Comparative evaluation of rumen metagenome community using qPCR and MG-RAST

AMB Express

Volumn 3, Issue , 2013, Pages 1-8

  Nathani, Neelam M ^a,c   Patel, Amrutlal K ^a   Dhamannapatil, Prakash S ^a   Kothari, Ramesh K ^b   Singh, Krishna M ^a   Joshi, Chaitanya G ^a  

^a Chhattisgarh Kamdhenu Vishwa Vidyalaya   (India)

^b Christ College   (India)

^c SAURASHTRA UNIVERSITY   (India)

Author keywords

Bubalus bubalis; Fibrobacter succinogens; Methanomicrobiales; MG RAST; Prevotella bryantii; Real time PCR; Ruminococcus flavefaciens; Selenomonas ruminantium

Indexed keywords

ARTICLE; BUFFALO; DNA EXTRACTION; DNA SEQUENCE; FIBROBACTER SUCCINOGENES; GENETIC DATABASE; METAGENOME; METAGENOMICS; METHANOMICROBIALES; NONHUMAN; PREVOTELLA; PYROSEQUENCING; REAL TIME POLYMERASE CHAIN REACTION; RNA GENE; ROUGHAGE; RUMINANT STOMACH; RUMINOCOCCUS FLAVEFACIENS; SELENOMONAS RUMINANTIUM;

EID: 84887131853     PISSN: None     EISSN: 21910855     Source Type: Journal    
DOI: 10.1186/2191-0855-3-1     Document Type: Article

References (32)

1. Attfield P, Gunasekera T, Boyd A, Deere D, Veal D (1999) Applications of flow cytometry to microbiology of food and beverage industries. Australas Biotechnol 9:159-166
2. Bekele AZ, Koike S, Kobayashi Y (2010) Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis. FEMS Microbiol Lett 305(1):49-57
3. Bryant MP (1959) Bacterial species of the rumen. Bacteriol Rev 23(3):125-153
4. Farrelly V, Rainey FA, Stackebrandt E (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61(7):2798-2801
5. Heid CA, Stevens J, Livak KJ, Williams PM (1996) Real time quantitative PCR. Genome Res 6(10):986-994
6. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18):4765-4774
7. Huijsdens XW, Linskens RK, Mak M, Meuwissen SG, Vandenbroucke-Grauls CM, Savelkoul PH (2002) Quantification of bacteria adherent to gastrointestinal mucosa by real-time PCR. J Clin Microbiol 40(12):4423-4427
8. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72(3):1719-1728
9. Klausegger A, Hell M, Berger A, Zinober K, Baier S, Jones N, Sperl W, Kofler B (1999) Gram type-specific broad-range PCR amplification for rapid detection of 62 pathogenic bacteria. J Clin Microbiol 37(2):464-466
10. Klieve AV, Hennessy D, Ouwerkerk D, Forster RJ, Mackie RI, Attwood GT (2003) Establishing populations of Megasphaera elsdenii YE34 and Butyrivibrio fibrisolvens YE44 in the rumen of cattle fed high grain diets. J Appl Microbiol 95:621-630
11. Koike S, Kobayashi Y (2001) Development and use of competitive PCR assays for the rumen cellulolytic bacteria: fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. FEMS Microbiol Lett 204(2):361-366
12. Langendijk PS, Schut F, Jansen GJ, Raangs GC, Kamphuis GR, Wilkinson MH, Welling GW (1995) Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl Environ Microbiol 61(8):3069-3075
13. Leser TD, Amenuvor JZ, Jensen TK, Lindecrona RH, Boye M, Moller K (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68(2):673-690
14. Lin YH, Chang BC, Chiang PW, Tang SL (2008) Questionable 16S ribosomal RNA gene annotations are frequent in completed microbial genomes. Gene 416(1-2):44-47
15. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Dymock D, Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64(2):795-799
16. McCarthy JE, Brimacombe R (1994) Prokaryotic translation: the interactive pathway leading to initiation. Trends Genet 10(11):402-407
17. McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R (2007) The national microbial pathogen database resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res 35(Database issue): D347-D353
18. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59(3):695-700
19. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33(17):5691-5702
20. Pilajun R, Wanapat M (2012) Microbial population in the rumen of swamp buffalo (Bubalus bubalis) as influenced by coconut oil and mangosteen peel supplementation. J Anim Physiol Anim Nutr (Berl) 97(3):439-445
21. Pryde SE, Richardson AJ, Stewart CS, Flint HJ (1999) Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig. Appl Environ Microbiol 65(12):5372-5377
22. Sahoo B, Saraswat ML, Haque N, Khan MY (2000) Energy balance and methane production in sheep fed chemically treated wheat straw. Small Ruminal Res 35:13-19
23. Shi Y, Weimer PJ (1996) Utilization of individual cellodextrins by three predominant ruminal cellulolytic bacteria. Appl Environ Microbiol 62(3):1084-1088
24. Stevenson DM, Weimer PJ (2007) 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 75(1):165-174
25. Suzuki MT, Taylor LT, DeLong EF (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl Environ Microbiol 66(11):4605-4614
26. Tajima K, Aminov RI, Nagamine T, Matsui H, Nakamura M, Benno Y (2001) Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl Environ Microbiol 67(6):2766-2774
27. Veal DA, Deere D, Ferrari B, Piper J, Attfield PV (2000) Fluorescence staining and flow cytometry for monitoring microbial cells. J Immunol Methods 243(1-2):191-210
28. Vinh NT, Wanapat M, Khejornsart P, Kongmun P (2011) Studies of diversity of rumen microorganisms and fermentation in swamp buffalo fed different diets. J Anim Vet Adv 10(4):406-414
29. von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21(3):213-229
30. Wanapat M, Cherdthong A (2009) Use of real-time PCR technique in studying rumen cellulolytic bacteria population as affected by level of roughage in swamp buffalo. Curr Microbiol 58(4):294-299
31. Wood J, Scott KP, Avgustin G, Newbold CJ, Flint HJ (1998) 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 64(10):3683-3689
32. Zinder SH (1993) Physiological ecology of methanogens. In: Ferry JG (ed) Methanogenesis: ecology, physiology, biochemistry and genetics. Springer, US, pp 128-206 doi:10.1186/2191-0855-3-551