Tavuklarda Sindirim Sistemi Mikrobiyotası ve Önemi

Yıl 2022, , 269 - 276, 30.12.2022

Kürşat Tetik , Barış Sareyyüpoğlu

https://doi.org/10.31196/huvfd.1141341

Öz

İnsanların beslenmesinde, güvenli ve kaliteli protein kaynakları sağlamak için, sürdürülebilir kanatlı eti ve yumurta üretimi oldukça önemlidir. Tavukların gastrointestinal (Gİ) yolu, besinlerin sindirilmesi, emilimi, bağışıklık sisteminin uyarılmasında ve patojen mikroorganizmaların dışlanmasında önemli bir rol oynayan karmaşık bir mikrobiyotayı barındırır. Son yıllarda bu konu hakkında yapılan araştırmalar mikrobiyotanın, konağın sağlık ve hastalık durumu üzerine büyük bir öneme sahip olduğunu göstermiştir. Bu makale, tavuk GI mikrobiyotanın oluşumu, fonksiyonu ve çeşitliliği hakkındaki mevcut bilgiler ile mikrobiyotanın çeşitliliğini etkileyen faktörleri gözden geçirilerek tanı yöntemleri hakkında genel bir bilgi niteliği taşımaktadır. Gelecekte mikrobiyotanın fonksiyonunun daha iyi anlaşılması, bize kanatlı sağlığı ve üretiminin iyileştirilmesi için yeni fırsatlar sağlayacaktır.

Anahtar Kelimeler

kümes hayvanları, bağırsak mikrobiyotası, mikrobiyom, 16S rRNA

Kaynakça

• 1. Allen, H. K., & Stanton, T. B. (2014). Altered egos: antibiotic effects on food animal microbiomes. Annual review of microbiology, 68, 297-315.
• 2. 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(2), 223-232. 3. Aßhauer, K. P., Wemheuer, B., Daniel, R., & Meinicke, P. (2015). Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics, 31(17), 2882-2884.
• 4. Ballou, A. L., Ali, R. A., Mendoza, M. A., Ellis, J., Hassan, H. M., Croom, W., & Koci, M. D. (2016). Development of the chick microbiome: how early exposure influences future microbial diversity. Frontiers in veterinary science, 3, 2.
• 5. Barnes, S. H., Allerbeck, K. R., Farah, B. G., Heunks, F. J., Inglehart, R. F., Jennings, M. K., Rosenmayr, L. (1979). Political action: Mass participation in five western democracies.
• 6. Blajman, J. E., Zbrun, M. V., Astesana, D. M., Berisvil, A. P., Scharpen, A. R., Fusari, M. L., Frizzo, L. S. (2015). Probióticos en pollos parrilleros: una estrategia para los modelos productivos intensivos. Revista argentina de microbiología, 47(4), 360-367.
• 7. Borda-Molina, D., Seifert, J., & Camarinha-Silva, A. (2018). Current perspectives of the chicken gastrointestinal tract and its microbiome. Computational and structural biotechnology journal, 16, 131-139.
• 8. Brisbin, J. T., Gong, J., Parvizi, P., & Sharif, S. (2010). Effects of lactobacilli on cytokine expression by chicken spleen and cecal tonsil cells. Clin. Vaccine Immunol., 17(9), 1337-1343.
• 9. Brisbin, J. T., Gong, J., & Sharif, S. (2008). Interactions between commensal bacteria and the gut-associated immune system of the chicken. Animal Health Research Reviews, 9(1), 101-110.
• 10. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Gordon, J. I. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature methods, 7(5), 335.
• 11. Carter, A. J., Adams, M. R., Woodward, M. J., & La Ragione, R. M. (2009). Control strategies for Salmonella colonization of poultry: The probiotic perspective. Food Sci Technol, 5, 103-115.
• 12. Castellanos, L. R., Donado-Godoy, P., León, M., Clavijo, V., Arevalo, A., Bernal, J. F., Hordijk, J. (2017). High heterogeneity of Escherichia coli sequence types harbouring ESBL/AmpC genes on IncI1 plasmids in the Colombian poultry chain. PloS one, 12(1), e0170777. 13. Chambers, J. R., & Gong, J. (2011). The intestinal microbiota and its modulation for Salmonella control in chickens. Food Research International, 44(10), 3149-3159.
• 14. Chaucheyras-Durand, F., & Durand, H. (2010). Probiotics in animal nutrition and health. Beneficial microbes, 1(1), 3-9.
• 15. Clavijo, V., & Flórez, M. J. V. (2018). The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: a review. Poultry science, 97(3), 1006-1021.
• 16. Clench, M. H., & Mathias, J. R. (1995). The avian cecum: a review. The Wilson Bulletin, 93-121.
• 17. Collado, M. C., Gueimonde, M., Hernandez, M., Sanz, Y., & Salminen, S. (2005). Adhesion of selected Bifidobacterium strains to human intestinal mucus and the role of adhesion in enteropathogen exclusion. Journal of food protection, 68(12), 2672-2678.
• 18. Danzeisen, J. L., Kim, H. B., Isaacson, R. E., Tu, Z. J., & Johnson, T. J. (2011). Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment. PloS one, 6(11).
• 19. Denbow, D. M. (2015). Gastrointestinal anatomy and physiology. In Sturkie's avian physiology (pp. 337-366): Elsevier.
• 20. Dho-Moulin, M., & Fairbrother, J. M. (1999). Avian pathogenic Escherichia coli (APEC).
• 21. Diaz-Sanchez, S., Hanning, I., Pendleton, S., & D’Souza, D. (2013). Next-generation sequencing: the future of molecular genetics in poultry production and food safety. Poultry science, 92(2), 562-572.
• 22. Diker, K. S. (2017). Hayvanlarda mikrobiyom - hayvan mikrobiyomu. Veteriner Hekimler Derneği Dergisi, 88(2), 122-132.
• 23. Engberg, R. M., Hedemann, M. S., Steenfeldt, S., & Jensen, B. B. (2004). Influence of whole wheat and xylanase on broiler performance and microbial composition and activity in the digestive tract. Poultry science, 83(6), 925-938.
• 24. Flint, H. J., Leitch, E., Duncan, S. H., Walker, A. W., Patterson, A. J., Rincon, M. T., Louis, P. (2006). Molecular approaches to the analysis of gastrointestinal microbial ecosystems: CAB Int. Washington DC.
• 25. Forder, R., Howarth, G., Tivey, D., & Hughes, R. (2007). Bacterial Modulation of Small Intestinal Goblet Cells and Mucin Composition During Early Posthatch Development of Poultry1. Poultry science, 86(11), 2396-2403.
• 26. Fraher, M. H., O'toole, P. W., & Quigley, E. M. (2012). Techniques used to characterize the gut microbiota: a guide for the clinician. Nature reviews Gastroenterology & hepatology, 9(6), 312.
• 27. Fricke, W. F., McDermott, P. F., Mammel, M. K., Zhao, S., Johnson, T. J., Rasko, D. A., LeClerc, J. E. (2009). Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry. Appl. Environ. Microbiol., 75(18), 5963-5971.
• 28. Gallo, R. L., & Hooper, L. V. (2012). Epithelial antimicrobial defence of the skin and intestine. Nature Reviews Immunology, 12(7), 503-516.
• 29. Gerritsen, J., Smidt, H., Rijkers, G. T., & de Vos, W. M. (2011). Intestinal microbiota in human health and disease: the impact of probiotics. Genes & nutrition, 6(3), 209-240.
• 30. Golder, H., Geier, M., Forder, R., Hynd, P., & Hughes, R. (2011). Effects of necrotic enteritis challenge on intestinal micro-architecture and mucin profile. British poultry science, 52(4), 500-506.
• 31. 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(3), 171-179.
• 32. Gürsoy, N. C., & Otlu, B. Mikrobiyota Çalışmalarında Moleküler Tanı Yöntemleri. JOURNAL OF BIOTECHNOLOGY AND STRATEGIC HEALTH RESEARCH, 1, 56-67.
• 33. Haghighi, H. R., Abdul-Careem, M. F., Dara, R. A., Chambers, J. R., & Sharif, S. (2008). Cytokine gene expression in chicken cecal tonsils following treatment with probiotics and Salmonella infection. Veterinary microbiology, 126(1-3), 225-233.
• 34. Hamady, M., Walker, J. J., Harris, J. K., Gold, N. J., & Knight, R. (2008). Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature methods, 5(3), 235-237.
• 35. Han, G. G., Kim, E. B., Lee, J., Lee, J.-Y., Jin, G., Park, J., Choi, Y.-J. (2016). Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens. Springerplus, 5(1), 911.
• 36. Hooper, L. V., Midtvedt, T., & Gordon, J. I. (2002). How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annual review of nutrition, 22(1), 283-307.
• 37. Hume, D. (2003). A treatise of human nature: Courier Corporation.
• 38. Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011). Human nutrition, the gut microbiome and the immune system. Nature, 474(7351), 327-336.
• 39. Kuda, T., Yokota, Y., Shikano, A., Takei, M., Takahashi, H., & Kimura, B. (2017). Dietary and lifestyle disease indices and caecal microbiota in high fat diet, dietary fibre free diet, or DSS induced IBD models in ICR mice. Journal of Functional Foods, 35, 605-614.
• 40. Kumar, S., Chen, C., Indugu, N., Werlang, G. O., Singh, M., Kim, W. K., & Thippareddi, H. (2018). Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens. PloS one, 13(2), e0192450.
• 41. Kumar, S., Dagar, S. S., Mohanty, A. K., Sirohi, S. K., Puniya, M., Kuhad, R. C., Puniya, A. K. (2011). Enumeration of methanogens with a focus on fluorescence in situ hybridization. Naturwissenschaften, 98(6), 457-472.
• 42. Lan, Y., Verstegen, M., Tamminga, S., & Williams, B. (2005). The role of the commensal gut microbial community in broiler chickens. World's Poultry Science Journal, 61(1), 95-104.
• 43. Langille, M. G., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Knight, R. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature biotechnology, 31(9), 814.
• 44. Lee, M. D., & Newell, D. G. (2006). Campylobacter in poultry: filling an ecological niche. Avian diseases, 50(1), 1-9.
• 45. Lu, H., Meng, X., & Yang, C. S. (2003). Enzymology of methylation of tea catechins and inhibition of catechol-O-methyltransferase by epigallocatechin gallate. Drug metabolism and disposition, 31(5), 572-579.
• 46. Lu, J., Idris, U., Harmon, B., Hofacre, C., Maurer, J. J., & Lee, M. D. (2003). Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Appl. Environ. Microbiol., 69(11), 6816-6824.
• 47. Luo, Q., Cui, H., Peng, X., Fang, J., Zuo, Z., Deng, J., Deng, Y. (2016). Dietary high fluorine alters intestinal microbiota in broiler chickens. Biological trace element research, 173(2), 483-491.
• 48. Macpherson, A. J., & Uhr, T. (2004). Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. science, 303(5664), 1662-1665.
• 49. Mancabelli, L., Ferrario, C., Milani, C., Mangifesta, M., Turroni, F., Duranti, S., van Sinderen, D. (2016). Insights into the biodiversity of the gut microbiota of broiler chickens. Environmental microbiology, 18(12), 4727-4738.
• 50. Messaoudi, S., Kergourlay, G., Dalgalarrondo, M., Choiset, Y., Ferchichi, M., Prévost, H.,Dousset, X. (2012). Purification and characterization of a new bacteriocin active against Campylobacter produced by Lactobacillus salivarius SMXD51. Food microbiology, 32(1), 129-134.
• 51. Mitsuhiro, F., & Jun-ichi, O. (1994). Nutritional and physiological characteristics in germ-free chickens. Comparative Biochemistry and Physiology Part A: Physiology, 109(3), 547-556.
• 52. Mwangi, W. N., Beal, R. K., Powers, C., Wu, X., Humphrey, T., Watson, M., Smith, A. L. (2010). Regional and global changes in TCRαβ T cell repertoires in the gut are dependent upon the complexity of the enteric microflora. Developmental & Comparative Immunology, 34(4), 406-417.
• 53. Nandi, S., Maurer, J. J., Hofacre, C., & Summers, A. O. (2004). Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter. Proceedings of the National Academy of Sciences, 101(18), 7118-7122.
• 54. Noy, Y., & Sklan, D. (1995). Digestion and absorption in the young chick. Poultry science, 74(2), 366-373.
• 55. Oakley, B. B., Lillehoj, H. S., Kogut, M. H., Kim, W. K., Maurer, J. J., Pedroso, A., Cox, N. A. (2014). The chicken gastrointestinal microbiome. FEMS microbiology letters, 360(2), 100-112.
• 56. Palmer, M. F., & Rolls, B. (1983). The activities of some metabolic enzymes in the intestines of germ-free and conventional chicks. British journal of nutrition, 50(3), 783-790.
• 57. Pan, D., & Yu, Z. (2014). Intestinal microbiome of poultry and its interaction with host and diet. Gut microbes, 5(1), 108-119.
• 58. Park, S., Hanning, I., Perrota, A., Bench, B., Alm, E., & Ricke, S. (2013). Modifying the gastrointestinal ecology in alternatively raised poultry and the potential for molecular and metabolomic assessment. Poultry science, 92(2), 546-561.
• 59. Patel, S., & Goyal, A. (2012). The current trends and future perspectives of prebiotics research: a review. 3 Biotech, 2(2), 115-125.
• 60. Pettersson, E., Lundeberg, J., & Ahmadian, A. (2009). Generations of sequencing technologies. Genomics, 93(2), 105-111.
• 61. Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic acids research, 35(21), 7188-7196.
• 62. Pryde, S. E., Duncan, S. H., Hold, G. L., Stewart, C. S., & Flint, H. J. (2002). The microbiology of butyrate formation in the human colon. FEMS microbiology letters, 217(2), 133-139.
• 63. Puniya, A. K., Singh, R., & Kamra, D. N. (2015). Rumen microbiology: from evolution to revolution. 64. Razmyar, J., Peighambari, S. M., & Zamani, A. H. (2017). Detection of a Newly Described Bacteriocin, Perfrin, Among C lostridium perfringens Isolates from Healthy and Diseased Ostriches and Broiler Chickens in Iran. Avian diseases, 61(3), 387-390.
• 65. Rehman, H., Vahjen, W., Kohl-Parisini, A., Ijaz, A., & Zentek, J. (2009). Influence of fermentable carbohydrates on the intestinal bacteria and enteropathogens in broilers. World's Poultry Science Journal, 65(1), 75-90.
• 66. 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(5), 319-335.
• 67. Sanderson, I. R. (2004). Short chain fatty acid regulation of signaling genes expressed by the intestinal epithelium. The Journal of nutrition, 134(9), 2450S-2454S.
• 68. Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Robinson, C. J. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol., 75(23), 7537-7541.
• 69. Sekelja, M., Rud, I., Knutsen, S., Denstadli, V., Westereng, B., Naes, T., & Rudi, K. (2012). Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin. Appl. Environ. Microbiol., 78(8), 2941-2948.
• 70. Servin, A. L., & Coconnier, M.-H. (2003). Adhesion of probiotic strains to the intestinal mucosa and interaction with pathogens. Best Practice & Research Clinical Gastroenterology, 17(5), 741-754.
• 71. Shang, Y., Kumar, S., Oakley, B., & Kim, W. K. (2018). Chicken gut microbiota: importance and detection technology. Frontiers in veterinary science, 5, 254.
• 72. Shaufi, M. A. M., Sieo, C. C., Chong, C. W., Gan, H. M., & Ho, Y. W. (2015). Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses. Gut pathogens, 7(1), 4.
• 73. Simpson, J. M., McCracken, V. J., Gaskins, H. R., & Mackie, R. I. (2000). Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA amplicons to monitor changes in fecal bacterial populations of weaning pigs after introduction of Lactobacillus reuteri strain MM53. Appl. Environ. Microbiol., 66(11), 4705-4714.
• 74. Smith, J. M. (2014). A review of avian probiotics. Journal of avian medicine and surgery, 28(2), 87-95.
• 75. Sommer, F., & Bäckhed, F. (2013). The gut microbiota masters of host development and physiology. Nature Reviews Microbiology, 11(4), 227-238.
• 76. Stanley, D., Geier, M. S., Hughes, R. J., Denman, S. E., & Moore, R. J. (2013). Highly variable microbiota development in the chicken gastrointestinal tract. PloS one, 8(12), e84290.
• 77. 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(10), 4301-4310.
• 78. Stanley, D., Keyburn, A. L., Denman, S. E., & Moore, R. J. (2012). Changes in the caecal microflora of chickens following Clostridium perfringens challenge to induce necrotic enteritis. Veterinary microbiology, 159(1-2), 155-162.
• 79. Stern, N., Clavero, M., Bailey, J., Cox, N., & Robach, M. (1995). Campylobacter spp. in broilers on the farm and after transport. Poultry science, 74(6), 937-941.
• 80. Stern, N., Svetoch, E., Eruslanov, B., Perelygin, V., Mitsevich, E., Mitsevich, I., Seal, B. (2006). Isolation of a Lactobacillus salivarius strain and purification of its bacteriocin, which is inhibitory to Campylobacter jejuni in the chicken gastrointestinal system. Antimicrobial agents and chemotherapy, 50(9), 3111-3116.
• 81. Stewart, E. J. (2012). Growing unculturable bacteria. Journal of bacteriology, 194(16), 4151-4160.
• 82. Tang, Y., Underwood, A., Gielbert, A., Woodward, M. J., & Petrovska, L. (2014). Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota. Appl. Environ. Microbiol., 80(2), 478-485.
• 83. Tellez, G., Higgins, S., Donoghue, A., & Hargis, B. (2006). Digestive physiology and the role of microorganisms. Journal of Applied Poultry Research, 15(1), 136-144.
• 84. Tilocca, B., Witzig, M., Rodehutscord, M., & Seifert, J. (2016). Variations of phosphorous accessibility causing changes in microbiome functions in the gastrointestinal tract of chickens. PloS one, 11(10).
• 85. Uni, Z., Noy, Y., & Sklan, D. (1999). Posthatch development of small intestinal function in the poult. Poultry science, 78(2), 215-222.
• 86. van der Wielen, P. W., Lipman, L. J., van Knapen, F., & Biesterveld, S. (2002). Competitive exclusion of Salmonella enterica serovar Enteritidis by Lactobacillus crispatus and Clostridium lactatifermentans in a sequencing fed-batch culture. Appl. Environ. Microbiol., 68(2), 555-559.
• 87. Van Immerseel, F., Cauwerts, K., Devriese, L., Haesebrouck, F., & Ducatelle, R. (2002). Feed additives to control Salmonella in poultry. World's Poultry Science Journal, 58(4), 501-513.
• 88. Van Immerseel, F., Rood, J. I., Moore, R. J., & Titball, R. W. (2009). Rethinking our understanding of the pathogenesis of necrotic enteritis in chickens. Trends in microbiology, 17(1), 32-36.
• 89. Vispo, C., & Karasov, W. H. (1997). The interaction of avian gut microbes and their host: an elusive symbiosis. In Gastrointestinal microbiology (pp. 116-155): Springer.
• 90. Walk, C., Bedford, M., Santos, T., Paiva, D., Bradley, J., Wladecki, H., McElroy, A. (2013). Extra-phosphoric effects of superdoses of a novel microbial phytase. Poultry science, 92(3), 719-725.
• 91. Wegener, H. C., Hald, T., Wong, L. F., Madsen, M., Korsgaard, H., Bager, F., Mølbak, K. (2003). Salmonella control programs in Denmark. Emerging infectious diseases, 9(7), 774. 92. Wei, S., Morrison, M., & Yu, Z. (2013). Bacterial census of poultry intestinal microbiome. Poultry science, 92(3), 671-683.
• 93. Zhu, X., & Joerger, R. (2003). Composition of microbiota in content and mucus from cecae of broiler chickens as measured by fluorescent in situ hybridization with group-specific, 16S rRNA-targeted oligonucleotide probes. Poultry science, 82(8), 1242-1249.
• 94. Zhu, X. Y., Zhong, T., Pandya, Y., & Joerger, R. D. (2002). 16S rRNA-based analysis of microbiota from the cecum of broiler chickens. Appl. Environ. Microbiol., 68(1), 124-137. 95. Zinicola, M., Higgins, H., Lima, S., Machado, V., Guard, C., & Bicalho, R. (2015). Shotgun metagenomic sequencing reveals functional genes and microbiome associated with bovine digital dermatitis. PloS one, 10(7).
• 96. Zoetendal, E. G., Akkermans, A. D., & De Vos, W. M. (1998). Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol., 64(10), 3854-3859.