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Items: 13


A communal catalogue reveals Earth's multiscale microbial diversity.

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.


Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.

Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R.

mSystems. 2015 Dec 22;1(1). pii: e00009-15. eCollection 2016 Jan-Feb.


Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.

Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ.

Microbiome. 2015 Mar 30;3:10. doi: 10.1186/s40168-015-0070-0. eCollection 2015.


Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.

Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R.

Front Microbiol. 2014 Jun 19;5:298. doi: 10.3389/fmicb.2014.00298. eCollection 2014.


A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system.

Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R.

Elife. 2013 Oct 15;2:e01104. doi: 10.7554/eLife.01104.


Advancing our understanding of the human microbiome using QIIME.

Navas-Molina JA, Peralta-Sánchez JM, González A, McMurdie PJ, Vázquez-Baeza Y, Xu Z, Ursell LK, Lauber C, Zhou H, Song SJ, Huntley J, Ackermann GL, Berg-Lyons D, Holmes S, Caporaso JG, Knight R.

Methods Enzymol. 2013;531:371-444. doi: 10.1016/B978-0-12-407863-5.00019-8.


Cohabiting family members share microbiota with one another and with their dogs.

Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R.

Elife. 2013 Apr 16;2:e00458. doi: 10.7554/eLife.00458.


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

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R.

ISME J. 2012 Aug;6(8):1621-4. doi: 10.1038/ismej.2012.8. Epub 2012 Mar 8.


Composition of human skin microbiota affects attractiveness to malaria mosquitoes.

Verhulst NO, Qiu YT, Beijleveld H, Maliepaard C, Knights D, Schulz S, Berg-Lyons D, Lauber CL, Verduijn W, Haasnoot GW, Mumm R, Bouwmeester HJ, Claas FH, Dicke M, van Loon JJ, Takken W, Knight R, Smallegange RC.

PLoS One. 2011;6(12):e28991. doi: 10.1371/journal.pone.0028991. Epub 2011 Dec 28.


Moving pictures of the human microbiome.

Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R.

Genome Biol. 2011;12(5):R50. doi: 10.1186/gb-2011-12-5-r50.


PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.

Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R.

Bioinformatics. 2011 Apr 15;27(8):1159-61. doi: 10.1093/bioinformatics/btr087. Epub 2011 Feb 23.


Examining the global distribution of dominant archaeal populations in soil.

Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N.

ISME J. 2011 May;5(5):908-17. doi: 10.1038/ismej.2010.171. Epub 2010 Nov 18.


Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4516-22. doi: 10.1073/pnas.1000080107. Epub 2010 Jun 3.

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