title: Bacterial biogeography of the human digestive tract.
abstract: We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated >32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing >95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with >99% Good's coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highly similar within individuals and largely distinct from those in stool. Within an individual, OTU overlap among broad site definitions (mouth, stomach/duodenum, colon and stool) ranged from 32-110 OTUs, 25 of which were common to all individuals and included OTUs affiliated with Faecalibacterium prasnitzii and the TM7 phylum. This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.
authors.affiliation: Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
authors.forename: Jennifer C
authors.initials: JC
authors.lastname: Stearns
authors.forename: Michael D J
authors.initials: MD
authors.lastname: Lynch
authors.forename: Dilani B
authors.initials: DB
authors.lastname: Senadheera
authors.forename: Howard C
authors.initials: HC
authors.lastname: Tenenbaum
authors.forename: Michael B
authors.initials: MB
authors.lastname: Goldberg
authors.forename: Dennis G
authors.initials: DG
authors.lastname: Cvitkovitch
authors.forename: Kenneth
authors.initials: K
authors.lastname: Croitoru
authors.forename: Gabriel
authors.initials: G
authors.lastname: Moreno-Hagelsieb
authors.forename: Josh D
authors.initials: JD
authors.lastname: Neufeld
mesh_terms: D000328:Adult; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D005260:Female; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D008297:Male; D054892:Metagenome / Q000235:genetics; D009928:Organ Specificity; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S