General microbiome research

  1. Mirzayi C, Renson A, Furlanello C, Sansone S, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo H, Buck GA, Bushman F, Casero D, Clarke G, Collado M, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Sartor BR, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone S, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L, Genomic Standards Consortium, Massive Analysis and Quality Control Society. 2021. Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine. DOI: 10.1038/s41591-021-01552-x.
  2. Widder S, Zhao J, Carmody LA, Zhang Q, Kalikin LM, Schloss PD, LiPuma JJ. 2021. Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways. The ISME Journal. DOI: 10.1038/s41396-021-01129-z.
  3. Baxter NT, Lesniak NA, Sinani H, Schloss PD, Koropatkin NM. 2019. The glucoamylase inhibitor acarbose has a diet-dependent and reversible effect on the murine gut microbiome. mSphere. 4: e00528-18. DOI: 10.1128/mSphere.00528-18.
  4. Sze MA, Schloss PD. 2019. The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data. mSphere. 4: e00163-19. DOI: 10.1128/mSphere.00163-19.
  5. Doherty MD, Ding T, Koumpouras C, Telesco SE, Monast C, Das A, Brodmerkel C, Schloss PD. 2018. Fecal microbiota signatures are associated with response to Ustekinumab therapy among Crohn’s Disease patients. mBio. 9: e02120-17. DOI: 10.1128/mBio.02120-17.
  6. Hannigan GD, Duhaime MB, Koutra D, Schloss PD. 2018. Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome. PLOS Comp Biol. 14: e1006099. DOI: 10.1371/journal.pcbi.1006099.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. Ding T, Schloss PD. 2014. Dynamics and associations of microbial community types across the human body. Nature. 509: 357-60. DOI: 10.1038/nature13178.
  14. 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.
  15. Schloss PD. 2014. Commentary: Microbiology: An integrated view of the skin microbiome. Appl Environ Microbiol. 514: 44-5. DOI: doi:10.1038/514044a.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature. 486: 207-14. DOI: 10.1038/nature11234.
  22. Human Microbiome Project Consortium. 2012. A framework for human microbiome research. Nature. 486: 215-21. DOI: 10.1038/nature11209.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. Robinson CJ, Schloss PD, Ramos Y, Raffa K, Handelsman J. 2010. Robustness of the bacterial community in the cabbage white butterfly larval midgut. Microb Ecology. 59: 199-211. DOI: 10.1007/s00248-009-9595-8.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. Schloss PD, Handelsman J. 2006. Toward a census of bacteria in soil. PLoS Comput Biol. 2: e92. DOI: 10.1371/journal.pcbi.0020092.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. Schloss PD, Handelsman J. 2003. Biotechnological prospects from metagenomics. Curr Opin Biotechnol. 14: 303-10. DOI: 10.1016/S0958-1669(03)00067-3.
  47. 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.
  48. 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.
  49. 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.
  50. 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.