Abstract
Diverse populations of rumen microorganisms in gut contribute to develop ability of breaking down fibrous foods, which are mostly unusable by humans (Owens FN, Goetsch AL (1988) Ruminal fermentation. In: Church DC (ed) The ruminant animal, digestive physiology and nutrition. Prentice-Hall, Englewood Cliffs, p 160). Rumen is having a larger population of microorganisms, more than a trillion organisms and wide diversity (hundreds of species and thousands of subspecies), per ounce of rumen contents (Xu et al., J Anim Sci 85:1024–1029, 2007). There are various traditional approaches through which overall performance of the rumen has been attempted to improve, e.g. plant secondary metabolites, microbial feed additives, chemical feed additives, selective stimulation of beneficial rumen microbes and selective inhibition of harmful rumen microbes. In spite of these, nowadays various new approaches are being used to improve our understanding of the relationships among the various rumen microorganisms and towards how they interact with their hosts (Chaucheyras-Durand and Ossa, Prof Anim Sci 30:1–12, 2014). To better characterize species in the rumen, new advanced technological aids such as gene sequencing and study of gene (genomics), protein (proteomics) and metabolite (metabolomics) expression are being frequently used. This chapter will majorly emphasize on recent tools used in exploring the diversity of rumen.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ametaj BN, Zebeli Q, Saleem F et al (2010) Metabolomics reveals unhealthy alterations in rumen metabolism with increased proportion of cereal grain in the diet of dairy cows. Metabolomics 6:583–594
Bond JJ, Dunne JC, Kwan FYS et al (2012) Carbohydrate transporting membrane proteins of the rumen bacterium, Butyrivibrio proteoclasticus. J Proteomics 75:3138–3144
Chaucheyras-Durand F, Ossa F (2014) The rumen microbiome: composition, abundance, diversity, and new investigative tools. Prof Anim Sci 30:1–12
Ciric M, Moon DC, Leahy LC et al (2014) Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. BMC Genomics 15:356
Collado MC, Sanz Y (2007a) Quantification of mucosa-adhered microbiota of lambs and calves by the use of culture methods and fluorescent in situ hybridization coupled with flow cytometry techniques. Vet Microbiol 121:299–306
Collado MC, Sanz Y (2007b) Characterization of the gastrointestinal mucosa associated microbiota of pigs and chickens using culture-based and molecular methodologies. J Food Prot 70:2799–2804
Collado MC, Isolauri E, Laitinen K et al (2008) Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am J Clin Nutr 88:894–899
Dunne JC, Li D, Kelly WJ et al (2012) Extracellular polysaccharide-degrading proteome of Butyrivibrio proteoclasticus. J Proteome Res 11(1):131–142
Eckburg PB, Bik EM, Bernstein CN et al (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638
Gong J, Yang C (2012) Advances in the methods for studying gut microbiota and their relevance to the research of dietary fiber functions. Food Res Int 48:916–929
Habib G, Raza M, Saleem M (2008) Effect of tree leaves with or without urea as a feed supplement on nutrient digestion and nitrogen balance in sheep. Anim Feed Sci Technol 144:335–343
Holligan S, Wang J, Cant JP et al (2013) A proteomics approach to detect tissue-wide adaptive changes in the pancreas associated with increased pancreatic α-amylase activity in domestic cattle (Bos taurus). Comp Biochem Physiol Part D Genomics Proteomics 8:65–71
Jami E, Mizrahi I (2012) Composition and similarity of bovine rumen microbiota across individual animals. PLoS One 7(3):e33306
Jayasri K, Padmaja K, Prasad PE (2014) Proteomics in animal health and production. IOSR J Agric Vet Sci 7:50–56
Jiang Y, Xie M, Chen W et al (2014) The sheep genome illuminates biology of the rumen and lipid metabolism. Science (New York, NY) 344:1168–1173
Kudva IT, Stanton TB, Lippolis JD (2014) The Escherichia coli O157:H7 bovine rumen fluid proteome reflects adaptive bacterial responses. BMC Microbiol 14:48
Lee JW, Lee SY (2009) Proteome-based physiological analysis of the metabolically engineered succinic acid producer Mannheimia succiniciproducens LPK7. Bioprocess Biosyst Eng. doi:10.1007/s00449-009-0339-4
Lee SJ, Song H, Lee SY (2006) Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production. Appl Environ Microbiol 72:1939–1948
Li M, Gong J, Cottrill M et al (2003) Evaluation of QIAamp® DNA Stool Mini Kit for ecological studies of gut microbiota. J Microbiol Methods 54:13–20
Li Z, Zhao H, Yang P et al (2013) Comparative quantitative analysis of gene expression profiles of glycoside hydrolase family 10 xylanases in the sheep rumen during a feeding cycle. Appl Environ Microbiol 79:1212–1220
Liang M-Y, Hou X-M, Qu B et al (2014) Functional analysis of FABP3 in the milk fat synthesis signaling pathway of dairy cow mammary epithelial cells. In Vitro Cell Dev Biol Anim. doi:10.1007/s11626-014-9780-z
Mohammadzadeh H, Yáñez-Ruiz DR, Martínez-Fernandez G et al (2014) Molecular comparative assessment of the microbial ecosystem in rumen and faeces of goats fed alfalfa hay alone or combined with oats. Anaerobe 29:52–58
Paliy O, Kenche H, Abernathy F et al (2009) High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray. Appl Environ Microbiol 75:3572–3579
Palma DG, Nadal I, Collado MC et al (2009) Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects. Br J Nutr 102:1154–1160
Palmer C, Bik EM, DiGiulio DB et al (2007) Development of the human infant intestinal microbiota. PLoS Biol 5:e177
Rajilic-Stojanovic M, Maathuis A, Heilig HGHJ et al (2010) Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis. Microbiology 156:3270–3281
Saleem F, Ametaj BN, Bouatra S et al (2012) A metabolomics approach to uncover the effects of grain diets on rumen health in dairy cows. J Dairy Sci 95:6606–6623
Sekhavati MH, Mesgaran MD, Nassiri MR et al (2009) Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal population s in both in vitro and in vivo systems. Mycol Res 113:1146–1153
Sidi-Boumedine K, Ellis RJ, Adam G et al (2014) Draft genome sequences of six ruminant Coxiella burnetii isolates of European origin. Genome Announc 2:e00285-14. doi:10.1128/genomeA. 00285-14
Snel J, Harmssen HJM, van der Wielen PWJJ et al (2002) Dietary strategies to influence the gastrointestinal microflora of young animals, and its potential to improve intestinal health. In: Blok MC et al (eds) Nutrition and health of the gastrointestinal tract. Wageningen Academic Publishers, Wageningen, pp 37–69
Teather RM (1985) Application of gene manipulation to rumen microflora. Can J Anim Sci 65:563–574
Vinayavekhin N, Homan EA, Saghatelian A (2010) Exploring disease through metabolomics. J Agric Food Chem 5:91–103
Wang T-Y, Chen H-L, Lu M-Y J et al (2011) Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses. Biotechnol Biofuel 4:24
Wang et al (2012) Effects of dietary composition on the rumen papillae tissue proteome of cows by the combination of two-dimensional gel electrophoresis and mass spectrometry. J Agri Biotechnol 20:1042–1047. ISSN 1674–7968 CN: 11-3342/S
Wang LF, Yang GY, Yang GQ et al (2014) Effect of zinc source on the expression of ZIPII transporter genes in Guanzhong dairy goats. Anim Feed Sci Technol. http://dx.doi.org/10.1016/j.anifeedsci.2014.06.006
Wishart DS, Lewis MJ, Morrissey JA et al (2008) The human cerebrospinal fluid metabolome. J Chromatogr B Anal Technol Biomed Life Sci 871:164–173
Yang Y, Wang J, Yuan T et al (2013) Proteome profile of bovine ruminal epithelial tissue based on GeLC–MS/MS. Biotechnol Lett 35:1831–1838
Zhao J, Bu D, Sun P et al (2014) Metabolomics analysis reveals large effect of roughage types on rumen microbial metabolic profile in dairy cows. Lett Appl Microbiol 59:79–85
Zoetendal EG, Collier CT, Koike S et al (2004) Molecular ecological analysis of the gastrointestinal microbiota: a review. J Nutr 134:65–472
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer India
About this chapter
Cite this chapter
Shrivastava, B. et al. (2015). ‘Omics’ Approaches to Understand and Manipulate Rumen Microbial Function. In: Puniya, A., Singh, R., Kamra, D. (eds) Rumen Microbiology: From Evolution to Revolution. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2401-3_15
Download citation
DOI: https://doi.org/10.1007/978-81-322-2401-3_15
Publisher Name: Springer, New Delhi
Print ISBN: 978-81-322-2400-6
Online ISBN: 978-81-322-2401-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)