Literature DB >> 25036628

Conducting a microbiome study.

Julia K Goodrich1, Sara C Di Rienzi1, Angela C Poole1, Omry Koren1, William A Walters2, J Gregory Caporaso3, Rob Knight4, Ruth E Ley5.   

Abstract

Human microbiome research is an actively developing area of inquiry, with ramifications for our lifestyles, our interactions with microbes, and how we treat disease. Advances depend on carefully executed, controlled, and reproducible studies. Here, we provide a Primer for researchers from diverse disciplines interested in conducting microbiome research. We discuss factors to be considered in the design, execution, and data analysis of microbiome studies. These recommendations should help researchers to enter and contribute to this rapidly developing field.
Copyright © 2014 Elsevier Inc. All rights reserved.

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Year:  2014        PMID: 25036628      PMCID: PMC5074386          DOI: 10.1016/j.cell.2014.06.037

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  102 in total

1.  Search and clustering orders of magnitude faster than BLAST.

Authors:  Robert C Edgar
Journal:  Bioinformatics       Date:  2010-08-12       Impact factor: 6.937

2.  Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5.

Authors:  Matam Vijay-Kumar; Jesse D Aitken; Frederic A Carvalho; Tyler C Cullender; Simon Mwangi; Shanthi Srinivasan; Shanthi V Sitaraman; Rob Knight; Ruth E Ley; Andrew T Gewirtz
Journal:  Science       Date:  2010-03-04       Impact factor: 47.728

3.  Antibiotics in early life alter the murine colonic microbiome and adiposity.

Authors:  Ilseung Cho; Shingo Yamanishi; Laura Cox; Barbara A Methé; Jiri Zavadil; Kelvin Li; Zhan Gao; Douglas Mahana; Kartik Raju; Isabel Teitler; Huilin Li; Alexander V Alekseyenko; Martin J Blaser
Journal:  Nature       Date:  2012-08-30       Impact factor: 49.962

4.  Obesity alters gut microbial ecology.

Authors:  Ruth E Ley; Fredrik Bäckhed; Peter Turnbaugh; Catherine A Lozupone; Robin D Knight; Jeffrey I Gordon
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-20       Impact factor: 11.205

5.  Gut microbiota from twins discordant for obesity modulate metabolism in mice.

Authors:  Vanessa K Ridaura; Jeremiah J Faith; Federico E Rey; Jiye Cheng; Alexis E Duncan; Andrew L Kau; Nicholas W Griffin; Vincent Lombard; Bernard Henrissat; James R Bain; Michael J Muehlbauer; Olga Ilkayeva; Clay F Semenkovich; Katsuhiko Funai; David K Hayashi; Barbara J Lyle; Margaret C Martini; Luke K Ursell; Jose C Clemente; William Van Treuren; William A Walters; Rob Knight; Christopher B Newgard; Andrew C Heath; Jeffrey I Gordon
Journal:  Science       Date:  2013-09-06       Impact factor: 47.728

Review 6.  Experimental and analytical tools for studying the human microbiome.

Authors:  Justin Kuczynski; Christian L Lauber; William A Walters; Laura Wegener Parfrey; José C Clemente; Dirk Gevers; Rob Knight
Journal:  Nat Rev Genet       Date:  2011-12-16       Impact factor: 53.242

7.  Structure, function and diversity of the healthy human microbiome.

Authors: 
Journal:  Nature       Date:  2012-06-13       Impact factor: 49.962

8.  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.

Authors:  J R Cole; Q Wang; E Cardenas; J Fish; B Chai; R J Farris; A S Kulam-Syed-Mohideen; D M McGarrell; T Marsh; G M Garrity; J M Tiedje
Journal:  Nucleic Acids Res       Date:  2008-11-12       Impact factor: 16.971

9.  Gut microbiomes of Malawian twin pairs discordant for kwashiorkor.

Authors:  Michelle I Smith; Tanya Yatsunenko; Mark J Manary; Indi Trehan; Rajhab Mkakosya; Jiye Cheng; Andrew L Kau; Stephen S Rich; Patrick Concannon; Josyf C Mychaleckyj; Jie Liu; Eric Houpt; Jia V Li; Elaine Holmes; Jeremy Nicholson; Dan Knights; Luke K Ursell; Rob Knight; Jeffrey I Gordon
Journal:  Science       Date:  2013-01-30       Impact factor: 47.728

10.  A core gut microbiome in obese and lean twins.

Authors:  Peter J Turnbaugh; Micah Hamady; Tanya Yatsunenko; Brandi L Cantarel; Alexis Duncan; Ruth E Ley; Mitchell L Sogin; William J Jones; Bruce A Roe; Jason P Affourtit; Michael Egholm; Bernard Henrissat; Andrew C Heath; Rob Knight; Jeffrey I Gordon
Journal:  Nature       Date:  2008-11-30       Impact factor: 49.962

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  227 in total

1.  The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation.

Authors:  Eduardo da Silva Fonseca; Raquel Silva Peixoto; Alexandre Soares Rosado; Fabiano de Carvalho Balieiro; James M Tiedje; Caio Tavora Coelho da Costa Rachid
Journal:  Microb Ecol       Date:  2017-06-21       Impact factor: 4.552

2.  Is the Oral Microbiome Associated with Blood Pressure in Older Women?

Authors:  Joshua H Gordon; Michael J LaMonte; Robert J Genco; Jiwei Zhao; Lu Li; Kathleen M Hovey; Maria Tsompana; Michael J Buck; Christopher A Andrews; Daniel I Mcskimming; Wei Zheng; Yijun Sun; Jean Wactawski-Wende
Journal:  High Blood Press Cardiovasc Prev       Date:  2019-06-24

Review 3.  Tick microbiome: the force within.

Authors:  Sukanya Narasimhan; Erol Fikrig
Journal:  Trends Parasitol       Date:  2015-04-27

4.  Considerations When Designing a Microbiome Study: Implications for Nursing Science.

Authors:  Katherine A Maki; Ana F Diallo; Mark B Lockwood; Alexis T Franks; Stefan J Green; Paule V Joseph
Journal:  Biol Res Nurs       Date:  2018-11-08       Impact factor: 2.522

5.  Tracking of Engineered Bacteria In Vivo Using Nonstandard Amino Acid Incorporation.

Authors:  Pichet Praveschotinunt; Noémie-Manuelle Dorval Courchesne; Ilona den Hartog; Chaochen Lu; Jessica J Kim; Peter Q Nguyen; Neel S Joshi
Journal:  ACS Synth Biol       Date:  2018-06-06       Impact factor: 5.110

6.  Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder.

Authors:  Tanya T Nguyen; Tomasz Kosciolek; Lisa T Eyler; Rob Knight; Dilip V Jeste
Journal:  J Psychiatr Res       Date:  2018-01-31       Impact factor: 4.791

7.  Systematic review: Gut microbiota in fecal samples and detection of colorectal neoplasms.

Authors:  Efrat L Amitay; Agne Krilaviciute; Hermann Brenner
Journal:  Gut Microbes       Date:  2018-05-15

8.  A Novel Combination of Fruits and Vegetables Prevents Diet-Induced Hepatic Steatosis and Metabolic Dysfunction in Mice.

Authors:  Weimin Guo; Dayong Wu; Maria C Dao; Lijun Li; Erin D Lewis; Edwin F Ortega; Heesun Eom; Michael Thomas; Mariana Nikolova-Karakashian; Mohsen Meydani; Simin N Meydani
Journal:  J Nutr       Date:  2020-11-19       Impact factor: 4.798

9.  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 10.  Toward Accurate and Quantitative Comparative Metagenomics.

Authors:  Stephen Nayfach; Katherine S Pollard
Journal:  Cell       Date:  2016-08-25       Impact factor: 41.582

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