Glyphosate is herbicide that is now widely used in agriculture. Glyphosate has a direct effect not only on plants but also on the gut microbiome of farm animals and poultry. This study examined the effects of glyphosate on the gut microbiome biomarkers of laying hens depending on their reproductive longevity. The results of the study revealed a relationship between glyphosate exposure, the composition of the gut microbiota, and the productive longevity of laying hens. It was found that the herbicide can induce changes in the bacterial community. Glyphosate had the most significant effect on the Firmicutes/Bacteroidota ratio. In the group with high reproductive longevity, glyphosate led to a 6.36

Xenobiotics have a negative impact on the composition and function of the intestinal microbiome; this requires measures to correct these disorders. The aim of the study was thus to conduct bioinformatic processing and analysis of NGS sequencing data of the intestinal (caecum) microbiome in broiler chickens, including the analysis of the taxonomic composition and predicted metabolic pathways. Experimental groups of broilers included: Group I fed the basic diet (BD); experimental Group II received BD and glyphosate; experimental Group III fed BD, glyphosate, and probiotic bacterial strains; and experimental Group IV received BD along with a combination of glyphosate, antibiotics, and probiotic bacterial strains. As a result, a reduction in the live weight of broilers by 4.2

Studying the microbiome of the cow’s reproductive system is crucial for maintaining the animals’ reproductive capacity. In 2025, the E. faecalis E-10 strain was isolated from the endometrium of a healthy Ayrshire cow kept at the Valaam Monastery eco-farm. The aim of the study was a whole-genome analysis of the strain using the MiSeq sequencer (Illumina, Inc., USA) and bioinformatics tools, including the Trimmomatic-0.38 ( http://www.usadellab.org/cms/?page=trimmomatic ), SPAdes-3.11.1 ( https://github.com/ablab/spades ), QUAST Version: 5.0.2 ( http://quast.sf.net ), BV-BRC ( https://www.bv-brc.org ), RAST ( https://rast.nmpdr.org ), KEGG ( https://www.kegg.jp ), Prokka ( https://github.com/tseemann/prokka ), and HMMER (hmmsearch) ( https://hmmer.org ) databases. Whole genome analysis of the E. faecalis E-10 strain showed that the genome consists of 108 contigs and has a total length of 2,882,409 bp, with a GC content of 37.49

Ensiling is the main method of preparing bulk forages for cattle in the conditions of the risk farming zone. This zone includes St. Petersburg and the Leningrad Oblast due to their geographical location and high humidity. To improve the efficiency of enzymatic processes during ensiling, various biopreparations of lactic acid bacteria that consist of one or more strains are used. However, the biotechnological potential of lactic acid bacteria involved in silage fermentation remains insufficiently studied. Thus, the selection of microorganisms for use in silages should always be carried out with all rigor and meet certain criteria. The aim of this study using metagenomic next-generation sequencing (NGS) and bioinformatics was to assess the efficiency of applying monocultures of lactic acid bacteria strains (Lactobacillus plantarum 50 and Enterococcus faecium 46). We further evaluated combining these strains for the ensiling process in a model laboratory experiment. As a result, it was shown that the greatest stability of microbiome and a high proportion of lactobacilli in the ensiled feeds, the best pH levels and silage quality were achieved using a combination of strains (L. plantarum 50 + E. faecium 46).

Inclusion of probiotic preparations in the diet has a complex positive effect on the body of ruminants. These supplements optimize digestive processes, stabilize the balance of rumen microflora, help to normalize metabolism and, as a result, increase overall productivity. A study was conducted aimed to study the effect of the enzyme-probiotic feed supplement “Profort” on the composition of the rumen microbiome of Black-and-White Holstein cows. During the experiment, cows of the experimental group received the probiotic “Profort.” At the end of the experiment, a comparison of the composition of the microbiome of cows in the experimental and control groups revealed significant and statistically reliable differences at the family level. In particular, an increase in the number of taxa including cellulolytic bacteria such as Oscillospiraceae, SR1, Flavobacteriaceae, and Weeksellaceae was noted. These bacteria play a key role in the decomposition of cellulose, the main component of plant feed, providing the animal with energy and nutrients. Changing in the number of taxa of lactic acid bacteria involved in the metabolism of lactic acid was shown. This indicates that the use of the feed additive “Profort” contributes to a more efficient usage of feed carbohydrates and prevents the accumulation of lactic acid in the rumen, which can lead to acidosis and a decrease in productivity.

There remains no consensus on the microbiological causes of endometritis in cows. The aim of this study, therefore, was to analyze the endometrial microbiome using metagenomic whole genome sequencing (WGS) with subsequent bioinformatic data analysis using high-yielding cows kept on an organic farm (Group 1A) compared to animals kept on a large industrial complex as follows: clinically healthy (Group 2A), with subclinical (Group 2B), or purulent-catarrhal endometritis (Group 2C). Using Illumina MiSeq platform, WGS results revealed that the dominant bacterial phyla were Bacillota in Groups 2A, 2B, and 2C, as well as Bacteroidota, Fusobacteriota, and Bacillota in Group 1A. In industrial farm conditions, subclinical and clinical endometritis was associated with an increase in the amount of Clostridium botulinum in the uterus (p < 0.05). In contrast to Group 2A, the dominant bacterial species in the organic eco-farm Group 1A were Bacteroides fragilis (55.1 ± 3.92

Various biological preparations of lactic acid bacteria are used to increase the efficiency of enzymatic processes during silage. The purpose of this study was to determine the effectiveness of using monocultures of lactic acid bacteria strains Lacticaseibacillus pracasei 6, Enterococcus faecium 46, and Lactobacillus plantarum 50 for the silage of a cereal-bean mixture in a model laboratory experiment. As a result, it was shown that the highest proportion of lactobacilli, faster acidification, better pH levels throughout the fermentation time, and higher metabolic energy were achieved using the L. plantarum 50 strain. All the strains used had antagonistic activity against clostridium, which may be due to both the synthesis of antimicrobial substances and rapid acidification of the medium. In general, the L. plantarum 50 strain is promising for use as an inoculum for silage of crop material and reducing the load of pathogenic microorganisms in ready-made canned food.

The article studies the safety of livestock products associated with the reduction of the spread of the most dangerous pathogens – Escherichia coli in canned feed for ruminants. Pathogenic E. coli are capable of producing various toxins and associated virulence factors that cause diseases in animals and humans. To analyze the genes of toxicity and virulence factors of E. coli, a collection of 72 samples of canned bulk feed (silage and haylage) prepared in 45 livestock complexes in St. Petersburg and the Leningrad Region was collected and analyzed. In this study, the presence of toxicity and virulence genes of Escherichia coli was analyzed: shiga toxin (stx1, stx 2), intimin (eae), enterohemolysin (ehxA) of enterobacteria using the PCR method. According to the degree of contamination of feeds with the studied genes, the most common among E. coli bacteria were the genes of toxicity of Shiga toxins of types 1 and 2 (41.7 and 37.5

The. aim of the. study was to evaluate the effect of compound feeds with reduced (by 5%) nutritional content of lysine, methionine and metabolic energy when lysine and methionine are included in them in various forms during their interaction with broiler sex on the transcription profile of key genes regulating antioxidant protection, the immune system, inflammation and apoptosis, productivity and barrier function of the gastrointestinal epithelium. Methods. The experiment was carried out at the “Zagorskoye” in 2024 on a poultry meat of the “Smena 9” cross from 1 to 35 days of age. Results. The live weight of rooster and hens in experimental groups II and IV was slightly higher compared to control I, whereas in group III it was lower. In many cases, changes in the composition of the diet of rooster and hens had a significant impact on the expression of a number of key genes. In roosters, PTGS2 expression in experimental groups II–IV increased sharply (from 4.9 to 52.0 times) compared with control I, whereas in hens it increased only 1.5–2.3 times. The expression of the Muc2 gene mRNA in hens decreased in experimental group II by 1.9 times compared with group I, whereas in roosters, on the contrary, it increased by 3.1 times.

Comparative analysis of immunologic and biochemical state of layers with high and low supposed production longevity has been given in the paper. The most pronounced differences have been found in total blood protein content that has been lower ($p \leqslant 0.05$) supposed productive longevity group than in group with supposed high productive longevity that is $69.7 \pm 0.69$ g/l against $52.0 \pm 1.16$ g/l.

Factors causing metabolic disorders in poultry bones may be divided by genetic, infectious and technologic ones. Feeds make up some 70% of costs for poultry growing and managing costs and that’s why lameness causes in connection with feeding have been considered in the paper.

The paper is designed to study of transformation in microbiota species content of poultry house air environment during transition and hot periods of year. The experiments have been carried out with industrial layer flock Loman White cross. The layers has been kept in poultry houses with cage keeping system. The experiment results show significant difference in air microbiologic composition in different year periods. Bacteria Ruminococcus, Lachnospiraceae, Rikenellaceae-RC9 gut group, Bacteroides genera that take part in organics decomposition prevailed in transitional period. During hot periods conditionally and pathogenic bacteria content has been risen in poultry shed. The research results confirm importance of air microbiota seasonal transformations control in poultry houses and necessity of poultry health management strategies and risks reduction.

Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreatic genes and blood physiology parameters after administering one maximum residue limit of herbicide glyphosate(GLY),two ANTs,and one anticoccidial drug(AD).A total of 260 Ross 308 broilers aged 1-40 d were divided into the following four groups of 65 birds each:control group,which was fed the main diet(MD),and three experimental groups,which were fed MD supplemented with GLY,GLY+ANTs(enrofloxacin and colistin methanesulfonate),and GLY+AD(ammonium maduramicin),respectively.The results showed that the addition of GLY,GLY+ANTs,and GLY+AD caused significant changes in the expression of several genes of physiological and economic importance.In particular,genes related to inflammation and apoptosis(interleukin 6(IL6),prostaglandin-endoperoxide synthase 2(PTGS2),and caspase 6(CASP6))were downregulated by up to 99.1%,and those related to antioxidant protection(catalase(CAT),superoxide dismutase 1(SOD1)and peroxiredoxin 6(PRDX6))by up to 98.6%,compared to controls.There was also a significant decline in the values of immunological characteristics in the blood serum observed in the experimental groups,and certain changes in gene expression were concordant with changes in the functioning of the pancreas and blood.The changes revealed in gene expression and blood indices in response to GLY,ANTs,and AD provide insights into the possible mechanisms of action of these agents at the molecular level.Specifically,these changes may be indicative of physiological mechanisms to overcome the negative effects of GLY,GLY+ANTs,and GLY+AD in broilers.

Background. Undesirable microflora can enter forage crops during harvesting with soil, which can contain various pathogenic microorganisms, including clostridia and enterobacteria, which enter it when manure is applied to fields as fertilizer. As a result, the silage may become unsuitable for use as animal feed. Purpose. Assess the presence of bacterial toxin genes in canned food on farms in the Leningrad region: shiga toxin (stx1, stx 2), intimin (eae), enterohemolysin (ehxA) of enterobacteria; alpha toxin (cpa), beta toxin (cpb) and epsilon toxin (etx) C. perfringens; binary toxin (cdtB), toxin A (tcdA) and B (tcdB) C. difficile. Materials and methods. The study used molecular biology methods: high-throughput sequencing of a fragment of the 16SpRNA gene to assess the microbial community of silage and PCR to assess the presence of toxin genes in the silage community. Based on the data obtained, a bioinformatics analysis was carried out. Results. As a result of the analysis of silage samples from most districts of the Leningrad region for the presence of genes for shiga toxin (stx1, stx 2), intimin (eae), enterohemolysin (ehxA) of enterobacteria; alpha toxin (cpa), beta toxin (cpb) and epsilon toxin (etx) C. perfringens; binary toxin (cdtB), toxin A (tcdA) and B (tcdB) C. difficile, silage samples were shown to be contaminated by several genetic determinants of bacterial toxicity using PCR. The genes for intimin, beta toxin and binary toxin were not identified in any of the samples examined. About 32% of the tested feeds were heavily contaminated with toxins. 23% of silos were found to be free of toxins. Conclusion. The data obtained indicate that rapid acidification of the silage mass by lactobacilli helps to reduce the development of pathogenic enterobacteria and clostridia.

The purpose of research is to study the effect of the probiotic Profort-T on the composition of the rumen microbiome of dairy cows using NGS sequencing, productivity and hematological parameters of the animals' blood serum. The experiment was carried out on black-and-white cows for 60 days. Analogue groups of 20 animals each were formed: control group I (received the basic diet (BD)) and experimental group II (received the BD diet and the Profort-T probiotic). The BD consisted of: silage – 42.26 kg; hay – 1.97; mixed feed – 14.67 kg; salt, chalk, soda. The cows of experimental group II received the probiotic Profort-T at the rate of 0.03 kg per 1 head from the day of admission to the new calving group. The feed additive was distributed manually to each head of experimental group II during the new calving period and partially during milking. The animals were kept under the same conditions. Animals are kept in tethered conditions. The rumen bacterial community was assessed by NGS sequencing using a MiSeq sequencer (Illumina, Inc., USA). The use of a probiotic (experimental group II) made it possible to increase the average daily milk yield from 14.9 to 22.0 % compared to the control (P ≤ 0.05) and reduce the content of somatic cells in cows’ milk from 21.6 to 33.5 % (P ≤ 0.05). NGS sequencing demonstrated that 21 phyla of microorga¬nisms were found in the rumen microflora of the studied cows. The most represented (P ≤ 0.05) bacteria in the rumen were bacteria of the phylum Bacteroidetes – from 46.6 ± 4.48 to 58.1 ± 5.52 %. The proportion of cellulolytic bacteria Candidatus Saccharibacteria increased in experimental group II at the end of the experiment compared to the control by 1.9 times (P ≤ 0.05). Microorganisms Proteobacteria and Fusobacteria decreased in experimental group II compared to the control by 5.7 and 1.8 times, respectively (P ≤ 0.05), i.e. the use of the Profort-T probiotic led to an improvement in the structure of the microbial community of the cow rumen.

Clostridioides difficile currently constitutes a major pathogen of the gastrointestinal tract, which poses a significant growing burden on medicine and veterinary medicine in many regions. A farm was assessed (feed table, silage pit, and feces (healthy animals, emaciated animals, and animals with mastitis)) for the presence of C. difficile toxins using the PCR method and for the microbiome in cow feed and feces using NGS technology, one month apart. C. difficile toxin A and binary toxin were detected in feed samples. C. difficile toxin genes were found in the feces of sick animals two to three times more often than in healthy animals. Analysis of the microbial community of cow feces revealed that, during the month, the animals experienced major changes in the community structure associated with the accumulation of pathogenic bacteria, in particular Paeniclostridium sp., as well as with the development of methanogenic archaea of the Methanobacteriaceae and associated microorganisms (Lachnospiraceae and Anaerovoracaceae), which may speak of a decrease in feed efficiency and, subsequently, animal productivity. Thus, it seems likely that C. difficile enters the gastrointestinal tract of animals through feed, while animals weakened by diseases are more sensitive to the reproduction of pathogens in the GIT due to a weakened organism.

Abstract. Understanding the relationships between the microbiome of the digestive system, the use of probiotic supplements and zootechnical indicators in cows is the key to developing new strategies to increase milk yields. Purpose of research to study the composition of the microflora of the digestive system chyme and dairy productivity of cows under the influence of a complex biological preparation. Research methods. The experiment was carried out on of cows of black-and-white holsteinized. Groups were formed: control group I (who received the main ration (MR)) and experimental group II (who received MR and the “AntiKlos” feed additive). The bacterial community of the scar was evaluated by NGS-sequencing, the intestinal microflora, litter and feed were evaluated using real-time PCR. Results showed that the use of the “AntiKlos” feed additive on livestock allowed to increase the average daily milk yield to 7.5 kg compared with control I (P = 0.05). The bacteria Bacteroidetes were the most abundantly represented (P ≤ 0.05) in the rumen – from 20.9 ± 4.36 and up to 55.3 ± 6.74 %. It was shown for the first time that under the influence of the introduction of the “AntiKlos” feed additive into the diet, there was also a 16.1-fold decrease in Fusobacteria phylum bacteria in experimental group II compared with control I (P < 0.05). In addition, the use of the “AntiKlos” feed additive led to the complete disappearance of such species as Streptococcus caprae, S. didelphis, Mycoplasma conjunctivae in the rumen, among which opportunistic and pathogenic forms are often found, which is the scientific novelty of the study. Similar bacterial taxa were found in the food from the feed table, litter and rectum of almost all the dairy cows studied. In the rectal chyme of cows of the experimental group, the number of taxa such as Clostridium spp., Enterobacteriaceae and Staphylococcus spp. decreased in comparison with control I (P ≤ 0.05). Thus it is necessary to pay attention to increasing the efficiency of animal husbandry by regulating the microbiomes of cows, as well as the microflora of feed and housing sites.

Relevance. The broad use of antimicrobials by agriculture and consumers motivation to buy antibiotic-free production form a basis to development of substitutes to antimicrobials. The goal of research was the analysis of antimicrobial resistance caused by veterinary antimicrobials administration to broilers, as well as the effect of metaprobiotic “Probiocid-Ultra” on antimicrobial resistance in dynamic.Methods. Three groups of broiler chickens were formed: I — control, who received the main diet, II — experimental, who received veterinary antibiotics enrofloxacin and colistin in addition to the diet of group I, III — experimental, who received the metaprobiotic “Probiocide-Ultra” in addition to the diet of group II. Gene expression analysis was performed using quantitative reverse transcription PCR. With inoculation to different media the antimicrobial resistance was examined with classical microbiological methods.Results. The dynamic of accumulation of antimicrobial resistance determinants caused by enrofloxacin and colistin administration to broilers was examined. Under the influence of enrofloxacin the increase in antimicrobial resistance to enrofloxacin itself, as well as to beta-lactams, tetracycline and colistin was observed. Under the influence of colistin the increase in antimicrobial resistance to colistin itself, as well as to enrofloxacin and beta-lactams was observed. The feed administration with metaprobiotic “Probiocid-Ultra” promoted noticeable decrease of the antimicrobial resistance genes amount, when analyzed with growth medium led to antimicrobial resistant enterobacteria vanished.

Silage can become a source of pathogenic bacteria and their toxins, which can cause diseases and reduce the productivity of dairy cows, promoting their constant carriage and circulation within the farm. The purpose of this work was to identify relationships between the presence of toxin genes of clostridia and enterobacteria and the diversity of microbial communities in feed, gastrointestinal tract, and cattle milk, as well as to assess the possibility of circulation of pathogens and their toxins within the farm. As a result of a comprehensive analysis of the presence of clostridia and enterobacteria toxins on the farm, feed samples were examined, including the feed table and silage pit, feces and milk. Contamination with various toxins was found to be present in all samples examined. Shiga toxins of enterobacteria, C. perfringens epsilon toxin and C. difficile toxins – toxin A and binary toxin have been detected in the silage. The C. perfringens epsilon toxin and alpha toxin genes were identified in the feces of sick and healthy cows. This indicates the possibility of pathogens circulating within the farm, which can persist even in clinically healthy individuals. Significant differences in the content of important groups of microorganisms were revealed in feces. The proportion of lactobacilli that have a negative effect on metabolic processes in the rumen - the development of lactic acidosis, was 5 times higher in the feces of animals with disease, and the proportion of representatives of lactate-utilizing bacteria of the order Veillonellales-Selenomonadales in the group of healthy animals was 3 times higher, according to compared to emaciated animals. Moreover, it was demonstrated that silage may be an important reservoir of Enterobacteriaceae and Clostridia toxins, as it contained a set of genetic determinants of toxicity from both Clostridia and Enterobacteriaceae.

To evaluate the effects of antibiotics and glyphosate, an experiment was conducted on 260 broilers. Four experimental groups were formed: I—control group, which received the basic diet (BD), II experimental group—BD with the addition of glyphosate; III experimental—OR with the addition of glyphosate and veterinary antibiotics enrofloxacin and colistin methanesulfonate; IV experimental—OR with the addition of glyphosate and ammonium maduramicin. Glyphosate and antibiotics combined with a herbicide altered the microbial community in broiler’s cecum. Genome-wide analysis made it possible to estimate the increase in the proportion of eukaryotic microorganisms and viruses under the influence of antibiotics. In the group of prokaryotic microorganisms, under the influence of glyphosate and antibiotics, significant changes were noted associated with a decrease in the proportion of bacteria, such as Faecalibacterium sp., Lawsonibacter sp., Lachnoclostridium sp. and Subdoligranulum sp., capable of producing butyrate and other short-chain fatty acids. These results indicate the negative impact of glyphosate in combination with antibiotics on the health and productivity of poultry, since these acids have a wide range of positive properties, for example, bacteriostatic, anti-inflammatory and proliferative effects.