Söhngen C, Bunk B, Podstawka A, Gleim D, Overmann J. BacDive--the Bacterial Diversity Metadatabase. Nucleic Acids Res. 2014;42:D592–9.
Article
Google Scholar
Söhngen C, Podstawka A, Bunk B, Gleim D, Vetcininova A, Reimer LC, et al. BacDive – The Bacterial Diversity Metadatabase in 2016. Nucleic Acids Res. 2015;44:D581–5.
Article
Google Scholar
Reimer LC, Söhngen C, Vetcininova A, Overmann J. Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase. J Biotechnol. 2017;261:187–93.
Article
CAS
Google Scholar
Richards MA, Cassen V, Heavner BD, Ajami NE, Herrmann A, Simeonidis E, et al. MediaDB: a database of microbial growth conditions in defined media. PLoS One. 2014;9:e103548.
Article
Google Scholar
Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk H-P, Gophna U, et al. Harnessing the landscape of microbial culture media to predict new organism–media pairings. Nat Commun [Internet]. 2015;6. Available from: https://doi.org/10.1038/ncomms9493
Barberán A, Caceres Velazquez H, Jones S, Fierer N. Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere [Internet]. 2017;2. Available from: https://doi.org/10.1128/mSphere.00237-17
Brbić M, Piškorec M, Vidulin V, Kriško A, Šmuc T, Supek F. The landscape of microbial phenotypic traits and associated genes. Nucleic Acids Res. 2016;44:10074–90.
PubMed
PubMed Central
Google Scholar
Mehta R, Singhal P, Singh H, Damle D, Sharma AK. Insight into thermophiles and their wide-spectrum applications. 3. Biotech. 2016;6:81.
Google Scholar
Wang Q, Cen Z, Zhao J. The survival mechanisms of thermophiles at high temperatures: an angle of omics. Physiology. 2015;30:97–106.
Article
CAS
Google Scholar
Stetter KO. Hyperthermophilic procaryotes. FEMS Microbiol Rev. Blackwell Publishing Ltd. 1996;18:149–58.
Article
CAS
Google Scholar
Boutz DR, Cascio D, Whitelegge J, Perry LJ, Yeates TO. Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. J Mol Biol. 2007;368:1332–44.
Article
CAS
Google Scholar
Bezsudnova EY, Boyko KM, Polyakov KM, Dorovatovskiy PV, Stekhanova TN, Gumerov VM, et al. Structural insight into the molecular basis of polyextremophilicity of short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus. Biochimie. 2012;94:2628–38.
Article
CAS
Google Scholar
Koga Y. Thermal adaptation of the archaeal and bacterial lipid membranes. Archaea. 2012;2012:789652.
Article
Google Scholar
van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, et al. Consistent mutational paths predict eukaryotic thermostability. BMC Evol Biol. 2013;13:7.
Article
Google Scholar
Burra PV, Kalmar L, Tompa P. Reduction in structural disorder and functional complexity in the thermal adaptation of prokaryotes. PLoS One. 2010;5:e12069.
Article
Google Scholar
Sabath N, Ferrada E, Barve A, Wagner A. Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation. Genome Biol Evol. 2013;5:966–77.
Article
Google Scholar
Kampmann M, Stock D. Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling. Nucleic Acids Res. 2004;32:3537–45.
Article
CAS
Google Scholar
Forterre P, Bouthier De La Tour C, Philippe H, Duguet M. Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from archaea to bacteria. Trends Genet. 2000;16:152–4.
Article
CAS
Google Scholar
Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 1998;14:442–4.
Article
CAS
Google Scholar
Counts JA, Zeldes BM, Lee LL, Straub CT, Adams MWW, Kelly RM. Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms. Wiley Interdiscip Rev Syst Biol Med [Internet]. 2017;9. Available from: https://doi.org/10.1002/wsbm.1377
Google Scholar
Swarup A, Lu J, DeWoody KC, Antoniewicz MR. Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8. Metab Eng. 2014;24:173–80.
Article
CAS
Google Scholar
Brumm PJ, Monsma S, Keough B, Jasinovica S, Ferguson E, Schoenfeld T, et al. Complete Genome Sequence of Thermus aquaticus Y51MC23. PLoS One. 2015;10:e0138674.
Article
Google Scholar
Selig M, Xavier KB, Santos H, Schönheit P. Comparative analysis of Embden-Meyerhof and Entner-Doudoroff glycolytic pathways in hyperthermophilic archaea and the bacterium Thermotoga. Arch Microbiol. 1997;167:217–32.
Article
CAS
Google Scholar
Brasen C, Esser D, Rauch B, Siebers B. Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation. Microbiol Mol Biol Rev. 2014;78:89–175.
Article
Google Scholar
Kengen SW, de Bok FA, van Loo ND, Dijkema C, Stams AJ, de Vos WM. Evidence for the operation of a novel Embden-Meyerhof pathway that involves ADP-dependent kinases during sugar fermentation by Pyrococcus furiosus. J Biol Chem. 1994;269:17537–41.
CAS
PubMed
Google Scholar
Ettema TJG, Ahmed H, Geerling ACM, van der Oost J, Siebers B. The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway. Extremophiles. 2008;12:75–88.
Article
CAS
Google Scholar
Cordova LT, Cipolla RM, Swarup A, Long CP, Antoniewicz MR. 13C metabolic flux analysis of three divergent extremely thermophilic bacteria: Geobacillus sp. LC300, Thermus thermophilus HB8, and Rhodothermus marinus DSM 4252. Metab Eng. 2017;44:182–90.
Article
CAS
Google Scholar
Kosuge T, Hoshino T. Lysine is synthesized through the alpha-aminoadipate pathway in Thermus thermophilus. FEMS Microbiol Lett. 1998;169:361–7.
CAS
PubMed
Google Scholar
Lee N-R, Lakshmanan M, Aggarwal S, Song J-W, Karimi IA, Lee D-Y, et al. Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27. Microb Cell Fact. 2014;13:61.
Article
Google Scholar
Oshima T. Unique polyamines produced by an extreme thermophile, Thermus thermophilus. Amino Acids. 2007;33:367–72.
Article
CAS
Google Scholar
Henne A, Brüggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, et al. The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol. Nature Publishing Group;. 2004;22:547.
Article
CAS
Google Scholar
Schäfers C, Blank S, Wiebusch S, Elleuche S, Antranikian G. Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism. Stand Genomic Sci. 2017;12:22.
Article
Google Scholar
Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, et al. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One. 2009;4:e4207.
Article
Google Scholar
Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, et al. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science. 2008;321:1670–3.
Article
CAS
Google Scholar
Fang M, Langman BM, Palmer DRJ. A stable analog of isochorismate for the study of MenD and other isochorismate-utilizing enzymes. Bioorg Med Chem Lett. 2010;20:5019–22.
Article
CAS
Google Scholar
DeCastro M-E, Rodríguez-Belmonte E, González-Siso M-I. Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes. Front Microbiol. 2016;7:1521.
Article
Google Scholar
Cowan DA, Ramond J-B, Makhalanyane TP, De Maayer P. Metagenomics of extreme environments. Curr Opin Microbiol. 2015;25:97–102.
Article
CAS
Google Scholar
Le PT, Makhalanyane TP, Guerrero LD, Vikram S, Van de Peer Y, Cowan DA. Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts. Genome Biol Evol. 2016;8:2737–47.
Article
CAS
Google Scholar
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999;27:29–34.
Article
CAS
Google Scholar
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45:D353–61.
Article
CAS
Google Scholar
Badhai J, Ghosh TS, Das SK. Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha. India. Front Microbiol. 2015;6:1166.
PubMed
Google Scholar
Saxena R, Dhakan DB, Mittal P, Waiker P, Chowdhury A, Ghatak A, et al. Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. Front Microbiol. 2016;7:2123.
Article
Google Scholar
Schomburg I, Jeske L, Ulbrich M, Placzek S, Chang A, Schomburg D. The BRENDA enzyme information system-From a database to an expert system. J Biotechnol. 2017;261:194–206.
Article
CAS
Google Scholar
UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015;43:D204–12.
Article
Google Scholar
Dehouck Y, Folch B, Rooman M. Revisiting the correlation between proteins’ thermoresistance and organisms’ thermophilicity. Protein Eng Des Sel. 2008;21:275–8.
Article
CAS
Google Scholar
da Costa MS, Santos H, Galinski EA. An overview of the role and diversity of compatible solutes in Bacteria and Archaea. Adv Biochem Eng Biotechnol. 1998;61:117–53.
CAS
PubMed
Google Scholar
Lamosa P, Burke A, Peist R, Huber R, Liu MY, Silva G, et al. Thermostabilization of proteins by diglycerol phosphate, a new compatible solute from the hyperthermophile Archaeoglobus fulgidus. Appl Environ Microbiol. 2000;66:1974–9.
Article
CAS
Google Scholar
Martins LO, Carreto LS, Da Costa MS, Santos H. New compatible solutes related to Di-myo-inositol-phosphate in members of the order Thermotogales. J Bacteriol. 1996;178:5644–51.
Article
CAS
Google Scholar
Zeldovich KB, Chen P, Shakhnovich EI. Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci U S A. 2007;104:16152–7.
Article
CAS
Google Scholar
Thiel T, Pratte B. Effect on heterocyst differentiation of nitrogen fixation in vegetative cells of the cyanobacterium Anabaena variabilis ATCC 29413. J Bacteriol. 2001;183:280–6.
Article
CAS
Google Scholar
Lundgren MR, Osborne CP, Christin P-A. Deconstructing Kranz anatomy to understand C4 evolution. J Exp Bot. 2014;65:3357–69.
Article
Google Scholar
Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev. 1981;45:316–54.
CAS
PubMed
PubMed Central
Google Scholar
Hiraishi A. Isoprenoid quinones as biomarkers of microbial populations in the environment. J Biosci Bioeng. 1999;88:449–60.
Article
CAS
Google Scholar
Goodacre NF, Gerloff DL, Uetz P. Protein Domains of Unknown Function Are Essential in Bacteria. MBio. 2013;5:e00744–13 – e00744–13.
PubMed
PubMed Central
Google Scholar
Mudgal R, Sandhya S, Chandra N, Srinivasan N. De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. Biol Direct. 2015;10:38.
Article
Google Scholar
Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, et al. Exploration of uncharted regions of the protein universe. PLoS Biol. 2009;7:e1000205.
Article
Google Scholar
Cleveland WS, Grosse E, Shyu WM. Chapter 8, Local regression models. In: Chambers JM, Hastie TJ, editors. Statistical Models in S. Wadsworth & Brooks/Cole; 1992.
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol. 1995;57:1.
Google Scholar
Johnson NL, Kotz S, Kemp AW. Univariate Discrete Distributions, Second Edition. New York: Wiley. p. 237–282.