Analysis of the relative content of probiotic bacteria in the intestines of farm animals using genetic methods

Probiotics are microorganisms that have beneficial properties that can have beneficial effects on the host organism. Chickens, pigs, and cattle are the most common farm animals around the world. In this regard, maintaining the microbial balance of the gut is an important task for veterinary medicine. It was previously established that probiotic efficacy has been proven for representatives of the genera Lactobacillus and Bifidobacterium, and Akkermansia and Faecalibacterium are considered as probiotics of a new generation. The aim of the work is a comparative analysis of the gut microbiome of chickens, pigs and cattle for the presence and relative content of probiotic microorganisms in it. Initially, the prevalence of phylum Bacteroides, Firmicutes, and Actinobacteria in the faeces of all the farm animals studied was shown. The Firmicutes phylum turned out to be the most widespread phylum isolated from chicken fecal samples, while the Bacteroides phylum dominated the gut microbiome of cows and pigs. When analyzing the relative content of proteobacteria, it was found that the intestinal microbiome of cows is represented by bacteria of the classes Betaproteobacteria and Epsilonproteobacteria, and in pigs almost exclusively by the class Epsilonproteobacteria. In the samples obtained from pigs, piglets and chickens, the dominance of bacteria of the genus Lactobacillus over Bifidobacterium was established. The simultaneous presence of probiotic bacteria of a new generation, Faecalobacterium prausnitzii and Akkermansia muciniphila, was identified only in faecal samples obtained from cows, while the relative abundance of bacteria Akkermansia muciniphila was 50.0 times higher than the number of Faecalobacterium prausnitzii in the samples. The bacterium Faecalobacterium prausnitzii was identified in pig faeces, and Akkermansia muciniphila was identified in chicken faeces. It is noteworthy that the presence of new generation probiotics in the intestines was not detected in piglets aged 5-10 days.

1. Gupta, V. Probiotics / V. Gupta, R. Garg // Indian Journal of Medical Microbiology. 2009:27(3):202-209. – DOI 10.4103/0255-0857.53201.

2. Fijan, S. Microorganisms with claimed probiotic properties: an overview of recent literature / S. Fijan // International Journal of Environmental Research and Public Health.2014:11(5):4745-5767. – DOI 10.3390/ijerph110504745.

3. Ouwehand, A. C. Probiotic approach to prevent antibiotic resistance / A. C. Ouwehand, S. Forssten, A. A. Hibberd, A. Lyra, B. Stahl // Annals of Medicine.2016:48(4):246-55. – DOI 10.3109/07853890.2016.1161232.

4. Ogata, T. Effect of Bifidobacterium longum BB536 administration on the intestinal environment, defecation frequency and fecal characteristics of human volunteers / T. Ogata, T. Nakamura, K. Anjitsu, T. Yaeshima, S. Takahashi, Y. Fukuwatari, N. Ishibashi, H. Hayasawa, T. Fujisawa, H. Iino // Bioscience and Microflora.1997:16(2):53- 58.

5. Tlaskalova-Hogenova, H. The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases / H. Tlaskalova-Hogenova, R. Stepankova, H. Kozakova, T. Hudcovic, L. Vannucci, L. Tuckova, P. Rossmann, T. Hrncir, M. Kverka, Z. Zakostelska, K. Klimesova, J. Pribylova, J. Bartova, D. Sanchez, P. Fundova, D. Borovska, D. Srutkova, Z. Zidek, M. Schwarzer, P. Drastich, D. P. Funda // Cellular and Molecular Immunology.2011:8 (2):110-120. – DOI 10.1038/cmi.2010.67.

6. Chang, C. J. Next generation probiotics in disease amelioration / C. J. Chang, T. L. Lin, Y. L. Tsai, T. R. Wu, W. F. Lai, C. C. Lu, H. C. Lai // Journal of Food and Drug Analysis.2019:27(3):615-622. – DOI 10.1016/j.jfda.2018.12.011.

7. Duncan, S. H. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. / S. H. Duncan, G. L. Hold, H. J. Harmsen, C. S. Stewart, H. J. Flint // The International Journal of Systematic and Evolutionary Microbiology.2002:52:2141-2146. – DOI 10.1099/00207713-52-6-2141.

8. Wang, X. M. Plasmids of diverse inc groups disseminate the fosfomycin resistance genefosa3 among Escherichia coli isolates from pigs, chickens, and dairy cows in northeast China / X. M. Wang, Z. Dong, S. Schwarz, Y. Zhu, X. Hua, Y. Zhang, S. Liu, W.J. Zhang // Antimicrobial Agents and Chemotherapy.2017:61(9):e00859-17. – DOI 10.1128/AAC.00859-17.

9. Berchieri, A. Jr. Observations on the persistence and vertical transmission of Salmonella enterica serovars Pullorum and Gallinarum in chickens: effect of bacterial and host genetic background / A. Jr. Berchieri, C. K. Murphy, K. Marston, P. A. Barrow // Avian Pathology.2001:30:221-231. – DOI 10.1080/03079450120054631.

10. Khan, S. The gut microbiota of laying hens and its manipulation with prebiotics and probiotics to enhance gut health and food safety / S. Khan, R.J. Moore, D. Stanley, K.K. Chousalkar // Applied and Environmental Microbiology.2020.86 (13):e00600-20. – DOI 10.1128/AEM.00600-20.

11. Hu, J. Gut microbiota-derived 3- phenylpropionic acid promotes intestinal epithelial barrier function via AhR signaling / J. Hu, J. Chen, X. Xu, Q. Hou, J. Ren, X. Yan // Microbiome.2023:11(1):102. – DOI 10.1186/s40168-023-01551-9.

12. He, Z. Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamaseproducing enteroaggregative Escherichia coli infection / Z. He, Y. Ma, S. Yang, S. Zhang, S. Liu, J. Xiao, Y. Wang, W. Wang, H. Yang, S. Li, Z. Cao // Microbiome.2022:10 (1):79. – DOI 10.1186/s40168-022-01269-0.

13. Yang, Y. W. Use of 16S rRNA genetargeted group-specific primers for real-time PCR analysis of predominant bacteria in mouse feces / Y. W. Yang, M. K. Chen, B. Y. Yang, X. J. Huang, X. R. Zhang, L. Q. He, J. Zhang, Z. C. Hua // Applied and Environmental Microbiology. 2015:81(19):6749- 56. – DOI 10.1128/AEM.01906-15.

14. Wise, M. G. Quantitative analysis of the intestinal bacterial community in one- to three-week-old commercially reared broiler chickens fed conventional or antibiotic-free vegetable-based diets / M. G. Wise, G. R. Siragusa // Journal of Applied Microbiology. 2007:102(4):1138-49. – DOI 10.1111/j.1365-2672.2006.03153.x.

15. Steed, H. Bacterial translocation in cirrhosis is not caused by an abnormal small bowel gut microbiota / H. Steed, G. T. Macfarlane, K. L. Blackett, S. Macfarlane, M. H. Miller, B. Bahrami, J. F. Dillon // FEMS Immunology and Medical Microbiology. 2011:63(3):346-54. – DOI 10.1111/ j.1574-695X.2011.00857.x.