Skip to main content

Metagenomic Insights into Herbivore Gut: An Application-Based Perspective

  • Chapter
  • First Online:

Abstract

‘Herbivores possess a fascinating gut ecosystem explicitly evolved to convert plant biomass into high quality proteins and energy constituents. In post-genomic era, the herbivore gut microbiota is viewed as capable sources of precious enzymes, genes and therapeutic biomolecules. Culture-independent metagenomic approaches have proven to be useful to unravel and utilize the gut microbiota for nutrition, health and industrial applications’.

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

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
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

Learn about institutional subscriptions

References

  • Azevedo AC, Bento CB, Ruiz JC, Queiroz MV, Mantovani HC (2015) Distribution and genetic diversity of bacteriocin gene clusters in rumen microbial genomes. Appl Environ Microbiol 81:7290–7304. doi:10.1128/AEM.01223-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Babcock DA, Wawrik B, Paul JH, McGuinness L, Kerkhof LJ (2007) Rapid screening of a large insert BAC library for specific 16S rRNA genes using TRFLP. J Microbiol Methods 71:156–161

    Article  CAS  PubMed  Google Scholar 

  • Bayer S, Kunert A, Ballschmiter M, Greiner-Stoeffele T (2010) Indication for a new lipolytic enzyme family: isolation and characterization of two esterases from a metagenomic library. J Mol Microbiol Biotechnol 18:181–187. doi:10.1159/000315459

    Article  CAS  PubMed  Google Scholar 

  • Beloqui A, Pita M, Polaina J, Martinez-Arias A, Golyshina OV, Zumarraga M (2006) Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: biochemical properties, structural analysis, and phylogenetic relationship. J Biol Chem 281:22933–22942

    Article  CAS  PubMed  Google Scholar 

  • Cheng F, Sheng J, Cai T, Jin J, Liu W, Lin Y, Du Y, Zhang M, Shen L (2012) A protease-insensitive feruloyl esterase from China Holstein cow rumen metagenomic library: expression, characterization, and utilization in ferulic acid release from wheat straw. J Agric Food Chem 60:2546–2553. doi:10.1021/jf204556u

    Article  CAS  PubMed  Google Scholar 

  • Cheng J, Huang S, Jiang H, Zhang Y, Li L, Wang J, Fan C (2016) Isolation and characterization of a non-specific endoglucanase from a metagenomic library of goat rumen. World J Microbiol Biotechnol 32(1):12. doi:10.1007/s11274-015-1957-4

    Article  PubMed  Google Scholar 

  • Dai X, Zhu Y, Luo Y, Song L, Liu D, Liu L, Chen F, Wang M, Li J, Zeng X, Dong Z, Hu S, Li L, Xu J, Huang L, Dong X (2012) Metagenomic insights into the fibrolytic microbiome in yak rumen. PLoS One 7:e40430. doi:10.1371/journal.pone.0040430

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Del Pozo MV, Fernández-Arrojo L, Gil-Martínez J, Montesinos A, Chernikova TN, Nechitaylo TY, Waliszek A, Tortajada M, Rojas A, Huws SA, Golyshina OV, Newbold CJ, Polaina J, Ferrer M, Golyshin PN (2012) Microbial beta-glucosidases from cow rumen metagenome enhance the saccharification of lignocellulose in combination with commercial cellulase cocktail. Biotechnol Biofuels 5:73. doi:10.1186/1754-6834-5-73

    Article  PubMed  PubMed Central  Google Scholar 

  • Diaz-Torres ML, McNab R, Spratt DA, Villedieu A, Hunt N, Wilson M, Mullany P (2003) Novel tetracycline resistance determined from the oral metagenome. Antimicrob Agents Chemother 47:1430–1432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duan CJ, Liu JL, Wu X, Tang JL, Feng JX (2010) Novel carbohydrate-binding module identified in a ruminal metagenomic endoglucanase. Appl Environ Microbiol 76:4867–4870. doi:10.1128/AEM.00011-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duan CJ, Xian L, Zhao GC, Feng Y, Pang H, Bai XL, Tang JL, Ma QS, Feng JX (2009) Isolation and partial characterization of novel genes encoding acidic cellulases from metagenome of buffalo rumens. J Appl Microbiol 107:245–256. doi:10.1111/j.1365-2672.2009.04202.x

    Article  CAS  PubMed  Google Scholar 

  • Feng Y, Duan CJ, Liu L, Tang JL, Feng JX (2009) Properties of a metagenome-derived beta-glucosidase from the contents of rabbit cecum. Biosci Biotechnol Biochem 73:1470–1473

    Article  CAS  PubMed  Google Scholar 

  • Feng Y, Duan CJ, Pang H, Mo XC, Wu CF, Yu Y, Hu YL, Wei J, Tang JL, Feng JX (2007) Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit caecum and characterization of the expressed cellulases. Appl Microbiol Biotechnol 75:319–328

    Article  CAS  PubMed  Google Scholar 

  • Ferrer M, Ghazi A, Beloqui A, Vieites JM, López-Cortés N, Marín-Navarro J, Nechitaylo TY, Guazzaroni ME, Polaina J, Waliczek A, Chernikova TN, Reva ON, Golyshina OV, Golyshin PN (2012) Functional metagenomics unveils a multifunctional glycosyl hydrolase from the family 43 catalysing the breakdown of plant polymers in the calf rumen. PLoS One 7:e38134. doi:10.1371/journal.pone.0038134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ferrer M, Beloqui A, Golyshina OV, Plou FJ, Neef A, Chernikova TN (2007) Biochemical structure features of a novel cyclodextrinase from cow rumen metagenome. Biotechnol J 2:207–213

    Article  CAS  PubMed  Google Scholar 

  • Findley SD, Mormile MR, Sommer-Hurley A, Zhang XC, Tipton P, Arnett K, Porter JH, Kerley M, Stacey G (2011) Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases. Appl Environ Microbiol 77:8106–8113. doi:10.1128/AEM.05925-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Firkins JL, Yu Z, Morrison M (2007) Ruminal nitrogen metabolism: perspectives for integration of microbiology and nutrition for dairy. J Dairy Sci 90(Suppl 1):E1–E16

    Article  PubMed  Google Scholar 

  • Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA (2008) Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 6:121–131. doi:10.1038/nrmicro1817

    Article  CAS  PubMed  Google Scholar 

  • Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR (2002) Isolation of antibiotics turbomycin A and B from a metagenome library of soil microbial DNA. Appl Environ Microbiol 68:4301–4306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo H, Feng Y, Mo X, Duan C, Tang J, Feng J (2008) Cloning and expression of beta-glucosidase gene umcel3G from metagenome of buffalo rumen and characterization of the translated product. Sheng Wu Gong Cheng Xue Bao 24:232–8 (Article in Chinese, abstract in English)

    Google Scholar 

  • Hall N (2007) Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 210:1518–1525

    Article  CAS  PubMed  Google Scholar 

  • Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249

    Article  CAS  PubMed  Google Scholar 

  • 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 331:463–467. doi:10.1126/science.1200387

    Article  CAS  PubMed  Google Scholar 

  • Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R (2016) MEGAN community edition - interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol 12(6):e1004957. doi:10.1371/journal.pcbi.1004957

    Article  PubMed  PubMed Central  Google Scholar 

  • Jones BV, Marchesi JR (2007) Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods 4:55–61

    Article  CAS  PubMed  Google Scholar 

  • Kohl KD, Connelly JW, Dearing MD, Forbey JS (2016) Microbial detoxification in the gut of a specialist avian herbivore, the Greater Sage-Grouse. FEMS Microbiol Lett 363(14):fnw144. doi:10.1093/femsle/fnw144

    Article  PubMed  Google Scholar 

  • Kumar M, Yadav A, Verma V, Singh B, Mal G, Nagpal R, Hemalatha R (2016) Bioengineered probiotics as a new hope for health and diseases: potential and prospects: an overview. Future Microbiol 11:585–600. doi:10.2217/fmb.16.4

    Article  CAS  PubMed  Google Scholar 

  • Lammle K, Zipper H, Breuer M, Hauer B, Buta C, Brunner H, Rupp S (2007) Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. J Biotechnol 127:575–592

    Article  PubMed  Google Scholar 

  • Lan PT, Sakamoto M, Sakata S, Benno Y (2006) Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov., and Bacteroides gallinarum sp. nov., isolated from chicken caecum. Int J Syst Evol Microbiol 56:2853–2859

    Article  CAS  PubMed  Google Scholar 

  • Liu K, Wang J, Bu D, Zhao S, McSweeny CS, Yu P, Li D (2009a) Isolation and biochemical characterization of two lipases from a metagenomic library of China Holstein cow rumen. Biochem Biophys Res Commun 385:605–611. doi:10.1016/j.bbrc.2009.05.110

    Article  CAS  PubMed  Google Scholar 

  • Liu L, Tang J, Feng J (2009b). Bacterial diversity in Guangxi buffalo rumen. Wei Sheng Wu Xue Bao 49:251–256 (Article in Chinese, abstract in English)

    Google Scholar 

  • Lopez-Cortes N, Reyes-Duarte D, Beloqui A, Polaina J, Ghazi I, Golyshina OV (2007) Catalytic role of conserved HQGE motif in the CE6 carbohydrate esterase family. FEBS Lett 581:4657–4662

    Article  CAS  PubMed  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA (2005) Genome sequencing in microfabricated high-density picolitre reactions. Nature 437:376–380

    CAS  PubMed  PubMed Central  Google Scholar 

  • Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386. doi:10.1186/1471-2105-9-386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nelson KE, Zinder SH, Hance I, Burr P, Odongo D, Wasawo D, Odenyo A, Bishop R (2003) Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: insights into an unexplored niche. Environ Microbiol 5:1212–1220

    Article  PubMed  Google Scholar 

  • Nguyen NH, Maruset L, Uengwetwanit T, Mhuantong W, Harnpicharnchai P, Champreda V, Tanapongpipat S, Jirajaroenrat K, Rakshit SK, Eurwilaichitr L, Pongpattanakitshote S (2012) Identification and characterization of a cellulase-encoding gene from the buffalo rumen metagenomic library. Biosci Biotechnol Biochem 76:1075–1084

    Article  CAS  PubMed  Google Scholar 

  • Nicholson MJ, Evans PN, Joblin KN (2007) Analysis of methanogens diversity in the rumen using temporal temperature gradient gel electrophoresis: identification of uncultured methanogens. Microb Ecol 54:141–150

    Article  CAS  PubMed  Google Scholar 

  • Palackal N, Lyon CS, Zaidi S, Luginbuhl P, Dupree P, Goubet F (2007) A multifunctional hybrid glycosyl hydrolase discovered in an uncultured microbial consortium from ruminant gut. Appl Microbiol Biotechnol 74:113–124

    Article  CAS  PubMed  Google Scholar 

  • Patel AB, Patel AK, Shah MP, Parikh IK, Joshi CG (2016) Isolation and characterization of novel multifunctional recombinant family 26 glycoside hydrolase from Mehsani buffalo rumen metagenome. Biotechnol Appl Biochem 63:257–265. doi:10.1002/bab.1358

    Article  CAS  PubMed  Google Scholar 

  • Prajapati VS, Purohit HJ, Raje DV, Parmar N, Patel AB, Jones OA, Joshi CG (2016) The effect of a high-roughage diet on the metabolism of aromatic compounds by rumen microbes: a metagenomic study using Mehsani buffalo (Bubalus bubalis). Appl Microbiol Biotechnol 100:1319–1331. doi:10.1007/s00253-015-7239-0

    Article  CAS  PubMed  Google Scholar 

  • Privé F, Newbold CJ, Kaderbhai NN, Girdwood SG, Golyshina OV, Golyshin PN, Scollan ND, Huws SA (2015) Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome. Appl Microbiol Biotechnol 99:5475–5485. doi:10.1007/s00253-014-6355-6

    Article  PubMed  PubMed Central  Google Scholar 

  • Rashamuse KJ, Visser DF, Hennessy F, Kemp J, Roux-van der Merwe MP, Badenhorst J, Ronneburg T, Francis-Pope R, Brady D (2013) Characterisation of two bifunctional cellulase-xylanase enzymes isolated from a bovine rumen metagenome library. Curr Microbiol 66:145–151. doi:10.1007/s00284-012-0251-z

    Article  CAS  PubMed  Google Scholar 

  • Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501–1506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shanks OC, Santo Domingo JW, Lamendella R, Kelty CA, Graham JE (2006) Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow faecal samples. Appl Environ Microbiol 72:4054–4060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shedova EN, Lunina NA, Berezina OV, Zverlov VV, Schwarz V, Velikodvorskaia GA (2009) Expression of the genes celA and XylA isolated from a fragment of metagenomic DNA in Escherichia coli. Mol Gen Mikrobiol Virusol 2:28–32 (Article in Russian, abstract in English)

    Google Scholar 

  • Singh B, Gautam SK, Verma V, Kumar M, Singh B (2008) Metagenomics in animals gastrointestinal tract-potential biotechnological prospects. Anaerobe 14:138–144. doi:10.1016/j.anaerobe.2008.03.002

    Article  CAS  PubMed  Google Scholar 

  • Singh B, Mal G, Bissi L, Marotta F (2016) The holy grail of designer probiotics: the probiotics with multiple health benefits. J Gastrointest Digestive Syst 6:2. doi:10.4172/2161-069X.1000415

    Google Scholar 

  • Singh KM, Jakhesara SJ, Koringa PG, Rank DN, Joshi CG (2012) Metagenomic analysis of virulence-associated and antibiotic resistance genes of microbes in rumen of Indian buffalo (Bubalus bubalis). Gene 507:146–151. doi:10.1016/j.gene.2012.07.037

    Article  CAS  PubMed  Google Scholar 

  • Toyoda A, Iio W, Mitsumori M, Minato H (2009) Isolation and identification of cellulose binding proteins from sheep rumen contents. Appl Environ Microbiol 75:1667–1673. doi:10.1128/AEM.01838-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • White BA, Lamed R, Bayer EA, Flint HJ (2014) Biomass utilization by gut microbiomes. Annu Rev Microbiol 68:279–296. doi:10.1146/annurev-micro-092412-155618

    Article  CAS  PubMed  Google Scholar 

  • Xu B, Xu W, Li J, Dai L, Xiong C, Tang X, Yang Y, Mu Y, Zhou J, Ding J, Wu Q, Huang Z (2015) Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation. BMC Genomics 16:174. doi:10.1186/s12864-015-1378-7

    Article  PubMed  PubMed Central  Google Scholar 

  • Xu J (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15:1713–1731

    Article  CAS  PubMed  Google Scholar 

  • Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI (2012) Human gut microbiome viewed across age and geography. Nature 486:222–227. doi:10.1038/nature11053

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wallace RJ, Rooke JA, McKain N, Duthie CA, Hyslop JJ, Ross DW, Waterhouse A, Watson M, Roehe R (2015) The rumen microbial metagenome associated with high methane production in cattle. BMC Genomics 16:839. doi:10.1186/s12864-015-2032-0

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhao S, Wang J, Bu D, Liu K, Zhu Y, Dong Z, Yu Z (2010) Novel glycoside hydrolases identified by screening a Chinese Holstein dairy cow rumen-derived metagenome library. Appl Environ Microbiol 76:6701–6705. doi:10.1128/AEM.00361-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou J, Bao L, Chang L, Liu Z, You C, Lu H (2012) Beta-xylosidase activity of a GH3 glucosidase/xylosidase from yak rumen metagenome promotes the enzymatic degradation of hemicellulosic xylans. Lett Appl Microbiol 54:79–87. doi:10.1111/j.1472-765X.2011.03175.x

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Birbal Singh .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Nature Singapore Pte Ltd.

About this chapter

Cite this chapter

Singh, B. et al. (2017). Metagenomic Insights into Herbivore Gut: An Application-Based Perspective. In: Kalia, V., Shouche, Y., Purohit, H., Rahi, P. (eds) Mining of Microbial Wealth and MetaGenomics. Springer, Singapore. https://doi.org/10.1007/978-981-10-5708-3_12

Download citation

Publish with us

Policies and ethics