Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China

BMC Microbiology

Volumn 13, Issue 1, 2013, Pages

  Li, Zhi Peng ^a   Liu, Han Lu ^a   Li, Guang Yu ^a   Bao, Kun ^a   Wang, Kai Ying ^a   Xu, Chao ^a   Yang, Yi Feng ^a   Yang, Fu He ^a   Wright, André Denis G ^b  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b UNIVERSITY OF VERMONT   (United States)

Author keywords

Ecology; Fiber; Prevotella; Tannin

Indexed keywords

RNA 16S; TANNIN;

ANIMAL FOOD; ANIMAL TISSUE; ARTICLE; BACTEROIDETES; CERVUS NIPPON; CHINA; CLOSTRIDIUM; DEER; DENATURING GRADIENT GEL ELECTROPHORESIS; EUBACTERIUM; FIBER; FORAGE; GENE LIBRARY; GENE SEQUENCE; MALE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PREVOTELLA; PREVOTELLA RUMINICOLA; PROTEOBACTERIA; RUMEN MICROORGANISM; RUMINANT STOMACH; SUCCINIVIBRIONACEAE;

ANIMALS; BACTERIA; BIOTA; CHINA; CLUSTER ANALYSIS; DIET; DIETARY FIBER; DNA, BACTERIAL; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; RUMEN; RUMINANTS; SEQUENCE ANALYSIS, DNA; TANNINS;

BACTERIA (MICROORGANISMS); BACTEROIDETES; CERVUS NIPPON; CLOSTRIDIUM POPULETI; EUBACTERIUM CELLULOSOLVENS; OTUS; PREVOTELLA; PREVOTELLA ALBENSIS; PREVOTELLA BREVIS; PREVOTELLA RUMINICOLA; PREVOTELLA SALIVAE; PREVOTELLA SHAHII; PREVOTELLA VERORALIS; SUCCINIVIBRIO DEXTRINOSOLVENS; ZEA MAYS;

EID: 84879809899     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-13-151     Document Type: Article

References (57)

1. Effective degradation of tannic acid by immobilized rumen microbes of a sika deer (Cervus nippon yesoensis) in winter. Hiura T, Hashidoko Y, Kobayashi Y, Tahara S, Anim Feed Sci Technol 2010 155 1 1 8 10.1016/j.anifeedsci.2009.09. 015
2. Captive roe deer (Capreolus capreolus) select for low amounts of tannic acid but not quebracho: fluctuation of preferences and potential benefits. Clauss M, Lason K, Gehrke J, Lechner-Doll M, Fickel J, Grune T, Jurgen Streich W, Comp Biochem Physiol B Biochem Mol Biol 2003 136 2 369 382 10.1016/S1096-4959(03)00244-6 14529762 (Pubitemid 38352765)
3. Does the complexity of the rumen microbial ecology preclude methane mitigation? Wright A-DG, Klieve AK, Animal Feed Sci. Technol. 2011 166-167 248 253
4. Rumen bacterial community transition during adaptation to high-grain diet. Tajima K, Arai S, Ogata K, Nagamine T, Matsui H, Nakamura M, Aminov RI, Benno Y, Anaerobe 2000 6 5 273 284 10.1006/anae.2000.0353
5. Prokaryote diversity in the rumen of yak (Bos grunniens) and Jinnan cattle (Bos taurus) estimated by 16S rDNA homology analyses. An DD, Dong XZ, Dong ZY, Anaerobe 2005 11 4 207 215 10.1016/j.anaerobe.2005.02.001 16701570 (Pubitemid 40724527)
6. Diversity and abundance of the bacterial 16S rRNA gene sequences in forestomach of alpacas (Lama pacos) and sheep (Ovis aries). Pei CX, Liu QA, Dong CS, Li HQ, Jiang JB, Gao WJ, Anaerobe 2010 16 4 426 432 10.1016/j.anaerobe. 2010.06.004 20558310
7. Phylogenetic analysis of 16S rRNA gene sequences reveals rumen bacterial diversity in Yaks (Bos grunniens). Yang LY, Chen J, Cheng XL, Xi DM, Yang SL, Deng WD, Mao HM, Mol Biol Rep 2010 37 1 553 562 10.1007/s11033-009-9794-x 19757178
8. Ruminal microbial digestion in free-living, in captive lichen-ded, and in Starved Reindeer (Rangifer tarandus tarandus) in winter. Aagnes TH, Sormo W, Mathiesen SD, Appl Environ Microbiol 1995 61 2 583 591 7574599
9. 16S rDNA library-based analysis of ruminal bacterial diversity. Edwards JE, McEwan NR, Travis AJ, Wallace RJ, Antonie Leeuwenhoek Int J Gen Mol Microbiol 2004 86 3 263 281 (Pubitemid 39517705)
10. Rumen microbes and fermentation of wild sika deer on the Shiretoko peninsula of Hokkaido Island, Japan. Ichimura Y, Yamano H, Takano T, Koike S, Kobayashi Y, Tanaka K, Ozaki N, Suzuki M, Okada H, Yamanaka M, Ecol Res 2004 19 4 389 395 10.1111/j.1440-1703.2004.00649.x (Pubitemid 39059356)
11. Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gradient gel electrophoresis, random sequencing, and statistical ecology approaches. Kocherginskaya SA, Aminov RI, White BA, Anaerobe 2001 7 3 119 134 10.1006/anae.2001.0378 (Pubitemid 32928200)
12. The host species affects the microbial community in the goat rumen. Shi PJ, Meng K, Zhou ZG, Wang YR, Diao QY, Yao B, Lett Appl Microbiol 2008 46 1 132 135 17971095
13. UniFrac: a new phylogenetic method for comparing microbial communities. Lozupone C, Knight R, Appl Environ Microbiol 2005 71 12 8228 8235 10.1128/AEM.71.12.8228-8235.2005 16332807 (Pubitemid 41803949)
14. 16S rDNA analysis of bacterial diversity in three fractions of cow rumen. Cho SJ, Cho KM, Shin EC, Lim WJ, Hong SY, Choi BR, Kang JM, Lee SM, Kim YH, Kim H, et al. J Microbiol Biotechnol 2006 16 1 92 101 (Pubitemid 43256982)
15. Bacterial diversity in the rumen of Gayals (Bos frontalis), Swamp buffaloes (Bubalus bubalis) and Holstein cow as revealed by cloned 16S rRNA gene sequences. Yang SL, Ma SC, Chen J, Mao HM, He YD, Xi DM, Yang LY, He TB, Deng WD, Mol Biol Rep 2010 37 4 2063 2073 10.1007/s11033-009-9664-6 19662514
16. Bacteria and archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Cunha IS, Barreto CC, Costa OYA, Bomfim MA, Castro AP, Kruger RH, Quirino BF, Anaerobe 2011 17 3 118 124 10.1016/j.anaerobe.2011.04.018 21575735
17. Characterization of bovine ruminal epithelial bacterial communities using 16S rRNA sequencing, PCR-DGGE, and qRT-PCR analysis. Li MJ, Zhou M, Adamowicz E, Basarab JA, Guan LL, Vet Microbiol 2012 155 1 72 80 10.1016/j.vetmic.2011.08. 007 21890283
18. Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. Pope PB, Mackenzie AK, Gregor I, Smith W, Sundset MA, McHardy AC, Morrison M, Eijsink VG, PLoS One 2012 7 6 38571 10.1371/journal.pone.0038571 22701672
19. Status of the phylogenetic diversity census of ruminal microbiomes. Kim M, Morrison M, Yu Z, FEMS Microbiol Ecol 2011 76 1 49 63 10.1111/j.1574-6941. 2010.01029.x 21223325
20. Effects of condensed tannins on endoglucanase activity and filter paper digestion by Fibrobacter succinogenes S85. Bae HD, McAllister TA, Yanke J, Cheng KJ, Muir AD, Appl Environ Microbiol 1993 59 7 2132 2138 16348990 (Pubitemid 23205800)
21. Microbial interactions with tannins: nutritional consequences for ruminants. McSweeney CS, Palmer B, McNeill DM, Krause DO, Anim Feed Sci Technol 2001 91 1-2 83 93 (Pubitemid 32515981)
22. Effects of sainfoin (Onobrychis viciifolia Scop.) condensed tannins on growth and proteolysis by four strains of ruminal bacteria. Jones GA, McAllister TA, Muir AD, Cheng KJ, Appl Environ Microbiol 1994 60 4 1374 1378 16349244 (Pubitemid 24113963)
23. The effect of condensed tannins from Lotus corniculatus on the proteolytic activities and growth of rumen bacteria. Min BR, Attwood GT, McNabb WC, Molan AL, Barry TN, Anim Feed Sci Technol 2005 121 1-2 45 58 (Pubitemid 40743096)
24. Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria. Koike S, Yoshitani S, Kobayashi Y, Tanaka K, FEMS Microbiol Lett 2003 229 1 23 30 10.1016/S0378-1097(03)00760-2 14659538 (Pubitemid 37504999)
25. Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Stevenson DM, Weimer PJ, Appl Microbiol Biotechnol 2007 75 1 165 174 10.1007/s00253-006-0802-y 17235560 (Pubitemid 46669229)
26. Novel rumen bacterial diversity in two geographically separated sub-species of reindeer. Sundset MA, Praesteng KE, Cann IK, Mathiesen SD, Mackie RI, Microb Ecol 2007 54 3 424 438 10.1007/s00248-007-9254-x 17473904 (Pubitemid 47554149)
27. Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis. Bekele AZ, Koike S, Kobayashi Y, FEMS Microbiol Lett 2010 305 1 49 57 10.1111/j.1574-6968.2010.01911.x 20158525
28. The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA genes. Wu S, Baldwin RL, Li W, Li C, Connor EE, Li RW, Metagenomics 2012 1 1 11
29. Interaction of ruminal bacteria in the production and utilization of maltooligosaccharides from starch. Cotta MA, Appl Environ Microbiol 1992 58 1 48 54 1539992
30. The cellular location of Prevotella ruminicola beta-1,4-D-endoglucanase and its occurrence in other strains of ruminal bacteria. Gardner RG, Wells JE, Russell JB, Wilson DB, Appl Environ Microbiol 1995 61 9 3288 3292 7574639
31. Phenotypic characterization of polysaccharidases produced by four Prevotella type strains. Matsui H, Ogata K, Tajima K, Nakamura M, Nagamine T, Aminov RI, Benno Y, Curr Microbiol 2000 41 1 45 49 10.1007/s002840010089 10919398 (Pubitemid 30395998)
32. Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, Attwood GT, McSweeney CS, FEMS Microbiol Rev 2003 27 5 663 693 10.1016/S0168-6445(03)00072-X 14638418 (Pubitemid 37456863)
33. Rumen microbial population dynamics during adaptation to a high-grain diet. Fernando SC, Purvis HT, Najar FZ, Sukharnikov LO, Krehbiel CR, Nagaraja TG, Roe BA, DeSilva U, Appl Environ Microbiol 2010 76 22 7482 7490 10.1128/AEM.00388-10 20851965
34. Bacterial diversity dynamics in rumen epithelium of wethers fed forage and mixed concentrate forage diets. Sadet-Bourgeteau S, Martin C, Morgavi DP, Vet Microbiol 2010 146 1-2 98 104 20554126
35. Vitamin B12-dependent propionate production by the ruminal bacterium Prevotella ruminicola 23. Strobel HJ, Appl Environ Microbiol 1992 58 7 2331 2333 1637169
36. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Purushe J, Fouts DE, Morrison M, White BA, Mackie RI, North American Consortium for Rumen B, Coutinho PM, Henrissat B, Nelson KE, Microb Ecol 2010 60 4 721 729 10.1007/s00248-010-9692-8 20585943
37. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA, Nat Rev Microbiol 2008 6 2 121 131 10.1038/nrmicro1817 18180751
38. Propionate precursors and other metabolic intermediates as possible alternative electron acceptors to methanogenesis in ruminal fermentation in vitro. Newbold CJ, Lopez S, Nelson N, Ouda JO, Wallace RJ, Moss AR, Br J Nutr 2005 94 1 27 35 10.1079/BJN20051445 16115329 (Pubitemid 41357806)
39. Molecular diversity of the rumen microbiome of Norwegian Reindeer on natural summer pasture. Sundset M, Edwards J, Cheng Y, Senosiain R, Fraile M, Northwood K, Praesteng KE, Glad T, Mathiesen S, Wright AD, Microb Ecol 2009 57 2 335 348 10.1007/s00248-008-9414-7 18604648
40. Inclusion of novel bacteria in rumen microbiology: need for basic and applied science. Kobayashi Y, Anim Sci J 2006 77 4 375 385 10.1111/j.1740-0929. 2006.00362.x (Pubitemid 44134184)
41. Analyses of the gene and amino acid sequence of the Prevotella (Bacteroides) ruminicola 23 xylanase reveals unexpected homology with endoglucanases from other genera of bacteria. Whitehead TR, Curr Microbiol 1993 27 1 27 33 10.1007/BF01576830 7763664 (Pubitemid 23171629)
42. Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum. Ramsak A, Peterka M, Tajima K, Martin JC, Wood J, Johnston MEA, Aminov RI, Flint HJ, Avgustin G, FEMS Microbiol Ecol 2000 33 1 69 79 10.1111/j.1574-6941.2000.tb00728.x 10922505 (Pubitemid 30462294)
43. Streptococcus caprinus sp. nov, a tannin-resistant ruminal bacterium from feral goats. Brooker JD, O'Donovan LA, Skene I, Clarke K, Blackall L, Muslera P, Lett Appl Microbiol 1994 18 6 313 318 10.1111/j.1472-765X.1994.tb00877.x (Pubitemid 24189047)
44. The tannin-degrading species Streptococcus gallolyticus and Streptococcus caprinus are subjective synonyms. Sly LI, Cahill MM, Osawa R, Fujisawa T, Int J Syst Bacteriol 1997 47 3 893 894 10.1099/00207713-47-3-893 9226925 (Pubitemid 27327792)
45. Isolation from a shea cake digester of a tannin-degrading Streptococcus gallolyticus strain that decarboxylates protocatechuic and hydroxycinnamic acids, and emendation of the species. Chamkha M, Patel BK, Traore A, Garcia JL, Labat M, Int J Syst Evol Microbiol 2002 52 Pt 3 939 944 12054261 (Pubitemid 34591223)
46. Tannic acid resistance in ruminal streptococcal isolates. Goel G, Puniya AK, Singh K, J Basic Microbiol 2005 45 3 243 245 10.1002/jobm.200410517 15900546 (Pubitemid 40850041)
47. Ovine ruminal microbes are capable of biotransforming hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Eaton HL, De Lorme M, Chaney RL, Craig AM, Microb Ecol 2011 62 2 274 286 10.1007/s00248-011-9809-8 21340737
48. Sporanaerobacter acetigenes gen nov., sp. nov., a novel acetogenic, facultatively sulfur-reducing bacterium. Hernandez-Eugenio G, Fardeau ML, Cayol JL, Patel BK, Thomas P, Macarie H, Garcia JL, Ollivierx P, Int J Syst Evol Microbiol 2002 52 Pt 4 1217 1223 12148631 (Pubitemid 34854982)
49. Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater. Chen S, Dong X, Int J Syst Evol Microbiol 2005 55 Pt 6 2257 2261 16280479 (Pubitemid 41646401)
50. Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. LaMontagne MG, Michel FC, Holden PA, Reddy CA, J Microbiol Methods 2002 49 3 255 264 10.1016/S0167-7012(01)00377-3 11869790 (Pubitemid 34183472)
51. 16S/23S rRNA sequencing. Lane DJ, Nucleic acid techniques in bacteria systematics New York: Wiley, Stackebrandt EGM, 1991 115 175
52. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Huber T, Faulkner G, Hugenholtz P, Bioinformatics 2004 20 14 2317 2319 10.1093/bioinformatics/bth226 15073015 (Pubitemid 39341624)
53. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, et al. Nucleic Acids Res 2009 37 141 D145 10.1093/nar/gkn879 19004872
54. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Appl Environ Microbiol 2009 75 23 7537 7541 10.1128/AEM.01541-09 19801464
55. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
56. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 10 2731 2739 10.1093/molbev/msr121 21546353
57. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Muyzer G, de Waal EC, Uitterlinden AG, Appl Environ Microbiol 1993 59 3 695 700 7683183 (Pubitemid 23072343)