Functional characterization reveals novel putative coding sequences in prevotella ruminicola genome extracted from rumen metagenomic studies

Journal of Molecular Microbiology and Biotechnology

Volumn 25, Issue 4, 2015, Pages 292-299

  Nathani, Neelam M ^a,b   Kothari, Ramesh K ^a   Patel, Amrutlal K ^b   Joshi, Chaitanya G ^b  

^a SAURASHTRA UNIVERSITY   (India)

^b Chhattisgarh Kamdhenu Vishwa Vidyalaya   (India)

Author keywords

Bacteroidetes; Carbohydrate active enzymes; Glycoside hydrolases; Prevotella ruminicola; Rumen microbiome

Indexed keywords

AMINO ACID DERIVATIVE; ARABINOGALACTAN; CARBOHYDRATE; CARBOXYLESTERASE; ENZYME; GLYCOSIDASE; GLYCOSYLTRANSFERASE; MONOSACCHARIDE; OLIGOSACCHARIDE; POLYSACCHARIDE LYASE; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; BOVINE; BUFFALO; CARBOHYDRATE METABOLISM; DNA BASE COMPOSITION; GENE SEQUENCE; HIGH FIBER DIET; HOST RANGE; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; PREVOTELLA RUMINICOLA; RUMEN MICROORGANISM; RUMINANT STOMACH; TAXONOMY; ANIMAL; BACTERIUM; CLASSIFICATION; ENZYMOLOGY; GENETICS; INTESTINE FLORA; ISOLATION AND PURIFICATION; MICROBIOLOGY; OPEN READING FRAME; PHYLOGENY; RUMEN;

ANIMALS; BACTERIA; BACTERIAL PROTEINS; BUFFALOES; CATTLE; GASTROINTESTINAL MICROBIOME; GENOME, BACTERIAL; METAGENOMICS; OPEN READING FRAMES; PHYLOGENY; PREVOTELLA RUMINICOLA; RUMEN;

EID: 84940668270     PISSN: 14641801     EISSN: 16602412     Source Type: Journal    
DOI: 10.1159/000437265     Document Type: Article

References (45)

1. Avgustin G, Wallace RJ, Flint H. Phenotypic diversity among ruminal isolates of Prevotella ruminicola: proposal of Prevotella brevis sp nov, Prevotella bryantii sp nov, and Prevotella albensis sp nov. and redefinition of Prevotella ruminicola. Int J Syst Bacteriol. 1997; 47: 484-488.
2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9: 75.
3. Bekele AZ, Koike S, Kobayashi Y. Genetic diversity and diet specificity of ruminal Prevotella revealed by. 16S rRNA gene-based analysis. FEMS Microbiol Lett. 2010; 305: 49-57.
4. Carr R, Shen-Orr SS, Borenstein E. Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PLoS Comput Biol. 2013; 9:e1003292.
5. Edwards J, McEwan N, Travis A, John Wallace R: 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie van Leeuwenhoek. 2004; 86: 263-281.
6. Fernando SC, Purvis HT, 2nd, Najar FZ, Sukharnikov LO, Krehbiel CR, Nagaraja TG, Roe BA, Desilva U. Rumen microbial population dynamics during adaptation to a highgrain diet. Appl Environ Microbiol. 2010; 76: 7482-7490.
7. Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM. The" most wanted" taxa from the human microbiome for whole genome sequencing. PloS One. 2012; 7:e41294.
8. Gruninger RJ, Sensen CW, McAllister TA, Forster RJ. Diversity of rumen bacteria in Canadian cervids. PloS One. 2014; 9:e89682.
9. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011; 331: 463-467.
10. Jami E, White BA, Mizrahi I. Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency. PloS One. 2014; 9:e85423.
11. Johnson EA, Reeses ET, Demain AL. Inhibition of Clostridium thermocellum cellulase by end products of cellulolysis. J Appl Biochem. 1982; 4: 8.
12. Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe SG, Bruce DC, Richardson PM, Lidstrom ME, Chistoserdova L. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. 2008; 26: 1029-1034.
13. Klieve AV, Bauchop T. Morphological diversity of ruminal bacteriophages from sheep and cattle. Appl Environ Microbiol. 1988; 54: 1637-1641.
14. Koike S, Kobayashi Y. Fibrolytic rumen bacteria: their ecology and function. Asian Aust J Anim Sci. 2009; 22: 131-138.
15. Koike S, Yoshitani S, Kobayashi Y, Tanaka K. Phylogenetic analysis of fiber-Associated rumen bacterial community and PCR detection of uncultured bacteria. FEMS Microbiol Lett. 2003; 229: 23-30.
16. Kong Y, Teather R, Forster R. Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages. FEMS Microbiol Ecol. 2010; 74: 612-622.
17. Konstantinidis KT, Braff J, Karl DM, DeLong EF. Comparative metagenomic analysis of a microbial community residing at a depth of. 4,000 meters at station ALOHA in the North Pacific subtropical gyre. Appl Environ Microbiol. 2009; 75: 5345-5355.
18. Lu G, Jiang L, Helikar RM, Rowley TW, Zhang L, Chen X, Moriyama EN. GenomeBlast: A web tool for small genome comparison. BMC Bioinformatics. 2006; 7(suppl. 4):S18.
19. Mannarelli BM, Ericsson LD, Stack RJ. Taxonomic relationships among strains of the anaerobic bacterium Bacteroides ruminicola determined by DNA and extracellular polysaccharide analysis. Appl Environ Microbiol. 1991; 57: 2975-2980.
20. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, Mc-Kenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005; 437: 376-380.
21. Martin J, Sykes S, Young S, Kota K, Sanka R, Sheth N, Orvis J, Sodergren E, Wang Z, Weinstock GM, Mitreva M. Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PloS One. 2012; 7:e36427.
22. McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R. Analysis Tool Web Services from the EMBL-EBI. Nucleic Acids Res. 2013; 41:W597-W600.
23. Meyer F, Paarmann D, D"Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. The metagenomics RAST Server - A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008; 9: 386.
24. Morvan B, Bonnemoy F, Fonty G, Gouet P. Quantitative determination of H2-utilizing acetogenic and sulfate-reducing bacteria and methanogenic archaea from digestive tract of different mammals. Curr Microbiol. 1996; 32: 129-133.
25. Nathani NM, Patel AK, Dhamannapatil PS, Kothari RK, Singh KM, Joshi CG. Comparative evaluation of rumen metagenome community using qPCR and MG-RAST. AMB Express. 2013; 3: 55.
26. Osborne JM, Dehority BA. Synergism in degradation and utilization of intact forage cellulose, hemicellulose, and pectin by three pure cultures of ruminal bacteria. Appl Environ Microbiol. 1989; 55: 2247-2250.
27. Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC. CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-Active enzymes in a newly sequenced organism using CAZy database. Glycobiology. 2010; 20: 1574-1584.
28. Parmar NR, Solanki JV, Patel AB, Shah TM, Patel AK, Parnerkar S, Kumar JI, Joshi CG. Metagenome of Mehsani buffalo rumen microbiota: an assessment of variation in feed-dependent phylogenetic and functional classification. J Mol Microbiol Biotechnol. 2014; 24: 249-261.
29. Patel V, Patel AK, Parmar NR, Patel AB, Reddy B, Joshi CG. Characterization of the rumen microbiome of Indian Kankrej cattle (Bos indicus) adapted to different forage diet. Appl Microbiol Biotechnol. 2014; 98: 9749-9761.
30. Purushe J, Fouts DE, Morrison M, White BA, Mackie RI, Coutinho PM, Henrissat B, Nelson KE. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb Ecol. 2010; 60: 721-729.
31. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Jian M, Zhou Y, Li Y, Zhang X, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010; 464: 59-65.
32. Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT. Accurate determination of microbial diversity from. 454 pyrosequencing data. Nat Methods. 2009; 6: 639-641.
33. Ramsak A, Peterka M, Tajima K, Martin JC, Wood J, Johnston EA, Aminov RI, Flint JH, Avgustin G. Unraveling the genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiol Ecol. 2000; 33: 69-79.
34. Rice P, Longden I, Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000; 16: 276-277.
35. Scheifinger CC, Wolin MJ. Propionate formation from cellulose and soluble sugars by combined cultures of Bacteroides succinogenes and Selenomonas ruminantium . Appl Microbiol. 1973; 26: 789-795.
36. Shi Y, Weimer PJ. Utilization of individual cellodextrins by three predominant ruminal cellulolytic bacteria. Appl Environ Microbiol. 1996; 62: 1084-1088.
37. Singh KM, Ahir VB, Tripathi AK, Ramani UV, Sajnani M, Koringa PG, Jakhesara S, Pandya PR, Rank DN, Murty DS, Kothari RK, Joshi CG. Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study. Mol Biol Rep. 2012; 39: 4841-4848.
38. Stevenson DM, Weimer PJ. Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-Time PCR. Appl Microbiol Biotechnol. 2007; 75: 165-174.
39. Storm E, Orskov ER. The nutritive value of rumen micro-organisms in ruminants. 1. Large-scale isolation and chemical composition of rumen micro-organisms. Br J Nutr. 1983; 50: 463-470.
40. Sundset MA, Praesteng KE, Cann IK, Mathiesen SD, Mackie RI. Novel rumen bacterial diversity in two geographically separated sub-species of reindeer. Microb Ecol. 2007; 54: 424-438.
41. Van Gylswyk NO. Enumeration and presumptive identification of some functional groups of bacteria in the rumen of dairy cows fed grass-silage based diets. FEMS Microbiol Ecol. 1990; 73: 243-254.
42. Wanapat M, Cherdthong A. Use of real-Time PCR technique in studying rumen cellulolytic bacteria population as affected by level of roughage in swamp buffalo. Curr Microbiol. 2009; 58: 294-299.
43. Whitford MF, Forster RJ, Beard CE, Gong J, Teather RM. Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned. 16S rRNA genes. Anaerobe. 1998; 4: 153-163.
44. Williams AG, Withers SE, Coleman GS. Glycoside hydrolases of rumen bacteria and protozoa. Curr Microbiol. 1984; 10: 7.
45. Wood J, Scott KP, Avgustin G, Newbold CJ, Flint HJ. Estimation of the relative abundance of different Bacteroides and Prevotella ribotypes in gut samples by restriction enzyme profiling of PCR-Amplified. 16S rRNA gene sequences. Appl Environ Microbiol. 1998; 64: 3683-3689.