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Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment.

Califf KJ, Schwarzberg-Lipson K, Garg N, Gibbons SM, Caporaso JG, Slots J, Cohen C, Dorrestein PC, Kelley ST.

mSystems. 2017 Jun 20;2(3). pii: e00016-17. doi: 10.1128/mSystems.00016-17. eCollection 2017 May-Jun.


Significant Impacts of Increasing Aridity on the Arid Soil Microbiome.

Neilson JW, Califf K, Cardona C, Copeland A, van Treuren W, Josephson KL, Knight R, Gilbert JA, Quade J, Caporaso JG, Maier RM.

mSystems. 2017 May 30;2(3). pii: e00195-16. doi: 10.1128/mSystems.00195-16. eCollection 2017 May-Jun.


Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study.

Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, Khoruts A, Geis E, Maldonado J, McDonough-Means S, Pollard EL, Roux S, Sadowsky MJ, Lipson KS, Sullivan MB, Caporaso JG, Krajmalnik-Brown R.

Microbiome. 2017 Jan 23;5(1):10. doi: 10.1186/s40168-016-0225-7.


mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG.

mSystems. 2016 Oct 18;1(5). pii: e00062-16. eCollection 2016 Sep-Oct.


Geography and Location Are the Primary Drivers of Office Microbiome Composition.

Chase J, Fouquier J, Zare M, Sonderegger DL, Knight R, Kelley ST, Siegel J, Caporaso JG.

mSystems. 2016 Apr 19;1(2). pii: e00022-16. eCollection 2016 Mar-Apr.


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.


cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies.

Chase JH, Bolyen E, Rideout JR, Caporaso JG.

mSystems. 2015 Dec 22;1(1). pii: e00010-15. eCollection 2016 Jan-Feb.


Open-Source Sequence Clustering Methods Improve the State Of the Art.

Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y, Zhou HW, Rognes T, Caporaso JG, Knight R.

mSystems. 2016 Feb 9;1(1). pii: e00003-15. eCollection 2016 Jan-Feb.


Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing.

Taylor DL, Walters WA, Lennon NJ, Bochicchio J, Krohn A, Caporaso JG, Pennanen T.

Appl Environ Microbiol. 2016 Nov 21;82(24):7217-7226. Print 2016 Dec 15.


Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.

Rideout JR, Chase JH, Bolyen E, Ackermann G, González A, Knight R, Caporaso JG.

Gigascience. 2016 Jun 13;5:27. doi: 10.1186/s13742-016-0133-6.


Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis.

Laubitz D, Harrison CA, Midura-Kiela MT, Ramalingam R, Larmonier CB, Chase JH, Caporaso JG, Besselsen DG, Ghishan FK, Kiela PR.

PLoS One. 2016 Apr 6;11(4):e0152044. doi: 10.1371/journal.pone.0152044. eCollection 2016.


Phylogenetic organization of bacterial activity.

Morrissey EM, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, Koch BJ, Liu CM, Hayer M, McHugh TA, Marks JC, Price LB, Hungate BA.

ISME J. 2016 Sep;10(9):2336-40. doi: 10.1038/ismej.2016.28. Epub 2016 Mar 4.


Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D, Knight R, Caporaso JG, Kelley ST.

Microbiome. 2016 Feb 24;4:11. doi: 10.1186/s40168-016-0153-6.


From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation.

Fuentes S, Barra B, Caporaso JG, Seeger M.

Appl Environ Microbiol. 2015 Nov 20;82(3):888-96. doi: 10.1128/AEM.02625-15. Print 2016 Feb 1.


Quantitative microbial ecology through stable isotope probing.

Hungate BA, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, Koch BJ, Liu CM, McHugh TA, Marks JC, Morrissey EM, Price LB.

Appl Environ Microbiol. 2015 Nov;81(21):7570-81. doi: 10.1128/AEM.02280-15. Epub 2015 Aug 21.


Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW.

Microbiome. 2015 Jul 31;3:34. doi: 10.1186/s40168-015-0098-1. eCollection 2015.


The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention.

McFadden RM, Larmonier CB, Shehab KW, Midura-Kiela M, Ramalingam R, Harrison CA, Besselsen DG, Chase JH, Caporaso JG, Jobin C, Ghishan FK, Kiela PR.

Inflamm Bowel Dis. 2015 Nov;21(11):2483-94. doi: 10.1097/MIB.0000000000000522.


Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography.

Marzinelli EM, Campbell AH, Zozaya Valdes E, Vergés A, Nielsen S, Wernberg T, de Bettignies T, Bennett S, Caporaso JG, Thomas T, Steinberg PD.

Environ Microbiol. 2015 Oct;17(10):4078-88. doi: 10.1111/1462-2920.12972. Epub 2015 Aug 4.


Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW.

Microbiome. 2015 May 20;3:20. doi: 10.1186/s40168-015-0081-x. eCollection 2015. Erratum in: Microbiome. 2015;3:34.


Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone.

Kang DW, DiBaise JK, Ilhan ZE, Crowell MD, Rideout JR, Caporaso JG, Rittmann BE, Krajmalnik-Brown R.

Anaerobe. 2015 Jun;33:33-41. doi: 10.1016/j.anaerobe.2015.01.005. Epub 2015 Jan 21.


A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples.

Rothrock MJ Jr, Hiett KL, Gamble J, Caudill AC, Cicconi-Hogan KM, Caporaso JG.

J Vis Exp. 2014 Dec 10;(94). doi: 10.3791/52161.


Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial.

Holscher HD, Caporaso JG, Hooda S, Brulc JM, Fahey GC Jr, Swanson KS.

Am J Clin Nutr. 2015 Jan;101(1):55-64. doi: 10.3945/ajcn.114.092064. Epub 2014 Nov 12.


Temporal variability is a personalized feature of the human microbiome.

Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, Leff JW, Vázquez-Baeza Y, Gonzalez A, Knight R, Dunn RR, Fierer N.

Genome Biol. 2014 Dec 3;15(12):531. doi: 10.1186/s13059-014-0531-y.


Advancing the microbiome research community.

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J; Scientists for Advancement of Microbiome Research, White O.

Cell. 2014 Oct 9;159(2):227-30. doi: 10.1016/j.cell.2014.09.022.


Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG.

PeerJ. 2014 Aug 21;2:e545. doi: 10.7717/peerj.545. eCollection 2014.


Individual diet has sex-dependent effects on vertebrate gut microbiota.

Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Org E, Parks B, Lusis AJ, Knight R, Caporaso JG, Svanbäck R.

Nat Commun. 2014 Jul 29;5:4500. doi: 10.1038/ncomms5500.


Conducting a microbiome study.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE.

Cell. 2014 Jul 17;158(2):250-262. doi: 10.1016/j.cell.2014.06.037.


Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.

Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA.

MBio. 2014 Jul 15;5(4):e01371-14. doi: 10.1128/mBio.01371-14.


Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity.

Bolnick DI, Snowberg LK, Caporaso JG, Lauber C, Knight R, Stutz WE.

Mol Ecol. 2014 Oct;23(19):4831-45. doi: 10.1111/mec.12846. Epub 2014 Jul 31.


Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch).

Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanbäck R.

Ecol Lett. 2014 Aug;17(8):979-87. doi: 10.1111/ele.12301. Epub 2014 May 22.


The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes.

Sahl JW, Caporaso JG, Rasko DA, Keim P.

PeerJ. 2014 Apr 1;2:e332. doi: 10.7717/peerj.332. eCollection 2014.


The personal human oral microbiome obscures the effects of treatment on periodontal disease.

Schwarzberg K, Le R, Bharti B, Lindsay S, Casaburi G, Salvatore F, Saber MH, Alonaizan F, Slots J, Gottlieb RA, Caporaso JG, Kelley ST.

PLoS One. 2014 Jan 29;9(1):e86708. doi: 10.1371/journal.pone.0086708. eCollection 2014.


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.


Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.


Meeting report: fungal its workshop (october 2012).

Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE.

Stand Genomic Sci. 2013 Apr 15;8(1):118-23. doi: 10.4056/sigs.3737409. eCollection 2013 Apr 15.


The Ecology of Microbial Communities Associated with Macrocystis pyrifera.

Michelou VK, Caporaso JG, Knight R, Palumbi SR.

PLoS One. 2013 Jun 19;8(6):e67480. doi: 10.1371/journal.pone.0067480. Print 2013.


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.


A meta-analysis of changes in bacterial and archaeal communities with time.

Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N.

ISME J. 2013 Aug;7(8):1493-506. doi: 10.1038/ismej.2013.54. Epub 2013 Apr 11.


Evidence for a persistent microbial seed bank throughout the global ocean.

Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA.

Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4651-5. doi: 10.1073/pnas.1217767110. Epub 2013 Mar 4.


From molecules to dynamic biological communities.

McDonald D, Vázquez-Baeza Y, Walters WA, Caporaso JG, Knight R.

Biol Philos. 2013 Mar;28(2):241-259. Epub 2013 Feb 5.


Bacterial diversity in two Neonatal Intensive Care Units (NICUs).

Hewitt KM, Mannino FL, Gonzalez A, Chase JH, Caporaso JG, Knight R, Kelley ST.

PLoS One. 2013;8(1):e54703. doi: 10.1371/journal.pone.0054703. Epub 2013 Jan 23.


Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21390-5. doi: 10.1073/pnas.1215210110. Epub 2012 Dec 10.


Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG.

Nat Methods. 2013 Jan;10(1):57-9. doi: 10.1038/nmeth.2276. Epub 2012 Dec 2.


Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R.

Curr Protoc Microbiol. 2012 Nov;Chapter 1:Unit 1E.5.. doi: 10.1002/9780471729259.mc01e05s27.


Diversity, distribution and sources of bacteria in residential kitchens.

Flores GE, Bates ST, Caporaso JG, Lauber CL, Leff JW, Knight R, Fierer N.

Environ Microbiol. 2013 Feb;15(2):588-96. doi: 10.1111/1462-2920.12036. Epub 2012 Nov 22.


Collaborative cloud-enabled tools allow rapid, reproducible biological insights.

Ragan-Kelley B, Walters WA, McDonald D, Riley J, Granger BE, Gonzalez A, Knight R, Perez F, Caporaso JG.

ISME J. 2013 Mar;7(3):461-4. doi: 10.1038/ismej.2012.123. Epub 2012 Oct 25. No abstract available.


Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR.

ISME J. 2013 Jan;7(1):50-60. doi: 10.1038/ismej.2012.79. Epub 2012 Jul 26.


Human gut microbiome viewed across age and geography.

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI.

Nature. 2012 May 9;486(7402):222-7. doi: 10.1038/nature11053.


The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites.

Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R.

J Allergy Clin Immunol. 2012 May;129(5):1204-8. doi: 10.1016/j.jaci.2012.03.010.


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.

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