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A High-Fat/High-Protein, Atkins-Type Diet Exacerbates Clostridioides (Clostridium) difficile Infection in Mice, whereas a High-Carbohydrate Diet Protects.

Mefferd CC, Bhute SS, Phan JR, Villarama JV, Do DM, Alarcia S, Abel-Santos E, Hedlund BP.

mSystems. 2020 Feb 11;5(1). pii: e00765-19. doi: 10.1128/mSystems.00765-19.


Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.

Doud DFR, Bowers RM, Schulz F, De Raad M, Deng K, Tarver A, Glasgow E, Vander Meulen K, Fox B, Deutsch S, Yoshikuni Y, Northen T, Hedlund BP, Singer SW, Ivanova N, Woyke T.

ISME J. 2020 Mar;14(3):659-675. doi: 10.1038/s41396-019-0557-y. Epub 2019 Nov 21.


Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea.

Hua ZS, Wang YL, Evans PN, Qu YN, Goh KM, Rao YZ, Qi YL, Li YX, Huang MJ, Jiao JY, Chen YT, Mao YP, Shu WS, Hozzein W, Hedlund BP, Tyson GW, Zhang T, Li WJ.

Nat Commun. 2019 Oct 8;10(1):4574. doi: 10.1038/s41467-019-12574-y.


Diverse respiratory capacity among Thermus strains from US Great Basin hot springs.

Zhou EM, Adegboruwa AL, Mefferd CC, Bhute SS, Murugapiran SK, Dodsworth JA, Thomas SC, Bengtson AJ, Liu L, Xian WD, Li WJ, Hedlund BP.

Extremophiles. 2020 Jan;24(1):71-80. doi: 10.1007/s00792-019-01131-6. Epub 2019 Sep 18.


Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures.

Thomas SC, Tamadonfar KO, Seymour CO, Lai D, Dodsworth JA, Murugapiran SK, Eloe-Fadrosh EA, Dijkstra P, Hedlund BP.

Front Microbiol. 2019 Jul 5;10:1427. doi: 10.3389/fmicb.2019.01427. eCollection 2019.


Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics.

Tan S, Liu J, Fang Y, Hedlund BP, Lian ZH, Huang LY, Li JT, Huang LN, Li WJ, Jiang HC, Dong HL, Shu WS.

ISME J. 2019 Aug;13(8):2044-2057. doi: 10.1038/s41396-019-0415-y. Epub 2019 Apr 8.


Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California.

Zhou EM, Xian WD, Mefferd CC, Thomas SC, Adegboruwa AL, Williams N, Murugapiran SK, Dodsworth JA, Ganji R, Li MM, Ding YP, Liu L, Woyke T, Li WJ, Hedlund BP.

Extremophiles. 2018 Nov;22(6):983-991. doi: 10.1007/s00792-018-1055-2. Epub 2018 Sep 15.


Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota.

Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ.

Nat Commun. 2018 Jul 19;9(1):2832. doi: 10.1038/s41467-018-05284-4.


Effect of the Synthetic Bile Salt Analog CamSA on the Hamster Model of Clostridium difficile Infection.

Howerton A, Seymour CO, Murugapiran SK, Liao Z, Phan JR, Estrada A, Wagner AJ, Mefferd CC, Hedlund BP, Abel-Santos E.

Antimicrob Agents Chemother. 2018 Sep 24;62(10). pii: e02251-17. doi: 10.1128/AAC.02251-17. Print 2018 Oct.


Synergistic plant-microbe interactions between endophytic bacterial communities and the medicinal plant Glycyrrhiza uralensis F.

Li L, Mohamad OAA, Ma J, Friel AD, Su Y, Wang Y, Musa Z, Liu Y, Hedlund BP, Li W.

Antonie Van Leeuwenhoek. 2018 Oct;111(10):1735-1748. doi: 10.1007/s10482-018-1062-4. Epub 2018 Mar 7.


Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation.

Xie W, Luo H, Murugapiran SK, Dodsworth JA, Chen S, Sun Y, Hedlund BP, Wang P, Fang H, Deng M, Zhang CL.

Environ Microbiol. 2018 Feb;20(2):734-754. doi: 10.1111/1462-2920.14004. Epub 2017 Dec 29.


Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs.

Becraft ED, Dodsworth JA, Murugapiran SK, Thomas SC, Ohlsson JI, Stepanauskas R, Hedlund BP, Swingley WD.

Front Microbiol. 2017 Oct 31;8:2082. doi: 10.3389/fmicb.2017.02082. eCollection 2017.


Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead.

Blunt SM, Sackett JD, Rosen MR, Benotti MJ, Trenholm RA, Vanderford BJ, Hedlund BP, Moser DP.

Sci Total Environ. 2018 May 1;622-623:1640-1648. doi: 10.1016/j.scitotenv.2017.10.052. Epub 2017 Oct 19.


Special Issue: the 3rd meeting of the Bergey's International Society for Microbial Systematics (BISMIS).

Hedlund BP, Sutcliffe IC, Trujillo ME.

Antonie Van Leeuwenhoek. 2017 Oct;110(10):1245-1246. doi: 10.1007/s10482-017-0935-2. No abstract available.


Reversible Reduction of Estrone to 17β-Estradiol by , , and Isolates from the Las Vegas Wash.

Blunt SM, Benotti MJ, Rosen MR, Hedlund BP, Moser DP.

J Environ Qual. 2017 Mar;46(2):281-287. doi: 10.2134/jeq2016.08.0286.


High-Quality Draft Genome Sequence of Thermocrinis jamiesonii GBS1T Isolated from Great Boiling Spring, Nevada.

Ganji R, Murugapiran SK, Ong JC, Manoharan N, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Duffy K, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Dodsworth JA, Hedlund BP.

Genome Announc. 2016 Oct 20;4(5). pii: e01112-16. doi: 10.1128/genomeA.01112-16.


High-Quality Draft Genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, Isolates from Tengchong, China.

Mefferd CC, Zhou EM, Yu TT, Ming H, Murugapiran SK, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Duffy K, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Williams AJ, Woyke T, Li WJ, Hedlund BP.

Genome Announc. 2016 Apr 28;4(2). pii: e00312-16. doi: 10.1128/genomeA.00312-16.


High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway.

Zhou EM, Murugapiran SK, Mefferd CC, Liu L, Xian WD, Yin YR, Ming H, Yu TT, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Shapiro N, Markowitz V, Ivanova N, Spunde A, Kyrpides N, Woyke T, Li WJ, Hedlund BP.

Stand Genomic Sci. 2016 Feb 27;11:20. doi: 10.1186/s40793-016-0140-3. eCollection 2016.


Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.

Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge J, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN.

Nat Commun. 2016 Jan 27;7:10476. doi: 10.1038/ncomms10476.


Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes.

Becraft ED, Dodsworth JA, Murugapiran SK, Ohlsson JI, Briggs BR, Kanbar J, De Vlaminck I, Quake SR, Dong H, Hedlund BP, Swingley WD.

Appl Environ Microbiol. 2015 Dec 4;82(4):992-1003. doi: 10.1128/AEM.03140-15. Print 2016 Feb 15.


High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism.

Hedlund BP, Murugapiran SK, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Duffy K, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Williams AJ, Cole JK, Dodsworth JA, Woyke T.

Genome Announc. 2015 Dec 3;3(6). pii: e01410-15. doi: 10.1128/genomeA.01410-15.


Thermocrinis jamiesonii sp. nov., a thiosulfate-oxidizing, autotropic thermophile isolated from a geothermal spring.

Dodsworth JA, Ong JC, Williams AJ, Dohnalkova AC, Hedlund BP.

Int J Syst Evol Microbiol. 2015 Dec;65(12):4769-75. doi: 10.1099/ijsem.0.000647. Epub 2015 Sep 29.


Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes.

Saw JH, Spang A, Zaremba-Niedzwiedzka K, Juzokaite L, Dodsworth JA, Murugapiran SK, Colman DR, Takacs-Vesbach C, Hedlund BP, Guy L, Ettema TJ.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140328. doi: 10.1098/rstb.2014.0328.


Uncultivated thermophiles: current status and spotlight on 'Aigarchaeota'.

Hedlund BP, Murugapiran SK, Alba TW, Levy A, Dodsworth JA, Goertz GB, Ivanova N, Woyke T.

Curr Opin Microbiol. 2015 Jun;25:136-45. doi: 10.1016/j.mib.2015.06.008. Epub 2015 Jun 23. Review.


Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics.

Nobu MK, Dodsworth JA, Murugapiran SK, Rinke C, Gies EA, Webster G, Schwientek P, Kille P, Parkes RJ, Sass H, Jørgensen BB, Weightman AJ, Liu WT, Hallam SJ, Tsiamis G, Woyke T, Hedlund BP.

ISME J. 2016 Feb;10(2):273-86. doi: 10.1038/ismej.2015.97. Epub 2015 Jun 19.


The changing landscape of microbial biodiversity exploration and its implications for systematics.

Hedlund BP, Dodsworth JA, Staley JT.

Syst Appl Microbiol. 2015 Jun;38(4):231-6. doi: 10.1016/j.syapm.2015.03.003. Epub 2015 Apr 2. Review.


Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China.

Hedlund BP, Reysenbach AL, Huang L, Ong JC, Liu Z, Dodsworth JA, Ahmed R, Williams AJ, Briggs BR, Liu Y, Hou W, Dong H.

Front Microbiol. 2015 Feb 27;6:157. doi: 10.3389/fmicb.2015.00157. eCollection 2015.


Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables.

Xie W, Zhang CL, Wang J, Chen Y, Zhu Y, de la Torre JR, Dong H, Hartnett HE, Hedlund BP, Klotz MG.

Environ Microbiol. 2015 May;17(5):1600-14. doi: 10.1111/1462-2920.12595. Epub 2014 Oct 13.


Impact of single-cell genomics and metagenomics on the emerging view of extremophile "microbial dark matter".

Hedlund BP, Dodsworth JA, Murugapiran SK, Rinke C, Woyke T.

Extremophiles. 2014 Sep;18(5):865-75. doi: 10.1007/s00792-014-0664-7. Epub 2014 Aug 12. Review.


Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.

Dodsworth JA, Gevorkian J, Despujos F, Cole JK, Murugapiran SK, Ming H, Li WJ, Zhang G, Dohnalkova A, Hedlund BP.

Int J Syst Evol Microbiol. 2014 Jun;64(Pt 6):2119-27. doi: 10.1099/ijs.0.055855-0. Epub 2014 Mar 27. Erratum in: Int J Syst Evol Microbiol. 2014 Sep;64(Pt 9):3331.


Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China.

Briggs BR, Brodie EL, Tom LM, Dong H, Jiang H, Huang Q, Wang S, Hou W, Wu G, Huang L, Hedlund BP, Zhang C, Dijkstra P, Hungate BA.

Environ Microbiol. 2014 Jun;16(6):1579-91. doi: 10.1111/1462-2920.12311. Epub 2013 Nov 14.


Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling.

Murugapiran SK, Huntemann M, Wei CL, Han J, Detter JC, Han C, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Pati A, Goodwin L, Peters L, Pitluck S, Lam J, McDonald AI, Dodsworth JA, Woyke T, Hedlund BP.

Stand Genomic Sci. 2013 Feb 25;7(3):449-68. doi: 10.4056/sigs.3667269. eCollection 2013.


The distribution and abundance of archaeal tetraether lipids in U.S. Great Basin hot springs.

Paraiso JJ, Williams AJ, Huang Q, Wei Y, Dijkstra P, Hungate BA, Dong H, Hedlund BP, Zhang CL.

Front Microbiol. 2013 Aug 28;4:247. doi: 10.3389/fmicb.2013.00247. eCollection 2013.


Wide distribution of autochthonous branched glycerol dialkyl glycerol tetraethers (bGDGTs) in U.S. Great Basin hot springs.

Hedlund BP, Paraiso JJ, Williams AJ, Huang Q, Wei Y, Dijkstra P, Hungate BA, Dong H, Zhang CL.

Front Microbiol. 2013 Aug 8;4:222. doi: 10.3389/fmicb.2013.00222. eCollection 2013.


Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia.

Cole JK, Gieler BA, Heisler DL, Palisoc MM, Williams AJ, Dohnalkova AC, Ming H, Yu TT, Dodsworth JA, Li WJ, Hedlund BP.

Int J Syst Evol Microbiol. 2013 Dec;63(Pt 12):4675-82. doi: 10.1099/ijs.0.053348-0. Epub 2013 Aug 15.


Insights into the phylogeny and coding potential of microbial dark matter.

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T.

Nature. 2013 Jul 25;499(7459):431-7. doi: 10.1038/nature12352. Epub 2013 Jul 14.


In situ production of branched glycerol dialkyl glycerol tetraethers in a great basin hot spring (USA).

Zhang CL, Wang J, Dodsworth JA, Williams AJ, Zhu C, Hinrichs KU, Zheng F, Hedlund BP.

Front Microbiol. 2013 Jul 9;4:181. doi: 10.3389/fmicb.2013.00181. eCollection 2013.


Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.

Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PS, Scholz MB, Lo CC, Raymond J, Quake SR, Hedlund BP.

Nat Commun. 2013;4:1854. doi: 10.1038/ncomms2884.


An integrated study reveals diverse methanogens, Thaumarchaeota, and yet-uncultivated archaeal lineages in Armenian hot springs.

Hedlund BP, Dodsworth JA, Cole JK, Panosyan HH.

Antonie Van Leeuwenhoek. 2013 Jul;104(1):71-82. doi: 10.1007/s10482-013-9927-z. Epub 2013 Apr 30.


Lateral gene transfer of family A DNA polymerases between thermophilic viruses, aquificae, and apicomplexa.

Schoenfeld TW, Murugapiran SK, Dodsworth JA, Floyd S, Lodes M, Mead DA, Hedlund BP.

Mol Biol Evol. 2013 Jul;30(7):1653-64. doi: 10.1093/molbev/mst078. Epub 2013 Apr 22.


Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment.

Peacock JP, Cole JK, Murugapiran SK, Dodsworth JA, Fisher JC, Moser DP, Hedlund BP.

PLoS One. 2013;8(3):e59927. doi: 10.1371/journal.pone.0059927. Epub 2013 Mar 29.


Cultivation and characterization of thermophilic Nitrospira species from geothermal springs in the US Great Basin, China, and Armenia.

Edwards TA, Calica NA, Huang DA, Manoharan N, Hou W, Huang L, Panosyan H, Dong H, Hedlund BP.

FEMS Microbiol Ecol. 2013 Aug;85(2):283-92. doi: 10.1111/1574-6941.12117. Epub 2013 Apr 11.


Community microrespirometry and molecular analyses reveal a diverse energy economy in Great Boiling Spring and Sandy's Spring West in the U.S. Great Basin.

Murphy CN, Dodsworth JA, Babbitt AB, Hedlund BP.

Appl Environ Microbiol. 2013 May;79(10):3306-10. doi: 10.1128/AEM.00139-13. Epub 2013 Mar 8.


Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin.

Murugapiran SK, Huntemann M, Wei CL, Han J, Detter JC, Han CS, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Lam J, McDonald AI, Dodsworth JA, Pati A, Goodwin L, Peters L, Pitluck S, Woyke T, Hedlund BP.

Genome Announc. 2013 Jan;1(1). pii: e00106-12. doi: 10.1128/genomeA.00106-12. Epub 2013 Jan 24.


A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing.

Hou W, Wang S, Dong H, Jiang H, Briggs BR, Peacock JP, Huang Q, Huang L, Wu G, Zhi X, Li W, Dodsworth JA, Hedlund BP, Zhang C, Hartnett HE, Dijkstra P, Hungate BA.

PLoS One. 2013;8(1):e53350. doi: 10.1371/journal.pone.0053350. Epub 2013 Jan 9.


Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities.

Cole JK, Peacock JP, Dodsworth JA, Williams AJ, Thompson DB, Dong H, Wu G, Hedlund BP.

ISME J. 2013 Apr;7(4):718-29. doi: 10.1038/ismej.2012.157. Epub 2012 Dec 13.


Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning.

Miller-Coleman RL, Dodsworth JA, Ross CA, Shock EL, Williams AJ, Hartnett HE, McDonald AI, Havig JR, Hedlund BP.

PLoS One. 2012;7(5):e35964. doi: 10.1371/journal.pone.0035964. Epub 2012 May 4.


Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs.

Dodsworth JA, McDonald AI, Hedlund BP.

FEMS Microbiol Ecol. 2012 Aug;81(2):446-54. doi: 10.1111/j.1574-6941.2012.01369.x. Epub 2012 Apr 18.


Potential role of Thermus thermophilus and T. oshimai in high rates of nitrous oxide (N2O) production in ∼80 °C hot springs in the US Great Basin.

Hedlund BP, McDonald AI, Lam J, Dodsworth JA, Brown JR, Hungate BA.

Geobiology. 2011 Nov;9(6):471-80. doi: 10.1111/j.1472-4669.2011.00295.x. Epub 2011 Sep 27.


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