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Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics.

Mosier AC, Justice NB, Bowen BP, Baran R, Thomas BC, Northen TR, Banfield JF.

MBio. 2013 Mar 12;4(2):e00484-12. doi: 10.1128/mBio.00484-12.


Cultivation and quantitative proteomic analyses of acidophilic microbial communities.

Belnap CP, Pan C, VerBerkmoes NC, Power ME, Samatova NF, Carver RL, Hettich RL, Banfield JF.

ISME J. 2010 Apr;4(4):520-30. doi: 10.1038/ismej.2009.139. Epub 2009 Dec 24.


Proteogenomic approaches for the molecular characterization of natural microbial communities.

Banfield JF, Verberkmoes NC, Hettich RL, Thelen MP.

OMICS. 2005 Winter;9(4):301-33.


New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS".

Goltsman DS, Dasari M, Thomas BC, Shah MB, VerBerkmoes NC, Hettich RL, Banfield JF.

Appl Environ Microbiol. 2013 Sep;79(17):5384-93. doi: 10.1128/AEM.00202-13. Epub 2013 May 3.


Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks.

Chokkathukalam A, Kim DH, Barrett MP, Breitling R, Creek DJ.

Bioanalysis. 2014 Feb;6(4):511-24. doi: 10.4155/bio.13.348. Review.


Interactions of the metal tolerant heterotrophic microorganisms and iron oxidizing autotrophic bacteria from sulphidic mine environment during bioleaching experiments.

Jeremic S, Beškoski VP, Djokic L, Vasiljevic B, Vrvić MM, Avdalović J, Gojgić Cvijović G, Beškoski LS, Nikodinovic-Runic J.

J Environ Manage. 2016 May 1;172:151-61. doi: 10.1016/j.jenvman.2016.02.041. Epub 2016 Mar 2.


Concentration of metabolites from low-density planktonic communities for environmental metabolomics using nuclear magnetic resonance spectroscopy.

Everroad RC, Yoshida S, Tsuboi Y, Date Y, Kikuchi J, Moriya S.

J Vis Exp. 2012 Apr 7;(62):e3163. doi: 10.3791/3163.


Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions.

Belnap CP, Pan C, Denef VJ, Samatova NF, Hettich RL, Banfield JF.

ISME J. 2011 Jul;5(7):1152-61. doi: 10.1038/ismej.2010.200. Epub 2011 Jan 13.


Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms.

Goltsman DS, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF.

Appl Environ Microbiol. 2009 Jul;75(13):4599-615. doi: 10.1128/AEM.02943-08. Epub 2009 May 8.


Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation.

Creek DJ, Chokkathukalam A, Jankevics A, Burgess KE, Breitling R, Barrett MP.

Anal Chem. 2012 Oct 16;84(20):8442-7. doi: 10.1021/ac3018795. Epub 2012 Sep 25.


Adaptation of intertidal biofilm communities is driven by metal ion and oxidative stresses.

Zhang W, Wang Y, Lee OO, Tian R, Cao H, Gao Z, Li Y, Yu L, Xu Y, Qian PY.

Sci Rep. 2013 Nov 11;3:3180. doi: 10.1038/srep03180.


Improved genome annotation through untargeted detection of pathway-specific metabolites.

Bowen BP, Fischer CR, Baran R, Banfield JF, Northen T.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S6. doi: 10.1186/1471-2164-12-S1-S6.


Recent advances in stable isotope-enabled mass spectrometry-based plant metabolomics.

Freund DM, Hegeman AD.

Curr Opin Biotechnol. 2017 Feb;43:41-48. doi: 10.1016/j.copbio.2016.08.002. Epub 2016 Sep 7. Review.


Proteomic and metabolomic profiles demonstrate variation among free-living and symbiotic vibrio fischeri biofilms.

Chavez-Dozal A, Gorman C, Nishiguchi MK.

BMC Microbiol. 2015 Oct 23;15:226. doi: 10.1186/s12866-015-0560-z.


Staphylococcus aureus metabolic response to changing environmental conditions - a metabolomics perspective.

Liebeke M, Lalk M.

Int J Med Microbiol. 2014 May;304(3-4):222-9. doi: 10.1016/j.ijmm.2013.11.017. Epub 2013 Dec 1. Review.


Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

Chen LX, Hu M, Huang LN, Hua ZS, Kuang JL, Li SJ, Shu WS.

ISME J. 2015 Jul;9(7):1579-92. doi: 10.1038/ismej.2014.245. Epub 2014 Dec 23.


Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities.

Justice NB, Pan C, Mueller R, Spaulding SE, Shah V, Sun CL, Yelton AP, Miller CS, Thomas BC, Shah M, VerBerkmoes N, Hettich R, Banfield JF.

Appl Environ Microbiol. 2012 Dec;78(23):8321-30. doi: 10.1128/AEM.01938-12. Epub 2012 Sep 21.


Ecological distribution and population physiology defined by proteomics in a natural microbial community.

Mueller RS, Denef VJ, Kalnejais LH, Suttle KB, Thomas BC, Wilmes P, Smith RL, Nordstrom DK, McCleskey RB, Shah MB, Verberkmoes NC, Hettich RL, Banfield JF.

Mol Syst Biol. 2010 Jun 8;6:374. doi: 10.1038/msb.2010.30.


Metal resistance in acidophilic microorganisms and its significance for biotechnologies.

Dopson M, Holmes DS.

Appl Microbiol Biotechnol. 2014 Oct;98(19):8133-44. doi: 10.1007/s00253-014-5982-2. Epub 2014 Aug 8. Review.


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