Diet alters both the structure and taxonomy of the ovine gut microbial ecosystem

DNA Research

Volumn 21, Issue 2, 2014, Pages 115-125

  Ellison, Melinda J ^a   Conant, Gavin C ^b   Cockrum, Rebecca R ^c   Austin, Kathy J ^a   Truong, Huan ^b   Becchi, Michela ^b   Lamberson, William R ^b   Cammack, Kristi M ^a  

^a UNIVERSITY OF WYOMING   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

^c Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

16S subunit; Microbiome; Ovis aries

Indexed keywords

DNA 16S; RIBOSOME DNA;

ANIMAL EXPERIMENT; ANIMAL FOOD; ARTICLE; BIOINFORMATICS; CONSENSUS SEQUENCE; CONTROLLED STUDY; DIET; DNA EXTRACTION; DNA SEQUENCE; ECOSYSTEM; FORAGE; GRAIN; INTESTINE; MALE; METAGENOME; MICROBIAL DIVERSITY; NONHUMAN; PHYLUM; PROKARYOTE; RUMINANT STOMACH; SEQUENCE DATABASE; SHEEP; TAXONOMY; ANIMAL; BACTERIA; CLASSIFICATION; GENETICS; MICROBIOLOGY;

ANIMALS; BACTERIA; DIET; DNA, RIBOSOMAL; ECOSYSTEM; METAGENOME; RUMEN; SEQUENCE ANALYSIS, DNA; SHEEP;

EID: 84899046818     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst044     Document Type: Article

References (43)

1. Tringe, S.G and Rubin, E.M. 2005, Metagenomics: DNA sequencing of environmental samples, Nat. Rev. Genet., 6, 805-14
2. Mackie, R.I. 2002, Mutualistic fermentative digestion in the gastrointestinal tract: Diversity and evolution, Integr. Comput. Biol., 42, 319-26
3. Ley, R.E., Lozupone, C.A., Hamady, M., Knight, R and Gordon, J.I. 2008, Worlds within worlds: Evolution of the vertebrate gutmicrobiota, Nat.Rev.Microbiol.,6, 776-88
4. Ley, R.E.,Hamady, M., Lozupone, C.,et al.2008, Evolutionof mammals andtheir gutmicrobes, Science,320,1647-51
5. Human Microbiome Project Consortium. 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207-14
6. Ley, R.E., Backhed, F., Turnbaugh, P., Lozupone, C.A., Knight, R.D and Gordon, J.I. 2005, Obesity alters gut microbial ecology, Proc. Natl. Acad. Sci. USA,102,11070-5
7. Turnbaugh, P.J., Ley, R.E., Mahowald, M.A., Magrini, V., Mardis, E.R and Gordon, J.I. 2006, An obesity-Associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027-31
8. Brulc, J.M., Antonopoulos, D.A., Miller, M.E., et al. 2009, Gene-centric metagenomics of the fiber-Adherent bovine rumen microbiome reveals forage specific glycoside hydrolases, Proc.Natl. Acad. Sci. USA,106,1948-53
9. Kim, M., Morrison, M and Yu, Z. 2011, Status of the phylogenetic diversity census of ruminal microbiomes, FEMS Microbiol. Ecol., 76, 49-63
10. Beja, O., Suzuki, M.T., Heidelberg, J.F., et al. 2002, Unsuspected diversityamongmarineaerobicanoxygenic phototrophs, Nature, 415, 630-3
11. Venter, J.C., Remington, K., Heidelberg, J.F., et al. 2004, Environmental genome shotgun sequencing of the Sargasso Sea, Science, 304, 66-74
12. Whitford, M.F., Forster, R.J., Beard, C.E., Gong, J and Teather, R.M. 1998, Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes, Anaerobe, 4, 153-63
13. Hess, M., Sczyrba, A., Egan, R., et al. 2011, Metagenomic discovery of biomass-Degrading genes and genomes from cow rumen, Science, 331, 463-7
14. Edwards, J.E., McEwan, N.R., Travis, A.J and John Wallace, R. 2004, 16S rDNA library-based analysis of ruminal bacterial diversity, Antonie Van Leeuwenhoek, 86, 263-81
15. Guan, L.L., Nkrumah, J.D., Basarab, J.A and Moore, S.S. 2008, Linkage of microbial ecology to phenotype: Correlation of rumen microbial ecology to cattle's feed efficiency, FEMS Microbiol. Lett., 288, 85-91
16. Zhou, M., Hernandez-Sanabria, E and Guan, L.L. 2009, Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies, Appl. Environ. Microbiol., 75, 6524-33
17. Kong, Y., Teather, R and Forster, R. 2010, Composition, spatial distribution, anddiversity of thebacterialcommunities in the rumen of cows fed different forages, FEMS Microbiol. Ecol., 74, 612-22
18. Pitta, D.W., Pinchak, E.,Dowd, S.E., et al. 2010,Rumenbacterial diversity dynamics associated with changing from bermudagrass hay to grazed winter wheat diets, Microb. Ecol., 59, 511-22
19. Cammack, K.M., Leymaster, K.A., Jenkins, T.G and Nielsen, M.K. 2005, Estimates of genetic parameters for feed intake, feeding behavior, and daily gain incomposite ramlambs, J. Anim. Sci., 83, 777-85
20. Ewing, B and Green, P. 1998, Base-calling of automated sequencer traces using phred. II. Error probabilities, Genome Res., 8, 186-94
21. Miller, C.S., Baker, B.J., Thomas, B.C., Singer, S.W and Banfield, J.F. 2011, EMIRGE: Reconstruction of fulllength ribosomal genes from microbial community short read sequencing data, Genome Biol., 12, R44
22. Langmead, B.,Trapnell, C., Pop, M.and Salzberg, S.L. 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25
23. Cole, J.R., Wang, Q., Cardenas, E., et al. 2009, The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis, Nucleic Acids Res., 37, D141-5
24. Benson, D.A., Cavanaugh, M., Clark, K., et al. 2013, GenBank, Nucleic Acids Res., 41, D36-42
25. Needleman, S.B and Wunsch, C.D. 1970, A general method applicable to the search for similarities in the amino acid sequence of two proteins, J. Mol. Biol., 48, 443-53
26. Li, D., Sajjapongse, K.,Truong, H.,Conant, G.andBecchi, M. 2013, A distributed CPU-GPU framework for pairwise alignments on large-scale sequence datasets. In: The 24th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP13), George Washington University, VA, pp. 329-38
27. Powell, A.J., Conant, G.C., Brown, D.E., Carbone, I and Dean, R.A. 2008, Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens, BMC Genomics, 9, 147
28. Sokal, R.R and Rohlf, F.J. 1995, Biometry, 3rd edition. W. H. Freeman and Company: New York
29. Wheeler, D.L., Church, D.M., Edgar, R., et al. 2004, Database resources of the National Center for Biotechnology Information: Update, Nucleic Acids Res., 32, D35-40
30. McGill, B.J., Etienne, R.S., Gray, J.S., et al. 2007, Species abundance distributions: Moving beyond single prediction theories to integration within an ecological framework, Ecol. Lett., 10, 995-1015
31. Izsák, J and Pavoine, S. 2012, Links between the species abundance distribution and the shape of the corresponding rank abundance curve, Ecol. Indicators, 14, 1-6
32. Press, W.H., Teukolsky, S.A., Vetterling, W.A and Flannery, B.P. 1992, Numerical Recipes in C. Cambridge University Press: New York
33. Conant, G.C. andWolfe, K.H. 2006, Functional partitioning of yeast co-expression networks after genome duplication, PLoS. Biol., 4, e109
34. Forster, P., Ramaswamy, V., Artaxo, P., et al. 2007, Changes in Atmospheric Constituents and in Radiative Forcing, In: Solomon, S., Qin, D. andManning, M., et al. (eds), Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press: Cambridge, UK.
35. Lana, R.R.P., Russell, J.B and Van Amburgh, M.E. 1998, The role of pH in regulating ruminal methane and ammonia production, J. Anim. Sci., 76, 2190-6
36. Unterseher, M., Jumpponen, A., Opik, M., et al. 2011, Species abundance distributions and richness estimations in fungal metagenomics-lessons learned from community ecology, Mol. Ecol., 20, 275-85
37. Bekele, A.Z., Koike, S and Kobayashi, Y. 2010, Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis, FEMS Microbiol. Lett., 305, 49-57
38. Stevenson, D.M and Weimer, P.J. 2007, Dominance of Prevotella and lowabundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-Time PCR, Appl. Microbiol. Biotechnol., 75, 165-74
39. Hillebrand, H., Bennett, D.M and Cadotte, M.W. 2008, Consequences of dominance: A review of evenness effects on local and regional ecosystem processes, Ecology, 89, 1510-20
40. Tuomisto, H. 2010, A consistent terminology for quantifying species diversity? Yes, it does exist, Oecologia, 164, 853-60
41. Torsvik, V.,Ovreas, L. andThingstad, T.F. 2002, Prokaryotic diversity-magnitude, dynamics, and controlling factors, Science, 296, 1064-6
42. Norberg, J., Swaney, D.P., Dushoff, J., Lin, J., Casagrandi, R and Levin, S.A. 2001, Phenotypic diversity and ecosystem functioning in changing environments: A theoretical framework, Proc. Natl. Acad. Sci. USA, 98, 11376-81
43. Nijs, I and Roy, J. 2000, How important are species richness, species evenness and interspecific differences to productivity? A mathematical model, Oikos, 88, 57-66