title: Comparative studies of the composition of bacterial microbiota associated with the ruminal content, ruminal epithelium and in the faeces of lactating dairy cows.
abstract: The objective of this research was to compare the composition of bacterial microbiota associated with the ruminal content (RC), ruminal epithelium (RE) and faeces of Holstein dairy cows. The RC, RE and faecal samples were collected from six Holstein dairy cows when the animals were slaughtered. Community compositions of bacterial 16S rRNA genes from RC, RE and faeces were determined using a MiSeq sequencing platform with bacterial-targeting universal primers 338F and 806R. UniFrac analysis revealed that the bacterial communities of RC, RE and faeces were clearly separated from each other. Statistically significant dissimilarities were observed between RC and faeces (P = 0.002), between RC and RE (P = 0.003), and between RE and faeces (P = 0.001). A assignment of sequences to taxa showed that the abundance of the predominant phyla Bacteroidetes was lower in RE than in RC, while a significant higher (P < 0.01) abundance of Proteobacteria was present in RE than in RC. When compared with the RC, the abundance of Firmicutes and Verrucomicrobia was higher in faeces, and RC contained a greater abundance of Bacteroidetes and Tenericutes. A higher proportions of Butyrivibrio and Campylobacter dominated RE as compared to RC. The faecal microbiota was less diverse than RC and dominated by genera Turicibacter and Clostridium. In general, these findings clearly demonstrated the striking compositional differences among RC, RE and faeces, indicating that bacterial communities are specific and adapted to the harbouring environment.
authors.affiliation: Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.
authors.forename: Jun-hua
authors.initials: JH
authors.lastname: Liu
authors.affiliation: Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.
authors.forename: Meng-ling
authors.initials: ML
authors.lastname: Zhang
authors.affiliation: Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.
authors.forename: Rui-yang
authors.initials: RY
authors.lastname: Zhang
authors.affiliation: Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.
authors.forename: Wei-yun
authors.initials: WY
authors.lastname: Zhu
authors.affiliation: Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.
authors.forename: Sheng-yong
authors.initials: SY
authors.lastname: Mao
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D058448:Biota; D002417:Cattle; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D004848:Epithelium / Q000382:microbiology*; D005243:Feces / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012417:Rumen / Q000382:microbiology*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
references.citation: Appl Environ Microbiol. 2011 May;77(9):2992-3001
references.pmid: 21378055
references.citation: Appl Environ Microbiol. 2006 Jul;72(7):5069-72
references.pmid: 16820507
references.citation: FEMS Microbiol Lett. 2007 Dec;277(2):205-9
references.pmid: 18031341
references.citation: Int J Syst Evol Microbiol. 2000 Mar;50 Pt 2:679-88
references.pmid: 10758875
references.citation: J Appl Bacteriol. 1979 Dec;47(3):443-55
references.pmid: 541305
references.citation: J Vet Med Sci. 1992 Feb;54(1):185-8
references.pmid: 1313704
references.citation: Br J Nutr. 1995 Apr;73(4):491-505
references.pmid: 7794867
references.citation: Bioinform Biol Insights. 2014 Jun 08;8:109-25
references.pmid: 24940050
references.citation: J Clin Microbiol. 2009 Apr;47(4):1199-201
references.pmid: 19204100
references.citation: Dis Markers. 2011;30(4):151-61
references.pmid: 21694441
references.citation: Appl Environ Microbiol. 2011 Aug 15;77(16):5770-81
references.pmid: 21705529
references.citation: Vet Microbiol. 2012 Feb 24;155(1):72-80
references.pmid: 21890283
references.citation: ISME J. 2012 Aug;6(8):1621-4
references.pmid: 22402401
references.citation: Vet Microbiol. 2010 Nov 20;146(1-2):98-104
references.pmid: 20554126
references.citation: J Anim Sci. 2010 Dec;88(12):3977-83
references.pmid: 20729286
references.citation: FEMS Microbiol Ecol. 2011 Apr;76(1):49-63
references.pmid: 21223325
references.citation: Appl Environ Microbiol. 2009 Sep;75(17):5489-95
references.pmid: 19617391
references.citation: Appl Environ Microbiol. 1993 Oct;59(10):3513-5
references.pmid: 8250575
references.citation: Curr Pharm Des. 2005;11(8):1047-53
references.pmid: 15777254
references.citation: Appl Environ Microbiol. 2007 Aug;73(16):5261-7
references.pmid: 17586664
references.citation: Bioinformatics. 2010 Jan 15;26(2):266-7
references.pmid: 19914921
references.citation: Appl Microbiol Biotechnol. 2013 Jul;97(14):6477-88
references.pmid: 23666481
references.citation: Animal. 2007 Aug;1(7):939-44
references.pmid: 22444795
references.citation: Anaerobe. 2013 Dec;24:12-9
references.pmid: 23994204
references.citation: J Anim Sci. 1996 Mar;74(3):678-84
references.pmid: 8707727
references.citation: Curr Microbiol. 2013 Sep;67(3):341-50
references.pmid: 23636494
references.citation: Appl Environ Microbiol. 1998 Mar;64(3):907-13
references.pmid: 9501430
references.citation: Vet Microbiol. 2012 Dec 7;160(3-4):496-500
references.pmid: 22749760
references.citation: Mol Biol Evol. 2009 Jul;26(7):1641-50
references.pmid: 19377059
references.citation: Appl Environ Microbiol. 2005 Dec;71(12):8228-35
references.pmid: 16332807
references.citation: J Bacteriol. 1995 Oct;177(20):5727-31
references.pmid: 7592315
references.citation: Biosci Biotechnol Biochem. 2005 Sep;69(9):1793-7
references.pmid: 16195605
references.citation: Gut. 2000 Apr;46(4):507-14
references.pmid: 10716680
references.citation: Bioinformatics. 2010 Oct 1;26(19):2460-1
references.pmid: 20709691
references.citation: Environ Microbiol. 2010 Jul;12(7):1842-54
references.pmid: 20236166
references.citation: Br J Nutr. 2014 Feb;111(3):387-402
references.pmid: 23931069
references.citation: Br J Nutr. 1979 Nov;42(3):553-7
references.pmid: 508714
references.citation: Nature. 2004 Dec 9;432(7018):750-3
references.pmid: 15592412
references.citation: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references.pmid: 19801464
references.citation: Appl Environ Microbiol. 2013 Jun;79(12):3744-55
references.pmid: 23584771
references.citation: Lett Appl Microbiol. 2008 Nov;47(5):367-73
references.pmid: 19146523
references.citation: J Appl Microbiol. 2006 Jun;100(6):1261-71
references.pmid: 16696673
references.citation: Am J Clin Nutr. 1979 Jan;32(1):139-48
references.pmid: 367141
references.citation: ISME J. 2012 Mar;6(3):531-41
references.pmid: 21938024
references.citation: J Bacteriol. 2000 Sep;182(17):4704-10
references.pmid: 10940008
references.citation: Vet Res. 1998 May-Aug;29(3-4):219-32
references.pmid: 9689739
references.citation: BMC Vet Res. 2012;8:237
references.pmid: 23217205
references.citation: Appl Environ Microbiol. 1980 Jan;39(1):233-41
references.pmid: 7356316
references.citation: Br J Nutr. 2014 Aug 14;112(3):416-27
references.pmid: 24846282