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BioMed Research International
Volume 2014, Article ID 267189, 10 pages
Research Article

High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

1Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001, India
2Xcelris Genomics Xcelris Labs Ltd, Old Premchandnagar Road, Opp. Satyagrah Chhavani, Bodakdev, Ahmedabad 380054, India
3Department of Animal Nutrition, Livestock Research Station, Sardarkrushinagar Dantiwada Agricultural University, Gujarat 385506, India

Received 27 February 2014; Revised 4 June 2014; Accepted 5 June 2014; Published 17 July 2014

Academic Editor: Neelu Nawani

Copyright © 2014 K. M. Singh et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. Miron, D. Ben-Ghedalia, and M. Morrison, “Invited review: adhesion mechanisms of rumen cellulolytic bacteria,” Journal of Dairy Science, vol. 84, pp. 1294–1309, 2001. View at Google Scholar
  2. P. B. Pope, A. K. Mackenzie, I. Gregor, W. Smith, M. A. Sundset, and A. C. McHardy, “Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci,” PloS ONE, vol. 7, Article ID e38571, 2012. View at Google Scholar
  3. E. Jami and I. Mizrahi, “Composition and similarity of bovine rumen microbiota across individual animals,” PloS One, vol. 7, article e33306, 2012. View at Google Scholar
  4. C. W. Forsberg, K. J. Cheng, and B. A. White, “Polysaccharide degradation in the rumen and large intestine,” in Gastrointestinal Microbiology, R. I. Mackie and B. A. White, Eds., vol. 1, pp. 319–379, Chapman & Hall, New York, NY, USA, 1997. View at Google Scholar
  5. D. J. Cosgrove, “Growth of the plant cell wall,” Nature Reviews Molecular Cell Biology, vol. 6, no. 11, pp. 850–861, 2005. View at Publisher · View at Google Scholar
  6. H. J. Flint and E. A. Bayer, “Plant cell wall breakdown by anaerobic microorganisms from the Mammalian digestive tract,” Annals of the New York Academy of Sciences, vol. 1125, pp. 280–288, 2008. View at Publisher · View at Google Scholar
  7. H. J. Flint, E. A. Bayer, M. T. Rincon, R. Lamed, and B. A. White, “Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis,” Nature Reviews Microbiology, vol. 6, pp. 121–131, 2008. View at Google Scholar
  8. J. M. Brulc, D. A. Antonopoulos, M. E. Miller et al., “Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 1948–1953, 2009. View at Google Scholar
  9. M. Hess, A. Sczyrba, R. Egan, T. W. Kim, H. Chokhawala, and G. Schroth, “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen,” Science, vol. 331, pp. 463–467, 2011. View at Publisher · View at Google Scholar
  10. B. L. Cantarel, P. M. Coutinho, C. Rancurel, T. Bernard, V. Lombard, and B. Henrissat, “The Carbohydrate-Active EnZymes database ( CAZy ): an expert resource for glycogenomics,” Nucleic Acids Research, vol. 37, pp. D233–D238, 2009. View at Google Scholar
  11. C. Bera-Maillet, E. Devillard, M. Cezette, J. P. Jouany, and E. Forano, “Xylanases and carboxymethylcellulases of the rumen protozoa Polyplastron multivesiculatum, Eudiplodinium maggii and Entodinium sp,” FEMS Microbiology Letters, vol. 244, pp. 149–156, 2005. View at Google Scholar
  12. M. Qi, P. Wang, N. O'Toole et al., “Snapshot of the eukaryotic gene expression in muskoxen rumen—a metatranscriptomic approach,” PloS ONE, vol. 6, Article ID e20521, 2011. View at Google Scholar
  13. D. Tilman, R. Socolow, J. A. Foley et al., “Beneficial biofuels—the food, energy, and environment trilemma,” Science, vol. 325, no. 5938, pp. 270–271, 2009. View at Google Scholar
  14. A. Henne, R. Daniel, R. A. Schmitz, and G. Gottschalk, “Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate,” Applied and Environmental Microbiology, vol. 65, no. 9, pp. 3901–3907, 1999. View at Google Scholar
  15. J. Handelsman, M. R. Rondon, S. F. Brady, J. Clardy, and R. M. Goodman, “Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products,” Chemistry & Biology, vol. 5, pp. R245–R249, 1998. View at Google Scholar
  16. F. Thomas, J. H. Hehemann, E. Rebuffet, M. Czjzek, and G. Michel, “Environmental and gut bacteroidetes: the food connection,” Frontiers in Microbiology, vol. 2, article 93, 2011. View at Google Scholar
  17. J. Stiverson, M. Morrison, and Z. Yu, “Populations of select cultured and uncultured bacteria in the rumen of sheep and the effect of diets and ruminal fractions,” International Journal of Microbiology, vol. 2011, Article ID 750613, 8 pages, 2011. View at Publisher · View at Google Scholar
  18. S. R. Gill, M. Pop, R. T. Deboy et al., “Metagenomic analysis of the human distal gut microbiome,” Science, vol. 312, pp. 1355–1395, 2006. View at Google Scholar
  19. P. J. Turnbaugh, M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, and R. E. Ley, “A core gut microbiome in obese and lean twins,” Nature, vol. 457, pp. 480–484, 2009. View at Google Scholar
  20. R. Lamendella, J. W. Domingo, S. Ghosh, J. Martinson, and D. B. Oerther, “Comparative fecal metagenomics unveils unique functional capacity of the swine gut,” BMC Microbiology, vol. 11, p. 103, 2011. View at Publisher · View at Google Scholar
  21. A. Qu, J. M. Brulc, M. K. Wilson, B. F. Law, and L. A. Theoret Joens Jr., “Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome,” PLoS ONE, vol. 3, Article ID e2945, 2008. View at Google Scholar
  22. K. S. Swanson, S. E. Dowd, J. S. Suchodolski et al., “Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice,” The ISME Journal, vol. 5, pp. 639–49, 2011. View at Google Scholar
  23. H. M. Tun, M. S. Brar, N. Khin, L. Jun, R. K. Hui, and S. E. Dowd, “Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing,” Journal of Microbiological Methods, vol. 88, pp. 369–376, 2012. View at Publisher · View at Google Scholar
  24. B. Xu, W. Xu, F. Yang et al., “Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds,” PloS One, vol. 8, article e56565, 2013. View at Google Scholar
  25. F. Warnecke, P. Luginbuhl, N. Ivanova et al., “Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite,” Nature, vol. 450, pp. 560–565, 2007. View at Publisher · View at Google Scholar
  26. J. E. Edwards, S. A. Huws, E. J. Kim, and A. H. KingstonSmith, “Characterization of the dynamics of initial bacterial colonization of nonconserved forage in the bovine rumen,” FEMS Microbiology Ecology, vol. 62, pp. 323–335, 2007. View at Publisher · View at Google Scholar
  27. F. Meyer, D. Paarmann, M. D'Souza et al., “The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes,” BMC Bioinformatics, vol. 9, p. 386, 2008. View at Google Scholar
  28. R. D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, and J. E. Pollington, “The Pfam protein families database,” Nucleic Acids Research, vol. 38, pp. D211–D222, 2010. View at Publisher · View at Google Scholar
  29. S. R. Eddy, “Profile hidden Markov models,” Bioinformatics, vol. 14, pp. 755–763, 1998. View at Google Scholar
  30. K. M. Singh, V. Ahir, A. K. Tripathi et al., “Metagenomic analysis of Surti buffalo 366 (Bubalus bubalis) rumen: a preliminary study,” Molecular Biology Reports, vol. 39, no. 4, pp. 4841–4484, 2012. View at Publisher · View at Google Scholar
  31. C. J. Duan, L. Xian, G. C. Zhao et al., “Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens,” Journal of Applied Microbiology, vol. 107, pp. 245–256, 2009. View at Google Scholar
  32. C.-J. Duan, J.-J. Liu, X. Wu, J.-L. Tang, and J.-X. Feng, “Novel carbohydrate-binding module identified in a ruminal metagenomic endoglucanase,” Applied and Environmental Microbiology, vol. 76, no. 14, pp. 4867–4870, 2010. View at Publisher · View at Google Scholar
  33. S. Y. Ding, M. T. Rincon, R. Lamed et al., “Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens,” Journal of Bacteriology, vol. 183, pp. 1945–1953, 2001. View at Google Scholar
  34. A. J. Harvey, M. Hrmova, R. De Gori, J. N. Varghese, and G. B. Fincher, “Comparative modelling of the three-dimensional structures of family 3 glycoside hydrolases,” Proteins, vol. 41, pp. 257–269, 2000. View at Publisher · View at Google Scholar
  35. R. C. Lee, M. Hrmova, R. A. Burton, J. Lahnstein, and G. B. Fincher, “Bifunctional family 3 glycoside hydrolases from barley with alpha-L-arabinofuranosidase and beta-D xylosidase activity. Characterization, primary structures, and COOH terminal processing,” Journal of Biological Chemistry, vol. 278, no. 7, pp. 5377–5387, 2003. View at Google Scholar
  36. Z. Bashir, V. K. Kondapalli, N. Adlakha et al., “Diversity and functional significance of cellulolytic microbes living in termite, pill-bug and stem-borer guts,” Scientific Reports, vol. 3, article 2558, 2013. View at Publisher · View at Google Scholar
  37. L. L. Lairson, B. Henrissat, G. J. Davies, and S. G. Withers, “Glycosyltransferases, structures, functions, and mechanisms,” Annual Review of Biochemistry, vol. 77, pp. 521–255, 2008. View at Publisher · View at Google Scholar
  38. D. M. Stevenson and P. J. Weimer, “Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real- time PCR,” Applied Microbiology and Biotechnology, vol. 75, pp. 165–174, 2007. View at Google Scholar
  39. E. Jami, B. A. White, and I. Mizrahi, “Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency,” PLoS ONE, vol. 9, no. 1, Article ID e85423, 2014. View at Google Scholar
  40. P. R. Pandya, K. M. Singh, S. Parnerkar, A. K. Tripathi, H. H. Mehta, and D. N. Rank, “Bacterial diversity in the rumen of Indian Surti buffalo (Bubalus bubalis), assessed by 16S rDNA analysis,” Journal of Applied Genetics, vol. 51, pp. 395–402, 2010. View at Publisher · View at Google Scholar
  41. D. P. Chandler, J. K. Fredrickson, and F. J. Brockman, “Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries,” Molecular Ecology, vol. 6, pp. 475–482, 1997. View at Google Scholar
  42. M. Li, G. B. Penner, E. Hernandez-Sanabria, M. Oba, and L. L. Guan, “Effects of sampling location and time, and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen,” Journal of Applied Microbiology, vol. 107, pp. 1924–1934, 2009. View at Publisher · View at Google Scholar
  43. K. M. Singh, A. K. Tripathi, P. R. Pandya, S. Parnerkar, D. N. Rank, and R. K. Kothari, “Use of real-time PCR technique in determination of major fibrolytic and non fibrolytic bacteria present in Indian Surti buffaloes (Bubalus bubalis),” Polish Journal of Microbiology, vol. 62, pp. 195–200, 2013. View at Google Scholar
  44. E. M. Rubin, “Genomics of cellulosic biofuels,” Nature, vol. 454, pp. 841–845, 2008. View at Google Scholar
  45. V. del Pozo Mercedes, L. Fernández-Arrojo, J. Gil-Martínez et al., “Microbial β-glucosidases from cow rumen metagenome enhance the saccharification of lignocellulose in combination with commercial cellulase cocktail,” Biotechnology for Biofuels, vol. 5, article 73, 2012. View at Google Scholar
  46. M. Zhang, R. Su, W. Qi, and Z. He, “Enhanced enzymatic hydrolysis of lignocellulose byoptimizing enzyme complexes,” Applied Biochemistry and Biotechnology, vol. 160, pp. 1407–1414, 2010. View at Google Scholar