Literature DB >> 21765408

Bayesian community-wide culture-independent microbial source tracking.

Dan Knights1, Justin Kuczynski, Emily S Charlson, Jesse Zaneveld, Michael C Mozer, Ronald G Collman, Frederic D Bushman, Rob Knight, Scott T Kelley.   

Abstract

Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments. We applied SourceTracker to microbial surveys from neonatal intensive care units (NICUs), offices and molecular biology laboratories, and provide a database of known contaminants for future testing.

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Mesh：

Year:  2011        PMID： 21765408      PMCID： PMC3791591          DOI： 10.1038/nmeth.1650

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  19 in total

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Authors:  Silvia G Acinas; Ramahi Sarma-Rupavtarm; Vanja Klepac-Ceraj; Martin F Polz
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3.  Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.

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Authors:  Christian L Lauber; Micah Hamady; Rob Knight; Noah Fierer
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5.  Alternative estimate of source distribution in microbial source tracking using posterior probabilities.

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Journal:  Water Res       Date:  2010-01-29       Impact factor: 11.236

6.  Novel application of a statistical technique, Random Forests, in a bacterial source tracking study.

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Journal:  Water Res       Date:  2010-05-31       Impact factor: 11.236

7.  Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators.

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8.  Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.

Authors:  Jens Reeder; Rob Knight
Journal:  Nat Methods       Date:  2010-09       Impact factor: 28.547

9.  Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants.

Authors:  M A Tanner; B M Goebel; M A Dojka; N R Pace
Journal:  Appl Environ Microbiol       Date:  1998-08       Impact factor: 4.792

Review 10.  Microbial source tracking: state of the science.

Authors:  Joyce M Simpson; Jorge W Santo Domingo; Donald J Reasoner
Journal:  Environ Sci Technol       Date:  2002-12-15       Impact factor: 9.028
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  408 in total

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Authors:  Sean M Gibbons; Tara Schwartz; Jennifer Fouquier; Michelle Mitchell; Naseer Sangwan; Jack A Gilbert; Scott T Kelley
Journal:  Appl Environ Microbiol       Date:  2014-11-14       Impact factor: 4.792

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Journal:  FEMS Microbiol Lett       Date:  2015-11-11       Impact factor: 2.742

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4.  Sediments and Soils Act as Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River.

Authors:  Christopher Staley; Trevor J Gould; Ping Wang; Jane Phillips; James B Cotner; Michael J Sadowsky
Journal:  Microb Ecol       Date:  2016-02-15       Impact factor: 4.552

5.  Quantifying the Relative Contributions of Environmental Sources to the Microbial Community in an Urban Stream under Dry and Wet Weather Conditions.

Authors:  Darshan Baral; Allison Speicher; Bruce Dvorak; David Admiraal; Xu Li
Journal:  Appl Environ Microbiol       Date:  2018-07-17       Impact factor: 4.792

6.  Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children.

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Journal:  Science       Date:  2016-02-19       Impact factor: 47.728

7.  Paneth cell defects in Crohn's disease patients promote dysbiosis.

Authors:  Ta-Chiang Liu; Bhaskar Gurram; Megan T Baldridge; Richard Head; Vy Lam; Chengwei Luo; Yumei Cao; Pippa Simpson; Michael Hayward; Mary L Holtz; Pavlos Bousounis; Joshua Noe; Diana Lerner; Jose Cabrera; Vincent Biank; Michael Stephens; Curtis Huttenhower; Dermot Pb McGovern; Ramnik J Xavier; Thaddeus S Stappenbeck; Nita H Salzman
Journal:  JCI Insight       Date:  2016-06-02

8.  Translocation and dissemination of commensal bacteria in post-stroke infection.

Authors:  Dragana Stanley; Linda J Mason; Kate E Mackin; Yogitha N Srikhanta; Dena Lyras; Monica D Prakash; Kulmira Nurgali; Andres Venegas; Michael D Hill; Robert J Moore; Connie H Y Wong
Journal:  Nat Med       Date:  2016-10-03       Impact factor: 53.440

Review 9.  Ancient and modern environmental DNA.

Authors:  Mikkel Winther Pedersen; Søren Overballe-Petersen; Luca Ermini; Clio Der Sarkissian; James Haile; Micaela Hellstrom; Johan Spens; Philip Francis Thomsen; Kristine Bohmann; Enrico Cappellini; Ida Bærholm Schnell; Nathan A Wales; Christian Carøe; Paula F Campos; Astrid M Z Schmidt; M Thomas P Gilbert; Anders J Hansen; Ludovic Orlando; Eske Willerslev
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-01-19       Impact factor: 6.237

10.  Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype.

Authors:  Leopoldo N Segal; Jose C Clemente; Jun-Chieh J Tsay; Sergei B Koralov; Brian C Keller; Benjamin G Wu; Yonghua Li; Nan Shen; Elodie Ghedin; Alison Morris; Phillip Diaz; Laurence Huang; William R Wikoff; Carles Ubeda; Alejandro Artacho; William N Rom; Daniel H Sterman; Ronald G Collman; Martin J Blaser; Michael D Weiden
Journal:  Nat Microbiol       Date:  2016-04-04       Impact factor: 17.745
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