Analyzing Gut Microbiome Diversity

Fecal samples were collected from each individual. Community DNA was prepared and used for pyrosequencing (454 Life Sciences), as well as for PCR and sequencing of bacterial 16S rRNA genes. Shotgun reads were mapped to reference genomes using the NCBI ‘non-redundant’ database, KEGG17 (link), STRING18 (link), CAZy (http://www.cazy.org/), and a 44-member human gut microbial genomes database. Metabolic reconstructions were performed based on CAZy, KEGG, and STRING annotations. The relative abundance of KEGG metabolic pathways is referred to as a ‘metabolic profile.’

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Turnbaugh P.J., Hamady M., Yatsunenko T., Cantarel B.L., Duncan A., Ley R.E., Sogin M.L., Jones W.J., Roe B.A., Affourtit J.P., Egholm M., Henrissat B., Heath A.C., Knight R, & Gordon J.I. (2008). A core gut microbiome in obese and lean twins. Nature, 457(7228), 480-484.

Publication 2008

16s rrna Bacterial genes Fecal Genomes Human Metabolic profile Microbial genomes Reconstructions

Corresponding Organization :

Other organizations : Centre National de la Recherche Scientifique, Washington University in St. Louis, Marine Biological Laboratory, University of South Carolina, University of Oklahoma, Enzo Life Sciences (United States), University of Colorado Boulder

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Variable analysis

independent variables

Collection of fecal samples from each individual

dependent variables

Composition of the microbial community DNA
Relative abundance of KEGG metabolic pathways (referred to as 'metabolic profile')

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the input information.

Annotations

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