Papers

Our research lab has many ways of outputting our discoveries. One of our primary approaches and the one our peers judge us by are our publications. Here are all of the papers generated by the lab along with PDF copies of the papers. Of course, a paper is just a way station along the scientific method. With this in mind, in 2014 we started to generate papers as reproducible documents that contain the code used to go from raw data to the final version of the manuscript that we submitted to the journal for review. We'd love it if you were able to take our data or code and build upon it to help your scientific story. Feel free to holler if you have questions about this process or about how we analyzed the data in our other publications.

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  • PDF version of published paper
  • Preprint version of manuscript
  • GitHub repository for paper
  • Raw data used in manuscript
  • Google Scholar page
  1. Hannigan GD, Duhaime MB, Koutra D, Schloss PD. 2017. Preprint: Biogeography & Environmental Conditions Shape Phage & Bacteria Interaction Networks Across The Human Microbiome.
  2. Hannigan GD, Duhaime MB, Ruffin IV MT, Koumpouras CC, Schloss PD. 2017. Preprint: Viral and Bacterial Communities of Colorectal Cancer.
  3. 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.
  4. Schloss PD. 2017. Preprinting Microbiology. mBio. 8: e00438-17. DOI: 10.1128/mBio.00438-17.
  5. Schloss PD, Johnston M, Casadevall A. 2017. Support Science by Publishing in Scientific Society Journals. mBio. 8: e01633-17. DOI: 10.1128/mBio.01633-17.
  6. 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.
  7. Sze MA, Schloss PD. 2017. Preprint: The effect of treatment on the microbiota of patients diagnosed with colonic lesions.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. Schloss PD. 2015. Commentary: Nurturing the microbiome field. Science. 350: 1044. DOI: 10.1126/science.350.6264.1044.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. Ding T, Schloss PD. 2014. Dynamics and associations of microbial community types across the human body. Nature. 509: 357-60. DOI: 10.1038/nature13178.
  28. 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.
  29. Schloss PD. 2014. Commentary: Microbiology: An integrated view of the skin microbiome. Appl Environ Microbiol. 514: 44-5. DOI: doi:10.1038/514044a.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. Schloss PD. 2013. Secondary structure improves OTU assignments of 16S rRNA gene sequences. ISME J. 7: 457-60. DOI: 10.1038/ismej.2012.102.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature. 486: 207-14. DOI: 10.1038/nature11234.
  42. Human Microbiome Project Consortium. 2012. A framework for human microbiome research. Nature. 486: 215-21. DOI: 10.1038/nature11209.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.
  53. Robinson CJ, Schloss PD, Ramos Y, Raffa K, Handelsman J. 2010. . Microb Ecol.. 59: 199-211. DOI: 10.1007/s00248-009-9595-8.
  54. 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.
  55. 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.
  56. 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.
  57. Schloss PD. 2009. A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One. 4: e8230. DOI: 10.1371/journal.pone.0008230.
  58. 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.
  59. 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.
  60. 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.
  61. 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.
  62. 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.
  63. 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.
  64. 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.
  65. 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.
  66. Schloss PD, Handelsman J. 2006. Toward a census of bacteria in soil. PLoS Comput Biol. 2: e92. DOI: 10.1371/journal.pcbi.0020092.
  67. 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.
  68. 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.
  69. 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.
  70. 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.
  71. 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.
  72. 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.
  73. 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.
  74. 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.
  75. 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.
  76. 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.
  77. 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.
  78. 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.
  79. Schloss PD, Handelsman J. 2003. Biotechnological prospects from metagenomics. Curr Opin Biotechnol. 14: 303-10. DOI: 10.1016/S0958-1669(03)00067-3.
  80. 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.
  81. 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.
  82. 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.
  83. 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.