Publications by authors named "Patrick D Schloss"

100Publications

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems.

mBio 2020 06 9;11(3). Epub 2020 Jun 9.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.00434-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7373189PMC
June 2020

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis.

Cell Rep 2020 Apr;31(1):107471

Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2020.03.035DOI Listing
April 2020

Coding-Complete RNA Virus Genomes Assembled from Murine Cecal Metatranscriptomes.

Microbiol Resour Announc 2020 Mar 19;9(12). Epub 2020 Mar 19.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/MRA.00018-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082449PMC
March 2020

The Proton Pump Inhibitor Omeprazole Does Not Promote Clostridioides difficile Colonization in a Murine Model.

mSphere 2019 11 20;4(6). Epub 2019 Nov 20.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphere.00693-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6887860PMC
November 2019

Reintroducing mothur: 10 Years Later.

Appl Environ Microbiol 2020 01 7;86(2). Epub 2020 Jan 7.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.02343-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6952234PMC
January 2020

Erratum for Baxter et al., "The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome".

mSphere 2019 May 22;4(3). Epub 2019 May 22.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphere.00347-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6531887PMC
May 2019

The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data.

mSphere 2019 05 22;4(3). Epub 2019 May 22.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphere.00163-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6531881PMC
May 2019

The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome.

mSphere 2019 02 6;4(1). Epub 2019 Feb 6.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphere.00528-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365613PMC
February 2019

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.

mBio 2018 11 20;9(6). Epub 2018 Nov 20.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.02248-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247079PMC
November 2018

Erratum for Sze and Schloss, "Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors".

mBio 2018 10 16;9(5). Epub 2018 Oct 16.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.02076-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191542PMC
October 2018

Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization.

mSphere 2018 06 27;3(3). Epub 2018 Jun 27.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphere.00261-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6021602PMC
June 2018

Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors.

mBio 2018 06 5;9(3). Epub 2018 Jun 5.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.00630-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989068PMC
June 2018

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research.

mBio 2018 06 5;9(3). Epub 2018 Jun 5.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.00525-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989067PMC
June 2018

In Defense of an Academic Career in Microbiology.

mSphere 2018 May-Jun;3(3). Epub 2018 May 2.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphere.00575-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932374PMC
October 2018

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome.

PLoS Comput Biol 2018 04 18;14(4):e1006099. Epub 2018 Apr 18.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5927471PMC
April 2018

Spatial Variation of the Native Colon Microbiota in Healthy Adults.

Cancer Prev Res (Phila) 2018 07 10;11(7):393-402. Epub 2018 Apr 10.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1940-6207.CAPR-17-0370DOI Listing
July 2018

Erratum for Sze and Schloss, "Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome".

mBio 2017 12 5;8(6). Epub 2017 Dec 5.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.01995-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717395PMC
December 2017

Erratum for Schloss et al., "Support Science by Publishing in Scientific Society Journals".

mBio 2017 11 21;8(6). Epub 2017 Nov 21.

Department of Molecular Microbiology & Immunology, Johns Hopkins University, Baltimore, Maryland, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.01926-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5698558PMC
November 2017

Normalization of the microbiota in patients after treatment for colonic lesions.

Microbiome 2017 Nov 16;5(1):150. Epub 2017 Nov 16.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-017-0366-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5689185PMC
November 2017

Support Science by Publishing in Scientific Society Journals.

mBio 2017 09 26;8(5). Epub 2017 Sep 26.

Department of Molecular Microbiology & Immunology, Johns Hopkins University, Baltimore, Maryland, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.01633-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5615203PMC
September 2017

Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes.

mSystems 2017 Jul-Aug;2(4). Epub 2017 Jul 25.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSystems.00063-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5527303PMC
July 2017

Preprinting Microbiology.

mBio 2017 05 23;8(3). Epub 2017 May 23.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.00438-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442452PMC
May 2017

OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units.

mSphere 2017 Mar-Apr;2(2). Epub 2017 Mar 8.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphereDirect.00073-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343174PMC
March 2017

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model.

Microbiome 2016 11 14;4(1):59. Epub 2016 Nov 14.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-016-0205-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109736PMC
November 2016

Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods.

mSystems 2016 Mar-Apr;1(2). Epub 2016 Apr 26.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSystems.00027-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069744PMC
April 2016

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome.

mBio 2016 08 23;7(4). Epub 2016 Aug 23.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.01018-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999546PMC
August 2016

Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer.

mSphere 2016 May-Jun;1(3). Epub 2016 May 11.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://msphere.asm.org/content/msph/1/3/e00102-16.full.pdf
Web Search
http://msphere.asm.org/lookup/doi/10.1128/mSphere.00102-16
Publisher Site
http://dx.doi.org/10.1128/mSphere.00102-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888883PMC
June 2016

Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis.

mSphere 2016 Jan-Feb;1(1). Epub 2015 Nov 4.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSphere.00001-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863627PMC
June 2016

Status of the Archaeal and Bacterial Census: an Update.

mBio 2016 05 17;7(3). Epub 2016 May 17.

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mBio.00201-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895100PMC
May 2016

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system.

PeerJ 2016 28;4:e1869. Epub 2016 Mar 28.

Department of Genomic Medicine, J. Craig Venter Institute , La Jolla, CA , USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.1869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824876PMC
April 2016

Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions.

Genome Med 2016 Apr 6;8(1):37. Epub 2016 Apr 6.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13073-016-0290-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823848PMC
April 2016

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units.

PeerJ 2015 8;3:e1487. Epub 2015 Dec 8.

Department of Microbiology and Immunology, University of Michigan-Ann Arbor , Ann Arbor, MI , United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.1487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675110PMC
December 2015

Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract.

Infect Immun 2015 Mar 22;83(3):934-41. Epub 2014 Dec 22.

Department of Internal Medicine/Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, Michigan, USA Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/IAI.02768-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333439PMC
March 2015

Low prevalence of Clostridium septicum fecal carriage in an adult population.

Anaerobe 2015 Apr 3;32:34-36. Epub 2014 Dec 3.

Division of Infectious Diseases, Department of Medicine, Vanderbilt University, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.anaerobe.2014.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385462PMC
April 2015

Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric peromyscus populations.

Appl Environ Microbiol 2015 Jan 31;81(1):396-404. Epub 2014 Oct 31.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.02303-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272734PMC
January 2015

Microbiology: An integrated view of the skin microbiome.

Nature 2014 Oct;514(7520):44-5

Department of Microbiology &Immunology, University of Michigan, Ann Arbor, Michigan 48109-5620, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/514044aDOI Listing
October 2014

The human gut microbiome as a screening tool for colorectal cancer.

Cancer Prev Res (Phila) 2014 Nov 7;7(11):1112-21. Epub 2014 Aug 7.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1940-6207.CAPR-14-0129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221363PMC
November 2014

The dynamics of a family's gut microbiota reveal variations on a theme.

Microbiome 2014 21;2:25. Epub 2014 Jul 21.

Department of Microbiology and Immunology, University of Michigan, 1520A Medical Science Research Building I, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/2049-2618-2-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109379PMC
July 2014

Structure of the gut microbiome following colonization with human feces determines colonic tumor burden.

Microbiome 2014 17;2:20. Epub 2014 Jun 17.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/2049-2618-2-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070349PMC
June 2014

Dynamics and associations of microbial community types across the human body.

Nature 2014 May 16;509(7500):357-60. Epub 2014 Apr 16.

Department of Microbiology and Immunology, 1500 W. Medical Center, University of Michigan, Ann Arbor, Michigan 48109, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nature13178
Publisher Site
http://dx.doi.org/10.1038/nature13178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139711PMC
May 2014

Mathematical modeling of primary succession of murine intestinal microbiota.

Proc Natl Acad Sci U S A 2014 Jan 23;111(1):439-44. Epub 2013 Dec 23.

Department of Microbiology and Immunology and Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.1311322111
Publisher Site
http://dx.doi.org/10.1073/pnas.1311322111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890833PMC
January 2014

The gut microbiome modulates colon tumorigenesis.

mBio 2013 Nov 5;4(6):e00692-13. Epub 2013 Nov 5.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://mbio.asm.org/cgi/doi/10.1128/mBio.00692-13
Publisher Site
http://dx.doi.org/10.1128/mBio.00692-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892781PMC
November 2013

Changes in cystic fibrosis airway microbiota at pulmonary exacerbation.

Ann Am Thorac Soc 2013 Jun;10(3):179-87

Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1513/AnnalsATS.201211-107OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960905PMC
June 2013

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

Appl Environ Microbiol 2013 Sep 21;79(17):5112-20. Epub 2013 Jun 21.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.01043-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973PMC
September 2013

Bioinformatics for the Human Microbiome Project.

PLoS Comput Biol 2012 29;8(11):e1002779. Epub 2012 Nov 29.

The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
https://dx.plos.org/10.1371/journal.pcbi.1002779
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1002779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510052PMC
April 2013

Secondary structure improves OTU assignments of 16S rRNA gene sequences.

ISME J 2013 Mar 27;7(3):457-60. Epub 2012 Sep 27.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ismej.2012.102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3578559PMC
March 2013

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs.

ISME J 2012 Dec 14;6(12):2257-68. Epub 2012 Jun 14.

Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109-1005, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ismej.2012.63DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504965PMC
December 2012

Stabilization of the murine gut microbiome following weaning.

Gut Microbes 2012 Jul-Aug;3(4):383-93. Epub 2012 Jun 12.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.

View Article

Download full-text PDF

Source
http://www.tandfonline.com/doi/abs/10.4161/gmic.21008
Publisher Site
http://dx.doi.org/10.4161/gmic.21008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463496PMC
January 2013

Decade-long bacterial community dynamics in cystic fibrosis airways.

Proc Natl Acad Sci U S A 2012 Apr 26;109(15):5809-14. Epub 2012 Mar 26.

Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1120577109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326496PMC
April 2012

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

PLoS One 2011 14;6(12):e27310. Epub 2011 Dec 14.

Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027310PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3237409PMC
August 2012

The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection.

Gut Microbes 2011 May-Jun;2(3):145-58. Epub 2011 May 1.

Department of Microbiology & Immunology, The University of Michigan, Ann Arbor, MI, 48109, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225775PMC
http://dx.doi.org/10.4161/gmic.2.3.16333DOI Listing
December 2011

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Authors:
Pelin Yilmaz Renzo Kottmann Dawn Field Rob Knight James R Cole Linda Amaral-Zettler Jack A Gilbert Ilene Karsch-Mizrachi Anjanette Johnston Guy Cochrane Robert Vaughan Christopher Hunter Joonhong Park Norman Morrison Philippe Rocca-Serra Peter Sterk Manimozhiyan Arumugam Mark Bailey Laura Baumgartner Bruce W Birren Martin J Blaser Vivien Bonazzi Tim Booth Peer Bork Frederic D Bushman Pier Luigi Buttigieg Patrick S G Chain Emily Charlson Elizabeth K Costello Heather Huot-Creasy Peter Dawyndt Todd DeSantis Noah Fierer Jed A Fuhrman Rachel E Gallery Dirk Gevers Richard A Gibbs Inigo San Gil Antonio Gonzalez Jeffrey I Gordon Robert Guralnick Wolfgang Hankeln Sarah Highlander Philip Hugenholtz Janet Jansson Andrew L Kau Scott T Kelley Jerry Kennedy Dan Knights Omry Koren Justin Kuczynski Nikos Kyrpides Robert Larsen Christian L Lauber Teresa Legg Ruth E Ley Catherine A Lozupone Wolfgang Ludwig Donna Lyons Eamonn Maguire Barbara A Methé Folker Meyer Brian Muegge Sara Nakielny Karen E Nelson Diana Nemergut Josh D Neufeld Lindsay K Newbold Anna E Oliver Norman R Pace Giriprakash Palanisamy Jörg Peplies Joseph Petrosino Lita Proctor Elmar Pruesse Christian Quast Jeroen Raes Sujeevan Ratnasingham Jacques Ravel David A Relman Susanna Assunta-Sansone Patrick D Schloss Lynn Schriml Rohini Sinha Michelle I Smith Erica Sodergren Aymé Spo Jesse Stombaugh James M Tiedje Doyle V Ward George M Weinstock Doug Wendel Owen White Andrew Whiteley Andreas Wilke Jennifer R Wortman Tanya Yatsunenko Frank Oliver Glöckner

Nat Biotechnol 2011 May;29(5):415-20

Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

View Article

Download full-text PDF

Source
https://darchive.mblwhoilibrary.org/bitstream/handle/1912/46
Web Search
http://www.nature.com/doifinder/10.1038/nbt.1823
Publisher Site
http://dx.doi.org/10.1038/nbt.1823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367316PMC
May 2011

Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis.

Appl Environ Microbiol 2011 May 18;77(10):3219-26. Epub 2011 Mar 18.

Department of Microbiology & Immunology; University of Michigan, Ann Arbor, MI 48109, USA.

View Article

Download full-text PDF

Source
http://aem.asm.org/lookup/doi/10.1128/AEM.02810-10
Publisher Site
http://dx.doi.org/10.1128/AEM.02810-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3126452PMC
May 2011

The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies.

PLoS Comput Biol 2010 Jul 8;6(7):e1000844. Epub 2010 Jul 8.

Department of Microbiology & Immunology, The University of Michigan, Ann Arbor, Michigan, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1000844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900292PMC
July 2010

A high-throughput DNA sequence aligner for microbial ecology studies.

PLoS One 2009 Dec 14;4(12):e8230. Epub 2009 Dec 14.

Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008230PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788221PMC
December 2009

Gut microbiota of an invasive subcortical beetle, Agrilus planipennis Fairmaire, across various life stages.

Environ Entomol 2008 Oct;37(5):1344-53

Department of Entomology, 1630 Linden Dr., 345 Russell Labs, University of Wisconsin-Madison, Madison, WI 53706, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1603/0046-225x(2008)37[1344:gmoais]2.0.co;2DOI Listing
October 2008

Novelty and uniqueness patterns of rare members of the soil biosphere.

Appl Environ Microbiol 2008 Sep 7;74(17):5422-8. Epub 2008 Jul 7.

Oklahoma State University, Department of Microbiology and Molecular Genetics, 1110 S. Innovation Way, Stillwater, OK 74074, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.00410-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2546616PMC
September 2008

Evaluating different approaches that test whether microbial communities have the same structure.

ISME J 2008 Mar 31;2(3):265-75. Epub 2008 Jan 31.

Department of Microbiology, University of Massachusetts--Amherst, Amherst, MA 01003, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ismej.2008.5DOI Listing
March 2008

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities.

BMC Bioinformatics 2008 Jan 23;9:34. Epub 2008 Jan 23.

Department of Microbiology, University of Massachusetts - Amherst, Amherst, MA 01003, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-9-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238731PMC
January 2008

The last word: books as a statistical metaphor for microbial communities.

Annu Rev Microbiol 2007 ;61:23-34

Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin 53706, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev.micro.61.011507.151712DOI Listing
December 2007

What is the extent of prokaryotic diversity?

Philos Trans R Soc Lond B Biol Sci 2006 Nov;361(1475):2023-37

School of Civil Engineering and Geosciences, University of Newcastle upon Tyne, Newcastle NE1 7RU, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1098/rstb.2006.1921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764926PMC
November 2006

Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.

Appl Environ Microbiol 2006 Oct;72(10):6773-9

Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA.

View Article

Download full-text PDF

Source
http://aem.asm.org/cgi/doi/10.1128/AEM.00474-06
Publisher Site
http://dx.doi.org/10.1128/AEM.00474-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1610290PMC
October 2006

Toward a census of bacteria in soil.

PLoS Comput Biol 2006 Jul 5;2(7):e92. Epub 2006 Jun 5.

Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.0020092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513271PMC
July 2006

Introducing TreeClimber, a test to compare microbial community structures.

Appl Environ Microbiol 2006 Apr;72(4):2379-84

Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.72.4.2379-2384.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449046PMC
April 2006

Molecular characterization of fungal community dynamics in the initial stages of composting.

FEMS Microbiol Ecol 2005 Jan;51(2):209-14

School of Chemical and Biomolecular Engineering, Olin Hall, Cornell University, Ithaca, NY 14853, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.femsec.2004.08.009DOI Listing
January 2005