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Original Articles

Correlation between genomic analyses with metatranscriptomic study reveals various functional pathways of Clostridium sartagoforme AAU1, a buffalo rumen isolate

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Pages 498-507 | Received 20 Feb 2015, Accepted 03 Aug 2015, Published online: 25 Oct 2015

References

  • Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 9:75–99. doi: 10.1186/1471-2164-9-75
  • Bergman EN. 1990. Energy contributions of volatile fatty acids from the gastrointestinal tract in various species. Physiol Rev. Apr;70:567–590.
  • Bettegowda C, Huang X, Lin J, Cheong I, Kohli M, Szabo SA, Zhang X, Diaz LA, Jr., Velculescu VE, Parmigiani G, et al. 2006. The genome and transcripto mes of the anti-tumor agent Clostridium novyi-NT. Nat Biotechnol. Dec;24:1573–1580. doi: 10.1038/nbt1256
  • Bond DR, Tsai BM, Russell JB. 1998. The diversion of lactose carbon through the tagatose pathway reduces the intracellular fructose 1,6-bisphosphate and growth rate of Streptococcus bovis. Appl Microbiol Biotechnol. May;49:600–605. doi: 10.1007/s002530051220
  • Cunin R, Glansdorff N, Pierard A, Stalon V. 1986. Biosynthesis and metabolism of arginine in bacteria. Microbiol Rev. Sep;50:314–352.
  • Dabrowski S, Zablotna E, Pietrewicz-Kubicz D, Dlugolecka A. 2012. Screening of environmental samples for bacteria producing 1,3-propanediol from glycerol. Acta Biochim Pol. 59:353–356.
  • Dineen SS, McBride SM, Sonenshein AL. 2010. Integration of metabolism and virulence by Clostridium difficile CodY. J Bacteriol. Oct;192:5350–5362. doi: 10.1128/JB.00341-10
  • Dineen SS, Villapakkam AC, Nordman JT, Sonenshein AL. 2007. Repression of Clostridium difficile toxin gene expression by CodY. J Mol Microbiol. Oct;66:206–219. doi: 10.1111/j.1365-2958.2007.05906.x
  • Drancourt M, Raoult D. 2005. Sequence-based identification of new bacteria: a proposition for creation of an orphan bacterium repository. J Clin Microbiol. Sep;43:4311–4315. doi: 10.1128/JCM.43.9.4311-4315.2005
  • Ghanem FM, Ridpath AC, Moore WE, Moore LV. 1991. Identification of Clostridium botulinum, Clostridium argentinense, and related organisms by cellular fatty acid analysis. J Clin Microbiol. Jun;29:1114–1124.
  • Hristov AN, Callaway TR, Lee C, Dowd SE. 2012. Rumen bacterial, archaeal, and fungal diversity of dairy cows in response to ingestion of lauric or myristic acid. J Anim Sci. Dec;90:4449–4457. doi: 10.2527/jas.2011-4624
  • Huang WM. 1996. Bacterial diversity based on type II DNA topoisomerase genes. Annu Rev Genet. 30:79–107. doi: 10.1146/annurev.genet.30.1.79
  • Hungate RE. 1957. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol. Mar;3:289–311. doi: 10.1139/m57-034
  • Hungate RE. 1966. In the rumen and its microbes. New York: Academic Press; p.  533.
  • Kemperman R, Jonker M, Nauta A, Kuipers OP, Kok J. 2003. Functional analysis of the gene cluster involved in production of the bacteriocin circularin A by Clostridium beijerinckii ATCC 25752. Appl Environ Microbiol. Oct;69:5839–5848. doi: 10.1128/AEM.69.10.5839-5848.2003
  • Kim P. 2004. Current studies on biological tagatose production using L-arabinose isomerase: a review and future perspective. Appl Microbiol Biotechnol. Aug;65:243–249.
  • Kopecny J, Hodrova B, Stewart CS. 1996. The isolation and characterization of a rumen chitinolytic bacterium. Lett Appl Microbiol. Sep;23:195–198. doi: 10.1111/j.1472-765X.1996.tb00063.x
  • Krieg NR, Holt JG, Sneath PHA, Staley JT, Williams ST. 1994. Bergey's manual of determinative bacteriology. 9th ed. Baltimore (MD): Williams & Wilkins.
  • Lewis VJ, Moss CW, Jones WL. 1967. Determination of volatile acid production of Clostridium by gas chromatography. Can J Microbiol. Aug;13:1033–1040. doi: 10.1139/m67-138
  • Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. Jan;42:D490–D495. doi: 10.1093/nar/gkt1178
  • Muniz S, Lacarta J, Pata MP, Jimenez JJ, Navarro E. 2014. Analysis of the diversity of substrate utilisation of soil bacteria exposed to Cd and earthworm activity using generalised additive models. Plos One. 9:e85057. doi: 10.1371/journal.pone.0085057
  • Nathani NM, Duggirala SM, Bhatt VD, KaPatel J, Joshi CG. 2014. Genomic analysis of a novel strain of Bacillus nealsonii, isolated from Surti buffalo rumen. Adv Biosci Biotechnol. 5:235–245. doi: 10.4236/abb.2014.53030
  • Nolling J, Breton G, Omelchenko MV, Makarova KS, Zeng Q, Gibson R, Lee HM, Dubois J, Qiu D, Hitti J, et al. 2001. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol. Aug;183:4823–4838. doi: 10.1128/JB.183.16.4823-4838.2001
  • Orpin CG. 1975. Studies on the rumen flagellate Neocallimastix frontalis. J Gen Microbiol. Dec;91:249–262. doi: 10.1099/00221287-91-2-249
  • Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC. 2010. CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database. Glycobiology. Dec;20:1574–1584. doi: 10.1093/glycob/cwq106
  • Seedorf H, Fricke WF, Veith B, Bruggemann H, Liesegang H, Strittmatter A, Miethke M, Buckel W, Hinderberger J, Li F, et al. 2008. The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci USA. Feb 12;105:2128–2133.
  • Sergeant MJ, Constantinidou C, Cogan TA, Bedford MR, Penn CW, Pallen MJ. 2014. Extensive microbial and functional diversity within the chicken cecal microbiome. Plos One. 9:e91941. doi: 10.1371/journal.pone.0091941
  • Shaw DR. 1962. Pyrophosphorolysis and enzymic synthesis of cytidine diphosphate glycerol and cytidine diphosphate ribitol. Biochem J. Feb;82:297–312. doi: 10.1042/bj0820297
  • Simunek J, Hodrova B, Bartonova H, Kopecny J. 2001. Chitinolytic bacteria of the mammal digestive tract. Folia Microbiol. 46:76–78. doi: 10.1007/BF02825892
  • Smuts HE, Lastovica AJ. 2011. Molecular characterization of the 16S rRNA gene of Helicobacter fennelliae isolated from stools and blood cultures from paediatric patients in South Africa. J Pathog. 2011:1–9. doi: 10.4061/2011/217376
  • Sonenshein AL. 2007. Control of key metabolic intersections in Bacillus subtilis. Nat Rev Microbiol. Dec;5:917–927. doi: 10.1038/nrmicro1772
  • Stevens L. 1970. The biochemical role of naturally occurring polyamines in nucleic acid synthesis. Biol Rev Camb Philos Soc. Feb;45:1–25. doi: 10.1111/j.1469-185X.1970.tb01073.x
  • Stutz HE, Quixley KW, McMaster LD, Reid SJ. 2007. Co-regulation of the nitrogen-assimilatory gene cluster in Clostridium saccharobutylicum. Microbiology. Sep;153:3081–3090. doi: 10.1099/mic.0.2007/005371-0
  • Sutcliffe IC, Russell RR. 1995. Lipoproteins of gram-positive bacteria. J Bacteriol. Mar;177:1123–1128.
  • Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. Aug;24:1596–1599. doi: 10.1093/molbev/msm092
  • Yu PL, Hodge RA, Li XP. 1990. In vitro expression of Lac-PTS and tagatose 1,6-bisphosphate aldolase genes from Lactococcus lactis subsp. cremoris plasmid pDI-21. Appl Microbiol Biotechnol. Sep;33:677–679. doi: 10.1007/BF00604936

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