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

Baxter NT, Lesniak NA, Sinani H, Schloss PD, Koropatkin NM.

mSphere. 2019 Feb 6;4(1). pii: e00528-18. doi: 10.1128/mSphere.00528-18.


Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280. No abstract available.


Nonsteroidal Anti-inflammatory Drugs Alter the Microbiota and Exacerbate Clostridium difficile Colitis while Dysregulating the Inflammatory Response.

Maseda D, Zackular JP, Trindade B, Kirk L, Roxas JL, Rogers LM, Washington MK, Du L, Koyama T, Viswanathan VK, Vedantam G, Schloss PD, Crofford LJ, Skaar EP, Aronoff DM.

MBio. 2019 Jan 8;10(1). pii: e02282-18. doi: 10.1128/mBio.02282-18.


Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.

Hannigan GD, Duhaime MB, Ruffin MT 4th, Koumpouras CC, Schloss PD.

MBio. 2018 Nov 20;9(6). pii: e02248-18. doi: 10.1128/mBio.02248-18.


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

Sze MA, Schloss PD.

MBio. 2018 Oct 16;9(5). pii: e02076-18. doi: 10.1128/mBio.02076-18. No abstract available.


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

Jenior ML, Leslie JL, Young VB, Schloss PD.

mSphere. 2018 Jun 27;3(3). pii: e00261-18. doi: 10.1128/mSphere.00261-18. Print 2018 Jun 27.


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

Sze MA, Schloss PD.

MBio. 2018 Jun 5;9(3). pii: e00630-18. doi: 10.1128/mBio.00630-18. Erratum in: MBio. 2018 Oct 16;9(5):.


In Defense of an Academic Career in Microbiology.

Schloss PD.

mSphere. 2018 May 2;3(3). pii: e00575-17. doi: 10.1128/mSphere.00575-17. eCollection 2018 May-Jun.


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

Hannigan GD, Duhaime MB, Koutra D, Schloss PD.

PLoS Comput Biol. 2018 Apr 18;14(4):e1006099. doi: 10.1371/journal.pcbi.1006099. eCollection 2018 Apr.


Spatial Variation of the Native Colon Microbiota in Healthy Adults.

Flynn KJ, Ruffin MT 4th, Turgeon DK, Schloss PD.

Cancer Prev Res (Phila). 2018 Jul;11(7):393-402. doi: 10.1158/1940-6207.CAPR-17-0370. Epub 2018 Apr 10.


Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn's Disease Patients.

Doherty MK, Ding T, Koumpouras C, Telesco SE, Monast C, Das A, Brodmerkel C, Schloss PD.

MBio. 2018 Mar 13;9(2). pii: e02120-17. doi: 10.1128/mBio.02120-17.


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

Sze MA, Schloss PD.

MBio. 2017 Dec 5;8(6). pii: e01995-17. doi: 10.1128/mBio.01995-17. No abstract available.


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

Schloss PD, Johnston M, Casadevall A.

MBio. 2017 Nov 21;8(6). pii: e01926-17. doi: 10.1128/mBio.01926-17. No abstract available.


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

Sze MA, Baxter NT, Ruffin MT 4th, Rogers MAM, Schloss PD.

Microbiome. 2017 Nov 16;5(1):150. doi: 10.1186/s40168-017-0366-3.


Support Science by Publishing in Scientific Society Journals.

Schloss PD, Johnston M, Casadevall A.

MBio. 2017 Sep 26;8(5). pii: e01633-17. doi: 10.1128/mBio.01633-17. Erratum in: MBio. 2017 Nov 21;8(6):.


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

Jenior ML, Leslie JL, Young VB, Schloss PD.

mSystems. 2017 Jul 25;2(4). pii: e00063-17. doi: 10.1128/mSystems.00063-17. eCollection 2017 Jul-Aug.


NLRP6 Protects Il10-/- Mice from Colitis by Limiting Colonization of Akkermansia muciniphila.

Seregin SS, Golovchenko N, Schaf B, Chen J, Pudlo NA, Mitchell J, Baxter NT, Zhao L, Schloss PD, Martens EC, Eaton KA, Chen GY.

Cell Rep. 2017 Jun 6;19(10):2174. doi: 10.1016/j.celrep.2017.05.074. No abstract available.


Preprinting Microbiology.

Schloss PD.

MBio. 2017 May 23;8(3). pii: e00438-17. doi: 10.1128/mBio.00438-17.


NLRP6 Protects Il10-/- Mice from Colitis by Limiting Colonization of Akkermansia muciniphila.

Seregin SS, Golovchenko N, Schaf B, Chen J, Pudlo NA, Mitchell J, Baxter NT, Zhao L, Schloss PD, Martens EC, Eaton KA, Chen GY.

Cell Rep. 2017 Apr 25;19(4):733-745. doi: 10.1016/j.celrep.2017.03.080. Erratum in: Cell Rep. 2017 Jun 6;19(10 ):2174.


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

Westcott SL, Schloss PD.

mSphere. 2017 Mar 8;2(2). pii: e00073-17. doi: 10.1128/mSphereDirect.00073-17. eCollection 2017 Mar-Apr.


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

Baxter NT, Koumpouras CC, Rogers MA, Ruffin MT 4th, Schloss PD.

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


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

Sze MA, Schloss PD.

MBio. 2016 Aug 23;7(4). pii: e01018-16. doi: 10.1128/mBio.01018-16. Erratum in: MBio. 2017 Dec 5;8(6):.


Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer.

Flynn KJ, Baxter NT, Schloss PD.

mSphere. 2016 May 11;1(3). pii: e00102-16. doi: 10.1128/mSphere.00102-16. eCollection 2016 May-Jun. Review.


Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis.

Zackular JP, Baxter NT, Chen GY, Schloss PD.

mSphere. 2015 Nov 4;1(1). pii: e00001-15. doi: 10.1128/mSphere.00001-15. eCollection 2016 Jan-Feb.


Status of the Archaeal and Bacterial Census: an Update.

Schloss PD, Girard RA, Martin T, Edwards J, Thrash JC.

MBio. 2016 May 17;7(3). pii: e00201-16. doi: 10.1128/mBio.00201-16.


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

Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK.

PeerJ. 2016 Mar 28;4:e1869. doi: 10.7717/peerj.1869. eCollection 2016.


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

Baxter NT, Ruffin MT 4th, Rogers MA, Schloss PD.

Genome Med. 2016 Apr 6;8(1):37. doi: 10.1186/s13073-016-0290-3.


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

Westcott SL, Schloss PD.

PeerJ. 2015 Dec 8;3:e1487. doi: 10.7717/peerj.1487. eCollection 2015.


Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

Beck JM, Schloss PD, Venkataraman A, Twigg H 3rd, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2015 Dec 1;192(11):1335-44. doi: 10.1164/rccm.201501-0128OC.


The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation.

Carmody LA, Zhao J, Kalikin LM, LeBar W, Simon RH, Venkataraman A, Schmidt TM, Abdo Z, Schloss PD, LiPuma JJ.

Microbiome. 2015 Apr 1;3:12. doi: 10.1186/s40168-015-0074-9. eCollection 2015.


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

Koenigsknecht MJ, Theriot CM, Bergin IL, Schumacher CA, Schloss PD, Young VB.

Infect Immun. 2015 Mar;83(3):934-41. doi: 10.1128/IAI.02768-14. Epub 2014 Dec 22.


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

Kopliku FA, Schubert AM, Mogle J, Schloss PD, Young VB, Aronoff DM.

Anaerobe. 2015 Apr;32:34-36. doi: 10.1016/j.anaerobe.2014.12.001. Epub 2014 Dec 3.


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

Baxter NT, Wan JJ, Schubert AM, Jenior ML, Myers P, Schloss PD.

Appl Environ Microbiol. 2015 Jan;81(1):396-404. doi: 10.1128/AEM.02303-14. Epub 2014 Oct 31.


Microbiology: An integrated view of the skin microbiome.

Schloss PD.

Nature. 2014 Oct 2;514(7520):44-5. doi: 10.1038/514044a. No abstract available.


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

Zackular JP, Rogers MA, Ruffin MT 4th, Schloss PD.

Cancer Prev Res (Phila). 2014 Nov;7(11):1112-21. doi: 10.1158/1940-6207.CAPR-14-0129. Epub 2014 Aug 7.


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

Schloss PD, Iverson KD, Petrosino JF, Schloss SJ.

Microbiome. 2014 Jul 21;2:25. doi: 10.1186/2049-2618-2-25. eCollection 2014.


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

Baxter NT, Zackular JP, Chen GY, Schloss PD.

Microbiome. 2014 Jun 17;2:20. doi: 10.1186/2049-2618-2-20. eCollection 2014.


Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls.

Schubert AM, Rogers MA, Ring C, Mogle J, Petrosino JP, Young VB, Aronoff DM, Schloss PD.

MBio. 2014 May 6;5(3):e01021-14. doi: 10.1128/mBio.01021-14.


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

Ding T, Schloss PD.

Nature. 2014 May 15;509(7500):357-60. doi: 10.1038/nature13178. Epub 2014 Apr 16.


Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis.

Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML.

Microbiome. 2013 Mar 4;1(1):9. doi: 10.1186/2049-2618-1-9.


Mathematical modeling of primary succession of murine intestinal microbiota.

Marino S, Baxter NT, Huffnagle GB, Petrosino JF, Schloss PD.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):439-44. doi: 10.1073/pnas.1311322111. Epub 2013 Dec 23.


The gut microbiome modulates colon tumorigenesis.

Zackular JP, Baxter NT, Iverson KD, Sadler WD, Petrosino JF, Chen GY, Schloss PD.

MBio. 2013 Nov 5;4(6):e00692-13. doi: 10.1128/mBio.00692-13.


Changes in cystic fibrosis airway microbiota at pulmonary exacerbation.

Carmody LA, Zhao J, Schloss PD, Petrosino JF, Murray S, Young VB, Li JZ, LiPuma JJ.

Ann Am Thorac Soc. 2013 Jun;10(3):179-87. doi: 10.1513/AnnalsATS.201211-107OC.


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

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD.

Appl Environ Microbiol. 2013 Sep;79(17):5112-20. doi: 10.1128/AEM.01043-13. Epub 2013 Jun 21.


Comparison of the respiratory microbiome in healthy nonsmokers and smokers.

Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2013 May 15;187(10):1067-75. doi: 10.1164/rccm.201210-1913OC.


Bioinformatics for the Human Microbiome Project.

Gevers D, Pop M, Schloss PD, Huttenhower C.

PLoS Comput Biol. 2012;8(11):e1002779. doi: 10.1371/journal.pcbi.1002779. Epub 2012 Nov 29. No abstract available.


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

Schloss PD.

ISME J. 2013 Mar;7(3):457-60. doi: 10.1038/ismej.2012.102. Epub 2012 Sep 27. No abstract available.

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