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Items: 1 to 50 of 102

1.

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.

2.

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment.

Shin B, Kim M, Zengler K, Chin KJ, Overholt WA, Gieg LM, Konstantinidis KT, Kostka JE.

Sci Rep. 2019 Feb 4;9(1):1239. doi: 10.1038/s41598-018-36567-x.

3.

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.

4.

Moving the cataloguing of the "uncultivated majority" forward.

Konstantinidis KT, Rossello-Mora R, Amann R.

Syst Appl Microbiol. 2019 Jan;42(1):3-4. doi: 10.1016/j.syapm.2018.12.001. Epub 2018 Dec 10. No abstract available.

PMID:
30558959
5.

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.

Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S.

Nat Commun. 2018 Nov 30;9(1):5114. doi: 10.1038/s41467-018-07641-9.

6.

imGLAD: accurate detection and quantification of target organisms in metagenomes.

Castro JC, Rodriguez-R LM, Harvey WT, Weigand MR, Hatt JK, Carter MQ, Konstantinidis KT.

PeerJ. 2018 Nov 2;6:e5882. doi: 10.7717/peerj.5882. eCollection 2018.

7.

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient.

Meziti A, Tsementzi D, Rodriguez-R LM, Hatt JK, Karayanni H, Kormas KA, Konstantinidis KT.

ISME J. 2019 Mar;13(3):767-779. doi: 10.1038/s41396-018-0307-6. Epub 2018 Nov 5.

PMID:
30397261
8.

Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics.

Zhang SY, Tsementzi D, Hatt JK, Bivins A, Khelurkar N, Brown J, Tripathi SN, Konstantinidis KT.

Environ Microbiol. 2019 Jan;21(1):182-196. doi: 10.1111/1462-2920.14439. Epub 2018 Nov 15.

PMID:
30325092
9.

Genomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains.

Pena-Gonzalez A, Rodriguez-R LM, Marston CK, Gee JE, Gulvik CA, Kolton CB, Saile E, Frace M, Hoffmaster AR, Konstantinidis KT.

mSystems. 2018 Aug 14;3(4). pii: e00065-18. doi: 10.1128/mSystems.00065-18. eCollection 2018 Jul-Aug.

10.

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.

11.

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria.

Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Malmstrom RR, Woyke T, Ulloa O, Konstantinidis KT, Thamdrup B, Stewart FJ.

ISME J. 2018 Nov;12(11):2706-2722. doi: 10.1038/s41396-018-0223-9. Epub 2018 Jul 10.

12.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
13.

Widely Used Benzalkonium Chloride Disinfectants Can Promote Antibiotic Resistance.

Kim M, Weigand MR, Oh S, Hatt JK, Krishnan R, Tezel U, Pavlostathis SG, Konstantinidis KT.

Appl Environ Microbiol. 2018 Aug 17;84(17). pii: e01201-18. doi: 10.1128/AEM.01201-18. Print 2018 Sep 1.

14.

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.

15.

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
16.

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.

17.

Genomic and Transcriptomic Insights into How Bacteria Withstand High Concentrations of Benzalkonium Chloride Biocides.

Kim M, Hatt JK, Weigand MR, Krishnan R, Pavlostathis SG, Konstantinidis KT.

Appl Environ Microbiol. 2018 May 31;84(12). pii: e00197-18. doi: 10.1128/AEM.00197-18. Print 2018 Jun 15.

18.

Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis.

Tsementzi D, Castro Gordillo J, Mahagna M, Gottlieb Y, Konstantinidis KT.

Environ Microbiol. 2018 May;20(5):1751-1764. doi: 10.1111/1462-2920.14104.

PMID:
29575448
19.

Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones.

Cardenas E, Orellana LH, Konstantinidis KT, Mohn WW.

Sci Rep. 2018 Feb 16;8(1):3142. doi: 10.1038/s41598-018-21197-0.

20.

Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano.

Viver T, Orellana L, González-Torres P, Díaz S, Urdiain M, Farías ME, Benes V, Kaempfer P, Shahinpei A, Ali Amoozegar M, Amann R, Antón J, Konstantinidis KT, Rosselló-Móra R.

Syst Appl Microbiol. 2018 May;41(3):198-212. doi: 10.1016/j.syapm.2017.12.004. Epub 2018 Jan 31.

PMID:
29429564
21.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

22.

Reply to the commentary "Uncultivated microbes-in need of their own nomenclature?"

Konstantinidis KT, Rosselló-Móra R, Amann R.

ISME J. 2018 Mar;12(3):653-654. doi: 10.1038/s41396-017-0011-y. Epub 2018 Jan 15. No abstract available.

23.

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.

24.

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.

25.

Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization.

Orellana LH, Chee-Sanford JC, Sanford RA, Löffler FE, Konstantinidis KT.

Appl Environ Microbiol. 2018 Jan 2;84(2). pii: e01646-17. doi: 10.1128/AEM.01646-17. Print 2018 Jan 15.

26.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893.

PMID:
28787424
27.

Uncultivated microbes in need of their own taxonomy.

Konstantinidis KT, Rosselló-Móra R, Amann R.

ISME J. 2017 Nov;11(11):2399-2406. doi: 10.1038/ismej.2017.113. Epub 2017 Jul 21.

28.

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
29.

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.

30.

Draft Genome Sequence of Bacillus cereus LA2007, a Human-Pathogenic Isolate Harboring Anthrax-Like Plasmids.

Pena-Gonzalez A, Marston CK, Rodriguez-R LM, Kolton CB, Garcia-Diaz J, Theppote A, Frace M, Konstantinidis KT, Hoffmaster AR.

Genome Announc. 2017 Apr 20;5(16). pii: e00181-17. doi: 10.1128/genomeA.00181-17.

31.

The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa.

Viver T, Orellana LH, Hatt JK, Urdiain M, Díaz S, Richter M, Antón J, Avian M, Amann R, Konstantinidis KT, Rosselló-Móra R.

Environ Microbiol. 2017 Aug;19(8):3039-3058. doi: 10.1111/1462-2920.13763. Epub 2017 May 11.

PMID:
28419691
32.

'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family.

Kleindienst S, Higgins SA, Tsementzi D, Chen G, Konstantinidis KT, Mack EE, Löffler FE.

Syst Appl Microbiol. 2017 Apr;40(3):150-159. doi: 10.1016/j.syapm.2016.12.001. Epub 2016 Dec 21.

PMID:
28292625
33.

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

Wang Y, Hatt JK, Tsementzi D, Rodriguez-R LM, Ruiz-Pérez CA, Weigand MR, Kizer H, Maresca G, Krishnan R, Poretsky R, Spain JC, Konstantinidis KT.

Appl Environ Microbiol. 2017 Mar 31;83(8). pii: e03321-16. doi: 10.1128/AEM.03321-16. Print 2017 Apr 15.

34.

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores.

Orellana LH, Rodriguez-R LM, Konstantinidis KT.

Nucleic Acids Res. 2017 Feb 17;45(3):e14. doi: 10.1093/nar/gkw900.

35.

Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe.

Zhang X, Johnston ER, Li L, Konstantinidis KT, Han X.

ISME J. 2017 Apr;11(4):885-895. doi: 10.1038/ismej.2016.180. Epub 2016 Dec 20.

36.

Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods.

Huang AD, Luo C, Pena-Gonzalez A, Weigand MR, Tarr CL, Konstantinidis KT.

Appl Environ Microbiol. 2017 Jan 17;83(3). pii: e02577-16. doi: 10.1128/AEM.02577-16. Print 2017 Feb 1.

37.

A Rieske-Type Oxygenase of Pseudomonas sp. BIOMIG1 Converts Benzalkonium Chlorides to Benzyldimethyl Amine.

Ertekin E, Konstantinidis KT, Tezel U.

Environ Sci Technol. 2017 Jan 3;51(1):175-181. doi: 10.1021/acs.est.6b03705. Epub 2016 Nov 20.

PMID:
27792326
38.

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ.

Nature. 2016 Aug 11;536(7615):179-83. Epub 2016 Aug 3.

39.

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, Schuur EA, Luo Y, Tiedje JM, Zhou J, Konstantinidis KT.

Front Microbiol. 2016 Apr 25;7:579. doi: 10.3389/fmicb.2016.00579. eCollection 2016.

40.

Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics.

Meziti A, Tsementzi D, Ar Kormas K, Karayanni H, Konstantinidis KT.

Environ Microbiol. 2016 Dec;18(12):4640-4652. doi: 10.1111/1462-2920.13303. Epub 2016 Apr 30.

PMID:
27001690
41.

Dynamic models of the complex microbial metapopulation of lake mendota.

Dam P, Fonseca LL, Konstantinidis KT, Voit EO.

NPJ Syst Biol Appl. 2016 Mar 24;2:16007. doi: 10.1038/npjsba.2016.7. eCollection 2016.

42.

Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments.

Ertekin E, Hatt JK, Konstantinidis KT, Tezel U.

Environ Sci Technol. 2016 Apr 19;50(8):4304-13. doi: 10.1021/acs.est.5b05959. Epub 2016 Mar 31.

PMID:
26992451
43.

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections.

Soto-Giron MJ, Rodriguez-R LM, Luo C, Elk M, Ryu H, Hoelle J, Santo Domingo JW, Konstantinidis KT.

Appl Environ Microbiol. 2016 Apr 18;82(9):2872-2883. doi: 10.1128/AEM.03529-15. Print 2016 May.

44.

Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils.

Higgins SA, Welsh A, Orellana LH, Konstantinidis KT, Chee-Sanford JC, Sanford RA, Schadt CW, Löffler FE.

Appl Environ Microbiol. 2016 May 2;82(10):2919-2928. doi: 10.1128/AEM.00243-16. Print 2016 May 15.

45.

Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium.

Kleindienst S, Higgins SA, Tsementzi D, Konstantinidis KT, Mack EE, Löffler FE.

Genome Announc. 2016 Mar 3;4(2). pii: e00037-16. doi: 10.1128/genomeA.00037-16.

46.

Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi.

Löffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Müller JA, Fullerton H, Zinder SH, Spormann AM.

Int J Syst Evol Microbiol. 2015 Jun;65(Pt 6):2015. doi: 10.1099/ijs.0.000308. No abstract available.

PMID:
26184667
47.

Microbial species delineation using whole genome sequences.

Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A.

Nucleic Acids Res. 2015 Aug 18;43(14):6761-71. doi: 10.1093/nar/gkv657. Epub 2015 Jul 6.

48.

Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy.

Weigand MR, Pena-Gonzalez A, Shirey TB, Broeker RG, Ishaq MK, Konstantinidis KT, Raphael BH.

Appl Environ Microbiol. 2015 Aug 15;81(16):5420-9. doi: 10.1128/AEM.01159-15. Epub 2015 Jun 5.

49.

Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities.

Tsementzi D, Poretsky R, Rodriguez-R LM, Luo C, Konstantinidis KT.

Environ Microbiol Rep. 2014 Dec;6(6):640-55.

PMID:
25756118
50.

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill.

Rodriguez-R LM, Overholt WA, Hagan C, Huettel M, Kostka JE, Konstantinidis KT.

ISME J. 2015 Sep;9(9):1928-40. doi: 10.1038/ismej.2015.5. Epub 2015 Feb 17.

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