Bacterial biogeography of the human digestive tract.

Scientific Reports
Jennifer C StearnsJosh D Neufeld

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.

References

May 24, 2001·Journal of Bacteriology·B J PasterF E Dewhirst
Feb 14, 2003·Lancet·Francisco Guarner, Juan-R Malagelada
Apr 24, 2003·Journal of Dental Research·P S KumarE J Leys
Mar 16, 2004·Proceedings of the National Academy of Sciences of the United States of America·Zhiheng PeiMartin J Blaser
Mar 26, 2005·Science·Fredrik BäckhedJeffrey I Gordon
Apr 16, 2005·Science·Paul B EckburgDavid A Relman
Jun 29, 2005·Circulation·James D BeckSteven Offenbacher
Jul 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ruth E LeyJeffrey I Gordon
Jan 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·Elisabeth M BikDavid A Relman
May 17, 2006·Anaerobe·Cynthia L Sears
Jul 6, 2006·Applied and Environmental Microbiology·T Z DeSantisG L Andersen
Aug 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Mitchell L SoginGerhard J Herndl
Feb 13, 2007·Proceedings of the National Academy of Sciences of the United States of America·Zhan GaoMartin J Blaser
Jun 26, 2007·Applied and Environmental Microbiology·Qiong WangJames R Cole
Jun 28, 2007·PLoS Biology·Chana PalmerPatrick O Brown
Aug 10, 2007·Journal of Clinical Microbiology·David N FredricksJeanne M Marrazzo
Jul 31, 2008·PloS One·Anders F AnderssonLars Engstrand
Oct 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Harry SokolPhilippe Langella
Oct 24, 2008·Journal of Dental Research·B J F KeijserW Crielaard
Nov 14, 2008·Proceedings of the National Academy of Sciences of the United States of America·Noah FiererRob Knight
Nov 20, 2008·Journal of Medical Microbiology·Tanja KuehbacherStephan J Ott
Dec 2, 2008·Nature·Peter J TurnbaughJeffrey I Gordon
Apr 21, 2009·Molecular Biology and Evolution·Morgan N PriceAdam P Arkin
May 30, 2009·Science·Elizabeth A GriceJulia A Segre
Oct 3, 2009·Journal of Microbiological Methods·Vladimir LazarevicPatrice François
Nov 7, 2009·Science·Elizabeth K CostelloRob Knight
Mar 6, 2010·Science·Matam Vijay-KumarAndrew T Gewirtz
Mar 20, 2010·Environmental Microbiology·Susan M HuseMitchell L Sogin
Mar 26, 2010·The ISME Journal·Elisabeth M BikDavid A Relman
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Jun 10, 2010·Current Gastroenterology Reports·R Daniel Lawson, Walter J Coyle
Jun 23, 2010·Proceedings of the National Academy of Sciences of the United States of America·Maria G Dominguez-BelloRob Knight
Jul 27, 2010·Journal of Bacteriology·Floyd E DewhirstWilliam G Wade
Aug 17, 2010·Bioinformatics·Robert C Edgar
Jun 1, 2011·Genome Biology·J Gregory CaporasoRob Knight
Jun 28, 2011·PloS One·Jorge M DinisCleber C Ouverney
Jul 1, 2011·The ISME Journal·Pedro Belda-FerreAlex Mira

❮ Previous
Next ❯

Citations

Sep 28, 2012·Genome Biology·Xochitl C MorganCurtis Huttenhower
Jul 19, 2012·PLoS Computational Biology·Karoline FaustCurtis Huttenhower
Mar 30, 2013·World Journal of Gastroenterology : WJG·Zi-Kai Wang, Yun-Sheng Yang
Oct 8, 2013·Applied and Environmental Microbiology·Jane M M NatividadElena F Verdu
Feb 10, 2016·Alimentary Pharmacology & Therapeutics·J TorresJ Hu
Oct 9, 2014·Proceedings of the National Academy of Sciences of the United States of America·Kieran C O'DohertyRobert G Beiko
Feb 25, 2014·Gastroenterology·Aleksandar D KosticDirk Gevers
Feb 4, 2014·Gastroenterology·Xochitl C Morgan, Curtis Huttenhower
Sep 20, 2012·Pharmacological Research : the Official Journal of the Italian Pharmacological Society·Stig Bengmark
May 1, 2012·The Journal of Allergy and Clinical Immunology·Luke K UrsellRob Knight
Mar 4, 2015·Cell Host & Microbe·Koji YasudaXochitl C Morgan
Sep 5, 2015·Current Opinion in Biotechnology·Smitha KrishnanKyongbum Lee
Sep 6, 2015·Gut·R H HuntJ Tack
Jan 28, 2015·Journal of Digestive Diseases·Christian SchulzPeter Malfertheiner
Nov 20, 2013·Journal of Digestive Diseases·Wen Ming WuLi Hua Peng
Oct 7, 2015·Frontiers in Microbiology·Natalie ChristianKeith Clay
Oct 23, 2014·MicrobiologyOpen·Esther JiménezJuan M Rodríguez
Apr 14, 2016·Digestive Diseases and Sciences·Erik J SniderJulian A Abrams
Dec 3, 2014·Internal Medicine Journal·G B Rogers
May 6, 2016·Frontiers in Microbiology·Ankit GuptaVineet K Sharma
Dec 18, 2013·Journal of Microbiological Methods·David Feria-GervasioJean-François Brugère
Oct 8, 2013·Veterinary Microbiology·Christopher J BarkerPeter Timms
Jun 25, 2013·FEMS Microbiology Reviews·Ines YangSebastian Suerbaum
Aug 6, 2013·FEMS Microbiology Reviews·Eva BoonRobert G Beiko
May 28, 2014·FEMS Microbiology Reviews·Mirjana Rajilić-Stojanović, Willem M de Vos
Jun 21, 2014·Immunity·Curtis HuttenhowerRamnik J Xavier
May 15, 2015·Cell Host & Microbe·Stéphane HacquardPaul Schulze-Lefert
Mar 25, 2015·Nature Reviews. Gastroenterology & Hepatology·R Balfour Sartor
Aug 22, 2013·Gut Microbes·Alexander Sheh, James G Fox
Mar 19, 2014·Gut Microbes·Joann Romano-KeelerJörn-Hendrik Weitkamp
Mar 20, 2014·Gut Microbes·Miriam E Martin, Jay V Solnick

❮ Previous
Next ❯

Methods Mentioned

BETA
Illumina
PCR
Illumina sequencing
biopsies

Software Mentioned

QIIME
USEARCH
FigTree
UCHIME
gplots
ggplot2
UniFrac
PyNAST
RAST
MG

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.