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Items: 1 to 50 of 455

1.

Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history.

Xu M, Stedtfeld RD, Wang F, Hashsham SA, Song Y, Chuang Y, Fan J, Li H, Jiang X, Tiedje JM.

Sci Total Environ. 2019 Nov 1;689:1172-1180. doi: 10.1016/j.scitotenv.2019.06.376. Epub 2019 Jun 24.

PMID:
31466157
2.

A general framework for quantitatively assessing ecological stochasticity.

Ning D, Deng Y, Tiedje JM, Zhou J.

Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):16892-16898. doi: 10.1073/pnas.1904623116. Epub 2019 Aug 7.

PMID:
31391302
3.

Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon.

Hale L, Feng W, Yin H, Guo X, Zhou X, Bracho R, Pegoraro E, Penton CR, Wu L, Cole J, Konstantinidis KT, Luo Y, Tiedje JM, Schuur EAG, Zhou J.

ISME J. 2019 Aug 5. doi: 10.1038/s41396-019-0485-x. [Epub ahead of print]

PMID:
31384013
4.

Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce.

Shen Y, Stedtfeld RD, Guo X, Bhalsod GD, Jeon S, Tiedje JM, Li H, Zhang W.

Environ Int. 2019 Oct;131:105031. doi: 10.1016/j.envint.2019.105031. Epub 2019 Jul 20.

5.

Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths.

Johnston ER, Hatt JK, He Z, Wu L, Guo X, Luo Y, Schuur EAG, Tiedje JM, Zhou J, Konstantinidis KT.

Proc Natl Acad Sci U S A. 2019 Jul 23;116(30):15096-15105. doi: 10.1073/pnas.1901307116. Epub 2019 Jul 8.

PMID:
31285347
6.

Global diversity and biogeography of bacterial communities in wastewater treatment plants.

Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown M, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A; Global Water Microbiome Consortium, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X, Zhou J.

Nat Microbiol. 2019 Jul;4(7):1183-1195. doi: 10.1038/s41564-019-0426-5. Epub 2019 May 13.

PMID:
31086312
7.

Consent insufficient for data release-Response.

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 May 3;364(6439):446. doi: 10.1126/science.aax7509. No abstract available.

PMID:
31048484
8.

Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence.

Pärnänen KMM, Narciso-da-Rocha C, Kneis D, Berendonk TU, Cacace D, Do TT, Elpers C, Fatta-Kassinos D, Henriques I, Jaeger T, Karkman A, Martinez JL, Michael SG, Michael-Kordatou I, O'Sullivan K, Rodriguez-Mozaz S, Schwartz T, Sheng H, Sørum H, Stedtfeld RD, Tiedje JM, Giustina SVD, Walsh F, Vaz-Moreira I, Virta M, Manaia CM.

Sci Adv. 2019 Mar 27;5(3):eaau9124. doi: 10.1126/sciadv.aau9124. eCollection 2019 Mar.

9.

Editorial: Environmental aspects of antibiotic resistance.

Tiedje JM.

FEMS Microbiol Ecol. 2019 Apr 1;95(4). pii: fiz019. doi: 10.1093/femsec/fiz019. No abstract available.

PMID:
30923814
10.

Climate warming accelerates temporal scaling of grassland soil microbial biodiversity.

Guo X, Zhou X, Hale L, Yuan M, Ning D, Feng J, Shi Z, Li Z, Feng B, Gao Q, Wu L, Shi W, Zhou A, Fu Y, Wu L, He Z, Van Nostrand JD, Qiu G, Liu X, Luo Y, Tiedje JM, Yang Y, Zhou J.

Nat Ecol Evol. 2019 Apr;3(4):612-619. doi: 10.1038/s41559-019-0848-8. Epub 2019 Mar 25.

PMID:
30911147
11.

Bacillus-Dominant Airborne Bacterial Communities Identified During Asian Dust Events.

Yoo K, Han I, Ko KS, Lee TK, Yoo H, Khan MI, Tiedje JM, Park J.

Microb Ecol. 2019 Oct;78(3):677-687. doi: 10.1007/s00248-019-01348-0. Epub 2019 Mar 23.

PMID:
30904989
12.

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.

13.

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.

14.

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.

15.

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.

PMID:
30375866
16.

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.

17.

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.

PMID:
30253298
18.

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.

19.

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.

20.

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.

21.

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.

PMID:
30052926
22.

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.

23.

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.

PMID:
29944836
24.

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.

25.

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.

26.

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.

27.

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.

PMID:
29802797
28.

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.

29.

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.

30.

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.

31.

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.

PMID:
29428982
32.

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.

PMID:
29408954
33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

PMID:
29196844
38.

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.

PMID:
29185915
39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

PMID:
28715138
44.

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.

PMID:
28663443
45.

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;:.

PMID:
28634640
46.

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.

47.

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.

48.

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.

PMID:
28525258
49.

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.

50.

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.

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