James M. Tiedje, Primary Publications (2009-2013):

  1. Cole, J.R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R.J. Farris, A.S. Kulam-Syed-Mohideen, D.M. McGarrell, T. Marsh, G.M. Garrity and J.M. Tiedje. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. (Database issue) 37:D141-D145; doi: 10.1093/nar/gkn879. [PubMed]

  2. Bakermans, C., R.E. Sloup, D.G. Zarka, J.M. Tiedje and M.F. Thomashow. 2008. Development and use of genetic system to identify genes required for efficient low-temperature growth of Psychrobacter arcticus 273-4. Extremophiles 13:21-30; doi: 10.1007/s00792-008-0193-3. [PubMed]

  3. Ramette A., J.M. Tiedje and A. Boetius. 2009. Impact of space, time and complex environments on microbial communities. Clin. Microbiol. Infection 15(s1):60-62; doi: 10.11141/j.169-0691.2008.02692.x. [PubMed]

  4. Yoder-Himes, D, P.S. Chain, Y. Zhu, O. Wurtzel, E.M. Rubin, J.M. Tiedje, R Sorek. 2009. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. PNAS 106:3976-3981; doi: 10.1073/pnas.0813403106 [PubMed]

  5. Bergholz, P.W., C. Bakermans and J.M. Tiedje. 2009. Psychrobacter arcticus 273-4 uses resource efficiency and molecular motin adaptations for subzero temperature growth. J. Bacteriol. 191:2340-2352; doi: 10.1128/JB.01377-08. [PubMed]

  6. Rodrigues, D.F., E.C. Jesus, H.L. Ayala-del-Río, V.H. Pellizari, D. Gilichinsky, L. Sepulveda-Torres and J.M. Tiedje. 2009. Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium. ISME Journal 3:658-665; doi: 10.1038/ismej.2009.25. [PubMed]

  7. Gao, H., Z.K. Yang, S. Barua, S.B. Reed, M.F. Romine, K.H. Nealson, J.K. Fredrickson, J.M. Tiedje and J. Zhou. 2009. Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA and NapA. ISME Journal, 3:1-11; doi: 10.1038/ismej.2009.40. [PubMed]

  8. Cardenas, E., J.R. Cole, J.M. Tiedje and J. Park. 2009. Microbial community analysis using RDPII (Ribosomal Database Project II): Methods, tools and new advances. Environ. Engr. Res., 14:3-9; doi: 10.4491/eer.2009.14.1.003. [pdf]

  9. Vishnivetskaya, T.A., S. Kathariou and J.M. Tiedje. 2009. The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 13:541-555; doi: 10.1007/s00792-009-0243-5. [PubMed]

  10. Rodríguez-Minguela, C.M., J.H.A. Apajalahti, B. Chai, J.R. Cole and J.M. Tiedje. 2009. Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact. Appl. Environ. Microbiol. 75:5100-5110; doi: 10.1128/AEM.00133-09. [PubMed]

  11. Jesus, E.C., T.L. Marsh, J.M. Tiedje and F.M. de S Moreira. 2009. Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME Journal 3:1004-1011; doi: 10.1038/ismej.2009.47. [PubMed]

  12. Sul, W.J., J-H. Park, J.F. Quensen, III, J.L.M. Rodrigues, L. Seliger, T.V. Tsoi, G.J. Zylstra and J.M. Tiedje. 2009. DNA-Stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl contaminated river sediments. Appl. Environ. Microbiol. 75:5501-5506; doi: 10.1128/AEM.00121-09. [PubMed]

  13. Konstantinidis, K.I., M.H. Serres, M.F. Romine, J.L.M.Rodrigues, J. Auchtung, L.A. McCue, M.S. Lipton, A. Obraztsova, C.S. Giometti, K.H. Nealson, J.K. Fredrickson and J.M. Tiedje. 2009. Comparative systems biology across an evolutionary gradient within the Shewanella genus. PNAS 106:15909-15914; doi: 10.1073/pnas.0902000106. [PubMed]

  14. Walk, S.T., E.W. Alm, D.M. Gordon, J.L. Ram, G.A. Toranzos, J.M. Tiedje and T.S. Whittam. 2009. Cryptic lineages of the Escherichia genus. Appl. Environ. Microbiol. 75:6534-6544; doi: 10.1128/AEM.01262-09. [PubMed]

  15. Parnell, J.J., V.J. Denef, J.Park, T. Tsoi and J.M. Tiedje. 2009. Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400. Biodegradation 21:147-156; doi: 10.1007/s10532-009-9289-4. [PubMed]

  16. Iwai, S., B. Chai, W.J. Sul, J.R. Cole, S.A. Hashsham and J.M. Tiedje. 2009. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME Journal 4:279-285; doi: 10.1038/ismej.2009.104. [PubMed]

  17. Van Nostrand, Joy D., W-M Wu, L. Wu, Y. Deng, J. Carley, S. Carroll, Z. He, B. Gu, J. Luo, C.S. Criddle, D.B. Watson, P.M. Jardine, T.L. Marsh, J.M. Tiedje, T.C. Hazen and J. Zhou. 2009. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ. Microbiol. 11:2611-2626; doi: 10.1111/j.1462-2920.2009.01986.x. [PubMed]

  18. Cole, J.R., K. Konstantidindis, R.J. Farris and J.M. Tiedje. 2010. Microbial diversity and phylogeny: Extending from rRNAs to genomes. pp. 1-19. In W-T Liu and J.K. Jansson (eds), Environmental Molecular Microbiology, Caister Academic Press. [book link]

  19. Yoder-Himes, D., K.T. Konstantinidis and J.M. Tiedje. 2010. Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS One 5(1):1-11 (e8724); doi: 10.1371/journal.pone.0008724. [PubMed]

  20. Ayala-del-Río, H., P.S. Chain, J.J. Grzymski, M.A. Ponder, N. Ivanova, P.W. Bergholz, G. Di Bartolo, L. Hauser, M. Land, C. Bakermans, D. Rodrigues, J. Klappenbach, D. Zarka, F. Larimer, P. Richardson, A. Murray, M. Thomashow and J.M. Tiedje. 2010. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl. Environ. Microbiol. 76:2304-2312; doi: 10.1128/AEM.02101-09. [PubMed]

  21. Oh, S., D.R. Yoder-Himes, J. Tiedje, J. Park and K.T. Konstantinidis. 2010. Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain. Appl. Environ. Microbiol. 76:2890-2988; doi: 10.1128/AEM.02826-09. [PubMed]

  22. Hemme, C., Y. Deng, T.J. Gentry, M.W. Fields, L. Wu, S. Barua, K. Barry, S.G. Tringe, D.B. Watson, Z. He, T.C. Hazen, J.M. Tiedje, E.M. Rubin and J. Zhou. 2010. Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME Journal 4:660-672; doi: 10.1038/ismej.2009.154. [PubMed]

  23. Jesus, E., E. Susilawati, S.L. Smith, Q. Wang, B. Chai, R. Farris, J.L.M. Rodrigues, K.D. Thelen and J.M. Tiedje. 2010. Bacterial communities in the rhizosphere of biofuel crops grown on marginal lands as evaluated by 16S rRNA gene pyrosequences. Bioenerg. Res. 3:20-27; doi: 10.1007/s12155-009-9073-7.

  24. Stres, B., L. Philippot, J. Faganeli and J.M. Tiedje, 2010. Frequent freeze-thaw cycles yield diminished yet resistant and responsive microbial communities in two temperate soils: a laboratory experiment. FEMS Microbiol Ecol. 74:323-335; doi: 10.1111/j.1574-6941.2010.00951.x. [PubMed]

  25. Cardenas. E., W-M Wu, M.B. Leigh, J. Carley, S. Carroll, T. Gentry, J. Luo, D. Watson, B. Gu, M. Ginder-Vogel, P.K. Kitanidis, P.M. Jardine, J. Zhou, C.S. Criddle, T.L. Marsh and J.M. Tiedje. 2010. A combined massively parallel sequencing-indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities. Appl. Environ. Microbiol. 76:6778-6786; doi: 10.1128/AEM.01097-10. [PubMed]

  26. Hinsa-Leasure, S., L. Bhavaraju, J. Rodrigues, C. Bakermans, D. Gilichinsky and J. Tiedje. 2010. Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample. FEMS Microbiol Ecol. 74:103-113; doi: 10.1111/j.1574-6941.2010.00945.x. [PubMed]

  27. Gao, H., S. Barua, Y. Liang, L. Wu, Y. Dong, S. Reed, J. Chen, D. Culley, D. Kennedy, Y. Yang, Z. He, K.H. Nealson, J.K. Fredrickson, J.M. Tiedje, M. Romine and J. Zhou. 2010. Impacts of Shewanella oneidensis c-type cytochromes on aerobic and anaerobic respiration. Microbiol Biotechnol. 3:455-466; doi: 10.1111/j.1751-7915.2010.00181.x. [PubMed]

  28. Teixeira, L., R.S. Peixoto1, J.C. Cury, W.J. Sul, V.H. Pellizari, J.Tiedje and A.S. Rosado. 2010. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME Journal 4:989-1001; doi: 10.1038/ismej.2010.35. [PubMed]

  29. Xu, M., W-M. Wu, L. Wu, Z. He, J.D. Van Nostrand, Y. Deng, J. Luo, J. Carley, M. Ginder-Vogel, T.J. Gentry, B. Gu,. D. Watson, P.M. Jardine, T.L. Marsh, J.M. Tiedje, T. Hazen, C.S. Criddle and J. Zhou. 2010. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME Journal 4:1060-1070; doi: 10.1038/ismej.2010.31. [PubMed]

  30. Cole, J.R., D.D. Myrold, C.H. Nakatsu, P.R. Owens, G. Kowalchuk, C. Tebbe and J.M. Tiedje. 2010. Development of Soil Metadata Standards for International DNA Sequence Databases. Proceedings, 19th World Congress of Soil Science, Brisbane, Australia, http://www.iuss.org/19th WCSS/WCSS_Main_Page.html. [pdf]

  31. Iwai, S., B. Chai, E. da C. Jesus, C.R. Penton, T.K. Lee, J.R. Cole and J.M. Tiedje.. 2011. Gene-targeted-metagenomics (GT-metagenomics) to explore the extensive diversity of genes of interest in microbial communities. pp. In Frans J. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. J. Wiley & Sons Press, Hoboken, NJ. [book link]

  32. Cole, James R., Qiong Wang, Benli Chai and James M. Tiedje. 2011. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. pp. In Frans J. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. J. Wiley & Sons Press, Hoboken, NJ. [book link]

  33. Brown, C.T. and J.M. Tiedje. 2011 Metagenomics: the paths forward. pp. In Frans J. de Bruijn (Ed.), Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. J. Wiley & Sons Press, Hoboken, NJ. [book link]

  34. Wu, W-M., J. Carley, D. Watson, B. Gu, S. Brooks, S.S. Kelly, K. Kemner, J.D. van Nostrand, L. Wu, M. Xu, J. Zhou, J. Luo, E. Cardenas, C. Hwang, M.W. Fields, T.L. Marsh, J.M. Tiedje, S.J. Green, J.E. Kostka, P.K. Kitanidis, P.M. Jardine and C.S. Criddle. 2011. Bioreduction and immobilization of uranium in situ: a case study at USA DOE Oak Ridge site, Tennessee. Acta Scientiae Circumstaniae (in Chinese) 31(3). [Abstract]

  35. Li, R. J.M. Auchtung, J.M. Tiedje and R.M. Worden. 2011. Shewanella oneidensis MR-1 chemotaxis in a diffusion gradient chamber. Environ. Sci. Technol. 45:1014-1020; doi: 10.1021/es102425p. [PubMed]

  36. Santos, H.F., J. Cury, F. Lima Carmo, A. Lopes Santos, J. Tiedje, J.D. van Elsas, A. Soares Rosado and R. Silva Peixoto. 2011. Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: Bacterial proxies for oil pollution. PLoS One 6(3):e16943; doi: 10.1371/journal.pone.0016943. [PubMed]

  37. Luo, C., S. Walk, D.M. Gordon, M. Feldgarden, J. Tiedje and K.T. Konstantinidis. 2011. Genome sequencing of environmental E. coli expands understanding of the ecology and speciation of the model bacterial species. PNAS 108:7200-7205; doi: 10.1073/pnas.1015622108. [PubMed]

  38. Iwai S., T.A. Johnson, B. Chai, S.A. Hashsham and J.M. Tiedje. 2011. Comparison of the specificity and efficacy of primers for aromatic dioxygenase gene analysis of environmental samples. Minireview. Appl. Environ. Microbiol. 77: 3551-3557; doi: 10.1128/AEM.00331-11. [PubMed]

  39. Cruz-García, Clarible, Alison E. Murray, Jorge L.M. Rodrigues, Jeffrey A. Gralnick, Lee Ann McCue, Margaret F. Romine, Frank E. Löffler and James M. Tiedje. 2011. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1. BMC Microbiology 11:64; doi: 10.1186/1471-2180-11-64. [PubMed]

  40. Patrauchan, M.A., J.J. Parnell, M.P. McLeod, C. Florizone, J.M. Tiedje and L.D. Eltis. 2011. Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400. Arch. Microbiol. (ePub ahead of print 26 Apr 11); doi: 10.1007/s00203-011-0705-x. [PubMed].

  41. Lee, T.K., J. Lee, W.J. Sul, S. Iwai, B. Chai, J.M. Tiedje, J. Park. 2011. Novel biphenyl oxidizing bacteria and dioxygenase genes from a Korean tidal mudflat. Appl. Environ. Microbiol. 77:3888-3891; doi: 10.1128/AEM.00023-11. [PubMed]

  42. Vishnivetskaya, T.A., S. Lucas, A. Copeland, A. Lapidus, T. Glavina del Rio, S. Kathariou, R.F. Ramaley, D.F. Rodrigues, C. Hendrix, P. Richardson and J.M. Tiedje. 2011. Complete genome sequence of the thermophilic bacterium Exiguobacterium sp. AT1b. J. Bacteriol. 193: 2880-2881; doi: 10.1128/JB.00303-11. [PubMed]

  43. Rodrigues, J.L.M., M.H. Serres and J.M. Tiedje. 2011. Large scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at genus level. Appl. Environ. Microbiol. (ePub ahead of print 3 Jun 11.) doi: 10.1128/AEM.00097-1. [PubMed]

  44. Sul, Woo Jun, James R Cole, Ederson da C Jesus, Qiong Wang, Ryan J Farris, Jordan A Fish and James M Tiedje. 2011. Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering. PNAS 108:14637-14642; doi: 10.1073/pnas.1111435108. [PubMed]

  45. Ahmad, Farhan, Gregoire Seyrig, Dieter M. Tourlousse, Robert D. Stedtfeld, James M. Tiedje and Syed A. Hashsham. 2011. A CCD-based fluorescence imaging system for real-time loop-mediated isothermal amplification-based rapid and sensitive detection of waterborne pathogens on microchips, Biomed. Microdevices 13:929-937; doi: 10.1007/s10544-011-9562-2.

  46. Santos, Adriana L, Jose F. Siqueira Jr., Isabela N. Rocas, Ederson C. Jesus, Alexandre S. Rosado, James M. Tiedje. 2011. Comparing the bacterial diversity of acute and chronic dental root canal infections. PLoS One 6(11):e28088; doi: 10.1371/journal.pone.0028088 [PubMed]

  47. Van Nostrand J.D., L. Wu, W.M. Wu, Z. Huang, T.J.Gentry, Y. Deng, J. Carley, S. Carroll, Z. He, B. Gu, J. Luo, C.S. Criddle, D.B. Watson, P.M. Jardine, T.L. Marsh, J.M. Tiedje, T.C. Hazen, J. Zhou. 2011. Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer. Appl Environ Microbiol. 77:3860-3869; doi: 10.1128/AEM.01981-10. [PubMed]

  48. Bakermans, C., P.W. Bergholz, D.F. Rodrigues, T.A. Vishnivetskaya, H.L. Ayala-del-Río and J.M. Tiedje. 2012. Genomic and expression analyses of cold-adapted microorganisms (Chapter 6). In Lyle Whyte and Robert Miller (Eds), Polar Microbiology: Life in a Deepfreeze. ASM Press, Washington. [book link]

  49. Liang, Chao, Ederson da C. Jesus, David S. Duncan, Randall D. Jackson, James M. Tiedje, Teri C. Balser. 2012. Soil microbial communities under model biofuel cropping systems in southern Wisconsin, USA: Impact of crop species and soil properties. Applied Soil Ecology 54:24-31; doi: 10.1016/j.apsoil.2011.11.015.

  50. Green, Stephan, Om Prakash, Puja Jasrotia, Will Overholt, Erick Cardenas, Daniela Hubbard, James Tiedje, David Watson, Christopher Schadt, Scott Brooks and Joel Kostka. 2012. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site. Appl Environ. Microbiol. 78(4):1039-1047; doi: 10.1128/AEM.06435-11. [PubMed]

  51. Caro-Quintero, Alejandro, Jennifer Auchtung, Jie Deng, Ingrid Brettar, Manfred Höfle, James M. Tiedje and Konstantinos T. Konstantinidis.. 2012. Genome sequencing of five Shewanella baltica strains recovered from the oxic-anoxic Interface of the Baltic Sea. J. Bacteriol. 194(5):1236 doi: 10.1128/JB.06468-11. [PubMed]

  52. Kim, Sang-Hoon, Christina Harzman, John K. Davis, Rachel Hutcheson, Joan B. Broderick, Terence L. Marsh, James M. Tiedje. 2012. Genome sequence of Desulfitobacterium hafniense DCB-2, a gram-positive anaerobe capable of dehalogenation and metal reduction. BMC Microbiology 12:21 doi: 10.1186/1471-2180-12-21. [PubMed]

  53. Looft T, T. A. Johnson, H.K. Allen, D.O. Bayles, D.P. Alt, R.D. Stedtfeld, W.J. Sul, T.M. Stedtfeld, B. Chai B, J. R. Cole, S.A. Hashsham, J.M.Tiedje and T.B. Stanton. 2012. In-feed antibiotic effects on the swine intestinal microbiome. PNAS 109(5):1691-1696; doi: 10.1073/pnas.1120238109. [PubMed]

  54. He, Ruo, Matthew J. Wooller, John W. Pohlman, Catharine Catranis, John Quensen, James M. Tiedje, Mary Beth Leigh. 2012. Identification of functionally active aerobic methanotrophs in sediments from an Arctic lake using stable isotope probing. Environ. Microbiol. 14(6):1403-19; doi: 10.1111/j.1462-2920.2012.02725.x. [PubMed]

  55. Stedtfeld, Robert D., Dieter M. Tourlousse, Gregoire Seyrig, Tiffany M. Stedtfeld, Maggie Kronlein, Scott Price, Farhan Ahmad, Erdogan Gulari, James M. Tiedje, Syed A. Hashsham. 2012. Gene-Z: A device for point of care genetic testing using a Smartphone. Lab on a Chip 12(8):1454-1462; doi: 10.1039/C2LC21226A.

  56. Li, Rui, James M. Tiedje, Chichia Chiu and Robert M. Worden. 2012. Soluble electron shuttles can mediate energy taxis toward insoluble electron acceptors. Environ Sci and Technol. 46:2813-2820; doi: 10.1021/es204302w.

  57. He, Ruo, Matthew J. Wooller, John W. Quensen, James M. Tiedje, Mary Beth Leigh. 2012. Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments. ISMEJ 6(10):1937-1948; doi: 10.1038/ismej.2012.34. [PubMed]

  58. He, Ruo, Matthew Wooller, John Pohlman, John Quensen, James Tiedje and Mary Leigh. 2012. Shifts in identity and activity of methanotrophs in Arctic lake sediments in response to temperature changes. Appl Environ. Microbiol ePub 20 April; doi: 10.1128/AEM.00853-12. [PubMed]

  59. Pell, Jason, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje and C. Titus Brown. 2012. Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. PNAS 109:13272-13277; doi: 10.1073/pnas.1121464109. [PubMed]

  60. Katharios-Lanwermeyer. S, M. Rakic-Martinez, S. Ratani, D. Elhanafi, J. M. Tiedje and S. Kathariou. 2012. Co-selection of cadmium and benzalkonium chloride resistance in conjugative transfer from non-pathogenic Listeria spp. to other listeriae. Appl Environ Microbiol. 8(21):7549-7556; doi: 10.1128/AEM.02245-12. [PubMed]

  61. Liang, Chao, David S. Duncan, Teri C. Balser, James M. Tiedje and Randall D. Jackson. 2012. Soil microbial residue storage linked to soil legacy under biofuel cropping systems in southern Wisconsin, USA. Soil Biol Biochem. 57:939-942; doi: 10.1016/j.soilbio.2012.09.006.

  62. Oh, Seungdae, Sarah Buddenborg, Deborah R. Yoder-Himes, James Tiedje and Konstantinos T. Konstantinidis. 2012. Genomic diversity of Escherichia isolates from diverse habitats. PLoS One 7(10):e47005; doi: 10.1371/journal.pone.0047005. [PubMed]

  63. Penton, Christopher R., Jonathan L. Deenik, Brian N. Popp, Greg L. Bruland, Pia Engstrom, Derek St. Louis and, James Tiedje. 2012. Importance of sub-surface rhizosphere-mediatedcoupled nitrification- denitrification in a flooded agroecosystem in Hawaii. Soil Biol Biochem. 57:362-373; doi: 10.1016/j.soilbio.2012.10.018.

  64. Rodrigues, Jorge L. M.; Vivian Pellizari, Rebecca Mueller, Kyunghwa Baek, Ederson da C. Jesus, Fabiana Paula, Babur Mirza, George Hamaoui, Siu Mui Tsai, Brigitte Feigl, James M. Tiedje, Brendan J.M. Bohannan and Klaus Nüsslein. 2013. Conversion of the Amazon Rainforest to agriculture results in biotic homogenization of soil bacterial communities. PNAS 110:988-993; doi: 10.1073/pnas.1220608110. [PubMed]

  65. Tourlousse, Dieter M., Farhan Ahmad, Robert D. Stedtfeld, Gregoire Seyrig, James M. Tiedje and Syed A. Hashsham. 2012. A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomed. Devices. 14:769-778; doi: 10.1007/s10544-012-9658-3.

  66. Vital, Marius, Christopher R. Penton, Qiong Wang, Vincent B. Young, Dion A. Antonopoulos, Mitchell L. Sogin, Hilary G. Morrison, Laura Raffals, Eugene B. Chang, Gary B. Huffnagle, Thomas M. Schmidt, James R. Cole and James M. Tiedje. 2013. A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. BMC Microbiome 1:8; doi: 10.1186/2049-2618-1-8.

  67. Young, Vincent B., Laura H. Raffals, Susan M. Huse, Marius Vital, Dongjuan Dai, Patrick D. Schloss, Jennifer M. Brulc, Dionysios A. Antonopoulos, Rose L. Arrieta, John H. Kwon, K. Gautham Reddy, Nathaniel A. Hubert, Sharon L. Grimm, Joseph H. Vineis, Sushila Dalal, Hilary G. Morrison, A. Murat Eren, Folker Meyer, Thomas M. Schmidt, James M. Tiedje, Eugene B. Chang and Mitchell L. Sogin. 2013. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. BMC Microbiome 1:9; doi: 10.1186/2049-2618-1-9

  68. Zhu, Yong-Guan, Timothy A. Johnson, Jian-Qiang Su, Min Qiao, Guang-Xia Guo, Robert D. Stedtfeld, Syed A. Hashsham and James M. Tiedje. 2013. Diverse and abundant antibiotic resistance genes in Chinese swine farms. PNAS 110:3435-3440; doi: 10.1073/pnas.1222743110 [PubMed]

  69. Rachid, Caio T. C. C., Adriana L. Santos, Marisa C. Piccolo, Fabiano C. Balieiro, Heitor L. C. Coutinho, Raquel S. Peixoto, James M. Tiedje and Alexandre S. Rosado. 2013. Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure. PLoS ONE 8:e59342; doi: 10.1371/journal.pone.0059342 [PubMed]

  70. Hinsa-Leasure, Shannon, Cassandra Koid, James M. Tiedje and Janna N. Schultzhaus. 2013. Biofilm formation by Psychrobacter arcticus and the role of a large adhesin in attachment to surfaces. Appl Environ Microbiol. 79:967-3973; doi: 10.1128/AEM.00867-13 PubMed]

  71. Sul, Woo Jun, Stella Asuming-Brempong, Qiong Wang. Dieter M. Tourlousse, C. Ryan Penton, Ye Deng, Jorge L. M. Rodrigues, Samuel G.K. Adiku, James W. Jones, Jizhong Zhou, James R. Cole and James M. Tiedje. 2013. Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biol Biochem. 65:33-38; doi: 10.1016/j.soilbio.2013.05.007

  72. Wang, Q., J.F. Quensen III, J.A. Fish, T.K. Lee, Y. Sun, J.M. Tiedje and J.R. Cole. 2013. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. mBio 4:e00592-13; doi: 10.1128/mBio.00592-13 [PubMed]

  73. Penton C.P., T.A. Johnson, J.F. Quensen III, S. Iwai, J.R. Cole and J.M. Tiedje. 2013. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. Front Microbiol. 4:279, doi: 10.3389/fmicb.2013.00279 [PubMed]

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