REVIEW

Rumial Microbes:Diversity and Quantification

  • MA Tao ,
  • DIAO Qiyu
Expand
  • Feed Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing 100081, China

Received date: 2015-07-02

  Online published: 2015-12-14

Abstract

Ruminants are able to utilize fibrous feed as a source of energy and nutrients due to the ruminal microbes, composed mainly of bacteria, fungi, and ciliate protozoa. Ruminal microbes play different roles in feed digestion and act synergistically to ferment dietary carbohydrates and proteins. This review reported the latest methods for assessment of ruminal microbial diversity, particularly molecular techniques, which allows people to gain new insights into rumen functions.

Cite this article

MA Tao , DIAO Qiyu . Rumial Microbes:Diversity and Quantification[J]. Chinese Journal of Animal Nutrition, 2015 , 27(12) : 3649 -3654 . DOI: 10.3969/j.issn.1006-267x.2015.12.001

References

[1] HOBSON P N,STEWART C S.The rumen microbial ecosystem[M].2nd ed.New York:Blackie Academic and Professional,1997.
[2] KRAUSE D O,NAGARAJA T G,WRIGHT A D,et al.Board-invited review:rumen microbiology:leading the way in microbial ecology[J].Journal of Animal Science,2013,91(1):331-341.  
[3] KIM M,MORRISON M,YU Z.Status of the phylogenetic diversity census of ruminal microbiomes[J].FEMS Microbiology Ecology,2011,76(1):49-63.  
[4] CHAUCHEYRAS-DURAND F,CHEVAUX E,MARTIN C,et al.Use of yeast probiotics in ruminants:effects and mechanisms of action on rumen pH, fibre degradation, and microbiota according to the diet[M].RIGOBELO E C.Probiotic in animals.Rijeka,Croatia:Tech,2012:119-162.
[5] BENSON A K,KELLY S A,LEGGE R,et al.Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors[J].Proceedings of the National Academy of Sciences of the United States of America,2010,107(44):18933-18938.  
[6] UYENO Y,SEKIGUCHI Y,TAJIMA K,et al.An rRNA-based analysis for evaluating the effect of heat stress on the rumen microbial composition of Holstein heifers[J].Anaerobe,2010,16(1):27-33.  
[7] RUSSELL J B,RYCHLIK J L.Factors that alter rumen microbial ecology[J].Science,2001,292(5519):1119-1122.  
[8] BEKELE A Z,KOIKE S,KOBAYASHI Y.Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis[J].FEMS Microbiology Letters,2010,305(1):49-57.  
[9] BOZAL N,MONTES M J,TUDELA E,et al.Characterization of several Psychrobacter strains isolated from Antarctic environments and description of Psychrobacter luti sp. nov. and Psychrobacter fozii sp. nov[J].International Journal of Systematic and Evolutionary Microbiology,2003,53(Pt 4):1093-1100.
[10] STEVENSON D M,WEIMER P J.Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR[J]. Applied Microbiology and Biotechnology,2007,75(1):165-174.  
[11] KONG Y,XIA Y,SEVIOUR R,et al.In situ identification of carboxymethyl cellulose-digesting bacteria in the rumen of cattle fed alfalfa or triticale[J].FEMS Microbiology Ecology,2012,80(1):159-167.  
[12] KOBAYASHI Y,SHINKAI T,KOIKE S.Ecological and physiological characterization shows that Fibrobacter succinogenes is important in rumen fiber digestion-review[J].Folia Microbiologica,2008,53(3):195-200.  
[13] JAMI E,MIZRAHI I.Composition and similarity of bovine rumen microbiota across individual animals[J].PLoS One,2012,7(3):e33306.
[14] JAMI E,MIZRAHI I.Similarity of the ruminal bacteria across individual lactating cows[J].Anaerobe,2012,18(3):338-343.  
[15] PITTA D P,PINCHAK W E,DOWD S E,et al.Rumen bacterial dynamics associated with changing from Bermudagrass hay to grazed winter wheat diets[J].Microbial Ecology,2010,59:511-522.
[16] JARVIS G N,KURTOVIC A,HAY A G,et al.The physiological and genetic diversity of bovine Streptococcus bovis strains(1)[J].FEMS Microbiology Ecology,2001,35(1):49-56.
[17] KOCHERGINSKAYA S A,AMINOV R I,WHITE B A.Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gradient gel electrophoresis, random sequencing, and statistical ecology approaches[J].Anaerobe,2001,7(3):119-134.  
[18] JANSSEN P H,KIRS M.Structure of the archaeal community of the rumen[J].Applied and Environmental Microbiology,2008,74(12):3619-3625.  
[19] MOSONI P,MARTIN C,FORANO E,et al.Long-term defaunation increases the abundance of cellulolytic Ruminococci and Methanogens but does not affect the bacterial and methanogen diversity in the rumen of sheep[J].Journal of Animal Science,2011,89(3):783-791.  
[20] BEIJER W H.Methane fermentation in the rumen of cattle[J].Nature,1952,170:576-577.
[21] YANAGITA K,KAMAGATA Y,KAWAHARASAKI M,et al.Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization[J].Bioscience Biotechnology and Biochemistry,2000,64(8):1737-1742.  
[22] SOLIVA C R,MEILE L,HINDRICHSEN I K,et al.Myristic acid supports the immediate inhibitory effect of lauric acid on ruminal methanogens and methane release[J].Anaerobe,2004,10(5):269-276.  
[23] OHENE-ADJEI S,TEATHER R M,IVAN M,et al.Postinoculation protozoan establishment and association patterns of methanogenic archaea in the ovine rumen[J].Applied and Environmental Microbiology,2007,73(14):4609-4618.  
[24] LEAHY S C,KELLY W J,ALTERMANN E,et al.The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions[J].PLoS One,2010,5(1):e8926.
[25] KIRSCHKE S,BOUSQUET P,CIAIS P,et al.Three decades of global methane sources and sinks[J].Nature Geoscience,2013,6(10):813-823.  
[26] 冯仰廉.反刍动物营养学[M].科学出版社,2004.
[27] SYLVESTER J T,KARNATI S K,YU Z,et al.Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR[J].Journal of Nutrition,2004,134(12):3378-3384.
[28] SKILLMAN L C,TOOVEY A F,WILLIAMS A J,et al.Development and validation of a real-time PCR method to quantify rumen protozoa and examination of variability between Entodinium populations in sheep offered a hay-based diet[J].Applied and Environmental Microbiology,2006,72(1):200-206.  
[29] TYMENSEN L,BARKLEY C,MCALLISTER T A.Relative diversity and community structure analysis of rumen protozoa according to T-RFLP and microscopic methods[J].Journal of Microbial Methods,2012,88(1):1-6.  
[30] MCSWEENEY C S,DENMAN S E,WRIGHT A D G,et al.Application of recent DNA/RNA-based techniques in rumen ecology[J].Asian-Australasian Journal of Animal Sciences,2007,20(2):283-294.
[31] GARCIA-MARTINEZ J,ACINAS S G,ANTON A I,et al.Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity[J].Journal of Microbial Methods,1999,36(1-2):55-64.  
[32] DENMAN S E,NICHOLSON M J,BROOKMAN J L,et al.Detection and monitoring of anaerobic rumen fungi using an ARISA method[J].Letters in Applied Microbiology,2008,47(6):492-499.  
[33] GRIFFITH G W,BAKER S,FLIEGEROVA K,et al.Anaerobic fungi:Neocallimastigomycota[J].IMA Fungus,2010,1(2):181-185.  
[34] LIGGENSTOFFER A S,YOUSSEF N H,COUGER M B,et al.Phylogenetic diversity and community structure of anaerobic gut fungi(phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores[J].ISME Journal,2010,4(10):1225-1235.  
[35] YOUSSEF N H,COUGER M B,STRUCHTEMEYER C G,et al. The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader[J].Applied and Enviromental Microbiology,2013,79(15):4620-4634.  
[36] OZKOSE E, THOMAS B J,DAVIES D R,et al.Cyllamyces aberensis gen. nov. sp. nov.,a new anaerobic gut fungus with branched sporangiophores isolated from cattle[J].Canadian Journal of Botany-Revue Canadienne de Botanique,2001,79(6):666-673.  
[37] BERG M M,YEOMAN C J,CHIA N,et al.Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome[J].Environmental Microbiology,2012,14(1):207-227.  
[38] CHAUCHEYRAS-DURAND F,MASSEGLIA S,FONTY G,et al.Influence of the composition of the cellulolytic flora on the development of hydrogenotrophic microorganisms, hydrogen utilization, and methane production in the rumens of gnotobiotically reared lambs[J].Applied and Environmental Microbiology,2010,76(24):7931-7937.  
[39] FONTY G,GOUET P,RATEFIARIVELO H,et al.Establishment of Bacteroides succinogenes and measurement of the main digestive parameters in the rumen of gnotoxenic lambs[J].Canadian Journal of Microbiology,1988,34(8):938-946.  
[40] FONTY G,GOUET P,JOUANY J P,et al.Ecological factors determining establishment of cellulolytic bacteria and protozoa in the rumens of meroxenic lambs[J].Journal of General and Applied Microbiology,1983,129(1):213-223.
[41] JAMI E,ISRAEL A,KOTSER A,et al.Exploring the bovine rumen bacterial community from birth to adulthood[J].ISME Journal,2013,7(6):1069-1079.  
Outlines

/