Pat Schloss

Professor, Frederick G. Novy Collegiate Professor of Microbiome Research
PI since 2006

Research areas

  • Colorectal cancer
  • C. difficile
  • Crohn's disease
  • microbial ecology
  • mothur


  • BS: Cornell University (1997)
  • PhD: Cornell University (2002)
  • Postdoc: University of Wisconsin (2006)
Pat Schloss


My interests span the breadth of microbiome research. My work in this field can be divided in to “wet” and “dry” components that are each a result of my interdisciplinary training and drive to look at microbial research questions differently. My interdisciplinary training motivates me to investigate bacteria as members of communities. This community-based approach has yielded recent publications from my laboratory where, instead of trying to link individual bacteria with pathogenesis, we seek to understand how entire microbial communities and subsets of those communities could be used to classify people by their health status or risk of disease. When I started pursuing these questions as a postdoc, we didn’t have the necessary computational tools to find the answers. So we made them ourselves. Trained as a biological engineer, I acquired the skills needed to develop several prominent computer programs for analyzing the DNA sequence data generated from microbial ecology experiments. Together, my papers describing these tools have been cited thousands of times. The ability to bridge biology and computational sciences has allowed me to leave a positive impact on a diverse array of important research questions spanning from colon cancer and Clostridium difficile infections to the soil and deep sea.

Schloss lab papers

  1. Schloss PD, Chaves B, Walker LP. 2000. The use of the analysis of variance to assess the influence of mixing during composting. Proc Biochem. 35: 675-84. DOI: 10.1016/S0032-9592(99)00117-X.
  2. Schloss PD, Walker LP. 2000. Measurement of process performance and variability in inoculated composting reactors using ANOVA and power analysis. Proc Biochem. 35: 931-42. DOI: 10.1016/S0032-9592(99)00156-9.
  3. Schloss PD, Walker LP. 2001. Assessment and improvement of process variable reproducibility in composting reactors. Trans ASAE. 44: 1021-31. DOI: 10.13031/2013.6223.
  4. Schloss PD, Hay AG, Wilson DB, Walker LP. 2003. Molecular assessment of inoculum efficacy and process reproducibility in composting using ARISA. Trans ASAE. 46: 919-27. DOI: 10.13031/2013.13568.
  5. Schloss PD, Handelsman J. 2003. Biotechnological prospects from metagenomics. Curr Opin Biotechnol. 14: 303-10. DOI: 10.1016/S0958-1669(03)00067-3.
  6. Schloss PD, Hay AG, Wilson DB, Walker LP. 2003. Tracking temporal changes of bacterial community fingerprints during the initial stages of composting. Microbiol Ecol. 46: 1-9. DOI: 10.1016/S0168-6496(03)00153-3.
  7. Schloss PD, Larget BR, Handelsman J. 2004. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol. 70: 5485-92. DOI: 10.1128/AEM.70.9.5485-5492.2004.
  8. Schloss PD, Handelsman J. 2004. Status of the microbial census. Microbiol Mol Biol Rev. 68: 686-91. DOI: 10.1128/MMBR.68.4.686-691.2004.
  9. Riesenfeld CS, Schloss PD, Handelsman J. 2004. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet. 38: 525-52. DOI: 10.1146/annurev.genet.38.072902.091216.
  10. Williamson LL, Borlee BR, Schloss PD, Guan C, Allen HK, Handelsman J. 2005. Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol. 71: 6335-44. DOI: 10.1128/AEM.71.10.6335-6344.2005.
  11. Schloss PD, Hay AG, Wilson DB, Gossett JM, Walker LP. 2005. Quantifying bacterial population dynamics in compost using 16S rRNA gene probes. Appl Microbiol Biotechnol. 66: 457-63. DOI: 10.1007/s00253-004-1727-y.
  12. Schloss PD, Handelsman J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 71: 1501-6. DOI: 10.1128/AEM.71.3.1501-1506.2005.
  13. Schloss PD, Handelsman J. 2005. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol. 6: 229. DOI: 10.1186/gb-2005-6-8-229.
  14. Hansgate AM, Schloss PD, Hay AG, Walker LP. 2005. Molecular characterization of fungal community dynamics in the initial stages of composting. FEMS Microbiol Ecol. 51: 209-14. DOI: 10.1016/j.femsec.2004.08.009.
  15. Vasanthakumar A, Delalibera I, Handelsman J, Klepzig KD, Schloss PD, Raffa KF. 2006. Characterization of gut-associated bacteria in larvae and adults of the southern pine beetle, Dendroctonus frontalis Zimmermann. Environ Entomol. 35: 1710-7.
  16. Schloss PD, Handelsman J. 2006. Introducing TreeClimber, a test to compare microbial community structures. Appl Environ Microbiol. 72: 2379-84. DOI: 10.1128/AEM.72.4.2379-2384.2006.
  17. Schloss PD, Delalibera I, Handelsman J, Raffa KF. 2006. Bacteria associated with the guts of two wood-boring beetles: Anoplophora glabripennis and Saperda vestita (Cerambycidae). Environ Entomol. 35: 625-9.
  18. Schloss PD, Handelsman J. 2006. Toward a census of bacteria in soil. PLoS Comput Biol. 2: e92. DOI: 10.1371/journal.pcbi.0020092.
  19. Schloss PD, Handelsman J. 2006. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol. 72: 6773-9. DOI: 10.1128/AEM.00474-06.
  20. Curtis TP, Head IM, Lunn M, Woodcock S, Schloss PD, Sloan WT. 2006. What is the extent of prokaryotic diversity?. Philos Trans R Soc Lond B Biol Sci. 361: 2023-37. DOI: 10.1098/rstb.2006.1921.
  21. Schloss PD, Handelsman J. 2007. The last word: books as a statistical metaphor for microbial communities. Annu Rev Microbiol. 61: 23-34. DOI: 10.1146/annurev.micro.61.011507.151712.
  22. Delalibera I, Vasanthakumar A, Burwitz BJ, Schloss PD, Klepzig KD, Handelsman J, Raffa KF. 2007. Composition of the bacterial community in the gut of the pine engraver, Ips pini (Say)(Coleoptera) colonizing red pine. Symbiosis. 43: 97-104.
  23. Vasanthakumar A, Handelsman J, Schloss PD, Bauer LS, Raffa KF. 2008. Gut microbiota of an invasive subcortical beetle, Agrilus planipennis Fairmaire, across various life stages. Environ Entomol. 37: 1344-53. DOI: 10.1093/ee/37.5.1344.
  24. Schloss PD, Handelsman J. 2008. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics. 9: 34. DOI: 10.1186/1471-2105-9-34.
  25. Schloss PD. 2008. Evaluating different approaches that test whether microbial communities have the same structure. ISME J. 2: 265-75. DOI: 10.1038/ismej.2008.5.
  26. Elshahed MS, Youssef NH, Spain AM, Sheik C, Najar FZ, Sukharnikov LO, Roe BA, Davis JP, Schloss PD, Bailey VL, Krumholz LR. 2008. Novelty and uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol. 74: 5422-8. DOI: 10.1128/AEM.00410-08.
  27. Schloss PD. 2009. A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One. 4: e8230. DOI: 10.1371/journal.pone.0008230.
  28. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 75: 7537-41. DOI: 10.1128/AEM.01541-09.
  29. Schloss PD, Allen HK, Klimowicz AK, Mlot C, Gross JA, Savengsuksa S, McEllin J, Clardy J, Ruess RW, Handelsman J. 2010. Psychrotrophic strain of Janthinobacterium lividum from a cold Alaskan soil produces prodigiosin. DNA Cell Biol. 29: 533-41. DOI: 10.1089/dna.2010.1020.
  30. Schloss PD. 2010. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol. 6: e1000844. DOI: 10.1371/journal.pcbi.1000844.
  31. Robinson CJ, Schloss PD, Ramos Y, Raffa K, Handelsman J. 2010. . Microb Ecol.. 59: 199-211. DOI: 10.1007/s00248-009-9595-8.
  32. Zhao J, Li J, Schloss PD, Kalikin LM, Raymond TA, Petrosino JF, Young VB, LiPuma JJ. 2011. Effect of sample storage conditions on culture-independent bacterial community measures in cystic fibrosis sputum specimens. J Clin Microbiol. 49: 3717-8. DOI: 10.1128/JCM.01189-11.
  33. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO. 2011. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 29: 415-20. DOI: 10.1038/nbt.1823.
  34. Schloss PD, Westcott SL. 2011. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. 77: 3219-26. DOI: 10.1128/AEM.02810-10.
  35. Schloss PD, Gevers D, Westcott SL. 2011. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One. 6: e27310. DOI: 10.1371/journal.pone.0027310.
  36. Reeves AE, Theriot CM, Bergin IL, Huffnagle GB, Schloss PD, Young VB. 2011. The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile infection. Gut Microbes. 2: 145-58. DOI: 10.4161/gmic.2.3.16333.
  37. Zhao J, Carmody LA, Kalikin LM, Li J, Petrosino JF, Schloss PD, Young VB, LiPuma JJ. 2012. Impact of enhanced Staphylococcus DNA extraction on microbial community measures in cystic fibrosis sputum. PLoS One. 7: e33127. DOI: 10.1371/journal.pone.0033127.
  38. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ, Young VB, LiPuma JJ. 2012. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci USA. 109: 5809-14. DOI: 10.1073/pnas.1120577109.
  39. Schloss PD, Schubert AM, Zackular JP, Iverson KD, Young VB, Petrosino JF. 2012. Stabilization of the murine gut microbiome following weaning. Gut Microbes. 3: 383-93. DOI: 10.4161/gmic.21008.
  40. Lesniewski RA, Jain S, Anantharaman K, Schloss PD, Dick GJ. 2012. The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J. 6: 2257-68. DOI: 10.1038/ismej.2012.63.
  41. Jumpstart Consortium Human Microbiome Project Data Generation Working Group. 2012. Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One. 7: e39315. DOI: 10.1371/journal.pone.0039315.
  42. Human Microbiome Project Consortium. 2012. A framework for human microbiome research. Nature. 486: 215-21. DOI: 10.1038/nature11209.
  43. Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature. 486: 207-14. DOI: 10.1038/nature11234.
  44. Gevers D, Pop M, Schloss PD, Huttenhower C. 2012. Bioinformatics for the Human Microbiome Project. PLoS Comput Biol. 8: e1002779. DOI: 10.1371/journal.pcbi.1002779.
  45. Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. 2012. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 8: e1002358. DOI: 10.1371/journal.pcbi.1002358.
  46. Zackular JP, Baxter NT, Iverson KD, Sadler WD, Petrosino JF, Chen GY, Schloss PD. 2013. The gut microbiome modulates colon tumorigenesis. mBio. 4: e00692-13. DOI: 10.1128/mBio.00692-13.
  47. 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. 2013. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome. 1: 9. DOI: 10.1186/2049-2618-1-9.
  48. Schloss PD. 2013. Secondary structure improves OTU assignments of 16S rRNA gene sequences. ISME J. 7: 457-60. DOI: 10.1038/ismej.2012.102.
  49. 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. 2013. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med. 187: 1067-75. DOI: 10.1164/rccm.201210-1913OC.
  50. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. 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. 79: 5112-20. DOI: 10.1128/AEM.01043-13.
  51. Carmody LA, Zhao J, Schloss PD, Petrosino JF, Murray S, Young VB, Li JZ, LiPuma JJ. 2013. Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Ann Am Thorac Soc. 10: 179-87. DOI: 10.1513/AnnalsATS.201211-107OC.
  52. Zackular JP, Rogers MA, Ruffin MT 4th, Schloss PD. 2014. The human gut microbiome as a screening tool for colorectal cancer. Cancer Prev Res (Phila). 7: 1112-21. DOI: 10.1158/1940-6207.CAPR-14-0129.
  53. Schubert AM, Rogers MA, Ring C, Mogle J, Petrosino JP, Young VB, Aronoff DM, Schloss PD. 2014. Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. mBio. 5: e01021-14. DOI: 10.1128/mBio.01021-14.
  54. Schloss PD, Iverson KD, Petrosino JF, Schloss SJ. 2014. The dynamics of a family's gut microbiota reveal variations on a theme. Microbiome. 2: 25. DOI: 10.1186/2049-2618-2-25.
  55. Schloss PD. 2014. Commentary: Microbiology: An integrated view of the skin microbiome. Appl Environ Microbiol. 514: 44-5. DOI: doi:10.1038/514044a.
  56. Marino S, Baxter NT, Huffnagle GB, Petrosino JF, Schloss PD. 2014. Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci USA. 111: 439-44. DOI: 10.1073/pnas.1311322111.
  57. Ding T, Schloss PD. 2014. Dynamics and associations of microbial community types across the human body. Nature. 509: 357-60. DOI: 10.1038/nature13178.
  58. Baxter NT, Zackular JP, Chen GY, Schloss PD. 2014. Structure of the gut microbiome following colonization with human feces determines colonic tumor burden. Microbiome. 2: 20. DOI: 10.1186/2049-2618-2-20.
  59. Zackular JP, Baxter NT, Chen GH, Schloss PD. 2015. Manipulation of the gut microbiota reveals role in colon tumorigenesis. mSphere. 1: e00001-e00015. DOI: 10.1128/mSphere.00001-15.
  60. Westcott SL, Schloss PD. 2015. De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units. PeerJ. 3: e1487. DOI: 10.7717/peerj.1487.
  61. Schubert AM, Sinani H, Schloss PD. 2015. Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile. mBio. 6: e00974-15. DOI: 10.1128/mBio.00974-15.
  62. Schloss PD. 2015. Commentary: Nurturing the microbiome field. Science. 350: 1044. DOI: 10.1126/science.350.6264.1044.
  63. Kopliku FA, Schubert AM, Mogle J, Schloss PD, Young VB, Aronoff DM. 2015. Low prevalence of Clostridium septicum fecal carriage in an adult population. Anaerobe. 32: 34-6. DOI: 10.1016/j.anaerobe.2014.12.001.
  64. Koenigsknecht MJ, Theriot CM, Bergin IL, Schumacher CA, Schloss PD, Young VB. 2015. Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract. Infect Immun. 83: 934-41. DOI: 10.1128/IAI.02768-14.
  65. Carmody LA, Zhao J, Kalikin LM, LeBar W, Simon RH, Venkataraman A, Schmidt TM, Abdo Z, Schloss PD, LiPuma JJ. 2015. The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation. Microbiome. 3: 12. DOI: 10.1186/s40168-015-0074-9.
  66. 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. 2015. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Am J Respir Crit Care Med. 192: 1335-44. DOI: 10.1164/rccm.201501-0128OC.
  67. Baxter NT, Wan JJ, Schubert AM, Jenior ML, Myers P, Schloss PD. 2015. Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric peromyscus populations. Appl Environ Microbiol. 81: 396-404. DOI: 10.1128/AEM.02303-14.
  68. Sze MA, Schloss PD. 2016. Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome. mBio. 7: e01018-16. DOI: 10.1128/mBio.01018-16.
  69. Schloss PD. 2016. Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods. mSystems. 1: e00027-16. DOI: 10.1128/mSystems.00027-16.
  70. Schloss PD, Girard RA, Martin T, Edwards J, Thrash JC. 2016. Status of the archaeal and bacterial census: an update. mBio. 7: e00201-16. DOI: 10.1128/mBio.00201-16.
  71. Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK. 2016. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ. 4: e1869. DOI: 10.7717/peerj.1869.
  72. Majid SA, Graw MF, Chatziefthimiou AD, Nguyen H, Richer R, Louge M, Sultan AA, Schloss P, Hay AG. 2016. Microbial Characterization of Qatari Barchan Sand Dunes. PLOS ONE. 11: e0161836. DOI: 10.1371/journal.pone.0161836.
  73. Flynn KJ, Baxter NT, Schloss PD. 2016. Metabolic and community synergy of oral bacteria in colorectal cancer. mSphere. 1: e00102-16. DOI: 10.1128/mSphere.00102-16.
  74. Baxter NT, Koumpouras CC, Rogers MA, Ruffin MT 4th, Schloss PD. 2016. DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model. Microbiome. 4: 59. DOI: 10.1186/s40168-016-0205-y.
  75. Baxter NT, Ruffin MT 4th, Rogers MA, Schloss PD. 2016. Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions. Genome Medicine. 8: 1. DOI: 10.1186/s13073-016-0290-3.
  76. Westcott SL, Schloss PD. 2017. OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units. mSphere. 2: e00073-17. DOI: 10.1128/mSphereDirect.00073-17.
  77. Seregin SS, Golovchenko N, Schaf B, Chen J, Pudlo NA, Mitchell J, Baxter NT, Zhao L, Schloss PD, Martens EC, Eaton KA, Chen GY. 2017. NLRP6 protects IL10-/- mice from colitis by limiting colonization of Akkermansia muciniphila. Cell Reports. . DOI: 10.1016/j.celrep.2017.03.080.
  78. Schloss PD. 2017. Preprinting Microbiology. mBio. 8: e00438-17. DOI: 10.1128/mBio.00438-17.
  79. Jenior ML, Leslie JL, Young VB, Schloss PD. 2017. Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments. mSystems. 2: e00063-17. DOI: 10.1128/mSystems.00063-17.