Metagenomics and CAZymes in Rumen: A review
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Authors
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Anju Kala
Indian Veterinary Research Institute
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Devki Nandan Kamra
Indian Veterinary Research Institute
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Lal Chandra Chaudhary
Indian Veterinary Research Institute
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Neeta Agarwal
Indian Veterinary Research Institute
Keywords:
Buffalo, CAZymes, Fiber, Metagenomics, Rrumen microbes.Abstract
Rumen is wonderful machinery that converts lignocellulsic biomass to high quality food, by virtue of the diverse microbiota it harbours. The composition of rumen ecosystem is shaped up by various factors including diet, individuality, age, geographic region, postfeeding time etc. Earlier culture based techeniques could study rumen microbes partially for the cultivable microbes. But, now it is known that about 90% of rumen microbes are unculturable, and the knowledge that we have till now seems very meager. With advent of new technologies as next generation sequencing, which studies the whole ruminal ecosystem at one time, has contributed tremendously to our existing knowledge. Approaches like metagenomics, metatranscriptomics have made it possible to study the structure and function of rumen microbes in their natural environment. The study of CAZymes has revealed that there is an array of hydrolytic enzymes in rumen that performs the deconstruction of fibrous feed material. Also, these enzymes are not only contributed by well known microbes’ viz. Fibrobacter and Ruminococcus, but by a very diverse microbiota including Roseburia, Porphryomonas, Balutia etc. So, metagenomics has added to our knowledge in many spheres of rumen microbiology, its composition and interactions in rumen. But the problem in this field is that a robust database is not available to compare the data obtained. Much work is required in field of analysis of metagenomic database establishment.
References
Achenbach L A and Coates J D. 2000. Disparity between bacterial phylogeny and physiology – comparing 16S rRNA sequences to assess relationships can be a powerful tool, but its limitations need to be considered. ASM News. 66: 714–715.
Agarwal, N., Agarwal, I., Kamra, D.N. and Chaudhary, L.C. 2000. Diurnal Variations in the activities of hydrolytic enzymes in different fractions of rumen contents of Murrah buffalo. J. Appl. Anim. Res. 18: 73-80.
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J-M, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Weissenbach J, Ehrlich SD and Bork P 2011. Enterotypes of the human gut microbiome. Nature. 473:174–180.
Brown Kav A, Benhar I., and Mizrahi, I. 2013. A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches .J Microbiol Methods. 95:272-279.
Brown Kav A, Sasson G., Jami E., Doron-Faigenboim A., Benhar I., and Mizrahi, I. 2012. Insights into the bovine rumen plasmidome. PNAS .109 (14) : 452–5457.
Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA. 2009. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A. 106:1948–1953. http://dx.doi.org/10.1073/pnas.0806191105.
de Menezes AB, Lewis E, O′Donovan M, O′Neill BF, Clipson N, et al. (2011) Microbiome analysis of dairy cows fed pasture or total mixed ration diets. FEMS Microbiology Ecology. 78: 256–265. doi: 10.1111/j.1574-6941.2011.01151.
Durso, L.M., Harhay, G.P., Smith, T.P., Bono, J.L., Desantis, T.Z., Harhay, D.M., Andersen, G.L., Keen, J.E., Laegreid, W.W., Clawson, M.L. 2010. Animal-to-animal variation in fecal microbial diversity among beef cattle. Appl Environ Microbiol. 76:4858–4862.
Edwards, E. J., McEwan, R. N., Travis, J. A. and Wallace, J R. 2004. 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie Van Leeuwenhoek. 86(3): 263-81.
Ekkers, D M, Cretoiu, M S, Kielak, A M and Elasas J D.2012.The great screen anomaly- a new frontier in product discovery through functional metagenomics. Appl Microbiol Biotechnol 93:1005-1020.
Ezer, A., Matalon, E., Jindou, S., Borovok, I., Atamna, N. 2008. Cell surface enzyme attachment is mediated by family 37 carbohydrate-binding modules, unique to Ruminococcus albus. J. Bacteriol. 190: 8220–22.
Ferrer, M., Golyshina, O. V., Chernikova, T. N., Khachane, A. N., Reyes-Duarte, D., Santos, V.A.P.M.D., Strompl. C,, Elborough, K., Jarvis, G., Neef, A., Yakimov, M.M., Timmis, K.N. and Golyshin, P.N. 2005. Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ. Microbiol.y 7: 1996–2010.
Fouts, D., Szpakowski, S., Purushe, J., Torralba, M., Waterman, R., et al. 2012. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS one 7: e48289. doi:10.1371/journal.pone.0048289
Gagen, E.J., Mosoni, P., Denman, S.E., Al Jasim, R, Mcsweeny, C.S. and Forano .2012.Methanogenic colonization does not significantly alter acetogn diversity in lambs isolated 17h after birth and raised aseptically. Microb. Ecol. 64:628-640.
Galbraith, E. A., Antonopoulos, D. A. and White, B. A.2004. Suppressive substractive hybdidization as a tool for identifying genetic diversity in an environmental metagenome : the rumen as a model. Environ. Microbiol 6:928-937.
Hobson, P.N. and Stewart, C. S. 1997. Rumen Microbial Ecosystem. (Dordecht: Springer).
Jami, E, Israel, A, Kotser A and Mizrahi I. 2013.Exploring the bovine rumen bacterial community from birth to adulthood. The International Society for Microbial Ecology. 7:1069–1079.
Kala, A. 2017. Effect of Diets and Essential Oils on Metagenomics of Rumen Microbes of Buffaloes. Ph.D. thesis submitted to Deemed University, Indian Veterinary Research Institute, Izatnagar, India.
Kala, A., Kamra, D.N., Kumar, A., Agarwal, N., Chaudhary, L.C., Joshi, C.G. 2017. Impact of levels of Total digestible nutrients on microbiome, enzyme profile and degradation of feeds in buffalo rumen. PLoS ONE 12(2), e0172051. https,//doi.org/10.1371/journal.pone.0172051.
Kala, A., Kamra, D.N., Agarwal, N. and Chaudhary, L.C.2017b. Effect of a blend of essential oils on buffalo rumen microbial and enzyme profiles and in vitro feed fermentation. Anim. Nutr.and Feed Technol. 17: 189-200. DOI: 10.5958/0974-181X.2017.00020.8
Kim, M., Morrison, M. and Yu, Z.2011.Status of phylogenetic diversity census of ruminal microbes.FEMS Microbiol. Ecol. 76:49-63
Kittelmann, S. and Janssen, P. H. 2011. Characterization of rumen ciliate community composition in domestic sheep,deer,and cattle, feeding on varying diets,by means of PCR-DGGE and clone libraries. FEMS Microbiol. Ecol .75: 468–481
Li, R.W., Connor, E.E., Li, C., Baldwin, V.I.R.L and Sparks, M.E .2012.Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environ. Microbiol. 14: 129–139. doi: 10.1111/j.1462-2920.2011.02543.
Li, Y., Ma, S., Zhang, X., Huang, S., Yang, H., Zhao, F., Yi, W., Yang, X.S. and Yi X. 2014. Evaluation of bacterial and archaeal diversity in the rumen of Xiangxi yellow cattle (Bos taurus) fed Miscanthus sinensis or common mixed feedstuff. Ann. Microbiol. 64(3): 1385-1394.
Lim, S., Seo, J., Choi, H., Yoon, D., Nam, J., Kim, H. 2013.Metagenome analysis of protein domain collocation within cellulase genes of goat rumen microbes. Asian-Austr J Anim Sci. 26: 1144-1151.
Mao, S., Zhang, M., Liu, J. and Zhu, W.201). Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle, membership and potential function Scientific Reports 5, Article number, 16116. doi, 10.1038/srep16116.
Morvan, B, Dore J, Rieu-Lesme F, Foucat L, Fonty G and Gouet, P.1994.Establishment of hydrogen - utilizing bacteria in rumen of new born lambs. FEMS Microbiol. Lett .117:249-256.
Naas, A. E., Mackenzie, A. K, Mravec, J., Schuckel, J., Wilates, W.G.T., Eijsink, V.G.H. and Pope, P. B.2014. Do rumen Bacteroidetes utilize an alternative mechanism for cellulose degradation? mBio. 5 (4):e01401-14.
Nardi, R. D., Marchesini, G., Shucong, L., Khafipour, E.K., Plaizier, J. C., Gianesella, M., Ricci, R., Andrighetto, I. and Segato, S. 2016. Metagenomic analysis of rumen microbial population in dairy heifers fed a high grain diet supplemented with dicarboxylic acids or polyphenols. BMC Veter. Res. 12: 29. doi,10.1186/s12917-016-0653-4.
Newbold, C.J., Lassalas, B. and Jouany, J. P. 1995.The importance of methanogens associated with ciliate protozoa in ruminal methane production in vitro. Lett. Appl. Microbiol. 21: 230–234.
Patel, D. D., Patel, A. K., Parmar, N. R., Shah, T. M., Patel, J. B., Pandya, P. R. and Joshi, C. G. 2014.Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet. Gene. 545: 88–94.
Patra, A.K., Kamra, D.N. and Agarwal, N. 2010. Effects of extracts of spices on rumen methanogenesis, enzyme activities and fermentation of feeds in vitro. J. Sci. Food Agri. 90 (3): 511–520.
Pope, P. B., Mackenzie, A. K., Gregor, I., Smith, W., Sundset, M. A., McHardy, A. C., Morrison, M., Eijsink, V. G. 2012. Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS One 7:e38571. http://dx.doi.org/10.1371/journal .pone.0038571.
Puniya, A. K., Singh, R., Kamra, D. N.2015.Rumen microbiology: From evolution to revolution (e- book).
Ross, E M, Petrovski S, Moate P J and Hayes B J. 2013. Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle. BMC Microbiol. 13:242 http://www.biomedcentral.com/1471-2180/13/242.
Shanks, O. C., Kelty, C. A., Archibeque, S., Jenkins, M., Newton, R. J., McLellan, S. L., Huse, S. M. and Sogin, M. L. 2011. Community structures of fecal bacteria in cattle from different animal feeding operations. Appl.and Environ. Microbiol. 77: 2992–3001.
Simon, C. and Daniel, R.2009.Achievements and new knowledge unraveled by metagenomic approaches.Appl. Microbiol. Biotechnol. 85:265-276.
Stevenson, D.M. and Weimer, P.J. 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.
Ushida, K., Newbold, C. J., Fonty, G., Morvan, B. and Jouany, J. P .1995. Interspecies hydrogen transfer between the rumen ciliate Polyplastron multivesiculatum and methanogenic bacteria. Proc. Jpn. So.c Rumen. Metabol .Physiol. 6: 61–63.
von Mering, C., Hugenholtz, P., Raes, J., Tringe, S. G., Doerks, T, Jensen, L. J., Ward, N. and Bork, P.2007. Quantitative phylogenetic assessment of microbial communities in diverse environments. Sci. 315: 1126–1130.
White, B.A., Lamed, R., Edward, A. Bayer, E.A., Harry J. and Flint, H.J. 2014. Biomass Utilization by Gut Microbiomes Annu. Rev. Microbiol. 68:279–96.
Wu, S., Baldwin, R.L. VI, Li, W., Li, C., Connor, E. E. and Li, R.W.2012.The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA gene. Metagenomics 1:e235571
Zhu, Z., Noel, S.J., Difford, G.F., Al-Soud, W.A., Brejnrod, A. and Sørensen, S.J. 2017. Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period. PLoS ONE 12(11): e0187858. https://doi.org/10.1371/journal.pone.0187858.
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