Skip to main content
SpringerLink
Log in

Microbiomes Associated with Animals: Implications for Livestock and Animal Production

  • Chapter
  • First Online:
The Brazilian Microbiome

Abstract

The Brazilian fauna is very diverse and domestic ruminants (cattle, sheep, goats, and buffalos) are particularly important to Brazil’s economy. Ruminants have developed a symbiotic relationship with anaerobic microorganisms, being able to convert fibrous plant materials into food products useful for human consumption, such as meat and milk. Analysis of the animal gut microbiome using next-generation sequencing studies suggests that the diversity and composition of the microbial communities co-diversified with their hosts, being influenced by diet composition, host genetics, geographical location, and environmental factors. Here we present an overview of the microbiome studies performed in the ruminant livestock of Brazil and discuss how the symbiotic relationship between ruminants and their microbes can affect the host productivity.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. SECOM (2012) Biodiversity in Brazil. Hyderabad, India

    Google Scholar 

  2. Brazil—Ministry of the Environment. Secretariat of Biodiversity and Forests—SBF (2015) Fifth National Report to the Convention on Biological Diversity: Brazil. Brasília

    Google Scholar 

  3. Instituto Brasileiro de Geografia e Estatística (IBGE)– (2015) Pesquisa da Pecuária Municipal 2013–2014. Rio de Janeiro: IBGE

    Google Scholar 

  4. Carnes A-AB das IE de (2015) Rebanho Bovino Brasileiro. http://www.abiec.com.br/3_rebanho.asp. Accessed 9 Apr 2016

  5. Bezerra LR, Sarmento JLR, Neto SG, de Paula NRO, Oliveira RL, do Rêgo WMF (2013) Residual feed intake: A nutritional tool for genetic improvement. Trop Anim Health Prod 45:1649–1661

    Article  PubMed  Google Scholar 

  6. Basarab JA, Beauchemin KA, Baron VS, Ominski KH, Guan LL, Miller SP, Crowley JJ (2013) Reducing GHG emissions through genetic improvement for feed efficiency: effects on economically important traits and enteric methane production. Animal 7(Suppl 2):303–315

    Article  PubMed  PubMed Central  Google Scholar 

  7. Jewell KA, CA MC, Odt CL, Weimer PJ, Suen G (2015) Ruminal bacterial community composition in dairy cows is dynamic over the course of two lactations and correlates with feed efficiency. Appl Environ Microbiol 81:4697–4710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Myer PR, Smith TPL, Wells JE, Kuehn LA, Freetly HC (2015) Rumen microbiome from steers differing in feed efficiency. PLoS One. doi:10.1371/journal.pone.0129174

  9. Jami E, White BA, Mizrahi I (2014) Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency. PLoS One. doi: 10.1371/journal.pone.0085423

  10. Mackie RI (2002) Mutualistic fermentative digestion in the gastrointestinal tract: diversity and evolution. Integr Comp Biol 42:319–326

    Article  PubMed  Google Scholar 

  11. Sender R, Fuchs S, Milo R (2016) Revised estimates for the number of human and bacteria cells in the body. bioRxiv 1–21

    Google Scholar 

  12. Moya A, Ferrer M (2016) Functional redundancy-induced stability of gut microbiota subjected to disturbance. Trends Microbiol. doi:10.1016/j.tim.2016.02.002

  13. Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332:970–974

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Modi SR, Collins JJ, Relman DA (2014) Antibiotics and the gut microbiota. J Clin Invest 124:4212–4218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Sankar SA, Lagier JC, Pontarotti P, Raoult D, Fournier PE (2015) The human gut microbiome, a taxonomic conundrum. Syst Appl Microbiol 38:276–286

    Article  CAS  PubMed  Google Scholar 

  16. Rosenberg E, Zilber-Rosenberg I (2016) Microbes drive evolution of animals and plants: the hologenome. MBio 7:1–8

    Article  Google Scholar 

  17. Zilber-Rosenberg I, Rosenberg E (2008) Role of microorganisms in the evolution of animals and plants: The hologenome theory of evolution. FEMS Microbiol Rev 32:723–735

    Article  CAS  PubMed  Google Scholar 

  18. Douglas AE, Lindsey RL (2016) Holes in the hologenome: Why host-microbial symbioses are not holobionts. MBio 7:1–7

    Google Scholar 

  19. Ley RE, Hamady M, Lozupone C et al (2008) Evolution of mammals and their gut microbes. Science 320:1647–1651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6:776–788

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Russell JB, Baldwin RL (1979) Comparison of substrate affinities among several rumen bacteria: a possible determinant of rumen bacterial competition. Appl Environ Microbiol 37:531–536

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Smith VH (2002) Effects of resource supplies on the structure and function of microbial communities. Antonie van Leeuwenhoek Int J Gen Mol Microbiol 81:99–106

    Article  CAS  Google Scholar 

  23. Mooshammer M, Wanek W, Zechmeister-Boltenstern S, Richter A (2014) Stoichiometric imbalances between terrestrial decomposer communities and their resources: Mechanisms and implications of microbial adaptations to their resources. Front Microbiol 5:1–10

    Article  Google Scholar 

  24. Østman B, Lin R, Adami C (2014) Trade-offs drive resource specialization and the gradual establishment of ecotypes. BMC Evol Biol 14:113

    Article  PubMed  PubMed Central  Google Scholar 

  25. Carbonero F, Oakley BB, Purdy KJ (2014) Metabolic flexibility as a major predictor of spatial distribution in microbial communities. PLoS One. doi: 10.1371/journal.pone.0085105

  26. Székely AJ, Langenheder S (2014) The importance of species sorting differs between habitat generalists and specialists in bacterial communities. FEMS Microbiol Ecol 87:102–112

    Article  PubMed  CAS  Google Scholar 

  27. Matias MG, Combe M, Barbera C, Mouquet N (2012) Ecological strategies shape the insurance potential of biodiversity. Front Microbiol 3:1–9

    Google Scholar 

  28. Rakoff-Nahoum S, Foster KR, Comstock LE (2016) The evolution of cooperation within the gut microbiota. Nature 533:255–259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Flint HJ, Scott KP, Duncan SH, Louis P, Forano E (2012) Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3:289–306

    Article  PubMed  PubMed Central  Google Scholar 

  30. Schink B (2002) Synergistic interactions in the microbial world. Antonie van Leeuwenhoek, Int J Gen Mol Microbiol 81:257–261

    Article  CAS  Google Scholar 

  31. Von Stockar U, Liu JS (1999) Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth. Biochim Biophys Acta—Bioenerg 1412:191–211

    Article  Google Scholar 

  32. Stephen AM, Cummings JH (1980) Mechanism of action of dietary fibre in the human colon. Nature 284:283–284

    Article  CAS  PubMed  Google Scholar 

  33. Colucci PE, Chase LE, Van Soest PJ (1982) Feed intake, apparent diet digestibility, and rate of particulate passage in dairy cattle. J Dairy Sci 65:1445–1456

    Article  Google Scholar 

  34. Malys MK, Campbell L, Malys N (2015) Symbiotic and antibiotic interactions between gut commensal microbiota and host immune system. Medicina 51:69–75

    Article  PubMed  Google Scholar 

  35. Kalmokoff ML, Bartlett F, Teather RM (1996) Are ruminal bacteria armed with bacteriocins? J Dairy Sci 79:2297–2308

    Article  CAS  PubMed  Google Scholar 

  36. Klimenko AI, Matushkin YG, Kolchanov NA, Lashin SA (2016) Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study. BMC Microbiol 16:S10

    Article  CAS  Google Scholar 

  37. Örmälä-Odegrip A-M, Ojala V, Hiltunen T, Zhang J, Bamford JK, Laakso J (2015) Protist predation can select for bacteria with lowered susceptibility to infection by lytic phages. BMC Evol Biol 15:81

    Article  PubMed  PubMed Central  Google Scholar 

  38. Chen H, Athar R, Zheng G, Williams HN (2011) Prey bacteria shape the community structure of their predators. ISME J 5:1314–1322

    Article  PubMed  PubMed Central  Google Scholar 

  39. Koskella B, Brockhurst MA (2014) Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev 38:916–931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Pérez J, Moraleda-Muñoz A, Marcos-Torres FJ, Muñoz-Dorado J (2015) Bacterial predation: 75 years and counting. Environ Microbiol 18:766–779

    Article  Google Scholar 

  41. Briner AE, Barrangou R (2016) Deciphering and shaping bacterial diversity through CRISPR. Curr Opin Microbiol 31:101–108

    Article  CAS  PubMed  Google Scholar 

  42. Jorth P, Whiteley M (2012) An evolutionary link between natural transformation and crispr adaptive immunity. MBio 3:1–7

    Article  CAS  Google Scholar 

  43. Polz MF, Alm EJ, Hanage WP (2013) Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet 29:170–175

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Ley RE, Peterson DA, Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:837–848

    Article  CAS  PubMed  Google Scholar 

  45. Weimer PJ (2015) Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations. Front Microbiol 6:296

    Article  PubMed  PubMed Central  Google Scholar 

  46. Shapira M (2016) Gut microbiotas and host evolution: scaling up symbiosis. Trends Ecol Evol 31:539–549

    Article  PubMed  Google Scholar 

  47. Minato H, Otsuka M, Shirasaka S, Itabashi H, Mitsumori M (1992) Colonization of microorganisms in the rumen of young calves. J Gen Appl Microbiol 38:447–456

    Article  Google Scholar 

  48. Stewart CS, Fonty G, Gouet P (1988) The establishment of rumen microbial communities. Anim Feed Sci Technol 21:69–97

    Article  Google Scholar 

  49. Huws SA, Mayorga OL, Theodorou MK, Onime LA, Kim EJ, Cookson AH, Newbold CJ, Kingston-Smith AH (2013) Successional colonization of perennial ryegrass by rumen bacteria. Lett Appl Microbiol 56:186–196

    Article  CAS  PubMed  Google Scholar 

  50. Hungate RE (1975) The rumen microbial ecosystem. Ann Rev Ecol Syst 6:39–66

    Article  CAS  Google Scholar 

  51. Rey M, Enjalbert F, Combes S, Cauquil L, Bouchez O, Monteils V (2014) Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential. J Appl Microbiol 116:245–257

    Article  CAS  PubMed  Google Scholar 

  52. Fonty G, Gouet P, Jouany JP, Senaud J (1987) Establishmentof the microflora and anerobic fungi in the rumen of lambs. J Gen Microbiol 133:1835–1843

    Google Scholar 

  53. Bryant MP, Small N, Bouma C, Robinson I (1958) Studies on the composition of the ruminal flora and fauna of young calves. J Dairy Sci 41:1747–1767

    Article  Google Scholar 

  54. Li RW, Connor EE, Li C, Baldwin Vi RL, Sparks ME (2012) Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environ Microbiol 14:129–139

    Article  PubMed  CAS  Google Scholar 

  55. Jami E, Israel A, Kotser A, Mizrahi I (2013) Exploring the bovine rumen bacterial community from birth to adulthood. ISME J 7:1069–1079

    Article  PubMed  PubMed Central  Google Scholar 

  56. 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 75:165–174

    Article  CAS  PubMed  Google Scholar 

  57. Kim M, Morrison M, Yu Z (2011) Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol Ecol 76:49–63

    Article  CAS  PubMed  Google Scholar 

  58. Wu S, Baldwin RL, Li W, Li C, Connor EE, Li RW (2012) The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA genes. Metagenomics 1:1–11

    Article  Google Scholar 

  59. Warner ACI (1962) Enumeration of rumen micro-organisms. J Gen Microbiol 28:119–128

    Article  CAS  PubMed  Google Scholar 

  60. Callaway TR, Dowd SE, Edrington TS, Anderson RC, Krueger N, Bauer N, Kononoff PJ, Nisbet DJ (2010) Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing. J Anim Sci 88:3977–3983

    Article  CAS  PubMed  Google Scholar 

  61. Hungate RE (1966) The rumen and its microbes. doi: 10.1002/jobm.19690090617

  62. Krause DO, Nagaraja TG, Wright ADG, Callaway TR (2013) Board-invited review: rumen microbiology: leading the way in microbial ecology. J Anim Sci 91:331–341

    Article  CAS  PubMed  Google Scholar 

  63. Kamra DN (2005) Rumen microbial ecosystem. Curr Sci 89:124–135

    CAS  Google Scholar 

  64. Hess M, Sczyrba A, Egan R et al (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463–467

    Article  CAS  PubMed  Google Scholar 

  65. Russell JB (2002) In: James B (ed) Rumen microbiology and its role in ruminant nutrition. Ithaca, NY: Russell Publishing.

    Google Scholar 

  66. Allison MJ (1978) Production of branched chain volatile fatty acids by certain anaerobic bacteria. Appl Environ Microbiol 35:872–877

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Wallace RJ, Atasoglu C, Newbold CJ (1999) Role of peptides in rumen microbial metabolism. Asian-Australas J Anim Sci 12:139–147

    Article  CAS  Google Scholar 

  68. Chen G, Russell JB (1989) More monensin-sensitive, ammonia producing bacteria from the rumen. Appl Environ Microbiol 55:1052–1057

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Russell JB, Strobel HJ, Chen GJ (1988) Enrichment and isolation of a ruminal bacterium with a very high specific activity of ammonia production. Appl Environ Microbiol 54:872–877

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Krause DO, Russell JB (1996) An rRNA approach for assessing the role of obligate amino acid-fermenting bacteria in ruminal amino acid degradation. Appl Environ Microbiol 62:815–821

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Bento CBP, de Azevedo AC, Detmann E, Mantovani HC (2015) Biochemical and genetic diversity of carbohydrate-fermenting and obligate amino acid-fermenting hyper-ammonia-producing bacteria from Nelore steers fed tropical forages and supplemented with casein. BMC Microbiol 15:28

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  72. Dehority BA (1969) Pectin fermenting bacteria isolated from the bovine rumen. J Bacteriol 99:189–196

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Mackie RI, Gilchrist FMC, Heath S (1984) An in vivo study of ruminal microorganisms influencing lactate turnover and its contribution to volatile fatty acid production. J Agric Sci Camb 103:37–51

    Article  CAS  Google Scholar 

  74. Henderson G, Cox F, Ganesh S, Jonker A, Young W, Janssen PH (2015) Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 5:14567

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Petri RM, Schwaiger T, Penner GB, Beauchemin KA, Forster RJ, McKinnon JJ, McAllister TA (2013) Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge. PLoS One 8:e83424

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  76. Santra A, Karim SA (2002) Influence of ciliate protozoa on biochemical changes and hydrolytic enzyme profile in the rumen ecosystem. J Appl Microbiol 92:801–811

    Article  CAS  PubMed  Google Scholar 

  77. Roger V, Grenet E, Jamot J, Bernalier A, Fonty G, Gouet P (1992) Degradation of maize stem by two rumen fungal species, Piromyces communis and Caecomyces communis, in pure cultures or in association with cellulolytic bacteria. Reprod Nutr Dev 32:321–329

    Article  CAS  PubMed  Google Scholar 

  78. Akin DE, Rigsby LL (1987) Mixed fungal populations and lignocellulosic tissue degradation in the bovine rumen. Appl Environ Microbiol 53:1987–1995

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Akin DE, Borneman WS (1990) Role of rumen fungi in fiber degradation. J Dairy Sci 114:3023–3032

    Article  Google Scholar 

  80. Theodorou MK, Mennim G, Davies DR, Zhu WY, Trinci a P, Brookman JL (1996) Anaerobic fungi in the digestive tract of mammalian herbivores and their potential for exploitation. Proc Nutr Soc 55:913–926

    Article  CAS  PubMed  Google Scholar 

  81. Klieve A V, Swain RA (1993) Estimation of ruminal bacteriophage numbers by pulsed-field gel electrophoresis and laser densitometry. Appl Environ Microbiol 59:2299–2303

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Swain RA, Nolan JV, Klieve AV (1996) Natural variability and diurnal fluctuations within the bacteriophage population of the rumen. Appl Environ Microbiol 62:994–997

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Klieve AV, Hegarty RS (1999) Opportunities for biological control of ruminal methanogenesis. Aust J Agric Res 50:1315–1319

    Article  Google Scholar 

  84. Ross EM, Petrovski S, Moate PJ, Hayes BJ (2013) Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle. BMC Microbiol 13:242

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  85. Instituto Brasileiro de Geografia e Estatística (IBGE) (2015) Produção da Pecuária Municipal 2014. Inst Bras Geogr e Estatística (IBGE). doi: ISSN 0101–4234

    Google Scholar 

  86. Cunha IS, Barreto CC, Costa OYA, Bomfim MA, Castro AP, Kruger RH, Quirino BF (2011) Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Anaerobe 17:118–124

    Article  PubMed  Google Scholar 

  87. Pfister JA, Malechek JC (1986) The voluntary forage intake and nutrition of goats and sheep in the semi-arid tropics of northeastern Brazil. J Anim Sci 63:1078–1086

    Article  CAS  PubMed  Google Scholar 

  88. Pimentel JCM, Filho JA de A, Júnior D do N, Crispim SMA, S e SSM d (1992) Composição botânica da dieta de ovinos em área de Caatinga raleada no Sertão do Ceará. Revista da Soc Bras Zootec 21:211–223

    Google Scholar 

  89. Lopes LD, de Souza Lima AO, Taketani RG, Darias P, da Silva LRF, Romagnoli EM, Louvandini H, Abdalla AL, Mendes R (2015) Exploring the sheep rumen microbiome for carbohydrate-active enzymes. Antonie Van Leeuwenhoek 108:15–30

    Article  CAS  PubMed  Google Scholar 

  90. Agrawal AR, Karim SA, Kumar R, Sahoo A, John PJ (2014) Review article sheep and goat production: basic differences, impact on climate and molecular tools for rumen microbiome study. PLoS One 3:684–706

    Google Scholar 

  91. Shi PJ, Meng K, Zhou ZG, Wang YR, Diao QY, Yao B (2008) The host species affects the microbial community in the goat rumen. Lett Appl Microbiol 46:132–135

    CAS  PubMed  Google Scholar 

  92. Lee HJ, Jung JY, YK O, Lee SS, Madsen EL, Jeon CO (2012) Comparative survey of rumen microbial communities and metabolites across one caprine and three bovine groups, using bar-coded pyrosequencing and 1H nuclear magnetic resonance spectroscopy. Appl Environ Microbiol 78:5983–5993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Cheng YF, Mao SY, Liu JX, Zhu WY (2009) Molecular diversity analysis of rumen methanogenic Archaea from goat in eastern China by DGGE methods using different primer pairs. Lett Appl Microbiol 48:585–592

    Article  CAS  PubMed  Google Scholar 

  94. Brulc JM, Antonopoulos DA, Miller ME et al (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA 106:1948–1953

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, Attwood GT, McSweeney CS (2003) Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiol Rev 27:663–693

    Article  CAS  PubMed  Google Scholar 

  96. United States Department of Agriculture (2016) Marketing and Trade Data–2016. http://www.usda.gov/. Accessed 28 Apr 2016

  97. Cabral S, De Campos S, Filho V, Detmann E (2008) Microbial efficiency and ruminal parameters in cattle fed diets based on tropical forage. Revista Bras Zootec 37:919–925

    Article  Google Scholar 

  98. Bento CBP, Azevedo AC, Gomes DI, Batista ED, Rufino LMA, Detmann E, Mantovani HC (2015) Effect of protein supplementation on ruminal parameters and microbial community fingerprint of Nelore steers fed tropical forages. Animal 10:44–54

    Article  PubMed  CAS  Google Scholar 

  99. de Jesus RB, Omori WP, de Lemos EGM, de Souza JAM (2015) Bacterial diversity in bovine rumen by metagenomic 16S rDNA sequencing and scanning electron microscopy. Acta Sci. Anim Sci 37:251–257

    Google Scholar 

  100. de Oliveira MNV, Jewell KA, Freitas FS, Benjamin LA, Tótola MR, Borges AC, Moraes CA, Suen G (2013) Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer. Vet Microbiol 164:307–314

    Article  PubMed  Google Scholar 

  101. Laguardia-Nascimento M, Branco KMGR, Gasparini MR, Giannattasio-Ferraz S, Leite LR, Araujo FMG, Salim AC de M, Nicoli JR, de Oliveira GC, Barbosa-Stancioli EF (2015) Vaginal microbiome characterization of Nelore cattle using metagenomic analysis. PLoS One 10:e0143294

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  102. de Menezes AB, Lewis E, O’Donovan M, O’Neill BF, Clipson N, Doyle EM (2011) Microbiome analysis of dairy cows fed pasture or total mixed ration diets. FEMS Microbiol Ecol 78:256–265

    Article  PubMed  CAS  Google Scholar 

  103. Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, Edrington TS (2008) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8:125

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  104. Shanks OC, Kelty CA, Archibeque S, Jenkins M, Newton RJ, McLellan SL, Huse SM, Sogin ML (2011) Community structures of fecal bacteria in cattle from different animal feeding operations. Appl Environ Microbiol 77:2992–3001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Jami E, Mizrahi I (2012) Composition and similarity of bovine rumen microbiota across individual animals. PLoS One 7:e33306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Ross EM, Moate PJ, Bath CR, Davidson SE, Sawbridge TI, Guthridge KM, Cocks BG, Hayes BJ (2012) High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing. BMC Genet 13:53

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Zoetendal EG, Raes J, Van Den Bogert B et al (2012) The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 6:1415–1426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Canavez FC, Luche DD, Stothard P et al (2012) Genome sequence and assembly of Bos indicus. J Hered 103:342–348

    Article  CAS  PubMed  Google Scholar 

  109. National Research Council (1981) The water buffalo: new prospects for an underutilized animal. Washington, DC National Academy Press.

    Google Scholar 

  110. FAOSTAT. Production, live animals. In: United Nations Food and Agriculture Organization. http://faostat3.fao.org/home/E. Accessed 21 Apr 2016

  111. Franzolin R, St-Pierre B, Northwood K, Wright ADG (2012) Analysis of rumen methanogen diversity in water buffaloes (Bubalus bubalis) under three different diets. Microb Ecol 64:131–139

    Article  CAS  PubMed  Google Scholar 

  112. Singh KM, Ahir VB, Tripathi AK et al (2012) Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study. Mol Biol Rep 39:4841–4848

    Article  CAS  PubMed  Google Scholar 

  113. Singh KM, Jisha TK, Reddy B, Parmar N, Patel A, Patel AK, Joshi CG (2015) Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S rRNA gene pyrosequencing. Mol Biol Rep 42:95–103

    Article  CAS  PubMed  Google Scholar 

  114. Lin B, Henderson G, Zou C, Cox F, Liang X, Janssen PH, Attwood GT (2015) Characterization of the rumen microbial community composition of buffalo breeds consuming diets typical of dairy production systems in Southern China. Anim Feed Sci Technol 207:75–84

    Article  CAS  Google Scholar 

  115. Franzolin R, Wright A-DG (2016) Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems. BMC Res Notes 9:1–5

    Article  CAS  Google Scholar 

  116. Hinsu AT, Parmar NR, Nathani NM, Pandit RJ, Patel AB, Patel AK, Joshi CG (2017) Functional gene profiling through metaRNAseq approach reveals diet-dependent variation in rumen microbiota of buffalo (Bubalus bubalis). Anaerobe 44:106–116

    Article  CAS  PubMed  Google Scholar 

  117. Henderson G, Cox F, Ganesh S, et al (2015) Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep. doi: 10.1038/srep14567

  118. White BA, Lamed R, Bayer EA, Flint HJ (2014) Biomass utilization by gut microbiomes. Annu Rev Microbiol 68:279–296

    Article  CAS  PubMed  Google Scholar 

  119. Ungerfeld EM (2014) Corrigendum: a theoretical comparison between two ruminal electron sinks. Front Microbiol 5:1–15

    Google Scholar 

  120. Weimer PJ, Stevenson DM, Mantovani HC, Man SLC (2010) Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents. J Dairy Sci 93:5902–5912

    Article  CAS  PubMed  Google Scholar 

  121. Mohammed R, Brink GE, Stevenson DM, Neumann AP, Beauchemin KA, Suen G, Weimer PJ (2014) Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay. Front Microbiol 5:1–11

    Article  Google Scholar 

  122. Petri RM, Schwaiger T, Penner GB, Beauchemin KA, Forster RJ, McKinnon JJ, McAllister TA (2013) Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge. PLoS One. doi: 10.1371/journal.pone.0083424

  123. 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 Env Microbiol 80:586–594

    Article  CAS  Google Scholar 

  124. Ransom-Jones E, Jones DL, McCarthy AJ, McDonald JE (2012) The Fibrobacteres: an important phylum of cellulose-degrading bacteria. Microb Ecol 63:267–281

    Article  CAS  PubMed  Google Scholar 

  125. Turnbaugh PJ, Ley RE, MA M, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031

    Article  PubMed  Google Scholar 

  126. Kittelmann S, Pinares-Patiño CS, Seedorf H, Kirk MR, Ganesh S, McEwan JC, Janssen PH (2014) Two different bacterial community types are linked with the low-methane emission trait in sheep. PLoS One 9:1–9

    Article  CAS  Google Scholar 

  127. Tajima S, Ogata K, Nagamine T, Matsui H, Nakamura M, Aminov RI, Benno Y (2000) Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe 6:273–284

    Article  CAS  Google Scholar 

  128. Petri RM, Forster RJ, Yang W, McKinnon JJ, TA MA (2012) Characterization of rumen bacterial diversity and fermentation parameters in concentrate fed cattle with and without forage. J Appl Microbiol 112:1152–1162

    Article  CAS  PubMed  Google Scholar 

  129. Morgavi DP, Kelly WJ, Janssen PH, Attwood GT (2013) Rumen microbial (meta)genomics and its application to ruminant production. Animal, 7 Suppl 1, 184–201. http://doi.org/10.1017/S1751731112000419

  130. Langille M, Zaneveld J, Caporaso JG, et al (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–21

    Google Scholar 

Download references

Acknowledgments

The authors gratefully acknowledge financial support from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; Brasília, Brazil), the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES; Brasília, Brazil), the Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG; Belo Horizonte, Brazil), and the INCT Ciência Animal.

Author information

Authors and Affiliations

  1. Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, Campus UFV, Viçosa, 36570-000, Brazil

    Hilario Cuquetto Mantovani, Déborah Romaskevis Gomes Lopes & Cláudia Braga Pereira Bento

  2. Federal University of Juiz de Fora, Governador Valadares, Brazil

    Marcelo Nagem de Oliveira

Authors
  1. Hilario Cuquetto Mantovani
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Déborah Romaskevis Gomes Lopes
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cláudia Braga Pereira Bento
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Marcelo Nagem de Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hilario Cuquetto Mantovani .

Editor information

Editors and Affiliations

  1. Soil Microbiology Laboratory – Department of Soil Science “Luiz de Queiroz” College of Agriculture, University of São Paulo – ESALQ/USP, Piracicaba, São Paulo, Brazil

    Victor Pylro

  2. Interdisciplinary Centre for Biotechnology Research (CIP-Biotec), Federal University of Pampa (UNIPAMPA), São Gabriel, Rio Grande do Sul, Brazil

    Luiz Roesch

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Mantovani, H.C., Lopes, D.R.G., Bento, C.B.P., de Oliveira, M.N. (2017). Microbiomes Associated with Animals: Implications for Livestock and Animal Production. In: Pylro, V., Roesch, L. (eds) The Brazilian Microbiome. Springer, Cham. https://doi.org/10.1007/978-3-319-59997-7_4

Download citation

Publish with us

Policies and ethics

Search

Navigation