Literature DB >> 22861806

Defining the human microbiome.

Luke K Ursell1, Jessica L Metcalf, Laura Wegener Parfrey, Rob Knight.   

Abstract

Rapidly developing sequencing methods and analytical techniques are enhancing our ability to understand the human microbiome, and, indeed, how the microbiome and its constituents are defined. This review highlights recent research that expands our ability to understand the human microbiome on different spatial and temporal scales, including daily time series datasets spanning months. Furthermore, emerging concepts related to defining operational taxonomic units, diversity indices, core versus transient microbiomes, and the possibility of enterotypes are discussed. Additional advances in sequencing technology and in our understanding of the microbiome will provide exciting prospects for exploiting the microbiota for personalized medicine.
© 2012 International Life Sciences Institute.

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Year:  2012        PMID: 22861806      PMCID: PMC3426293          DOI: 10.1111/j.1753-4887.2012.00493.x

Source DB:  PubMed          Journal:  Nutr Rev        ISSN: 0029-6643            Impact factor:   7.110


  71 in total

1.  Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.

Authors:  Les Dethlefsen; David A Relman
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-16       Impact factor: 11.205

2.  A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.

Authors:  Yijun Sun; Yunpeng Cai; Susan M Huse; Rob Knight; William G Farmerie; Xiaoyu Wang; Volker Mai
Journal:  Brief Bioinform       Date:  2011-04-27       Impact factor: 11.622

3.  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

Review 4.  Development of the human gastrointestinal microbiota and insights from high-throughput sequencing.

Authors:  Maria Gloria Dominguez-Bello; Martin J Blaser; Ruth E Ley; Rob Knight
Journal:  Gastroenterology       Date:  2011-05       Impact factor: 22.682

5.  Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

Authors:  Amber L Hartman; Sean Riddle; Timothy McPhillips; Bertram Ludäscher; Jonathan A Eisen
Journal:  BMC Bioinformatics       Date:  2010-06-12       Impact factor: 3.169

Review 6.  Direct sequencing of the human microbiome readily reveals community differences.

Authors:  Justin Kuczynski; Elizabeth K Costello; Diana R Nemergut; Jesse Zaneveld; Christian L Lauber; Dan Knights; Omry Koren; Noah Fierer; Scott T Kelley; Ruth E Ley; Jeffrey I Gordon; Rob Knight
Journal:  Genome Biol       Date:  2010-05-05       Impact factor: 13.583

7.  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

8.  Identifying genetic determinants needed to establish a human gut symbiont in its habitat.

Authors:  Andrew L Goodman; Nathan P McNulty; Yue Zhao; Douglas Leip; Robi D Mitra; Catherine A Lozupone; Rob Knight; Jeffrey I Gordon
Journal:  Cell Host Microbe       Date:  2009-09-17       Impact factor: 21.023

Review 9.  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

10.  Statistical methods for detecting differentially abundant features in clinical metagenomic samples.

Authors:  James Robert White; Niranjan Nagarajan; Mihai Pop
Journal:  PLoS Comput Biol       Date:  2009-04-10       Impact factor: 4.475

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  228 in total

Review 1.  Interactions between host and gut microbiota in domestic pigs: a review.

Authors:  Yadnyavalkya Patil; Ravi Gooneratne; Xiang-Hong Ju
Journal:  Gut Microbes       Date:  2019-11-24

Review 2.  Candida albicans Pathogenesis: Fitting within the Host-Microbe Damage Response Framework.

Authors:  Mary Ann Jabra-Rizk; Eric F Kong; Christina Tsui; M Hong Nguyen; Cornelius J Clancy; Paul L Fidel; Mairi Noverr
Journal:  Infect Immun       Date:  2016-09-19       Impact factor: 3.441

Review 3.  The Microbiome and Osteosarcopenic Obesity in Older Individuals in Long-Term Care Facilities.

Authors:  Julia E Inglis; Jasminka Z Ilich
Journal:  Curr Osteoporos Rep       Date:  2015-10       Impact factor: 5.096

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

Review 5.  From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity.

Authors:  Jessica I Rivera-Pérez; Alfredo A González; Gary A Toranzos
Journal:  Microbiol Spectr       Date:  2017-01

6.  The potential influence of the microbiota and probiotics on women during long spaceflights.

Authors:  Camilla Urbaniak; Gregor Reid
Journal:  Womens Health (Lond)       Date:  2016-02-22

Review 7.  The microbiome of the urinary tract--a role beyond infection.

Authors:  Samantha A Whiteside; Hassan Razvi; Sumit Dave; Gregor Reid; Jeremy P Burton
Journal:  Nat Rev Urol       Date:  2015-01-20       Impact factor: 14.432

8.  Fecal microbiomes of non-human primates in Western Uganda reveal species-specific communities largely resistant to habitat perturbation.

Authors:  Aleia I McCord; Colin A Chapman; Geoffrey Weny; Alex Tumukunde; David Hyeroba; Kelly Klotz; Avery S Koblings; David N M Mbora; Melissa Cregger; Bryan A White; Steven R Leigh; Tony L Goldberg
Journal:  Am J Primatol       Date:  2013-11-27       Impact factor: 2.371

9.  Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children.

Authors:  S Murugesan; M Ulloa-Martínez; H Martínez-Rojano; F M Galván-Rodríguez; C Miranda-Brito; M C Romano; A Piña-Escobedo; M L Pizano-Zárate; C Hoyo-Vadillo; J García-Mena
Journal:  Eur J Clin Microbiol Infect Dis       Date:  2015-03-12       Impact factor: 3.267

10.  Investigators' perspectives on translating human microbiome research into clinical practice.

Authors:  M J Slashinski; S N Whitney; L S Achenbaum; W A Keitel; S A McCurdy; A L McGuire
Journal:  Public Health Genomics       Date:  2013-04-24       Impact factor: 2.000

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