Literature DB >> 25367129

Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis.

Maomeng Tong1, Jonathan P Jacobs2, Ian H McHardy1, Jonathan Braun1.   

Abstract

Dysbiosis of host-associated commensal microbiota is emerging as an important factor in risk and phenotype of immunologic, metabolic, and behavioral diseases. Accurate analysis of microbial composition and functional state in humans or mice requires appropriate collection and pre-processing of biospecimens. Methods to sample luminal and mucosal microbiota from human or mouse intestines and to profile microbial phylogenetic composition using 16S rRNA sequencing are presented here. Data generated using the methods in this unit can be used for downstream quantitative analysis of microbial ecology.
Copyright © 2014 John Wiley & Sons, Inc.

Entities:  

Keywords:  16S rRNA; Illumina sequencing; intestinal microbiota; lavage; mucosal microbiota

Mesh：

Substances：

Year:  2014        PMID： 25367129      PMCID： PMC4457454          DOI： 10.1002/0471142735.im0741s107

Source DB:  PubMed          Journal:  Curr Protoc Immunol        ISSN： 1934-3671


  18 in total

Review 1.  Host-gut microbiota metabolic interactions.

Authors:  Jeremy K Nicholson; Elaine Holmes; James Kinross; Remy Burcelin; Glenn Gibson; Wei Jia; Sven Pettersson
Journal:  Science       Date:  2012-06-06       Impact factor: 47.728

Review 2.  Molecular eco-systems biology: towards an understanding of community function.

Authors:  Jeroen Raes; Peer Bork
Journal:  Nat Rev Microbiol       Date:  2008-09       Impact factor: 60.633

3.  Bacterial community variation in human body habitats across space and time.

Authors:  Elizabeth K Costello; Christian L Lauber; Micah Hamady; Noah Fierer; Jeffrey I Gordon; Rob Knight
Journal:  Science       Date:  2009-11-05       Impact factor: 47.728

4.  Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Authors:  Justin Kuczynski; Jesse Stombaugh; William Anton Walters; Antonio González; J Gregory Caporaso; Rob Knight
Journal:  Curr Protoc Microbiol       Date:  2012-11

5.  QIIME allows analysis of high-throughput community sequencing data.

Authors:  J Gregory Caporaso; Justin Kuczynski; Jesse Stombaugh; Kyle Bittinger; Frederic D Bushman; Elizabeth K Costello; Noah Fierer; Antonio Gonzalez Peña; Julia K Goodrich; Jeffrey I Gordon; Gavin A Huttley; Scott T Kelley; Dan Knights; Jeremy E Koenig; Ruth E Ley; Catherine A Lozupone; Daniel McDonald; Brian D Muegge; Meg Pirrung; Jens Reeder; Joel R Sevinsky; Peter J Turnbaugh; William A Walters; Jeremy Widmann; Tanya Yatsunenko; Jesse Zaneveld; Rob Knight
Journal:  Nat Methods       Date:  2010-04-11       Impact factor: 28.547

6.  Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.

Authors:  J Gregory Caporaso; Christian L Lauber; William A Walters; Donna Berg-Lyons; James Huntley; Noah Fierer; Sarah M Owens; Jason Betley; Louise Fraser; Markus Bauer; Niall Gormley; Jack A Gilbert; Geoff Smith; Rob Knight
Journal:  ISME J       Date:  2012-03-08       Impact factor: 10.302

7.  HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota.

Authors:  Ian H McHardy; Xiaoxiao Li; Maomeng Tong; Paul Ruegger; Jonathan Jacobs; James Borneman; Peter Anton; Jonathan Braun
Journal:  Microbiome       Date:  2013-10-12       Impact factor: 14.650

8.  Gut microbiota disturbance during antibiotic therapy: a multi-omic approach.

Authors:  Ana Elena Pérez-Cobas; María José Gosalbes; Anette Friedrichs; Henrik Knecht; Alejandro Artacho; Kathleen Eismann; Wolfgang Otto; David Rojo; Rafael Bargiela; Martin von Bergen; Sven C Neulinger; Carolin Däumer; Femke-Anouska Heinsen; Amparo Latorre; Coral Barbas; Jana Seifert; Vitor Martins dos Santos; Stephan J Ott; Manuel Ferrer; Andrés Moya
Journal:  Gut       Date:  2012-12-12       Impact factor: 23.059

9.  Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.

Authors:  Alison R Erickson; Brandi L Cantarel; Regina Lamendella; Youssef Darzi; Emmanuel F Mongodin; Chongle Pan; Manesh Shah; Jonas Halfvarson; Curt Tysk; Bernard Henrissat; Jeroen Raes; Nathan C Verberkmoes; Claire M Fraser; Robert L Hettich; Janet K Jansson
Journal:  PLoS One       Date:  2012-11-28       Impact factor: 3.240

10.  A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease.

Authors:  Maomeng Tong; Xiaoxiao Li; Laura Wegener Parfrey; Bennett Roth; Andrew Ippoliti; Bo Wei; James Borneman; Dermot P B McGovern; Daniel N Frank; Ellen Li; Steve Horvath; Rob Knight; Jonathan Braun
Journal:  PLoS One       Date:  2013-11-19       Impact factor: 3.240
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  34 in total

1.  Indigenous Microbiota Protects against Inflammation-Induced Osteonecrosis.

Authors:  D W Williams; H E Vuong; S Kim; A Lenon; K Ho; E Y Hsiao; E C Sung; R H Kim
Journal:  J Dent Res       Date:  2020-02-28       Impact factor: 6.116

2.  Microbial, metabolomic, and immunologic dynamics in a relapsing genetic mouse model of colitis induced by T-synthase deficiency.

Authors:  Jonathan P Jacobs; Lin Lin; Maryam Goudarzi; Paul Ruegger; Dermot P B McGovern; Albert J Fornace; James Borneman; Lijun Xia; Jonathan Braun
Journal:  Gut Microbes       Date:  2016-11-22

3.  High-protein diet improves sensitivity to cholecystokinin and shifts the cecal microbiome without altering brain inflammation in diet-induced obesity in rats.

Authors:  Lixin Wang; Jonathan P Jacobs; Venu Lagishetty; Pu-Qing Yuan; Shuping V Wu; Mulugeta Million; Joseph R Reeve; Joseph R Pisegna; Yvette Taché
Journal:  Am J Physiol Regul Integr Comp Physiol       Date:  2017-07-19       Impact factor: 3.619

4.  Metformin alters the duodenal microbiome and decreases the incidence of pancreatic ductal adenocarcinoma promoted by diet-induced obesity.

Authors:  Tien S Dong; Hui-Hua Chang; Meg Hauer; Venu Lagishetty; William Katzka; Enrique Rozengurt; Jonathan P Jacobs; Guido Eibl
Journal:  Am J Physiol Gastrointest Liver Physiol       Date:  2019-09-23       Impact factor: 4.052

Review 5.  Diagnostic and Prognostic Microbial Biomarkers in Inflammatory Bowel Diseases.

Authors:  Marla Dubinsky; Jonathan Braun
Journal:  Gastroenterology       Date:  2015-08-15       Impact factor: 22.682

6.  Helicobacter pylori and gut microbiota in multiple sclerosis versus Alzheimer's disease: 10 pitfalls of microbiome studies.

Authors:  Ah-Mee Park; Seiichi Omura; Mitsugu Fujita; Fumitaka Sato; Ikuo Tsunoda
Journal:  Clin Exp Neuroimmunol       Date:  2017-07-23

Review 7.  A review and roadmap of the skin, lung and gut microbiota in systemic sclerosis.

Authors:  Shannon Teaw; Monique Hinchcliff; Michelle Cheng
Journal:  Rheumatology (Oxford)       Date:  2021-12-01       Impact factor: 7.580

8.  Early life adversity predicts brain-gut alterations associated with increased stress and mood.

Authors:  Elena J L Coley; Emeran A Mayer; Vadim Osadchiy; Zixi Chen; Vishvak Subramanyam; Yurui Zhang; Elaine Y Hsiao; Kan Gao; Ravi Bhatt; Tien Dong; Priten Vora; Bruce Naliboff; Jonathan P Jacobs; Arpana Gupta
Journal:  Neurobiol Stress       Date:  2021-05-25

9.  Surgically Induced Changes in Gut Microbiome and Hedonic Eating as Related to Weight Loss: Preliminary Findings in Obese Women Undergoing Bariatric Surgery.

Authors:  Claudia P Sanmiguel; Jonathan Jacobs; Arpana Gupta; Tiffany Ju; Jean Stains; Kristen Coveleskie; Venu Lagishetty; Anna Balioukova; Yijun Chen; Erik Dutson; Emeran A Mayer; Jennifer S Labus
Journal:  Psychosom Med       Date:  2017-10       Impact factor: 3.864

10.  The Intestinal Microbiome Predicts Weight Loss on a Calorie-Restricted Diet and Is Associated With Improved Hepatic Steatosis.

Authors:  Tien S Dong; Kayti Luu; Venu Lagishetty; Farzaneh Sedighian; Shih-Lung Woo; Benjamin W Dreskin; William Katzka; Candace Chang; Yi Zhou; Nerea Arias-Jayo; Julianne Yang; Aaron I Ahdoot; Jason Ye; Zhaoping Li; Joseph R Pisegna; Jonathan P Jacobs
Journal:  Front Nutr       Date:  2021-07-08
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