Molecular Nutrition

Diversity of Ruminal and Fecal Microbiota of Goat

  • WANG Jiwen ,
  • WANG Lizhi ,
  • YAN Tianhai ,
  • GUO Wei ,
  • XU Qin
Expand
  • Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China

Received date: 2015-02-02

  Online published: 2015-08-13

Abstract

This experiment was conducted to explore structure and composition of ruminal and fecal microbiota of goat. Six ten-month-old Boer goats were fed a diet consisting of 30% concentrate and 70% roughage. After 14-day experiment, the rumen fluid (R group) and feces (F group) were sampled [each group had 3 replicates (samples)]. Total DNA of rumen content and feces samples were extracted, and universal prokaryote primers were used to target the V4 to V5 hypervariable region of 16S rRNA, finally the products were sequenced on MiSeq Illumina sequencing platform. The results showed as follows: 1) a total of 227 729 sequences across all rumen content and fecal samples were generated, and the total number of operational taxonomic units (OTUs) detected by the cluster analysis reached 13 601. 2) The 99.337% of all OTUs belonged to bacteria. The most abundant phyla in F and R groups was Firmicutes(65.400%) and Bacteroidetes (60.188%), respectively. 3) One hundred and twenty nine families were detected in all samples. The most abundant families found in F group was Ruminococcaceae (37.705%), which was extremely significantly higher than that in R group (P<0.01); the most abundant families found in R group was Prevotellaceae (29.959%), which was extremely significantly higher than that in F group (P<0.01). 4) Two hundred and twenty nine genera were detected in all samples. The most abundant genus found in F and R groups was unclassified Ruminococcaceae (26.914%) and Prevotella (28.621%), respectively. 5) The analysis revealed 14 genera shared by all 12 samples. Among them, the most abundant genus was Clostridium_Ⅳ(1.748%). It is concluded that there is a significant difference between ruminal and fecal microbiota, and there are many unclassified microbiomes that have high relative abundance in the rumen, which need further investigations.

Cite this article

WANG Jiwen , WANG Lizhi , YAN Tianhai , GUO Wei , XU Qin . Diversity of Ruminal and Fecal Microbiota of Goat[J]. Chinese Journal of Animal Nutrition, 2015 , 27(8) : 2559 -2571 . DOI: 10.3969/j.issn.1006-267x.2015.08.030

References

[1] MACKIE R I,WHITE B A.Recent advances in rumen microbial ecology and metabolism:potential impact on nutrient output[J].Journal of Dairy Science,1990,73(10):2971-2995.  

[2] RUSSELL J B,RYCHLIK J L.Factors that alter rumen microbial ecology[J].Science,2001,292(5519):1119-1122.  

[3] EL-MEADAWAY A,MIR Z,MIR P S,et al.Relative efficacy of inocula from rumen fluid or faecal solution for determining in vitro digestibility and gas production[J].Canadian Journal of Animal Science,1998,78(4):673-679.  

[4] HESPELL R B,AKIN D E,DEHORITY B A.Bacteria,fungi,and protozoa of the rumen[C]//MACKIE R I,WHITE B A,ISAACSON R E.Gastrointestinal microbiology.New York:Chapman and Hall,1997.

[5] YANG L Y,CHEN J,CHENG X L,et al.Phylogenetic analysis of 16S rRNA gene sequences reveals rumen bacterial diversity in Yaks(Bos grunniens)[J].Molecular Biology Reports,2010,37(1):553-562.  

[6] PACE N R.A molecular view of microbial diversity and the biosphere[J].Science,1997,276(5313):734-740.  

[7] EDWARDS J E,HUWS S A,KIM E J,et al.Characterization of the dynamics of initial bacterial colonization of nonconserved forage in the bovine rumen[J].FEMS Microbiology Ecology,2007,62(3):323-335.  

[8] HIGHLANDER S K.High throughput sequencing methods for microbiome profiling:application to food animal systems[J].Animal Health Research Reviews,2012,13(01):40-53.  

[9] SANDRI M,MANFRIN C,PALLAVICINI A,et al.Microbial biodiversity of the liquid fraction of rumen content from lactating cows[J].Animal,2014,8(04):572-579.  

[10] REY M,ENJALBERT F,COMBES S,et al.Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential[J].Journal of Applied Microbiology,2014,116(2):245-257.  

[11] DE OLIVEIRA M N V,JEWELL K A,FREITAS F S,et al.Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer[J].Veterinary Microbiology,2013,164(3):307-314.

[12] 张丽英.饲料分析及饲料质量检测技术[M].北京:中国农业大学出版社,2003.

[13] CAPORASO J G,LAUBER C L,WALTERS W A,et al.Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample[J].Proceedings of the National Academy of Sciences,2011,108(Suppl.1):4516-4522.  

[14] CAPORASO J G,KUCZYNSKI J,STOMBAUGH J,et al.QIIME allows analysis of high-throughput community sequencing data[J].Nature Methods,2010,7(5):335-336.  

[15] SCHLOSS P D,WESTCOTT S L,RYABIN T,et al.Introducing mothur:open-source,platform-independent,community-supported software for describing and comparing microbial communities[J].Applied and Environmental Microbiology,2009,75(23):7537-7541.  

[16] EDGAR R C.Search and clustering orders of magnitude faster than BLAST[J].Bioinformatics,2010,26(19):2460-2461.  

[17] CAPORASO J G,BITTINGER K,BUSHMAN F D,et al.PyNAST:a flexible tool for aligning sequences to a template alignment[J].Bioinformatics,2010,26(2):266-267.  

[18] COLE J R,WANG Q,CARDENAS E,et al.The Ribosomal Database Project:improved alignments and new tools for rRNA analysis[J].Nucleic Acids Research,2009,37(suppl.1):D141-D145.  

[19] DOWD S E,CALLAWAY T R,WOLCOTT R D,et al.Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing(bTEFAP)[J].BMC Microbiology,2008,8(1):125.  

[20] LETTAT A,NOZIÈRE P,SILBERBERG M,et al.Rumen microbial and fermentation characteristics are affected differently by bacterial probiotic supplementation during induced lactic and subacute acidosis in sheep[J].BMC Microbiology,2012,12(1):142.  

[21] VAN BAALE M J,SARGEANT J M,Gnad D P,et al.Effect of forage or grain diets with or without monensin on ruminal persistence and fecal Escherichia coli O157:H7 in cattle[J].Applied and Environmental Microbiology,2004,70(9):5336-5342.  

[22] VAN DONKERSGOED J,GRAHAM T,GANNON V.The prevalence of verotoxins,Escherichia coli O157:H7,and Salmonella in the feces and rumen of cattle at processing[J].The Canadian Veterinary Journal,1999,40(5):332.

[23] HUO W,ZHU W,MAO S.Impact of subacute ruminal acidosis on the diversity of liquid and solid-associated bacteria in the rumen of goats[J].World Journal of Microbiology and Biotechnology,2014,30(2):669-680.  

[24] MIN B R,SOLAIMAN S,SHANGE R,et al.Gastrointestinal bacterial and methanogenic archaea diversity dynamics associated with condensed tannin-containing pine bark diet in goats using 16S rDNA amplicon pyrosequencing[J/OL].International Journal of Microbiology,2014.http://dx.doi.org/10.1155/2014/141909.

[25] KIM M,MORRISON M,YU Z.Status of the phylogenetic diversity census of ruminal microbiomes[J].FEMS Microbiology Ecology,2011,76(1):49-63.  

[26] JAMI E,MIZRAHI I.Composition and similarity of bovine rumen microbiota across individual animals[J].PloS One,2012,7(3):e33306.  

[27] 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.  

[28] 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.  

[29] AVGUTIN G,WALLACE R J,FLINT H J.Phenotypic diversity among ruminal isolates of Prevotella ruminicola:proposal of Prevotella brevis sp.nov.,Prevotella bryantii sp.nov.,and Prevotella albensis sp.nov.and redefinition of Prevotella ruminicola[J].International Journal of Systematic Bacteriology,1997,47(2):284-288.

[30] PURUSHE J,FOUTS D E,MORRISON M,et al.Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii:insights into their environmental niche[J].Microbial Ecology,2010,60(4):721-729.  

[31] WOOD T M,WILSON C A,STEWART C S.Preparation of the cellulase from the cellulolytic anaerobic rumen bacterium Ruminococcus albus and its release from the bacterial cell wall[J].Biochemical Journal,1982,205:129-137.  

[32] DOERNER K C,WHITE B A.Assessment of the endo-1,4-beta-glucanase components of Ruminococcus flavefaciens FD-1[J].Applied and Environmental Microbiology,1990,56(6):1844-1850.

[33] GIRIJA D,DEEPA K,XAVIER F,et al.Analysis of cow dung microbiota-a metagenomic approach[J].Indian Journal of Biochemistry,2013,12:372-378.

[34] DE JESÙS-LABOY K M,GODOY-VITORINO F,PICENO Y M,et al.Comparison of the fecal microbiota in feral and domestic goats[J].Genes,2011,3(1):1-18.

[35] GU S,CHEN D,ZHANG J N,et al.Bacterial community mapping of the mouse gastrointestinal tract[J].PloS One,2013,8(10):e74957.  

[36] SUEN G,STEVENSON D M,BRUCE D C,et al.Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7[J].Journal of Bacteriology,2011,193(19):5574-5575.  

[37] FRANK D N,AMAND A L S,FELDMAN R A,et al.Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases[J].Proceedings of the National Academy of Sciences,2007,104(34):13780-13785.  

[38] HUWS S A,KIM E J,LEE M R F,et al.As yet uncultured bacteria phylogenetically classified as Prevotella,Lachnospiraceae incertae sedis and unclassified Bacteroidales,Clostridiales and Ruminococcaceae may play a predominant role in ruminal biohydrogenation[J].Environmental Microbiology,2011,13(6):1500-1512.  

[39] DEFNOUN S,AMBROSIO M,GARCIA J L,et al.Degradation of cinnamate via β-oxidation to benzoate by a defined,syntrophic consortium of anaerobic bacteria[J].Current Microbiology,2003,46(1):0047-0052.  

[40] FREY J C,PELL A N,Berthiaume R,et al.Comparative studies of microbial populations in the rumen,duodenum,ileum and faeces of lactating dairy cows[J].Journal of Applied Microbiology,2010,108(6):1982-1993.

[41] 冯仰廉.反刍动物营养学[M].北京:科学出版社,2004.

[42] WILLIAMS A G,COLEMAN G S.The rumen protozoa[M].New York:Springer-Verlag; 1992.
Outlines

/