1932

Abstract

Knowledge gained from early and recent studies that define the functions of microbial populations within the rumen microbiome is essential to allow for directed rumen manipulation strategies. A large number of omic studies have focused on carbohydrate active enzymes either for improved fiber digestion within the animal or for use in industries such as biofuels. Studies of the rumen microbiome with respect to methane production and abatement strategies have led to initiatives for defining the microbiome of low- and high-methane-emitting animals while ensuring optimal feed conversion. With advances in omic technologies, the ability to link host genetics and the rumen microbiome by studying all the biological components (holobiont) through the use of hologenomics has begun. However, a program to culture and isolate microbial species for the purpose of standard microbial characterization to aid in assigning function to genomic data remains critical, especially for genes of unknown function.

Keyword(s): ecologymethanemicrobiomeomicsxenobiotic
Loading

Article metrics loading...

/content/journals/10.1146/annurev-animal-022114-110705
2015-02-16
2024-12-02
Loading full text...

Full text loading...

/deliver/fulltext/animal/3/1/annurev-animal-022114-110705.html?itemId=/content/journals/10.1146/annurev-animal-022114-110705&mimeType=html&fmt=ahah

Literature Cited

  1. Woese CR. 1987. Bacterial evolution. Microbiol. Rev. 51:221–71 [Google Scholar]
  2. Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. PNAS 74:5463–67 [Google Scholar]
  3. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. PNAS 82:6955–59 [Google Scholar]
  4. Stahl DA, Flesher B, Mansfield HR, Montgomery L. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1079–84 [Google Scholar]
  5. McSweeney CS, Mackie RI, Odenyo AA, Stahl DA. 1993. Development of an oligonucleotide probe targeting 16S rRNA and its application for detection and quantitation of the ruminal bacterium Synergistes jonesii in a mixed-population chemostat. Appl. Environ. Microbiol. 59:1607–12 [Google Scholar]
  6. Lin CZ, Flesher B, Capman WC, Amann RI, Stahl DA. 1994. Taxon specific hybridization probes for fiber-digesting bacteria suggest novel gut-associated Fibrobacter. Syst. Appl. Microbiol. 17:418–24 [Google Scholar]
  7. Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143–69 [Google Scholar]
  8. Yanagita K, Kamagata Y, Kawaharasaki M, Suzuki T, Nakamura Y, Minato H. 2000. Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization. Biosci. Biotechnol. Biochem. 64:1737–42 [Google Scholar]
  9. Tajima K, Nagamine T, Matsui H, Nakamura M, Aminov RI. 2001. Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol. Lett. 200:67–72 [Google Scholar]
  10. Whitford MF, Forster RJ, Beard CE, Gong J, Teather RM. 1998. Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4:153–63 [Google Scholar]
  11. Krause DO, Russell JB. 1996. How many ruminal bacteria are there?. J. Dairy Sci. 79:1467–75 [Google Scholar]
  12. Edwards JE, McEwan NR, Travis AJ, Wallace RJ. 2004. 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie van Leeuwenhoek 86:263–81 [Google Scholar]
  13. Attwood GT, Kelly WJ, Altermann EH, Moon CD, Leahy S, Cookson AL. 2008. Application of rumen microbial genome information to livestock systems in the postgenomic era. Aust. J. Exp. Agric. 48:695–700 [Google Scholar]
  14. Fouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC et al. 2012. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLOS ONE 7:e48289 [Google Scholar]
  15. Henderson G, Cox F, Kittelmann S, Miri VH, Zethof M et al. 2013. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLOS ONE 8:e74787 [Google Scholar]
  16. von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T et al. 2007. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315:1126–30 [Google Scholar]
  17. Henderson G, Naylor GE, Leahy SC, Janssen PH. 2010. Presence of novel, potentially homoacetogenic bacteria in the rumen as determined by analysis of formyltetrahydrofolate synthetase sequences from ruminants. Appl. Environ. Microbiol. 76:2058–66 [Google Scholar]
  18. Denman SE, Tomkins NW, McSweeney CS. 2007. Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol. Ecol. 62:313–22 [Google Scholar]
  19. Gagen EJ, Denman SE, Padmanabha J, Zadbuke S, Al Jassim R et al. 2010. Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach. Appl. Environ. Microbiol. 76:7785–95 [Google Scholar]
  20. Wright A-DG, Williams AJ, Winder B, Christophersen CT, Rodgers SL, Smith KD. 2004. Molecular diversity of rumen methanogens from sheep in Western Australia. Appl. Environ. Microbiol. 70:1263–70 [Google Scholar]
  21. 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. 67:2766–74 [Google Scholar]
  22. Denman SE, McSweeney CS. 2006. Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiol. Ecol. 58:572–82 [Google Scholar]
  23. Sylvester JT, Karnati SK, Yu Z, Morrison M, Firkins JL. 2004. Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. J. Nutr. 134:3378–84 [Google Scholar]
  24. Crosby B, Collier B, Thomas DY, Teather RM, Erfle JD. 1984. Cloning and expression in Escherichia coli of cellulase genes from Bacteroides succinogenes. Fifth Canadian Bioenergy R&D Seminar Hasnain S. 573–76 London: Elsevier Appl. Sci. Publ [Google Scholar]
  25. McGavin MJ, Forsberg CW, Crosby B, Bell AW, Dignard D, Thomas DY. 1989. Structure of the cel-3 gene from Fibrobacter succinogenes S85 and characteristics of the encoded gene product, endoglucanase 3. J. Bacteriol. 171:5587–95 [Google Scholar]
  26. Teather RM, Erfle JD. 1990. DNA sequence of a Fibrobacter succinogenes mixed-linkage β-glucanase (1,3-1,4-β-d-glucan 4-glucanohydrolase) gene. J. Bacteriol. 172:3837–41 [Google Scholar]
  27. Hazlewood GP, Davidson K, Laurie JI, Romaniec MP, Gilbert HJ. 1990. Cloning and sequencing of the celA gene encoding endoglucanase A of Butyrivibrio fibrisolvens strain A46. J. Gen. Microbiol. 136:2089–97 [Google Scholar]
  28. Flint HJ, McPherson CA, Bisset J. 1989. Molecular cloning of genes from Ruminococcus flavefaciens encoding xylanase and β(1-3,1-4)glucanase activities. Appl. Environ. Microbiol. 55:1230–33 [Google Scholar]
  29. Cunningham C, McPherson CA, Martin J, Harris WJ, Flint HJ. 1991. Sequence of a cellulase gene from the rumen anaerobe Ruminococcus flavefaciens 17. Mol. Gen. Genet. 228:320–23 [Google Scholar]
  30. Xue GP, Orpin CG, Gobius KS, Aylward JH, Simpson GD. 1992. Cloning and expression of multiple cellulase cDNAs from the anaerobic rumen fungus Neocallimastix patriciarum in Escherichia coli. J. Gen. Microbiol. 138:1413–20 [Google Scholar]
  31. Xue G-P, Gobius KS, Orpin CG. 1992. A novel polysaccharide hydrolase cDNA (celD) from Neocallimastix patriciarum encoding three multi-functional catalytic domains with high endoglucanase, cellobiohydrolase and xylanase activities. J. Gen. Microbiol. 138:2397–403 [Google Scholar]
  32. Zhou L, Xue GP, Orpin CG, Black GW, Gilbert HJ, Hazlewood GP. 1994. Intronless celB from the anaerobic fungus Neocallimastix patriciarum encodes a modular family A endoglucanase. Biochem. J. 297:Pt. 2359–64 [Google Scholar]
  33. Garcia-Vallvé S, Romeu A, Palau J. 2000. Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol. Biol. Evol 17:352–61 [Google Scholar]
  34. Ricard G, McEwan NR, Dutilh BE, Jouany JP, Macheboeuf D et al. 2006. Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics 7:22 [Google Scholar]
  35. Baar C, Eppinger M, Raddatz G, Simon J, Lanz C et al. 2003. Complete genome sequence and analysis of Wolinella succinogenes. PNAS 100:11690–95 [Google Scholar]
  36. Leahy SC, Kelly WJ, Ronimus RS, Wedlock N, Altermann E, Attwood GT. 2013. Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies. Animal 7:Suppl. 2235–43 [Google Scholar]
  37. Jun HS, Qi M, Ha JK, Forsberg CW. 2007. Fibrobacter succinogenes, a dominant fibrolytic ruminal bacterium: transition to the post genomic era. Asian-Australas. J. Anim. Sci. 20:802–10 [Google Scholar]
  38. Brumm P, Mead D, Boyum J, Drinkwater C, Deneke J et al. 2011. Functional annotation of Fibrobacter succinogenes S85 carbohydrate active enzymes. Appl. Biochem. Biotechnol. 163:649–57 [Google Scholar]
  39. Suen G, Weimer PJ, Stevenson DM, Aylward FO, Boyum J et al. 2011. The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLOS ONE 6:e18814 [Google Scholar]
  40. Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A et al. 2009. Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLOS ONE 4:e6650 [Google Scholar]
  41. Morgavi DP, Kelly WJ, Janssen PH, Attwood GT. 2013. Rumen microbial (meta) genomics and its application to ruminant production. Animal 7:184–201 [Google Scholar]
  42. Youssef NH, Couger MB, Struchtemeyer CG, Liggenstoffer AS, Prade RA et al. 2013. The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl. Environ. Microbiol. 79:4620–34 [Google Scholar]
  43. Kelly WJ, Leahy SC, Altermann E, Yeoman CJ, Dunne JC et al. 2010. The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment. PLOS ONE 5:e11942 [Google Scholar]
  44. Purushe J, Fouts DE, Morrison M, White BA, Mackie RI et al. 2010. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb. Ecol. 60:721–29 [Google Scholar]
  45. Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ et al. 2010. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLOS ONE 5:e8926 [Google Scholar]
  46. Nagar-Anthal KR, Worrell VE, Teal R, Nagle DP. 1996. The pterin lumazine inhibits growth of methanogens and methane formation. Arch. Microbiol. 166:136–40 [Google Scholar]
  47. Poulsen M, Schwab C, Jensen BB, Engberg RM, Spang A et al. 2013. Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat. Commun. 4:1428 [Google Scholar]
  48. Schnoes AM, Brown SD, Dodevski I, Babbitt PC. 2009. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLOS Comput. Biol 5:e1000605 [Google Scholar]
  49. Galperin MY, Koonin EV. 2010. From complete genome sequence to ‘complete’ understanding?. Trends Biotechnol 28:398–406 [Google Scholar]
  50. Dodd D, Moon Y-H, Swaminathan K, Mackie RI, Cann IKO. 2010. Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes. J. Biol. Chem. 285:30261–73 [Google Scholar]
  51. Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D et al. 2005. Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ. Microbiol. 7:1996–2010 [Google Scholar]
  52. Droge J, McHardy AC. 2012. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief. Bioinform. 13:646–55 [Google Scholar]
  53. Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M et al. 2011. Taxonomic metagenome sequence assignment with structured output models. Nat. Methods 8:191–92 [Google Scholar]
  54. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. 2013. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31:533–38 [Google Scholar]
  55. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43 [Google Scholar]
  56. Zhou F, Olman V, Xu Y. 2008. Barcodes for genomes and applications. BMC Bioinform. 9:546 [Google Scholar]
  57. Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC et al. 2009. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. PNAS 106:1948–53 [Google Scholar]
  58. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H et al. 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463–67 [Google Scholar]
  59. Pope PB, Denman SE, Jones M, Tringe SG, Barry K et al. 2010. Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. PNAS 107:14793–98 [Google Scholar]
  60. Pope PB, Smith W, Denman SE, Tringe SG, Barry K et al. 2011. Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 333:646–48 [Google Scholar]
  61. Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E et al. 2011. Snapshot of the eukaryotic gene expression in muskoxen rumen—a metatranscriptomic approach. PLOS ONE 6:e20521 [Google Scholar]
  62. Raes J, Bork P. 2008. Molecular eco-systems biology: towards an understanding of community function. Nat. Rev. Microbiol. 6:693–99 [Google Scholar]
  63. Benson AK, Kelly SA, Legge R, Ma F, Low SJ et al. 2010. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. PNAS 107:18933–38 [Google Scholar]
  64. Goopy JP, Donaldson A, Hegarty R, Vercoe PE, Haynes F et al. 2014. Low-methane yield sheep have smaller rumens and shorter rumen retention time. Br. J. Nutr. 111:578–85 [Google Scholar]
  65. Meng Q, Kerley MS, Ludden PA, Belyea RL. 1999. Fermentation substrate and dilution rate interact to affect microbial growth and efficiency. J. Anim. Sci. 77:206–14 [Google Scholar]
  66. Hegarty RS, Goopy JP, Herd RM, McCorkell B. 2007. Cattle selected for lower residual feed intake have reduced daily methane production. J. Anim. Sci. 85:1479–86 [Google Scholar]
  67. Zhou M, Hernandez-Sanabria E, Guan LL. 2009. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Appl. Environ. Microbiol. 75:6524–33 [Google Scholar]
  68. Carberry CA, Waters SM, Kenny DA, Creevey CJ. 2014. Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet type. Appl. Environ. Microbiol. 80:586–94 [Google Scholar]
  69. Jones RJ. 1981. Does ruminal metabolism of mimosine explain the absence of Leucaena toxicity in Hawaii?. Aust. Vet. J. 57:55–56 [Google Scholar]
  70. Padmanabha J, Halliday JM, Denman SE, Davis CK, Shelton HM, McSweeney CS. 2014. Is there genetic diversity in the ‘leucaena bug’ Synergistes jonesii which may reflect ability to degrade leucaena toxins?. Trop. Grassl. Forrajes Trop. 2:112–15 [Google Scholar]
  71. Graham SR, Dalzell SA, Ngu NT, Davis CK, Greenway D et al. 2013. Efficacy, persistence and presence of Synergistes jonesii in cattle grazing leucaena in Queensland: on-farm observations pre- and post-inoculation. Anim. Prod. Sci. 53:1065–74 [Google Scholar]
  72. Halliday JM, Padmanabha J, McSweeney CS, Kerven G, Shelton HM. 2013. Leucaena toxicity: a new perspective on the most widely used forage tree legume. Trop. Grassl. Forrajes Trop. 1:1–11 [Google Scholar]
  73. Allison MJ, Mayberry WR, McSweeney CS, Stahl DA. 1992. Synergistes jonesii, gen. nov., sp. nov.: a rumen bacterium that degrades toxic pyridinediols. Syst. Appl. Microbiol. 15:522–29 [Google Scholar]
  74. Davis CK, Webb RI, Sly LI, Denman SE, McSweeney CS. 2012. Isolation and survey of novel fluoroacetate-degrading bacteria belonging to the phylum Synergistetes. FEMS Microbiol. Ecol. 80:671–84 [Google Scholar]
  75. Gregg K, Hamdorf B, Henderson K, Kopecny J, Wong C. 1998. Genetically modified ruminal bacteria protect sheep from fluoroacetate poisoning. Appl. Environ. Microbiol. 64:3496–98 [Google Scholar]
  76. Gregg K, Cooper CL, Schafer DJ, Sharpe H, Beard CE et al. 1994. Detoxification of the plant toxin fluoroacetate by a genetically modified rumen bacterium. Biotechnology 12:1361–65 [Google Scholar]
  77. Padmanabha J, Gregg K, McSweeney CS, Prideaux C, Ford M. 2004. Protection of cattle from fluoroacetate poisoning by genetically modified ruminal bacteria. Sci. Access 1:293 [Google Scholar]
  78. Hugenholtz P, Hooper SD, Kyrpides NC. 2009. Focus: Synergistetes. Environ. Microbiol. 11:1327–29 [Google Scholar]
  79. Bell AT, Newton GL, Everist SL, Legg J. 1955. Acacia georginae poisoning of cattle and sheep. Aust. Vet. J. 31:249–57 [Google Scholar]
  80. Baena S, Fardeau M-L, Ollivier B, Labat M, Thomas P et al. 1999. Aminomonas paucivorans gen. nov., sp. nov., a mesophilic, anaerobic, amino-acid-utilizing bacterium. Int. J. Syst. Bacteriol. 49:975–82 [Google Scholar]
  81. Ganesan A, Chaussonnerie S, Tarrade A, Dauga C, Bouchez T et al. 2008. Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum ‘Synergistetes’, isolated from an anaerobic sludge digester. Int. J. Syst. Evol. Microbiol. 58:2003–12 [Google Scholar]
  82. Menes RJ, Muxi L. 2002. Anaerobaculum mobile sp. nov., a novel anaerobic, moderately thermophilic, peptide-fermenting bacterium that uses crotonate as an electron acceptor, and emended description of the genus Anaerobaculum. Int. J. Syst. Evol. Microbiol. 52:157–64 [Google Scholar]
  83. Zavarzina DG, Zhilina TN, Tourova TP, Kuznetsov BB, Kostrikina NA, Bonch-Osmolovskaya EA. 2000. Thermanaerovibrio velox sp. nov., a new anaerobic, thermophilic, organotrophic bacterium that reduces elemental sulfur, and emended description of the genus Thermanaerovibrio. Int. J. Syst. Evol. Microbiol. 50:1287–95 [Google Scholar]
  84. Díaz-Cárdenas C, López G, Patel BKC, Baena S. 2010. Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring. Int. J. Syst. Evol. Microbiol. 60:850–53 [Google Scholar]
  85. Surkov AV, Dubinina GA, Lysenko AM, Glockner FO, Kuever J. 2001. Dethiosulfovibrio russensis sp. nov., Dethiosulfovibrio marinus sp. nov. and Dethiosulfovibrio acidaminovorans sp. nov., novel anaerobic, thiosulfate- and sulfer-reducing bacteria isolated from ‘Thiodendron' sulfer mats in different saline environments. Int. J. Syst. Evol. Microbiol. 51:327–37 [Google Scholar]
  86. Gill HS, Shu Q, Leng RA. 2000. Immunization with Streptococcus bovis protects against lactic acidosis in sheep. Vaccine 18:2541–48 [Google Scholar]
  87. Wright AD, Kennedy P, O'Neill CJ, Toovey AF, Popovski S et al. 2004. Reducing methane emissions in sheep by immunization against rumen methanogens. Vaccine 22:3976–85 [Google Scholar]
  88. Williams YJ, Popovski S, Rea SM, Skillman LC, Toovey AF et al. 2009. A vaccine against rumen methanogens can alter the composition of archaeal populations. Appl. Environ. Microbiol. 75:1860–66 [Google Scholar]
  89. Wedlock DN, Janssen PH, Leahy SC, Shu D, Buddle BM. 2013. Progress in the development of vaccines against rumen methanogens. Animal 7:Suppl. 2244–52 [Google Scholar]
  90. Asanuma N, Hino T. 2000. Activity and properties of fumarate reductase in ruminal bacteria. J. Gen. Appl. Microbiol. 46:119–25 [Google Scholar]
  91. Gregg K, Allen G, Beard C. 1996. Genetic manipulation of rumen bacteria: from potential to reality. Aust. J. Agric. Res. 47:247–56 [Google Scholar]
  92. Gilbert HJ, Hazlewood GP, Laurie JI, Orpin CG, Xue GP. 1992. Homologous catalytic domains in a rumen fungal xylanase: evidence for gene duplication and prokaryotic origin. Mol. Microbiol. 6:2065–72 [Google Scholar]
  93. Xue GP, Denman SE, Glassop D, Johnson JS, Dierens LM et al. 1995. Modification of a xylanase cDNA isolated from an anaerobic fungus Neocallimastix patriciarum for high-level expression in Escherichia coli. J. Biotechnol. 38:269–77 [Google Scholar]
  94. Xue GP, Johnson JS, Bransgrove KL, Gregg K, Beard CE et al. 1997. Improvement of expression and secretion of a fungal xylanase in the rumen bacterium Butyrivibrio fibrisolvens OB156 by manipulation of promoter and signal sequences. J. Biotechnol. 54:139–48 [Google Scholar]
  95. Krause DO, Bunch RJ, Dalrymple BD, Gobius KS, Smith WJ et al. 2001. Expression of a modified Neocallimastix patriciarum xylanase in Butyrivibrio fibrisolvens digests more fibre but cannot effectively compete with highly fibrolytic bacteria in the rumen. J. Appl. Microbiol. 90:388–96 [Google Scholar]
  96. Denman S, Xue GP, Patel B. 1996. Characterization of a Neocallimastix patriciarum cellulase cDNA (celA) homologous to Trichoderma reesei cellobiohydrolase II. Appl. Environ. Microbiol. 62:1889–96 [Google Scholar]
  97. Vercoe PE, Gregg K. 1995. Sequence and transcriptional analysis of an endoglucanase gene from Ruminococcus albus AR67. Anim. Biotechnol. 6:59–71 [Google Scholar]
  98. Dalrymple BP, Cybinski DH, Layton I, McSweeney CS, Xue GP et al. 1997. Three Neocallimastix patriciarum esterases associated with the degradation of complex polysaccharides are members of a new family of hydrolases. Microbiology 143:Pt. 82605–14 [Google Scholar]
  99. McSweeney CS, Dalrymple BP, Gobius KS, Kennedy PM, Krause DO et al. 1999. The application of rumen biotechnology to improve the nutritive value of fibrous feedstuffs: pre- and post-ingestion. Livest. Prod. Sci. 59:265–83 [Google Scholar]
  100. Flint HJ. 1994. Molecular genetics of obligate anaerobes from the rumen. FEMS Microbiol. Lett. 121:259–67 [Google Scholar]
  101. Houle D, Govindaraju DR, Omholt S. 2010. Phenomics: the next challenge. Nat. Rev. Genet. 11:855–66 [Google Scholar]
  102. Alberch P. 1991. From genes to phenotype: dynamical systems and evolvability. Genetica 84:5–11 [Google Scholar]
  103. McSweeney C, Mackie R. 2012. Micro-organisms and ruminant digestion: state of knowledge, trends and future prospects. Backgr. Study Pap. No. 61, FAO Comm. Genet. Resour. Food Agric., Rome
/content/journals/10.1146/annurev-animal-022114-110705
Loading
/content/journals/10.1146/annurev-animal-022114-110705
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error