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      Fecal Microbiota in Premature Infants Prior to Necrotizing Enterocolitis


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          Intestinal luminal microbiota likely contribute to the etiology of necrotizing enterocolitis (NEC), a common disease in preterm infants. Microbiota development, a cascade of initial colonization events leading to the establishment of a diverse commensal microbiota, can now be studied in preterm infants using powerful molecular tools. Starting with the first stool and continuing until discharge, weekly stool specimens were collected prospectively from infants with gestational ages ≤32 completed weeks or birth weights≤1250 g. High throughput 16S rRNA sequencing was used to compare the diversity of microbiota and the prevalence of specific bacterial signatures in nine NEC infants and in nine matched controls. After removal of short and low quality reads we retained a total of 110,021 sequences. Microbiota composition differed in the matched samples collected 1 week but not <72 hours prior to NEC diagnosis. We detected a bloom (34% increase) of Proteobacteria and a decrease (32%) in Firmicutes in NEC cases between the 1 week and <72 hour samples. No significant change was identified in the controls. At both time points, molecular signatures were identified that were increased in NEC cases. One of the bacterial signatures detected more frequently in NEC cases (p<0.01) matched closest to γ -Proteobacteria. Although this sequence grouped to the well-studied Enterobacteriaceae family, it did not match any sequence in Genbank by more than 97%. Our observations suggest that abnormal patterns of microbiota and potentially a novel pathogen contribute to the etiology of NEC.

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          Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

          We constructed error-correcting DNA barcodes that allow one run of a massively parallel pyrosequencer to process up to 1,544 samples simultaneously. Using these barcodes we processed bacterial 16S rRNA gene sequences representing microbial communities in 286 environmental samples, corrected 92% of sample assignment errors, and thus characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.
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            Metagenomics: genomic analysis of microbial communities.

            Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology. This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.
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              Necrotizing enterocolitis: treatment based on staging criteria.

              Neonatal necrotizing enterocolitis is the most important cause of acquired gastrointestinal morbidity or mortality among low birthweight infants. Prematurity alone is probably the only identifiable risk factor. Although the etiology is unknown NEC has many similarities to an infectious disease. Proper staging helps improve reporting and the management of NEC.

                Author and article information

                Role: Editor
                PLoS One
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                6 June 2011
                : 6
                : 6
                : e20647
                [1 ]Department of Microbiology and Cell Sciences and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
                [2 ]Department of Pediatrics, University of Florida, Gainesville, Florida, United States of America
                [3 ]Department of Pediatrics, University of Florida, Jacksonville, Florida, United States of America
                [4 ]Department of Statistics and Genetics Institute, University of Florida, Gainesville, Florida, United States of America
                [5 ]Clinical & Translational Science Institute, University of Florida, Gainesville, Florida, United States of America
                Indian Institute of Science, India
                Author notes

                Conceived and designed the experiments: VM JN RS MH GC DT. Performed the experiments: VM CMY MU LN JN RS MH. Analyzed the data: VM CMY JN DT XW YS MU LN RS MH GC. Contributed reagents/materials/analysis tools: VM JN RS. Wrote the paper: VM CMY JN RS MH GC XW. Bioinformatics/stats tool development: XW YS GC.

                Mai 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.
                : 8 March 2011
                : 5 May 2011
                Page count
                Pages: 7
                Research Article
                Bacterial Pathogens
                Emerging Infectious Diseases
                Host-Pathogen Interaction
                Medical Microbiology
                Microbial Ecology
                Microbial Pathogens
                Gastroenterology and Hepatology
                Pediatric Gastroenterology
                Infectious Diseases
                Bacterial Diseases
                Enterobacter Infections
                Gastrointestinal Infections
                Pediatric Critical Care
                Pediatric Gastroenterology



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