Current Microbiology

, Volume 67, Issue 2, pp 130–137

Comparative Analysis of Microbial Profiles in Cow Rumen Fed with Different Dietary Fiber by Tagged 16S rRNA Gene Pyrosequencing

  • Honglada Thoetkiattikul
  • Wuttichai Mhuantong
  • Thanaporn Laothanachareon
  • Sithichoke Tangphatsornruang
  • Virote Pattarajinda
  • Lily Eurwilaichitr
  • Verawat Champreda
Article
  • 1.3k Downloads

Abstract

The ruminal microbiome of cattle plays an important role not only in animal health and productivity but also in food safety and environment. Microbial profiles of rumen fluid obtained from dairy cows fed on three different fiber/starch diet compositions were characterized. Tagged 16S rRNA gene pyrosequencing and statistical analysis revealed that the dominant ruminal bacteria shared by all three sample groups belonged to phyla Bacteroidetes, Firmicutes, and Proteobacteria. However, the relative abundance of these bacterial groups was markedly affected by diet composition. In animals fed with a high fiber diet, the fibrolytic and cellulolytic bacteria Lachnospiraceae, Ruminococcaceae, and Fibrobacteraceae were found in highest abundance compared with animals fed other diets with lower fiber content. The polysaccharide-degrading Prevotellaceae and Flavobacteriaceae bacteria were most abundant in the rumen of cows fed on diet with the highest starch content. These data highlight the ruminal microbiome’s ability to adapt to feed composition and also provide a basis for the development of feed formulation systems designed to improve livestock productivity.

References

  1. 1.
    Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 3:e2836PubMedCrossRefGoogle Scholar
  2. 2.
    Avguštin G, Ramšak A, Peterka M (2001) Systematics and evolution of ruminal species of the genus Prevotella. Folia Microbiol 46:40–44CrossRefGoogle Scholar
  3. 3.
    Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Micro Methods 55:541–555CrossRefGoogle Scholar
  4. 4.
    Belanche A, Doreau M, Edwards JE, Moorby JM, Pinloche E, Newbold CJ (2012) Shifts in the rumen microbiota dute to the type of carbohydrate and level of protein ingested by dairy cattle are associated with changes in rumen fermentation. J Nutr 142:1684–1692PubMedCrossRefGoogle Scholar
  5. 5.
    Bretschger O, Osterstock JB, Pinchak WE, Ishii S, Nelson KE (2010) Microbial fuel cells and microbial ecology: applications in ruminant health and production research. Microb Ecol 59:415–427PubMedCrossRefGoogle Scholar
  6. 6.
    Buee M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184(2):449–456PubMedCrossRefGoogle Scholar
  7. 7.
    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 88:3977–3983PubMedCrossRefGoogle Scholar
  8. 8.
    Chu HM, Guo RT, Lin TW, Chou CC, Shr HL, Lai HL, Tang TY, Cheng KJ, Selinger BL, Wang AH (2004) Structures of Selenomonas ruminantiumphytase in complex with persulfated phytate: dSP phytase fold and mechanism for sequential substrate hydrolysis. Structure 12:2015–2024PubMedCrossRefGoogle Scholar
  9. 9.
    Domingo MC, Huletsky A, Boissinot M, Bernard KA, Picard FJ, Bergeron MG (2008) Ruminococcus gauvreauii sp. nov., a glycopeptide-resistant species isolated from a human faecal specimen. Int J Syst Evol Microbiol 58:1393–1397PubMedCrossRefGoogle Scholar
  10. 10.
    Dowd SE, Callaway TR, Wallcott 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 ampliconpyrosequencing (bTEFAP). Microbiology 8:125PubMedGoogle Scholar
  11. 11.
    Edgar RC, Haas BJ, Clemente JC, Quince C, Knight (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200PubMedCrossRefGoogle Scholar
  12. 12.
    Edwards JE, McEwan NR, Travis AJ, Wallace RJ (2004) 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie Van Leeuwenhoek 86:263–281CrossRefGoogle Scholar
  13. 13.
    Evans NJ, Brown JM, Murray RD, Getty B, Birtles RJ, Hart CA, Carter SD (2011) Characterization of novel bovine gastrointestinal tract Treponema isolates and comparison with bovine digital dermatitis treponemes. Appl Environ Microbiol 77:138–177PubMedCrossRefGoogle Scholar
  14. 14.
    Fernando SC, Purvis HT II, Najar FZ, Sukharnikov LO, Krehbiel CR, Nagaraja TG, Roe BA, DeSilva U (2010) Rumen microbial population dynamics during adaptation to a high-grain diet. Appl Environ microbiol 76(22):7482–7490PubMedCrossRefGoogle Scholar
  15. 15.
    Graber JR, Leadbetter JR, Breznak JA (2004) Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the first Spirochetes isolated from termite guts. Appl Environ Microbiol 70:1315–1320PubMedCrossRefGoogle Scholar
  16. 16.
    Hamberger A, Horn MA, Dumont MG, Murrell JC, Drake HL (2008) Anaerobic consumers of monosaccharides in a moderately acidic fen. Appl Environ Microbiol 74:3112–3120PubMedCrossRefGoogle Scholar
  17. 17.
    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 (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 33:463–467CrossRefGoogle Scholar
  18. 18.
    Humblot C, Guyot JP (2009) Pyrosequencing of tagged 16S rRNA gene amplicons for rapid deciphering of the microbiomes of fermented foods such as pearl millet slurries. Appl Environ Microbiol 75:4354–4361PubMedCrossRefGoogle Scholar
  19. 19.
    Jami E, Mizrahi I (2012) Composition and similarity of bovine rumen microbiota across individual animals. PLoS One 7(3):e33306PubMedCrossRefGoogle Scholar
  20. 20.
    Janssen PH, Kirs M (2008) Structure of the archaeal community of the rumen. Appl Environ Microbiol 74(12):3619–3625PubMedCrossRefGoogle Scholar
  21. 21.
    Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer NA (2009) Comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3(4):442–453PubMedCrossRefGoogle Scholar
  22. 22.
    Kabel MA, Yeoman CJ, Han Y, Dodd D, Abbas CA, de Bont JA, Morrison M, Cann IKO, Mackie RI (2011) Biochemical characterization and relative expression levels of multiple carbohydrate esterases of the xylanolytic rumen bacterium Prevotella ruminicola 23 grown on an ester-enriched substrate. Appl Environ Microbiol 77(16):5671–5681PubMedCrossRefGoogle Scholar
  23. 23.
    Kamra DN (2005) Rumen microbial ecosystem. Curr Sci 89:124–135Google Scholar
  24. 24.
    Kebreab E, Dijkstra J, Bannink A, France J (2009) Recent advances in modeling nutrient utilization in ruminants. J Anim Sci 87:E111–E122PubMedCrossRefGoogle Scholar
  25. 25.
    Kopecný J, Zorec M, Mrázek J, Kobayashi Y, Marinsek-Logar R (2003) Butyrivibrio hungatei sp. nov. and Pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen. Int J Syst Evol Microbiol 53:201–209PubMedCrossRefGoogle Scholar
  26. 26.
    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 27:663–693PubMedCrossRefGoogle Scholar
  27. 27.
    Lee HJ, Jung JY, Oh YK, Lee SS, Madsen EL, Jeon CO (2012) Comparative survey of rumen microbial communities and metabolites across caprine and three bovine groups, using bar-coded pyrosequencing and 1H nuclear magnetic resonance spectroscopy. Appl Environ Microbiol 78:5983–5993PubMedCrossRefGoogle Scholar
  28. 28.
    Lou J, Dawson KA, Strobel HJ (1997) Glycogen biosynthesis via UDP-glucose in the ruminal bacterium Prevotella bryantii B1(4). Appl Environ Microbiol 63(11):4355–4359PubMedGoogle Scholar
  29. 29.
    Matsui H, Ogata K, Tajima K, Nakamura M, Nagamine T, Aminov RI, Benno Y (2000) Phenotypic characterization of polysaccharidases produced by four Prevotella type strains. Curr Microbiol 41:45–49PubMedCrossRefGoogle Scholar
  30. 30.
    Meyer M, Stenzel U, Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3(2):267–278PubMedCrossRefGoogle Scholar
  31. 31.
    Moore LV, Moore WE (1994) Oribaculum catoniae gen. nov., sp. nov.; Catonella morbi gen. nov., sp. nov.; Hallella seregens gen. nov., sp. nov.; Johnsonella ignava gen. nov., sp. nov.; and Dialister pneumosintes gen. nov., comb. nov., nom. rev., Anaerobic gram negative bacilli from the human gingival crevice. Int J Syst Bacteriol 44:187–192PubMedCrossRefGoogle Scholar
  32. 32.
    Morotomi M, Nagai F, Watanabe Y (2011) Christensenella minuta gen. nov., sp. nov., isolated from human faeces that forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov. Int J Syst Evol Microbiol 62(Pt 1):144–149PubMedGoogle Scholar
  33. 33.
    Pitta DW, Pinchak E, Dowd SE, Osterstock J, Gontcharova V, Youn E, Dorton K, Yoon I, Min BR, Fulford JD, Wickersham TA, Malinowski DP (2010) Rumen bacterial diversity dynamics associated with changing from Bermuda grass hay to grazed winter wheat diets. Microb Ecol 59:511–522PubMedCrossRefGoogle Scholar
  34. 34.
    Ramšak A, Peterka M, Tajima K, Martin JC, Wood J, Johnston MEA, Aminov RI, Flint HJ, Avguštin G (2000) Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiol Ecol 33:69–79PubMedCrossRefGoogle Scholar
  35. 35.
    Sanapareddy N, Hamp TJ, Gonzalez LC, Hilger HA, Fodor AA, Clinton SM (2009) Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. Appl Environ Microbiol 75(6):1688–1696PubMedCrossRefGoogle Scholar
  36. 36.
    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541PubMedCrossRefGoogle Scholar
  37. 37.
    Stanley K, Jones K (2003) Cattle and sheep farms as reservoirs of Campylobacter. J Appl Microbiol 94:13–104SCrossRefGoogle Scholar
  38. 38.
    Tajima K, Aminov RI, Nagamine T, Ogata K, Nakamura M (1999) Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol Ecol 29:159–169CrossRefGoogle Scholar
  39. 39.
    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 67:2766–2774PubMedCrossRefGoogle Scholar
  40. 40.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 24(8):1596–1599PubMedCrossRefGoogle Scholar
  41. 41.
    Van den Bogert B, de Vos Willem M, Zoetendal EG, Kleerebezem M (2011) Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol 77(6):2071–2080PubMedCrossRefGoogle Scholar
  42. 42.
    Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naıve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ microbiol 73(16):5261–5267PubMedCrossRefGoogle Scholar
  43. 43.
    Zoetendal EG, Rajilic-Stojanovic M, DeVos WM (2009) High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57:1605–1615CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Honglada Thoetkiattikul
    • 1
  • Wuttichai Mhuantong
    • 1
  • Thanaporn Laothanachareon
    • 1
  • Sithichoke Tangphatsornruang
    • 2
  • Virote Pattarajinda
    • 3
  • Lily Eurwilaichitr
    • 1
  • Verawat Champreda
    • 1
  1. 1.Enzyme Technology Laboratory, Bioresources Technology UnitNational Center for Genetic Engineering and Biotechnology (BIOTEC)Khlong LuangThailand
  2. 2.Genomic Research Laboratory, Genome InstituteNational Center for Genetic Engineering and BiotechnologyKhlong LuangThailand
  3. 3.Department of Animal Science, Faculty of AgricultureKhon Kaen UniversityKhon KaenThailand

Personalised recommendations