Hostname: page-component-848d4c4894-75dct Total loading time: 0 Render date: 2024-05-27T07:45:14.926Z Has data issue: false hasContentIssue false
  • English
  • Français

The use of multiple restriction enzymes in terminal restriction fragment length polymorphism analysis and identification of performance-related caecal bacterial groups in growing broiler chickens

Published online by Cambridge University Press:  08 July 2015

R. RUIZ ,
A. BARROSO-DELJESÚS ,
L. LARA  and
L. A. RUBIO
R. RUIZ
Affiliation:
Fisiología y Bioquímica de la Nutrición Animal (EEZ, CSIC), Profesor Albareda 1, 18008 Granada, Spain
A. BARROSO-DELJESÚS
Affiliation:
Unidad de Genómica, Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, PTS Granada, Avda. del Conocimiento s/n, Armilla, 18016 Granada, Spain
L. LARA
Affiliation:
Fisiología y Bioquímica de la Nutrición Animal (EEZ, CSIC), Profesor Albareda 1, 18008 Granada, Spain
L. A. RUBIO*
Affiliation:
Fisiología y Bioquímica de la Nutrición Animal (EEZ, CSIC), Profesor Albareda 1, 18008 Granada, Spain
*
*To whom all correspondence should be addressed. Email: lrubio@eez.csic.es
Get access Rights & Permissions [Opens in a new window]

Summary

Four restriction enzymes (AluI, HhaI, MspI and RsaI), either individually or in combination, were used in terminal restriction fragment length polymorphism (T-RFLP) analysis to: (i) characterize the chicken intestinal bacterial community; and (ii) tentatively identify intestinal bacterial groups related with increased performance parameters in broiler chickens. Balanced commercial diets free of any feed antibiotics were offered to broilers assigned randomly to one of the five dietary treatments: control (C) (commercial diet with no additive), inulin (I), fructose caramel, propyl propane thiosulphonate (PTS-O)-45 and PTS-O-90. Except for the inulin-supplemented diet, multivariate statistical analysis of T-RFLP profiles based on individual enzymes or their combinations showed that the caecal bacterial community composition was significantly different among diets, particularly between the control and the supplemented diets. Individual RsaI and the combination AluI + RsaI proved to be the most useful to discriminate between dietary treatments. Clostridiaceae 1, Lachnospiraceae, Ruminococcaceae and Micrococcaceae were tentatively identified as those families most likely to be implicated in defining the caecal microbiota composition of growing broiler chickens, and also as those most closely related with differences in productive parameters.

Type
Animal Research Papers
Information
The Journal of Agricultural Science , Volume 153 , Issue 8 , November 2015 , pp. 1491 - 1505
Check for updates
Copyright
Copyright © Cambridge University Press 2015 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

Apajalahti, J., Kettunen, A. & Graham, H. (2004). Characteristics of the gastrointestinal microbial communities, with special reference to the chicken. World's Poultry Science Journal 60, 223–232.CrossRefGoogle Scholar
Apajalahti, J. H. A., Kettunen, A., Nurminen, P. H., Jatila, H. & Holben, W. E. (2003). Selective plating underestimates abundance and shows differential recovery of bifidobacterial species from human feces. Applied and Environmental Microbiology 69, 5731–5735.CrossRefGoogle ScholarPubMed
Barnes, E. M. (1979). The intestinal microflora of poultry and game birds during life and after storage. Journal of Applied Bacteriology 46, 407–419.CrossRefGoogle ScholarPubMed
Beckmann, L., Simon, O. & Vahjen, W. (2006). Isolation and identification of mixed linked β-glucan degrading bacteria in the intestine of broiler chickens and partial characterization of respective 1,3-1,4-β-glucanase activities. Journal of Basic Microbiology 46, 175–185.CrossRefGoogle ScholarPubMed
Boros, D., Marquardt, R. R. & Guenter, W. (1998). Site of exoenzyme action in gastrointestinal tract of broiler chicks. Canadian Journal of Animal Science 78, 599–602.CrossRefGoogle Scholar
Bray, J. R. & Curtis, J. T. (1957). An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs 27, 325–349.CrossRefGoogle Scholar
Chee, S. H., Iji, P. A., Choct, M., Mikkelsen, L. L. & Kocher, A. (2010). Characterisation and response of intestinal microflora and mucins to manno-oligosaccharide and antibiotic supplementation in broiler chickens. British Poultry Science 51, 368–380.CrossRefGoogle ScholarPubMed
Chen, C. Y., Yu, C., Chen, S. W., Chen, B. J. & Wang, H. T. (2013). Effect of yeast with bacteriocin from rumen bacteria on growth performance, caecal flora, caecal fermentation and immunity function of broiler chicks. Journal of Agricultural Science, Cambridge 151, 287–297.CrossRefGoogle Scholar
Clarke, K. R. (1993). Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology 18, 117–143.CrossRefGoogle Scholar
Clarke, K. R. & Warwick, R. M. (2001). Changes in Marine Communities: an Approach to Statistical Analysis and Interpretation, 2nd ed. Plymouth, UK: PRIMER-E, Ltd., Plymouth Marine Laboratory.Google Scholar
Delzenne, N. M. & Cani, P. D. (2011). Interaction between obesity and the gut microbiota: relevance in nutrition. Annual Review of Nutrition 21, 15–31.CrossRefGoogle Scholar
Dunbar, J., Ticknor, L. O. & Kuske, C. R. (2001). Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Applied and Environmental Microbiology 67, 190–197.CrossRefGoogle ScholarPubMed
European Union (2003). Regulation (EC) No 1831/2003 of the European Parliament and of the Council of 22 September 2003 on additives for use in animal nutrition. Official Journal of the European Union L268, 29–43.Google Scholar
Frick, J. S. & Autenrieth, I. B. (2013). The gut microflora and its variety of roles in health and disease. In Between Pathogenicity and Commensalism (Eds Dobrindt, U., Hacker, J. H. & Svanborg, C.), pp. 273–289. Current Topics in Microbiology and Immunology, Vol. 358. Berlin: Springer-Verlag.CrossRefGoogle Scholar
Gaggìa, F., Mattarelli, P. & Biavati, B. (2010). Probiotics and prebiotics in animal feeding for safe food production. International Journal of Food Microbiology 141(Suppl. 1), S15–S28.CrossRefGoogle ScholarPubMed
Geier, M. S., Torok, V. A., Allison, G. E., Ophel-Keller, K. & Hughes, R. J. (2009). Indigestible carbohydrates alter the intestinal microbiota but do not influence the performance of broiler chickens. Journal of Applied Microbiology 106, 1540–1548.CrossRefGoogle Scholar
Gong, J., Forster, R. J., Yu, H., Chambers, J. R., Wheatcroft, R., Sabour, P. M. & Chen, S. (2002). Molecular analysis of bacterial populations in the ileum of broiler chickens and comparison with bacteria in the cecum. FEMS Microbiology Ecology 41, 171–179.CrossRefGoogle ScholarPubMed
Greiner, T. & Bäckhed, F. (2011). Effects of the gut microbiota on obesity and glucose homeostasis. Trends in Endocrinology and Metabolism 22, 117–123.CrossRefGoogle ScholarPubMed
Højberg, O., Canibe, N., Poulsen, H. D., Hedemann, M. S. & Jensen, B. B. (2005). Influence of dietary zinc oxide and copper sulfate on the gastrointestinal ecosystem in newly weaned piglets. Applied and Environmental Microbiology 71, 2267–2277.CrossRefGoogle ScholarPubMed
Huang, H.-D., Wang, W., Ma, T., Li, G.-Q., Liang, F.-L. & Liu, R.-L. (2009). Sphingomonas sanxanigenens sp. nov., isolated from soil. International Journal of Systematic and Evolutionary Microbiology 59, 719–723.CrossRefGoogle ScholarPubMed
Jozefiak, D., Rutkowski, A., Kaczmarek, S., Jensen, B. B., Engberg, R. M. & Højberg, O. (2010). Effect of β -glucanase and xylanase supplementation of barley- and rye-based diets on cecal microbiota of broiler chickens. British Poultry Science 51, 546–557.CrossRefGoogle ScholarPubMed
Kaplan, C. W., Astaire, J. C., Sanders, M. E., Reddy, B. S. & Kitts, C. L. (2001). 16S Ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus NCFM. Applied and Environmental Microbiology 67, 1935–1939.CrossRefGoogle ScholarPubMed
Kent, A. D., Smith, D. J., Benson, B. J. & Triplett, E. W. (2003). Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Applied and Environmental Microbiology 69, 6768–6776.CrossRefGoogle ScholarPubMed
Lu, J., Idris, U., Harmon, B., Hofacre, C., Maurer, J. J. & Lee, M. D. (2003 a). Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Applied and Environmental Microbiology 69, 6816–6824.CrossRefGoogle ScholarPubMed
Lu, J., Sanchez, S., Hofacre, C., Maurer, J. J., Harmon, B. G. & Lee, M. D. (2003 b). Evaluation of broiler litter with reference to the microbial composition as assessed by using 16S rRNA and functional gene markers. Applied and Environmental Microbiology 69, 901–908.CrossRefGoogle Scholar
Mead, G. C. (1989). Microbes of the avian cecum: types present and substrates utilized. Journal of Experimental Zoology 252(Suppl. 3), 48–54.CrossRefGoogle Scholar
Ministerio de la Presidencia (2005). Real decreto 1201/2005, de 10 de Octubre, sobre protección de los animales utilizados para experimentación y otros fines científicos (royal decree 1201/2005, of October 10, on the protection of animals used for experimental and other scientific purposes). BOE (Diario oficial Boletín Oficial del Estado) 252, 34367–34391. Available online from: http://www.boe.es/buscar/doc.php?id=BOE-A-2005-17344 (verified May 2015).Google Scholar
Nava, G. M., Attene-Ramos, M. S., Gaskins, H. R. & Richards, J. D. (2009). Molecular analysis of microbial community structure in the chicken ileum following organic acid supplementation. Veterinary Microbiology 137, 345–353.CrossRefGoogle ScholarPubMed
Ortiz Mellet, C. & García Fernández, J. M. (2010). Difructose Dianhydrides (DFAs) and DFA enriched products as functional foods. Topics in Current Chemistry 294, 49–77.CrossRefGoogle Scholar
Park, S., Ku, Y. K., Seo, M. J., Kim, D. Y., Yeon, Y. E., Lee, K. M., Jeong, S. C., Yoon, W. K., Harn, C. H. & Kim, H. M. (2006). Principal component analysis and discriminant analysis (PCA-DA) for discriminating profiles of terminal restriction fragment length polymorphism (T-RFLP) in soil bacterial communities. Soil Biology and Biochemistry 38, 2344–2349.CrossRefGoogle Scholar
Patel, G. B., Khan, A. W., Agnew, B. J. & Colvin, J. R. (1980). Isolation and characterization of an anaerobic, cellulolytic microorganism, Acetivibrio cellulolyticus gen. nov., sp. nov. International Journal of Systematic Bacteriology 30, 179–185.CrossRefGoogle Scholar
Peinado, M. J., Ruiz, R., Echávarri, A., Aranda-Olmedo, I. & Rubio, L. A. (2013 a). Garlic derivative PTS-O modulates intestinal microbiota composition and improves digestibility in growing broiler chickens. Animal Feed Science and Technology 181, 87–92.CrossRefGoogle Scholar
Peinado, M. J., Echávarri, A., Ruiz, R., Suárez-Pereira, E., Ortiz Mellet, C., García Fernández, J. M. & Rubio, L. A. (2013 b). Effects of inulin and di-d-fructose dianhydride-enriched caramels on intestinal microbiota composition and performance of broiler chickens. Animal 7, 1779–1788.CrossRefGoogle ScholarPubMed
Pourabedin, M., Xu, Z., Baurhoo, B., Chevaux, E. & Zhao, X. (2014). Effects of mannan oligosaccharide and virginiamycin on the cecal microbial community and intestinal morphology of chickens raised under suboptimal conditions. Canadian Journal of Microbiology 60, 255–266.CrossRefGoogle ScholarPubMed
Rehman, H., Hellweg, P., Taras, D. & Zentek, J. (2008). Effects of dietary inulin on the intestinal short chain fatty acids and microbial ecology in broiler chickens as revealed by denaturing gradient gel electrophoresis. Poultry Science 87, 783–789.CrossRefGoogle ScholarPubMed
Rehman, H. U., Vahjen, W., Awad, W. A. & Zentek, J. (2007). Indigenous bacteria and bacterial metabolic products in the gastrointestinal tract of broiler chickens. Archives of Animal Nutrition 61, 319–335.CrossRefGoogle ScholarPubMed
Ruiz, R., García, M. P., Lara, A. & Rubio, L. A. (2010). Garlic derivatives (PTS and PTS-O) differently affect the ecology of swine faecal microbiota in vitro . Veterinary Microbiology 144, 110–117.CrossRefGoogle ScholarPubMed
Ruiz, R. & Rubio, L. A. (2009). Lyophilisation improves the extraction of PCR-quality community DNA from pig faecal samples. Journal of the Science of Food and Agriculture 89, 723–727.CrossRefGoogle Scholar
Stanley, D., Hughes, R. J. & Moore, R. J. (2014). Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease. Applied Microbiology and Biotechnology 98, 4301–4310.CrossRefGoogle ScholarPubMed
Thayer, D. W. (1976). Facultative wood-digesting bacteria from the hind-gut of the termite Reticulitermes hesperus . Journal of General Microbiology 95, 287–296.CrossRefGoogle Scholar
Torok, V. A., Ophel-Keller, K., Loo, M. & Hughes, R. J. (2008). Application of methods for identifying broiler chicken gut bacterial species linked with increased energy metabolism. Applied and Environmental Microbiology 74, 783–791.CrossRefGoogle ScholarPubMed
Torok, V. A., Allison, G. E., Percy, N. J., Ophel-Keller, K. & Hughes, R. J. (2011 a). Influence of antimicrobial feed additives on broiler commensal posthatch gut microbiota development and performance. Applied and Environmental Microbiology 77, 3380–3390.CrossRefGoogle ScholarPubMed
Torok, V. A., Hughes, R. J., Mikkelsen, L. L., Pérez-Maldonado, R. P., Balding, K., MacAlpine, R., Percy, N. J. & Ophel-Keller, K. (2011 b). Identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials. Applied and Environmental Microbiology 77, 5868–5878.CrossRefGoogle ScholarPubMed
Vispo, C. & Karasov, W. H. (1997). The interaction of avian gut microbes and their host: an elusive symbiosis. In Gastrointestinal Microbiology. 1. Gastrointestinal Ecosystem and Fermentations (Eds Mackie, R. J. & White, B. A.), pp. 116–155. New York: Chapman and Hall.CrossRefGoogle Scholar
Viveros, A., Chamorro, S., Pizarro, M., Arija, I., Centeno, C. & Brenes, A. (2011). Effects of dietary polyphenol-rich grape products on intestinal microflora and gut morphology in broiler chicks. Poultry Science 90, 566–578.CrossRefGoogle ScholarPubMed
Wang, H. T., Li, Y. H., Chou, I. P., Hsieh, Y. H., Chen, B. J. & Chen, C. Y. (2011). Albusin B modulates lipid metabolism and increases antioxidant defence in broiler chickens by a proteomic approach. Journal of the Science of Food and Agriculture 93, 284–292.CrossRefGoogle Scholar
Wei, S., Morrison, M. & Yu, Z. (2013). Bacterial census of poultry intestinal microbiome. Poultry Science 92, 671–683.CrossRefGoogle ScholarPubMed
Widmer, F., Hartmann, M., Frey, B. & Kolliker, R. (2006). A novel strategy to extract specific phylogenetic sequence information from community TRFLP. Journal of Microbiological Methods 66, 512–520.CrossRefGoogle ScholarPubMed
Yin, Y., Lei, F., Zhu, L., Li, S., Wu, Z., Zhang, R., Gao, G. F., Zhu, B. & Wang, X. (2010). Exposure of different bacterial inocula to new born chicken affects gut microbiota development and ileum gene expression. ISME Journal 4, 367–376.CrossRefGoogle Scholar
Supplementary material: File

Ruiz supplementary material

Dataset S1

Download Ruiz supplementary material(File)
File 44.6 KB
Supplementary material: File

Ruiz supplementary material

Dataset S2

Download Ruiz supplementary material(File)
File 157.9 KB
Supplementary material: File

Ruiz supplementary material

Figure S1

Download Ruiz supplementary material(File)
File 451.7 KB