Hayvan Sağlığında Mikrobiyota ve İşlevi
Özet
Bu derleme çalışması, hayvanlarda mikrobiyotanın tanımını, yapısını, çeşitliliğini, üstlendiği biyolojik işlevleri ve konak sağlığı ile olan çok yönlü ilişkisini kapsamlı bir şekilde incelemektedir. Doğumla birlikte şekillenmeye başlayan mikrobiyota; başta gastrointestinal sistem olmak üzere deri, solunum ve ürogenital sistem gibi farklı organ ve dokularda kolonize olan karmaşık mikrobiyal topluluklardan oluşmaktadır. Mikrobiyotanın kararlı yapısının bozulması olarak tanımlanan disbiyozis durumu, bağışıklık sistemini, metabolizmayı, üreme sağlığını ve genel hayvan refahını olumsuz yönde etkilemektedir. Beslenme biçimi, barınma koşulları, mevsimsel değişiklikler ve ilaç kullanımı gibi çevresel etmenler ile yaş, ırk, cinsiyet ve genetik yapı gibi konakçıya özgü faktörler mikrobiyota kompozisyonunun şekillenmesinde rol oynamaktadır. Bağırsak-beyin ekseni aracılığıyla merkezi sinir sistemiyle çift yönlü iletişim kuran mikrobiyota, konak davranışları, stres yanıtları ve bilişsel süreçler üzerinde de belirleyici bir etkiye sahiptir. Ayrıca kanatlı hayvanlar, ruminantlar ve domuzlarda yürütülen metagenomik araştırmalar, sağlıklı bir mikrobiyal kompozisyonun patojen kolonizasyonunu baskıladığını, selüloz ve nişasta fermantasyonu ile uçucu yağ asitlerinin üretimini sağladığını, yemden yararlanma oranını artırdığını ve et, süt ile yumurta verimliliğini yükselttiğini ortaya koymaktadır. Sonuç olarak, hayvan mikrobiyotasının güncel durumunun takibi ve rasyon düzenlemeleriyle modüle edilmesi, hastalıklardan korunma, hayvan sağlığının geliştirilmesi ve hayvancılıkta ekonomik verimliliğin artırılması açısından kritik bir önem taşımaktadır.
This review study comprehensively examines the definition, structure, diversity, biological functions, and multifaceted relationship of the microbiota in animals with host health. Beginning to take shape at birth, the microbiota consists of complex microbial communities that colonize various organs and tissues, primarily the gastrointestinal system, as well as the skin, respiratory, and urogenital systems. The disruption of the stable microbiota structure, defined as dysbiosis, adversely affects the immune system, metabolism, reproductive health, and overall animal welfare. Environmental factors such as diet, housing conditions, seasonal changes, and medication use, alongside host-specific factors like age, breed, sex, and genetic structure, play a key role in shaping microbiota composition. Communicating bi-directionally with the central nervous system via the gut-brain axis, the microbiota also exerts a decisive influence on host behavior, stress responses, and cognitive processes. Furthermore, metagenomic research in poultry, ruminants, and swine reveals that a healthy microbial composition suppresses pathogen colonization, enables volatile fatty acid production through cellulose and starch fermentation, enhances feed efficiency, and improves meat, milk, and egg yields. In conclusion, monitoring the status of animal microbiota and modulating it through ration adjustments carries critical importance for disease prevention, animal health enhancement, and increasing economic productivity in livestock farming.
Referanslar
Carding S, Verbeke K, Vipond D.T, Corfe B M, Owen L. J. Dysbiosis of the gut microbiota in disease. Microbial ecology in health and disease, 2015; 26(1), 26191.
Li H, Sun J, Du J, Wang F, Fang R, Yu C, et al. Clostridium butyricum exerts a neuroprotective effect in a mouse model of traumatic brain injury via the gut-brain axis. Neurogastroenterology & Motility, 2018; 30(5), e13260.
Küllük E, Dalgın D. Veteriner Sahada Güncel Mikrobiyota Kavramı. Etlik Veteriner Mikrobiyoloji Dergisi, 2021;32 (1): 77-88 . DOI: 10.35864/evmd.674349.
Goulet O. Potential role of the intestinal microbiota in programming health and disease, Nutrition Reviews, 2015;73(suppl_1):32-40.
Roquetto AR, Monteiro NES, Moura CS, et al. Green propolis modulates gut microbiota, reduces endotoxemia and expression of TLR4 pathway in mice fed a high-fat diet. Food Research International. 2015;76:796-803.
Huang Y, Shi X, Li Z, et al. Possible association of Firmicutes in the gut microbiota of patients with major depressive disorder. Neuropsychiatric Disease and Treatment. 2018;14:3329.
Dickerson F, Severance E, Yolken R. The microbiome, immunity, and schizophrenia and bipolar disorder. Brain, Behavior, and Immunity. 2017;62:46-52. doi: 10.1016/j.bbi.2016.12.010.
Firkins JL, Yu Z. Ruminant nutrition symposium: how to use data on the rumen microbiome to improve our understanding of ruminant nutrition. Journal of Animal Science, 2015; 93, 1450–1470. doi: 10.2527/jas.2014-8754.
Waite DW, Taylor MW. Exploring the avian gut microbiota: current trends and future directions. Frontiers in Microbiology. 2015;3:673. doi: 10.3389/fmicb.2015.00673.
Kekeç AI, İkiz S, Çelik B, et al. Dişi Sığırlarda Mikrobiyota ve Üreme Sağlığı. Animal Health Production and Hygiene. 2019;8(2):674-677.
Lloyd-Price J, Arze C, Ananthakrishnan A N, Schirmer M, Avila-Pacheco J, Poon T. W., et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature, 2019;569, 655–662.
Guinane CM, Cotter PD. Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therapeutic advances in gastroenterology, 2013; 6(4), 295-308.
Bahrndorff S, Alemu T, Alemneh T, et al. The microbiome of animals: implications for conservation biology. International journal of genomics, 2016.
Lundberg R, Scharch C, Sandvang D. The link between broiler flock heterogeneity and cecal microbiome composition. Animal microbiome. 2021;3(1):1-14.
Pelicia K, Mendes AA, Saldanha ESPB, et al. Use of Prebiotics and Probiotics of Bacterial and Yeast Origin For Free-Range Broiler Chickens. British Journal of Poultry Science. 2004; 6(3):163-169.
Karaoğlu M, Durdağ H. The İnfluence of Dietary Probiotic (Saccharomyces Cerevisiae) Supplementation and Different Slaughter Age on The Performance, Slaughter and Carcass Properties of Broilers. Internatıonal Journal Poultry Science. 2005;4:309-316.
Zhu, L, Wu Q, Dai J, et al. Evidence of cellulose metabolism by the giant panda gut microbiome. Proceedings of the National Academy of Sciences. 2011;108(43):17714-17719.
Rodrigues Hoffmann A, Patterson AP, Diesel A, et al. The skin microbiome in healthy and allergic dogs. PloS one, 2014;9(1):e83197.
Cheng Y, Fox S, Pemberton D, et al. The Tasmanian devil microbiome—implications for conservation and management. Microbiome. 2015;3(1):1-11.
Lokmer A, Wegner KM. Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection. The ISME Journal, 2015;9(3):670-682.
Suchodolski JS, Foster ML, Sohail MU. The fecal microbiome in cats with diarrhea. PloS one. 2015;10(5):e0127378.
Costa MC, Weese JS. Understanding the intestinal microbiome in health and disease. Veterinary Clinics of North America: Equine Practice. 2018;34:1–12.
Çelik C. The Core Microbiome And Antimicrobial Resistant Microorganisms In Horses. In. 3rd International Conference on Food, Agriculture and Veterinary, B.Kır and S. Seydosoglu (Ed), 19 -20 June 2021, Izmir, Turkey, (pp. 556-570).
Isaiah A, Parambeth JC, Steiner JM, et al. The fecal microbiome of dogs with exocrine pancreatic insufficiency. Anaerobe, 2017; 45, 50-58.
Dorn ES, Tress B, Suchodolski JS, et al. Bacterial microbiome in the nose of healthy cats and in cats with nasal disease. PLoS One. 2017;12(6):e0180299.
Lucyshyn DR, Maggs DJ, Cooper AE, et al. Feline conjunctival microbiota in a shelter: effects of time, upper respiratory disease and famciclovir administration. Journal of Feline Medicine and Surgery, 2021; 23(4), 316-330.
Seddik H, Xu L, Wang Y,et al. A rapid shift to high-grain diet results in dynamic changes in rumen epimural microbiome in sheep. Animal, 2019; 13(8), 1614-1622.
Minozzi G, Biscarini F, Dalla Costa E, et al. Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions. Animals, 2021; 11(1), 4.
Morrison PK, Newbold CJ, Jones E, et al. The equine gastrointestinal microbiome: impacts of age and obesity. Frontiers in microbiology, 2018; 9, 3017.
Timsit E, McMullen C, Amat S, et al. Respiratory bacterial microbiota in cattle: from development to modulation to enhance respiratory health. Veterinary Clinics: Food Animal Practice. 2020;36(2): 297-320.
Mir RA, Schaut RG, Allen HK, et al. Cattle intestinal microbiota shifts following Escherichia coli O157: H7 vaccination and colonization. PloS one. 2019;14(12):e0226099.
Oikonomou G, Addis MF, Chassard, C. Milk microbiota: what are we exactly talking about?. Frontiers in microbiology. 2020;11:60.
Swartz JD, Lachman M, Westveer K, et al. Characterization of the vaginal microbiota of ewes and cows reveals a unique microbiota with low levels of lactobacilli and near-neutral pH. Frontiers in veterinary science. 2014;1:19.
Zeineldin M, Barakat R, Elolimy A, et al. Synergetic action between the rumen microbiota and bovine health. Microbial pathogenesis. 2018;124:106-115.
Pitta DW, Indugu N, Kumar S, et al. Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows. Anaerobe, 2016; 38, 50-60.
Barnes EM, Mead GC, Barnum DA,et al. The intestinal flora of the chicken in the period 2 to 6 weeks of age, with particular reference to the anaerobic bacteria. British poultry science, 1972; 13(3), 311-326.
Salanitro JP, Fairchilds IG, Zgornicki YD. Isolation, culture characteristics, and identification of anaerobic bacteria from the chicken cecum. Applied microbiology, 1974; 27(4), 678-687.
Wei S, Morrison M, Yu Z. Bacterial census of poultry intestinal microbiome. Poultry science, 2013; 92(3), 671-683.
Kartzinel TR, Hsing JC, Musili PM, et al. Covariation of diet and gut microbiome in African megafauna. Proceedings of the National Academy of Sciences, 2019; 116(47), 23588-23593.
Roggenbuck M, Sauer C, Poulsen M, et al. The giraffe (Giraffa camelopardalis) rumen microbiome. FEMS microbiology ecology, 2014; 90(1), 237-246.
Yao R, Xu L, Hu T, et al. The “wildness” of the giant panda gut microbiome and its relevance to effective translocation. Global Ecology and Conservation, 2019; 18, e00644.
Martinson VG, Danforth BN, Minckley RL, et al. A simple and distinctive microbiota associated with honey bees and bumble bees. Molecular Ecology. 2011;20(3):619-628.
Amato KR, Yeoman CJ, Kent A, et al. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. The ISME journal. 2013;7(7):1344-1353.
Wong AC, Chaston JM, Douglas AE. The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis. The ISME journal. 2013;7(10):1922-1932.
David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559-563.
Goodrich JK, Di Rienzi SC, Poole AC, et al. Conducting a microbiome study. Cell. 2014;158:250–62.
Kers JG, Velkers FC, Fischer EAJ, et al. Take care of the environment: housing conditions affect the interplay of nutritional interventions and intestinal microbiota in broiler chickens. Animal Microbiome. 2019;1:1–14.
Cuscó A, Belanger JM, Gershony L, et al. Individual signatures and environmental factors shape skin microbiota in healthy dogs. Microbiome, 2017; 5(1), 1-15.
Costa MC, Arroyo L G, Allen-Vercoe E, Stämpfli, H R, Kim P T, Sturgeon A, & Weese S. Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene. PLoS (Public Library of Science) One, 2012; 7(7), e41484.
Bermingham EN, Kittelmann S, Young W, et al. Short-term feeding of wet and dry diets alters the faecal bacterial populations in the domestic cat (Felis catus). British Journal of Nutrition, 2011; 106, 49–52.
Bermingham EN, Young W, Kittelmann S, et al. Dietary format alters fecal bacterial populations in the domestic cat (Felis catus). Microbiologyopen, 2013; 2(1), 173-181.
O'Donnell MM, Harris HMB, Jeffery IB, et al. The core faecal bacterial microbiome of Irish Thoroughbred racehorses. Letters in applied microbiology. 2013;57(6):492-501.
Kauter A, Epping L, Semmler T, et al. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. Animal Microbiome. 2019;1(1):1-15.
Ross AA, Müller KM, Weese JS, et al. Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia. Proceedings of the National Academy of Sciences. 2018;115(25):E5786-E5795.
Moloney RD, Desbonnet L, Clarke G, Dinan T G., & Cryan, J. F. The microbiome: stress, health and disease. Mammalian genome, 2014; 25(1), 49-74.
Paz HA, Anderson CL, Muller MJ, et al. Rumen bacterial community composition in Holstein and Jersey cows is different under same dietary condition and is not affected by sampling method. Frontiers in microbiology, 2016; 7,1206.
Li F, Li C, Chen Y, et al. Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle. Microbiome, 2019; 7(1), 1-17.
Danzeisen JL, Kim HB, Isaacson RE,et al. Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment. PloS one, 2011; 6(11), e27949. doi: 10.1371/journal.pone.0027949
Ballou AL, Ali RA, Mendoza MA, et al. Development of the chick microbiome: how early exposure influences future microbial diversity. Frontiers in veterinary science; 2016; 3, 2. doi: 10.3389/fvets.2016.00002
Crhanova M, Hradecka H, Faldynova M, et al. Immune response of chicken gut to natural colonization by gut microflora and to Salmonella enterica serovar enteritidis infection. Infection and immunity, 2011; 79(7), 2755-2763.
Collins SM, Bercik P. The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease. Gastroenterology, 2009; 136(6), 2003-2014.
Koca O, Dönmez N. İkinci beyin: Bağırsak. Atatürk Üniversitesi Veteriner Bilimleri Dergisi. 2020;15 (2):187-195. DOI: 10.17094/ataunivbd.701620.
Kelly D L, Lyon D E, Yoon S L, & Horgas A. L. The microbiome and cancer: Implications for oncology nursing science. Cancer nursing, 2016; 39(3), E56-E62.
Zheng P, Zeng B, Zhou C, Liu M, Fang Z, Xu X., ... & Xie, P. Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism. Molecular psychiatry, 2016; 21(6), 786-796.
Buffington SA, Di Prisco GV, Auchtung TA, et al. Microbial reconstitution reverses maternal diet-induced social and synaptic deficits in offspring. Cell. 2016;165(7):1762-1775.
Erny D, de Angelis ALH, Jaitin D, et al. Host microbiota constantly control maturation and function of microglia in the CNS. Nature neuroscience, 2015; 18(7), 965-977.
Vuong HE, Yano JM, Fung TC, et al. The microbiome and host behavior. Annual review of neuroscience. 2017;40:21-49.
Dosmann A, Bahet N, Gordon DM. Experimental modulation of external microbiome affects nestmate recognition in harvester ants (Pogonomyrmex barbatus). PeerJ 2016;4: e1566
Haberecht S, Bajagai YS, Moore RJ, et al. Poultry feeds carry diverse microbial communities that influence chicken intestinal microbiota colonisation and maturation. AMB Express. 2020;10(1):1-10.
Yadav S, Jha R. Strategies to modulate the intestinal microbiota and their effects on nutrient utilization, performance, and health of poultry. Journal of animal science and biotechnology. 2019;10(1): 1-11.
Holscher HD, Bauer LL, Gourineni V, et al. Agave inulin supplementation afects the fecal microbiota of healthy adults participating in a randomized, double-blind, placebocontrolled, crossover trial. Journal of Nutrition. 2015; 145(9):2025–2032. doi:https://doi. org/10.3945/jn.115.217331.
Koecher KJ, Thomas W, Slavin JL. Healthy subjects experience bowel changes on enteral diets: addition of a fber blend attenuates stool weight and gut bacteria decreases without changes in gas. Journal of Parenteral and Enteral Nutrition. 2015;39(3):337–343. doi:https://doi.org/10.1177/0148607113510523.
Fruge AD, Van der Pol W, Rogers LQ, et al. Fecal Akkermansia muciniphila is associated with body composition and microbiota diversity in overweight and obese women with breast cancer participating in a presurgical weight loss trial. Journal of the Academy of Nutrition and Dietetics. 2018;120(4):650-659 doi:https://doi.org/10.1016/j.jand.2018.08.164.
Mathlouthi N, Mallet S, Saulnier L, et al. Effects of xylanase and ∝-glucanase addition on performance, nutrient digestibility, and physico-chemical conditions in the small intestine contents and caecal microflora of broiler chickens fed a wheat and barley-based diet. Animal Research. 2002;51(05):395–406.
Gangadoo S, Dinev I, Chapman J, et al. Selenium nanoparticles in poultry feed modify gut microbiota and increase abundance of Faecalibacterium prausnitzii. Applied microbiology and biotechnology. 2018;102(3):1455-1466.
Deusch S, Tilocca B, Camarinha-Silva A, et al. News in livestock research—use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals. Computational and structural biotechnology journal. 2015;13:55-63.
Jami E, Mizrahi I. Composition and similarity of bovine rumen microbiota across individual animals. PloS one, 2012; 7(3): e33306.
Carberry CA, Kenny DA, Han S, et al. Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle. Applied and environmental microbiology. 2012;78(14):4949-4958.
Guan LL, Nkrumah JD, Basarab JA, et al. Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency. FEMS microbiology letters. 2008;288(1):85-91.
Lopes DRG, de Souza Duarte M, La Reau AJ, et al. Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers. Journal of animal science and biotechnology,.2021;12(1):1-17.
Zhang YK, Zhang XX, Li FD, et al. Characterization of the rumen microbiota and its relationship with residual feed intake in sheep. Animal. 2021;15(3):100161.
Castillo-Gonzalez AR, Burrola-Barraza ME, Dominguez-Viveros J, Chavez-Martinez A. Rumen microorganisms and fermentation Microorganismos y fermentación ruminal. Archivos de medicina veterinaria, 2014; 46(3), 349-361.
Ratti RP, Botta LS, Sakamoto IK, et al. Production of H2 from cellulose by rumen microorganisms: effects of inocula pre-treatment and enzymatic hydrolysis. Biotechnology letters, 2014; 36(3), 537-546.
Fernando SC, Ii HTP, Najar FZ, et al. Rumen microbial population dynamics during adaptation to a high-grain diet. Applied and environmental microbiology, 2010; 76(22), 7482-7490.
Chen Y, Oba M, Guan LL. Variation of bacterial communities and expression of Toll-like receptor genes in the rumen of steers differing in susceptibility to subacute ruminal acidosis. Veterinary microbiology, 2012; 159(3-4), 451-459.
Duskova D, Marounek M. Fermentation of pectin and glucose and activity of pectin-degrading enzymes in the rumen bacterium Lachnospira multiparus. Letters in Applied Microbiology, 33(2), 159-163.
Yang H, Huang X, Fang S, et al. Unraveling the fecal microbiota and metagenomic functional capacity associated with feed efficiency in pigs. Frontiers in microbiology, 2017; 8, 1555.
Mach N, Berri M, Estellé J, et al. Early-life establishment of the swine gut microbiome and impact on host phenotypes: role of early-life gut microbiome on pigs’ health. Environmental microbiology reports, 2015; 7: 554–569.
Niu Q, Li P, Hao S, Zhang Y, Kim SW, Li H, et al. Dynamic distribution of the gut microbiota and the relationship with apparent crude fiber digestibility and growth stages in pigs. Scientific reports, 2015; 5(1), 1-7.
Singh KM, Shah TM, Reddy B, et al. Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers. Journal of applied genetics, 2014; 55(1), 145-154.
Tan Z, Yang T, Wang Y, Xing K, et al. Metagenomic analysis of cecal microbiome identified microbiota and functional capacities associated with feed efficiency in Landrace finishing pigs. Frontiers in microbiology, 2017; 8, 1546.
Wang H, Ni X, Qing X, et al. Live probiotic Lactobacillus johnsonii BS15 promotes growth performance and lowers fat deposition by improving lipid metabolism, intestinal development, and gut microflora in broilers. Frontiers in Microbiology. 2017; 8, 1073. doi: 10.3389/fmicb.2017.01073.
Lamendella R, Santo Domingo JW, Ghosh S, et al. Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC microbiology, 2011; 11(1), 1-17.