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Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils.

Feng J, Penton CR, He Z, Van Nostrand JD, Yuan MM, Wu L, Wang C, Qin Y, Shi ZJ, Guo X, Schuur EAG, Luo Y, Bracho R, Konstantinidis KT, Cole JR, Tiedje JM, Yang Y, Zhou J.

MBio. 2019 Feb 26;10(1). pii: e02521-18. doi: 10.1128/mBio.02521-18.


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.


Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils.

Khan MAW, Bohannan BJM, Nüsslein K, Tiedje JM, Tringe SG, Parlade E, Barberán A, Rodrigues JLM.

FEMS Microbiol Ecol. 2019 Feb 1;95(2). doi: 10.1093/femsec/fiy230.


Long-Term Effect of Different Fertilization and Cropping Systems on the Soil Antibiotic Resistome.

Wang F, Xu M, Stedtfeld RD, Sheng H, Fan J, Liu M, Chai B, Soares de Carvalho T, Li H, Li Z, Hashsham SA, Tiedje JM.

Environ Sci Technol. 2018 Nov 20;52(22):13037-13046. doi: 10.1021/acs.est.8b04330. Epub 2018 Nov 8.


Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota.

Vital M, Howe A, Bergeron N, Krauss RM, Jansson JK, Tiedje JM.

Appl Environ Microbiol. 2018 Nov 15;84(23). pii: e01562-18. doi: 10.1128/AEM.01562-18. Print 2018 Dec 1.


Bioavailability of tetracycline to antibiotic resistant Escherichia coli in water-clay systems.

Zhang Y, Boyd SA, Teppen BJ, Tiedje JM, Zhang W, Zhu D, Li H.

Environ Pollut. 2018 Dec;243(Pt B):1078-1086. doi: 10.1016/j.envpol.2018.09.059. Epub 2018 Sep 15.


Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States.

Mackelprang R, Grube AM, Lamendella R, Jesus EDC, Copeland A, Liang C, Jackson RD, Rice CW, Kapucija S, Parsa B, Tringe SG, Tiedje JM, Jansson JK.

Front Microbiol. 2018 Aug 15;9:1775. doi: 10.3389/fmicb.2018.01775. eCollection 2018.


More replenishment than priming loss of soil organic carbon with additional carbon input.

Liang J, Zhou Z, Huo C, Shi Z, Cole JR, Huang L, Konstantinidis KT, Li X, Liu B, Luo Z, Penton CR, Schuur EAG, Tiedje JM, Wang YP, Wu L, Xia J, Zhou J, Luo Y.

Nat Commun. 2018 Aug 9;9(1):3175. doi: 10.1038/s41467-018-05667-7.


New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.

Kroeger ME, Delmont TO, Eren AM, Meyer KM, Guo J, Khan K, Rodrigues JLM, Bohannan BJM, Tringe SG, Borges CD, Tiedje JM, Tsai SM, Nüsslein K.

Front Microbiol. 2018 Jul 23;9:1635. doi: 10.3389/fmicb.2018.01635. eCollection 2018.


Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements.

Stedtfeld RD, Guo X, Stedtfeld TM, Sheng H, Williams MR, Hauschild K, Gunturu S, Tift L, Wang F, Howe A, Chai B, Yin D, Cole JR, Tiedje JM, Hashsham SA.

FEMS Microbiol Ecol. 2018 Sep 1;94(9). doi: 10.1093/femsec/fiy130.


Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection.

Zhang AN, Li LG, Ma L, Gillings MR, Tiedje JM, Zhang T.

Microbiome. 2018 Jul 21;6(1):130. doi: 10.1186/s40168-018-0516-2.


Antibiotic Resistome Associated with Small-Scale Poultry Production in Rural Ecuador.

Guo X, Stedtfeld RD, Hedman H, Eisenberg JNS, Trueba G, Yin D, Tiedje JM, Zhang L.

Environ Sci Technol. 2018 Aug 7;52(15):8165-8172. doi: 10.1021/acs.est.8b01667. Epub 2018 Jul 10.


The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM, Cole JR, Konstantinidis KT.

Nucleic Acids Res. 2018 Jul 2;46(W1):W282-W288. doi: 10.1093/nar/gky467.


Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass.

Guo X, Zhou X, Hale L, Yuan M, Feng J, Ning D, Shi Z, Qin Y, Liu F, Wu L, He Z, Van Nostrand JD, Liu X, Luo Y, Tiedje JM, Zhou J.

Front Microbiol. 2018 May 31;9:954. doi: 10.3389/fmicb.2018.00954. eCollection 2018.


Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient.

Roley SS, Duncan DS, Liang D, Garoutte A, Jackson RD, Tiedje JM, Robertson GP.

PLoS One. 2018 Jun 1;13(6):e0197320. doi: 10.1371/journal.pone.0197320. eCollection 2018.


Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra.

Liang J, Xia J, Shi Z, Jiang L, Ma S, Lu X, Mauritz M, Natali SM, Pegoraro E, Penton CR, Plaza C, Salmon VG, Celis G, Cole JR, Konstantinidis KT, Tiedje JM, Zhou J, Schuur EAG, Luo Y.

Glob Chang Biol. 2018 Oct;24(10):4946-4959. doi: 10.1111/gcb.14325. Epub 2018 Jun 12.


Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity.

Rodriguez-R LM, Gunturu S, Tiedje JM, Cole JR, Konstantinidis KT.

mSystems. 2018 Apr 10;3(3). pii: e00039-18. doi: 10.1128/mSystems.00039-18. eCollection 2018 May-Jun.


Comment on "The whole-soil carbon flux in response to warming".

Xiao J, Yu F, Zhu W, Xu C, Zhang K, Luo Y, Tiedje JM, Zhou J, Cheng L.

Science. 2018 Feb 23;359(6378). pii: eaao0218. doi: 10.1126/science.aao0218.


Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation.

Li B, Wu WM, Watson DB, Cardenas E, Chao Y, Phillips DH, Mehlhorn T, Lowe K, Kelly SD, Li P, Tao H, Tiedje JM, Criddle CS, Zhang T.

Appl Environ Microbiol. 2018 Apr 16;84(9). pii: e02885-17. doi: 10.1128/AEM.02885-17. Print 2018 May 1.


Draft genome of the fungicidal biological control agent Burkholderia anthina strain XXVI.

de Los Santos-Villalobos S, Kremer JM, Parra-Cota FI, Hayano-Kanashiro AC, García-Ortega LF, Gunturu SK, Tiedje JM, He SY, Peña-Cabriales JJ.

Arch Microbiol. 2018 Jul;200(5):803-810. doi: 10.1007/s00203-018-1490-6. Epub 2018 Feb 10.


ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes.

Yin X, Jiang XT, Chai B, Li L, Yang Y, Cole JR, Tiedje JM, Zhang T.

Bioinformatics. 2018 Jul 1;34(13):2263-2270. doi: 10.1093/bioinformatics/bty053.


Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection.

Etchebarne BE, Li Z, Stedtfeld RD, Nicholas MC, Williams MR, Johnson TA, Stedtfeld TM, Kostic T, Khalife WT, Tiedje JM, Hashsham SA, Hughes MJ.

Front Microbiol. 2017 Dec 12;8:2211. doi: 10.3389/fmicb.2017.02211. eCollection 2017.


How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?

Rodriguez-R LM, Castro JC, Kyrpides NC, Cole JR, Tiedje JM, Konstantinidis KT.

Appl Environ Microbiol. 2018 Mar 1;84(6). pii: e00014-18. doi: 10.1128/AEM.00014-18. Print 2018 Mar 15.


Divergence in Gene Regulation Contributes to Sympatric Speciation of Shewanella baltica Strains.

Deng J, Auchtung JM, Konstantinidis KT, Caro-Quintero A, Brettar I, Höfle M, Tiedje JM.

Appl Environ Microbiol. 2018 Jan 31;84(4). pii: e02015-17. doi: 10.1128/AEM.02015-17. Print 2018 Feb 15.


Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study.

Šket R, Treichel N, Kublik S, Debevec T, Eiken O, Mekjavić I, Schloter M, Vital M, Chandler J, Tiedje JM, Murovec B, Prevoršek Z, Likar M, Stres B.

PLoS One. 2017 Dec 6;12(12):e0188556. doi: 10.1371/journal.pone.0188556. eCollection 2017.


Correction to: The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation.

Fonseca EDS, Peixoto RS, Rosado AS, Balieiro FC, Tiedje JM, Rachid CTCDC.

Microb Ecol. 2018 Jan;75(1):192. doi: 10.1007/s00248-017-1122-8.


Antibiotic Resistance Gene Detection in the Microbiome Context.

Do TT, Tamames J, Stedtfeld RD, Guo X, Murphy S, Tiedje JM, Walsh F.

Microb Drug Resist. 2018 Jun;24(5):542-546. doi: 10.1089/mdr.2017.0199. Epub 2017 Nov 29.


MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome.

Williams MR, Stedtfeld RD, Tiedje JM, Hashsham SA.

Front Microbiol. 2017 Sep 27;8:1896. doi: 10.3389/fmicb.2017.01896. eCollection 2017. Review.


Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD.

Stedtfeld RD, Chai B, Crawford RB, Stedtfeld TM, Williams MR, Xiangwen S, Kuwahara T, Cole JR, Kaminski NE, Tiedje JM, Hashsham SA.

Front Microbiol. 2017 Sep 7;8:1708. doi: 10.3389/fmicb.2017.01708. eCollection 2017.


TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal.

Stedtfeld RD, Brett Sallach J, Crawford RB, Stedtfeld TM, Williams MR, Waseem H, Johnston CT, Li H, Teppen BJ, Kaminski NE, Boyd SA, Tiedje JM, Hashsham SA.

Appl Microbiol Biotechnol. 2017 Oct;101(19):7409-7415. doi: 10.1007/s00253-017-8460-9. Epub 2017 Aug 15.


Corrigendum: The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms.

Muziasari WI, Pitkänen LK, Sørum H, Stedtfeld RD, Tiedje JM, Virta M.

Front Microbiol. 2017 Aug 2;8:1491. doi: 10.3389/fmicb.2017.01491. eCollection 2017.


Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil.

Yuan MM, Zhang J, Xue K, Wu L, Deng Y, Deng J, Hale L, Zhou X, He Z, Yang Y, Van Nostrand JD, Schuur EAG, Konstantinidis KT, Penton CR, Cole JR, Tiedje JM, Luo Y, Zhou J.

Glob Chang Biol. 2018 Jan;24(1):297-307. doi: 10.1111/gcb.13820. Epub 2017 Sep 1.


Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes.

Robertson GP, Hamilton SK, Barham BL, Dale BE, Izaurralde RC, Jackson RD, Landis DA, Swinton SM, Thelen KD, Tiedje JM.

Science. 2017 Jun 30;356(6345). pii: eaal2324. doi: 10.1126/science.aal2324. Review.


The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation.

Fonseca EDS, Peixoto RS, Rosado AS, Balieiro FC, Tiedje JM, Rachid CTCDC.

Microb Ecol. 2018 Jan;75(1):183-191. doi: 10.1007/s00248-017-1014-y. Epub 2017 Jun 21. Erratum in: Microb Ecol. 2017 Dec 2;:.


Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB.

Munir A, Waseem H, Williams MR, Stedtfeld RD, Gulari E, Tiedje JM, Hashsham SA.

Microarrays (Basel). 2017 May 29;6(2). pii: E9. doi: 10.3390/microarrays6020009.


Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device.

Williams MR, Stedtfeld RD, Stedtfeld TM, Tiedje JM, Hashsham SA.

Biomed Microdevices. 2017 Sep;19(3):45. doi: 10.1007/s10544-017-0191-2.


Bioavailability of Soil-Sorbed Tetracycline to Escherichia coli under Unsaturated Conditions.

Chen Z, Zhang W, Wang G, Zhang Y, Gao Y, Boyd SA, Teppen BJ, Tiedje JM, Zhu D, Li H.

Environ Sci Technol. 2017 Jun 6;51(11):6165-6173. doi: 10.1021/acs.est.7b00590. Epub 2017 May 19.


Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study.

Šket R, Treichel N, Debevec T, Eiken O, Mekjavic I, Schloter M, Vital M, Chandler J, Tiedje JM, Murovec B, Prevoršek Z, Stres B.

Front Physiol. 2017 May 4;8:250. doi: 10.3389/fphys.2017.00250. eCollection 2017.


TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome.

Stedtfeld RD, Stedtfeld TM, Fader KA, Williams MR, Bhaduri P, Quensen J, Zacharewski TR, Tiedje JM, Hashsham SA.

FEMS Microbiol Ecol. 2017 May 1;93(5). doi: 10.1093/femsec/fix058.


Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers.

Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae JC, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, Tiedje JM, Upham BL, Hashsham SA.

J Environ Manage. 2017 Aug 1;198(Pt 1):213-220. doi: 10.1016/j.jenvman.2017.04.079. Epub 2017 Apr 29.


Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner.

Srinivasan V, Stedtfeld RD, Tourlousse DM, Baushke SW, Xin Y, Miller SM, Pham T, Rouillard JM, Gulari E, Tiedje JM, Hashsham SA.

J Microbiol Methods. 2017 Aug;139:15-21. doi: 10.1016/j.mimet.2017.04.009. Epub 2017 Apr 23.


Warming enhances old organic carbon decomposition through altering functional microbial communities.

Cheng L, Zhang N, Yuan M, Xiao J, Qin Y, Deng Y, Tu Q, Xue K, Van Nostrand JD, Wu L, He Z, Zhou X, Leigh MB, Konstantinidis KT, Schuur EA, Luo Y, Tiedje JM, Zhou J.

ISME J. 2017 Aug;11(8):1825-1835. doi: 10.1038/ismej.2017.48. Epub 2017 Apr 21.


Virulence factor activity relationships (VFARs): a bioinformatics perspective.

Waseem H, Williams MR, Stedtfeld T, Chai B, Stedtfeld RD, Cole JR, Tiedje JM, Hashsham SA.

Environ Sci Process Impacts. 2017 Mar 22;19(3):247-260. doi: 10.1039/c6em00689b. Review.


Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices.

Williams MR, Stedtfeld RD, Waseem H, Stedtfeld T, Upham B, Khalife W, Etchebarne B, Hughes M, Tiedje JM, Hashsham SA.

Anal Methods. 2017 Feb 28;9(8):1229-1241. doi: 10.1039/C6AY03405E. Epub 2017 Jan 31.


The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms.

Muziasari WI, Pitkänen LK, Sørum H, Stedtfeld RD, Tiedje JM, Virta M.

Front Microbiol. 2017 Jan 6;7:2137. doi: 10.3389/fmicb.2016.02137. eCollection 2016. Erratum in: Front Microbiol. 2017 Aug 02;8:1491.


Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms.

Meyer KM, Klein AM, Rodrigues JL, Nüsslein K, Tringe SG, Mirza BS, Tiedje JM, Bohannan BJ.

Mol Ecol. 2017 Mar;26(6):1547-1556. doi: 10.1111/mec.14011. Epub 2017 Feb 10.


Strategies to improve reference databases for soil microbiomes.

Choi J, Yang F, Stepanauskas R, Cardenas E, Garoutte A, Williams R, Flater J, Tiedje JM, Hofmockel KS, Gelder B, Howe A.

ISME J. 2017 Apr;11(4):829-834. doi: 10.1038/ismej.2016.168. Epub 2016 Dec 9. No abstract available.


Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria.

de Carvalho TS, Jesus ED, Barlow J, Gardner TA, Soares IC, Tiedje JM, Moreira FM.

Ecology. 2016 Oct;97(10):2760-2771. doi: 10.1002/ecy.1513. Epub 2016 Sep 9.


Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in <25min.

Ahmad F, Stedtfeld RD, Waseem H, Williams MR, Cupples AM, Tiedje JM, Hashsham SA.

J Microbiol Methods. 2017 Jan;132:27-33. doi: 10.1016/j.mimet.2016.11.010. Epub 2016 Nov 14.


Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils.

Wang F, Stedtfeld RD, Kim OS, Chai B, Yang L, Stedtfeld TM, Hong SG, Kim D, Lim HS, Hashsham SA, Tiedje JM, Sul WJ.

Environ Sci Technol. 2016 Dec 6;50(23):12621-12629. Epub 2016 Nov 18.


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