Bacterial census of poultry intestinal microbiome

Poultry Science

Volumn 92, Issue 3, 2013, Pages 671-683

  Wei, S ^a   Morrison, M ^a,b   Yu, Z ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b CSIRO   (Australia)

Author keywords

16S rRNA; Chicken; Intestinal microbiome; Na ve analysis; Turkey

Indexed keywords

EID: 84874403622     PISSN: 00325791     EISSN: 15253171     Source Type: Journal    
DOI: 10.3382/ps.2012-02822     Document Type: Article

References (42)

1. Barnes, E. M., G. C. Mead, D. A. Barnum, and E. G. Harry. 1972. The intestinal flora of the chicken in the period 2 to 6 weeks of age, with particular reference to the anaerobic bacteria. Br. Poult. Sci. 13:311-326.
2. Bjerrum, L., R. M. Engberg, T. D. Leser, B. B. Jensen, K. Finster, and K. Pedersen. 2006. Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques. Poult. Sci. 85:1151-1164.
3. Brisbin, J. T., J. Gong, and S. Sharif. 2008. Interactions between commensal bacteria and the gut-associated immune system of the chicken. Anim. Health Res. Rev. 9:101-110.
4. Callaway, T. R., S. E. Dowd, R. D. Wolcott, Y. Sun, J. L. McReynolds, T. S. Edrington, J. A. Byrd, R. C. Anderson, N. Krueger, and D. J. Nisbet. 2009. Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing. Poult. Sci. 88:298-302.
5. Edgar, R. C., B. J. Haas, J. C. Clemente, C. Quince, and R. Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194-2200.
6. Edwards, J. E., N. R. McEwan, A. J. Travis, and R. John Wallace. 2004. 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie van Leeuwenhoek 86:263-281.
7. Gong, J., R. J. Forster, H. Yu, J. R. Chambers, R. Wheatcroft, P. M. Sabour, and S. Chen. 2002. Molecular analysis of bacterial populations in the ileum of broiler chickens and comparison with bacteria in the cecum. FEMS Microbiol. Ecol. 41:171-179.
8. Haas, B. J., D. Gevers, A. M. Earl, M. Feldgarden, D. V. Ward, G. Giannoukos, D. Ciulla, D. Tabbaa, S. K. Highlander, E. Sodergren, B. Methe, T. Z. DeSantis, J. F. Petrosino, R. Knight, and B. W. Birren. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21:494-504.
9. Hollister, A. G., D. E. Corrier, D. J. Nisbet, R. C. Beier, and J. R. Deloach. 1994. Comparison of effects of chicken cecal microorganisms maintained in continuous culture and provision of dietary lactose on cecal colonization by Salmonella typhimurium in turkey poults and broiler chicks. Poult. Sci. 73:640-647.
10. Jankowski, J., J. Juskiewicz, K. Gulewicz, A. Lecewicz, B. A. Slominski, and Z. Zdunczyk. 2009. The effect of diets containing soybean meal, soybean protein concentrate, and soybean protein isolate of different oligosaccharide content on growth performance and gut function of young turkeys. Poult. Sci. 88:2132-2140.
11. Kim, M., M. Morrison, and Z. Yu. 2011. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol. Ecol. 76:49-63.
12. Larue, R., Z. Yu, V. A. Parisi, A. R. Egan, and M. Morrison. 2005. Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ. Microbiol. 7:530-543.
13. Lee, J. E., S. Lee, J. Sung, and G. Ko. 2011. Analysis of human and animal fecal microbiota for microbial source tracking. ISME J. 5:362-365.
14. Lemos, L. N., R. R. Fulthorpe, and L. F. W. Roesch. 2012. Low sequencing efforts bias analyses of shared taxa in microbial communities. Folia Microbiol. (Praha) 57:409-413.
15. Lozupone, C., and R. Knight. 2005. UniFrac: A new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
16. Lu, J., and J. S. Domingo. 2008. Turkey fecal microbial community structure and functional gene diversity revealed by 16S rRNA gene and metagenomic sequences. J. Microbiol. 46:469-477.
17. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.-H. Schleifer. 2004. ARB: A software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
18. Meyer, F., D. Paarmann, M. D'Souza, R. Olson, E. M. Glass, M. Kubal, T. Paczian, A. Rodriguez, R. Stevens, A. Wilke, J. Wilkening, and R. A. Edwards. 2008. The metagenomics RAST server-A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386.
19. Nordentoft, S., L. Molbak, L. Bjerrum, J. De Vylder, F. Van Immerseel, and K. Pedersen. 2011. The influence of the cage system and colonisation of Salmonella Enteritidis on the microbial gut flora of laying hens studied by T-RFLP and 454 pyrosequencing. BMC Microbiol. 11:187.
20. Ondov, B. D., N. H. Bergman, and A. M. Phillippy. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12:385.
21. Owens, B., L. Tucker, M. A. Collins, and K. J. McCracken. 2008. Effects of different feed additives alone or in combination on broiler performance, gut microflora and ileal histology. Br. Poult. Sci. 49:202-212.
22. Palander, S., M. Näsi, and P. Palander. 2010. Digestibility and energy value of cereal-based diets in relation to digesta viscosity and retention time in turkeys and chickens at different ages estimated with different markers. Arch. Anim. Nutr. 64:238-253.
23. Qu, A., J. M. Brulc, M. K. Wilson, B. F. Law, J. R. Theoret, L. A. Joens, M. E. Konkel, F. Angly, E. A. Dinsdale, R. A. Edwards, K. E. Nelson, and B. A. White. 2008. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS ONE 3:e2945.
24. Roesch, L. F. W., R. R. Fulthorpe, A. Riva, G. Casella, A. K. M. Hadwin, A. D. Kent, S. H. Daroub, F. A. O. Camargo, W. G. Farmerie, and E. W. Triplett. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1:283-290.
25. Ruiz, V., D. Ruiz, A. G. Gernat, J. L. Grimes, J. G. Murillo, M. J. Wineland, K. E. Anderson, and R. O. Maguire. 2008. The effect of quicklime (CaO) on litter condition and broiler performance. Poult. Sci. 87:823-827.
26. Saengkerdsub, S., R. C. Anderson, H. H. Wilkinson, W.-K. Kim, D. J. Nisbet, and S. C. Ricke. 2007. Identification and quantification of methanogenic Archaea in adult chicken ceca. Appl. Environ. Microbiol. 73:353-356.
27. Saitou, N., and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
28. Salanitro, J. P., I. G. Fairchilds, and Y. D. Zgornicki. 1974. Isolation, culture characteristics, and identification of anaerobic bacteria from the chicken cecum. Appl. Microbiol. 27:678-687.
29. Schloss, P. D., and J. Handelsman. 2004. Status of the microbial census. Microbiol. Mol. Biol. Rev. 68:686-691.
30. Schloss, P. D., and J. Handelsman. 2006. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl. Environ. Microbiol. 72:6773-6779.
31. Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, R. A. Lesniewski, B. B. Oakley, D. H. Parks, C. J. Robinson, J. W. Sahl, B. Stres, G. G. Thallinger, D. J. Van Horn, and C. F. Weber. 2009. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
32. Scupham, A. J. 2007a. Examination of the microbial ecology of the avian intestine in vivo using bromodeoxyuridine. Environ. Microbiol. 9:1801-1809.
33. Scupham, A. J. 2007b. Succession in the intestinal microbiota of preadolescent turkeys. FEMS Microbiol. Ecol. 60:136-147.
34. Scupham, A. J., T. G. Patton, E. Bent, and D. O. Bayles. 2008. Comparison of the cecal microbiota of domestic and wild turkeys. Microb. Ecol. 56:322-331.
35. Stanley, D., S. E. Denman, R. J. Hughes, M. S. Geier, T. M. Crowley, H. Chen, V. R. Haring, and R. J. Moore. 2012a. Intestinal microbiota associated with differential feed conversion efficiency in chickens. Appl. Microbiol. Biotechnol. http://dx.doi. org/10.1007/s00253-011-3847-5.
36. Stanley, D., A. L. Keyburn, S. E. Denman, and R. J. Moore. 2012b. Changes in the caecal microflora of chickens following Clostridium perfringens challenge to induce necrotic enteritis. Vet. Microbiol. 159:155-162.
37. Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
38. Yegani, M., and D. R. Korver. 2008. Factors affecting intestinal health in poultry. Poult. Sci. 87:2052-2063.
39. Youssef, N. H., and M. S. Elshahed. 2008. Species richness in soil bacterial communities: A proposed approach to overcome sample size bias. J. Microbiol. Methods 75:86-91.
40. Yu, Z., M. Yu, and M. Morrison. 2006. Improved serial analysis of V1 ribosomal sequence tags (SARST-V1) provides a rapid, comprehensive, sequence-based characterization of bacterial diversity and community composition. Environ. Microbiol. 8:603-611.
41. Yue, J. C., and M. K. Clayton. 2005. A similarity measure based on species proportions. Comm. Statist. Theory Methods 34:2123-2131.
42. Zhu, X. Y., T. Zhong, Y. Pandya, and R. D. Joerger. 2002. 16S rRNA-based analysis of microbiota from the cecum of broiler chickens. Appl. Environ. Microbiol. 68:124-137.