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      Structure and function of the healthy pre-adolescent pediatric gut microbiome.

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          Abstract

          The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although human gut microbiota are recognized to change as we age, information regarding the structure and function of the gut microbiome during childhood is limited. Using 16S rRNA gene and shotgun metagenomic sequencing, we characterized the structure, function, and variation of the healthy pediatric gut microbiome in a cohort of school-aged, pre-adolescent children (ages 7-12 years). We compared the healthy pediatric gut microbiome with that of healthy adults previously recruited from the same region (Houston, TX, USA).

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          Most cited references74

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            QIIME allows analysis of high-throughput community sequencing data.

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              Search and clustering orders of magnitude faster than BLAST.

              Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets. Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch.
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                Author and article information

                Journal
                Microbiome
                Microbiome
                Springer Science and Business Media LLC
                2049-2618
                2049-2618
                Aug 26 2015
                : 3
                Affiliations
                [1 ] Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA. holliste@bcm.edu.
                [2 ] Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA. holliste@bcm.edu.
                [3 ] Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.
                [4 ] Bioinformatics Research Laboratory, Baylor College of Medicine, Houston, TX, USA.
                [5 ] Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.
                [6 ] Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA.
                [7 ] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
                [8 ] Children's Nutrition Research Center, Houston, TX, USA.
                [9 ] Pediatric Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Houston, TX, USA.
                [10 ] Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
                [11 ] Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA.
                [12 ] Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA.
                Article
                10.1186/s40168-015-0101-x
                10.1186/s40168-015-0101-x
                4550057
                26306392
                267dfe4e-eeb6-4cd2-a9df-15fc442c14a7
                History

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