Yildirim EA, Laptev GYu, Tiurina DG, Filippova VA, Ilina LA, Novikova NI, Sokolova KA, Ponomareva ES, Zaikin VA, Klyuchnikova IA, Bolshakov VN, Korochkina EA, Romanov MN.

Animal Husbandry and Fodder Production. 2025. Vol. 108. No. 3. Р. 21-35.

doi:10.33284/2658-3135-108-3-21

Original article

Comparison of the endometrial microbiome of cows under eco-farm conditions in the early and late dry periods

 

Elena A Yildirim1,2, Georgy Yu Laptev3, Daria G Tiurina4, Valentina A Filippova5,6,

Larisa A Ilina7,8, Natalia I Novikova9, Kseniya A Sokolova10,11, Ekaterina S Ponomareva12,

Vasily A Zaikin13, Irina A Klyuchnikova14, Vladislav N Bolshakov15, Elena A Korochkina16, Michael  N Romanov17,18,19,20                                                                                            

1,3,4,5,7,9,10,12,13,15Molecular Genetics and Microbiomics Laboratory, BIOTROF+ Ltd, Pushkin, St. Petersburg, Russia

2,6,8,11,14,17St. Petersburg State Agrarian University, Pushkin, St. Petersburg, Russia

16St. Petersburg State University of Veterinary Medicine, St. Petersburg, Russia

18School of Natural Sciences, University of Kent, Canterbury, Kent, UK

19Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand

20Federal Research Center for Animal Husbandry named after Academy Member LK Ernst, Dubrovitsy, Russia

1,2deniz@biotrof.ru, https://orcid.org/0000-0002-5846-4844

3georg-laptev@rambler.ru, https://orcid.org/0000-0002-8795-6659

4tiurina2@biotrof.ru, https://orcid.org/0000-0001-9001-2432

5,6filippova@biotrof.ru, https://orcid.org/0000-0001-8789-9837

7,8ilina@biotrof.ru, https://orcid.org/0000-0003-2789-4844

9natalia-iv-nov@rambler.ru, https://orcid.org/0000-0002-9647-4184

10,11kalitkina.xeniya@gmail.com, https://orcid.org/0000-0002-9541-6839

12kate@biotrof.ru, https://orcid.org/0000-0002-4336-8273

13dfcx@biotrof.ru, https://orcid.org/0009-0006-8029-9955

14klyuchnikova.irinaa@yandex.ru, https://orcid.org/0009-0008-6484-1235

15bvn@biotrof.ru, https://orcid.org/0000-0001-9764-327X

16e.kora@mail.ru, https://orcid.org/0000-0002-7011-4594

17,18,19,20m.romanov@kent.ac.uk, https://orcid.org/0000-0003-3584-4644

Abstract. The system of keeping and feeding cows in eco-farms is close to their natural habitat, which ensures a low incidence of postpartum endometritis. However, in late dry period, compared to the early one, the risk of uterine microbiome disorder and morbidity increases. The aim of the study was to determine the differences in the structure and functions of the uterine microbiome of clinically healthy Ayrshire cows (n=3) at the beginning and end of the dry period in the conditions of the Valaam Monastery eco-farm using the method of targeted NGS sequencing. During NGS sequencing of the endometrial microbiome, 9 superphyla and phyla of microorganisms were found in the early dry period, and significantly less in the late period. The endometrial microbiome of cows in the eco-farm conditions contained a significant number of representatives of the Moraxellaceae family (8.7±0.54 in the early dry period and 26.1±2.26% in the late dry period). The content of Lactobacillaceae in the early dry period of cows was 6.0±0.39%. In the late dry period, the number of these bacteria decreased by 12.9 times compared to the early one. Bioinformatics analysis allowed us to identify and annotate 392 potential metabolic pathways of the endometrial microbiota. Comparing the early and late dry periods in cows, a statistically significant change in the functional activity of 28 of these pathways was found. Under the conditions of an eco-farm, a diverse and abundant taxonomic composition of the microbiota was revealed in the reproductive tract of cows, in particular, an increased content of lactobacilli compared to the results obtained in the study of animals on industrial farms.

Keywords: cows, Ayrshire breed, organic farm, microbiome, endometrium, NGS sequencing, bioinformatics, predicted metabolic pathways

Acknowledgments: the   work   was   supported   by   the  Russian  Science  Foundation, Project No. 24-16-00131.

For citation: Yildirim EA, Laptev GYu, Tiurina DG, Filippova VA, Ilina LA, Novikova NI, Sokolova KA, Ponomareva ES, Zaikin VA, Klyuchnikova IA, Bolshakov VN, Korochkina EA, Romanov MN. Comparison  of  the  endometrial  microbiome  of  cows under eco-farm conditions in the early and late dry periods. Animal Husbandry and Fodder Production. 2025;108(3):21-35. (In Russ.). https://doi.org/10.33284/2658-3135-108-3-21

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Information about the authors:

Elena A Yildirim, Dr Sci. (Biology), Biotechnologist at the Laboratory of Molecular Genetics and Microbiomics, Limited Liability Company "BIOTROF+", 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia; Professor at the Department of Large Animal Husbandry, Saint Petersburg State Agrarian University, 2/2 Peterburgskoye Highway, Pushkin, Saint Petersburg, 196601, Russia, tel.: +7 (921) 310-70-92.

Georgy Yu Laptev, Dr Sci. (Biology), General Director, Limited Liability Company "BIOTROF+", 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia; Professor at the Department of Large Animal Husbandry, Saint Petersburg State Agrarian University, 2/2 Peterburgskoye Highway, Pushkin, Saint Petersburg, 196601, Russia, tel.: +7 (812) 322-85-50.

Darya G Tiurina, Cand. Sci. (Economic), Senior Biotechnologist at the Laboratory of Molecular Genetics and Microbiomics, Limited Liability Company "BIOTROF+", 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia, tel.: +7 (921) 752-19-66.

Valentina A Filippova, Senior Biotechnologist at the Laboratory of Molecular Genetics and Microbiomics, Limited Liability Company "BIOTROF+", 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia; Head of the Laboratory at the Department of Large Animal Husbandry, Saint Petersburg State Agrarian University, 2/2 Peterburgskoye Highway, Pushkin, Saint Petersburg, 196601, Russia, tel.: +7 (905) 220-65-08.

Larisa A Ilina, Head of the Laboratory of Molecular Genetics and Microbiomics, Limited Liability Company "BIOTROF+", 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia; Professor at the Department of Large Animal Husbandry, Saint Petersburg State Agrarian University, 2/2 Peterburgskoye Highway, Pushkin, Saint Petersburg, 196601, Russia, tel.: +7 (911) 206-57-23.

Natalia I Novikova, Cand. Sci. (Biology), Deputy General Director, Limited Liability Company "BIOTROF+", 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia, tel.: +7 (812) 322-85-50.

Ksenia A Sokolova, Biotechnologist at the Laboratory of Molecular Genetics and Microbiomics, Limited Liability Company "BIOTROF+", 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia; Assistant at the Department of Large Animal Husbandry, Saint Petersburg State Agrarian University, 2/2 Peterburgskoye Highway, Pushkin, Saint Petersburg, 196601, Russia, tel.: +7 (988) 627-33-85.

Ekaterina S Ponomareva, Biotechnologist at the Laboratory of Molecular Genetics and Microbiomics, Limited Liability Company "BIOTROF+", 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia, tel.: +7 (960) 241-41-31.

Vasily A Zaikin, Biotechnologist at the Laboratory of Molecular Genetics and Microbiomics, Limited Liability Company "BIOTROF+", 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia, tel.: +7 (981) 976-41-77.

Irina A Klyuchnikova, Postgraduate Student at the Department of Large Animal Husbandry, Saint Petersburg State Agrarian University, 2/2 Peterburgskoye Highway, Pushkin, Saint Petersburg, 196601, Russia, tel.: +7 (900) 652-34-89.

Vladislav N Bolshakov, Cand. Sci. (Agriculture), Limited Liability Company "BIOTROF+", Senior Sales Manager, 19 Zagrebskiy Blvd, Saint Petersburg, 192284, Russia, tel.: +7 (812) 172-03-52.

Elena A Korochkina, Dr Sci. (Veterinary), Associate Professor at the Department of Obstetrics and Operative Surgery, Saint Petersburg State University of Veterinary Medicine, 5 Chernigovskaya St, Saint Petersburg, 196084, Russia, tel.: +7 (812) 388-22-35.

Michael N Romanov, Cand. Sci. (Biology), 60 Dubrovitsy village, Podolsk City district, Moscow region, 142132, Russia.

The article was submitted 05.06.2025; approved after reviewing 25.06.2025; accepted for publication 15.09.2025.

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