a preterm neonate versus those who delivered at term.
    Full-text · Article · May 2014
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    • "Where specific PCR, serology and culture focus on a defined set of candidate pathogens, deep sequencing presents a relatively unbiased survey of RNA or DNA sequences present in a sample. Furthermore, this approach does not rely on microbial recovery and isolation, an important attribute given that the microbiome is diverse and, for the most part, cannot be readily cultured.[7] Limitations of the deep sequencing approach for diagnosing infections include: the possible introduction of contaminating sequences into the preparation, difficulties with identifying sequences not included in reference databases (e.g. "
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    ABSTRACT: Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue.
    Full-text · Article · Apr 2014 · PLoS ONE
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    • "The number of centroids detected in each sample that passed QC ranged from 2563 (from a sample taken from the posterior vaginal fornix: when healthy, such samples exhibit the lowest-diversity microbe communities of all studied body sites (25)) to 4 128 821 (from a distal gut sample, the most complex of all human-associated microbial communities (25)), with a median of 94 135 (from an oral sample). As examples, one core gene (encoding a sigma factor subunit of RNA polymerase) for Bacteroides ovatus—a bacterium commonly found in the human gut (26,27)—was observed in 81.53% of all GI-tract samples, and in <5% of samples sequenced from all other body sites. "
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    ABSTRACT: Microbial genome sequencing is one of the longest-standing areas of biological database development, but high-throughput, low-cost technologies have increased its throughput to an unprecedented number of new genomes per year. Several thousand microbial genomes are now available, necessitating new approaches to organizing information on gene function, phylogeny and microbial taxonomy to facilitate downstream biological interpretation. MetaRef, available at, is a novel online resource systematically cataloguing a comprehensive pan-genome of all microbial clades with sequenced isolates. It organizes currently available draft and finished bacterial and archaeal genomes into quality-controlled clades, reports all core and pan gene families at multiple levels in the resulting taxonomy, and it annotates families' conservation, phylogeny and consensus functional information. MetaRef also provides a comprehensive non-redundant reference gene catalogue for metagenomic studies, including the abundance and prevalence of all gene families in the >700 shotgun metagenomic samples of the Human Microbiome Project. This constitutes a systematic mapping of clade-specific microbial functions within the healthy human microbiome across multiple body sites and can be used as reference for identifying potential functional biomarkers in disease-associate microbiomes. MetaRef provides all information both as an online browsable resource and as downloadable sequences and tabular data files that can be used for subsequent offline studies.
    Full-text · Article · Nov 2013 · Nucleic Acids Research
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