Simple SummarySalmonellosis is among the most common infectious poultry diseases that also represent a high risk to human health. The pathological process caused by Salmonella enterica serovar Enteritidis (SE) triggers in the caecum the expression of certain genes, e.g., avian β-defensins (gallinacins), cytokines (interleukins), etc. On the other hand, gut microbiota influences the infection potential of pathogens. The present study aimed at revealing the differential expression of genes associated with the immune system and changes in the bacterial communities in the intestine of growing chickens in response to SE infection. We also tested a feed additive, essential oils-based phytobiotic Intebio, as a potential alternative to antibiotics and showed effects of its administration on the caecal microbiome composition and the expression of some genes related to immunity. The phytobiotic showed its efficiency for application in poultry rearing and production.AbstractThis study was performed to investigate the differential expression of eight immunity genes and the bacterial profiles in the caecum of growing chickens challenged with Salmonella enterica serovar Enteritidis (SE) at 1 and 23 days post inoculation (dpi) in response to SE infection at 19 days of age and administration of the phytobiotic Intebio. Following infection, the genes CASP6 and IRF7 were upregulated by greater than twofold. Chicks fed Intebio showed at 1 dpi upregulation of AvBD10, IL6, IL8L2, CASP6 and IRF7. At 23 dpi, expression of AvBD11, IL6, IL8L2, CASP6 and IRF7 lowered in the experiment subgroups as compared with the control. Examination of the caecal contents at 1 dpi demonstrated a significant decrease in the microbial biodiversity in the infected subgroup fed normal diet. Bacterial content of Lactobacillus and Bacillus declined, while that of Enterobacteriaceae rose. In the infected subgroup fed Intebio, a pronounced change in composition of the microflora was not observed. In the early infection stages, the phytobiotic seemed to promote response to infection. Subsequently, an earlier suppression of the inflammatory reaction took place in chickens fed Intebio. Thus, use of Intebio as a drug with phytobiotic activity in chickens, including those infected with Salmonella, proved to be promising.

One of the main roles in poultry resistance to infections caused by Salmonella is attributed to host immunity and intestinal microbiota. We conducted an experiment that involved challenging Lohmann White laying hens with Salmonella Enteritidis (SE), feeding them a diet supplemented with an EOs-based phytobiotic Intebio®. At 1 and 7 days post-inoculation, the expression profiles of eight genes related to immunity, transport of nutrients in the intestine, and metabolism were examined. Cecal microbiome composition and blood biochemical/immunological indices were also explored and egg production traits recorded. As a result, the SE challenge of laying hens and Intebio® administration had either a suppressive or activating effect on the expression level of the studied genes (e.g., IL6 and BPIFB3), the latter echoing mammalian/human tissue-specific expression. There were also effects of the pathogen challenge and phytobiotic intake on the cecal microbiome profiles and blood biochemical/immunological parameters, including those reflecting the activity of the birds’ immune systems (e.g., serum bactericidal activity, β-lysine content, and immunoglobulin levels). Significant differences between control and experimental subgroups in egg performance traits (i.e., egg weight/number/mass) were also found. The phytobiotic administration suggested a positive effect on the welfare and productivity of poultry.

The reindeer (Rangifer tarandus L.) is a unique animal inhabitant of arctic regions. Low ambient temperatures and scant diets (primarily, lichens) have resulted in different evolutional adaptations, including the composition of the ruminal microbiota. In the study presented here, the effects of seasonal and regional aspects of the composition of the ruminal microbiota in reindeer (Nenets breed, 38 animals) were studied (wooded tundra from the Yamalo-Nenetski Autonomous District (YNAD) vs. from the Nenetski Autonomous District (NAD)). The ruminal content of calves (n = 12) and adult animals (n = 26, 15 males and 11 females) was sampled in the summer (n = 16) and winter seasons (n = 22). The composition of the ruminal microbial population was determined by the V3-V4 16S rRNA gene region sequencing. It was found that the population was dominated by Bacteroidetes and Firmicutes phyla, followed by Spirochaetes and Verrucomicrobia. An analysis of the community using non-metric multidimensional scaling and Bray–Curtis similarity metrics provided evidence that the most influential factors affecting the composition of ruminal microbiota are the region (p = 0.001) and season (p = 0.001); heat map analysis revealed several communities that are strongly affected by these two factors. In the summer season, the following communities were significantly larger compared to in the winter season: Coriobactriaceae, Erysipelothrihaceae, and Mycoplasmataceae. The following communities were significantly larger in the winter season compared to in summer: Paraprevotellaceae, Butyrivibrio spp., Succiniclasticum spp., Coprococcus spp., Ruminococcus spp., and Pseudobutyrivibrio spp. In NAD (tundra), the following communities were significantly larger in comparison to YNAD (wooded tundra): Verrucomicrobia (Verruco-5), Anaerolinaceae, PeHg47 Planctomycetes, cellulolytic Lachnospiraceae, and Succiniclasticum spp. The following bacterial groups were significantly larger in YNAD in comparison to NAD: cellulolytic Ruminococaceae, Dehalobacteriaceae, Veillionelaceae, and Oscilospira spp. The significant differences in the ruminal microbial population were primarily related to the ingredients of diets, affected by region and season. The summer-related increases in the communities of certain pathogens (Mycoplasmataceae, Fusobacterium spp., Porphyromonas endodentalis) were found. Regional differences were primarily related to the ratio of the species involved in ruminal cellulose degradation and ruminal fatty acids metabolism; these differences reflect the regional dissimilarities in botanical diet ingredients.

Study of probiotic microorganisms which can produce enzymes and amino acids is important to develop biologicals to prevent disease and increase productivity in poultry. Lactbacillus sp. and Bifidobacterium sp. are widely used as probiotics due to their adhesive ability and antipathogenic activity. Bacillus sp. and yeasts Saccharomyces sp. are less examined but considered perspective as probiotic agents due to antibiotic activity and some other helpful features. Using T-RFLP (Terminal Restriction Fragment Length Polymorphism) and Real-Time PCR we compared number and composition of caecum microbiome in 37-day old Cobb 500 broiler chicken. In group I the chickens were fed with balanced combined fodder. In group II the chickens were fed with the same combined fodder supplemented with a probiotic which contained Saccharomyces sp. living cells, and in group III this probiotic was replaced by a probiotic product Cellobacterin-T. Chickens' caecum microbiome contained various taxa including several unidentified phylotypes in addition to commonly found gut microorganisms. Phylum Firmcutes (mainly cellulolytic and amylolitic Clostridia) and Bacillus sp., Lactobacillus sp., Enterococcus sp. which possess anti-bacterial activity are identified as predominating taxa. In addition, various opportunistic and pathogenic microorganism were found including causative agents of respiratory diseases (Pasteurellaceae, Mycoplasma sp., etc.). Both probiotics resulted in an increase of total caecum microbiome and a decreased of its biodiversity. The most remarkable changes we found in the chickens fed with yeast probiotic. Caecum microbiome community of the broilers from group II showed the lowest Shannon index and Simpson index. Cellobacterin-T had the highest probiotic effect. In the broilers from group III the microbiome Bacillus sp. counts increased 1.38-fold, Lactobacillus sp. number was 1.47 times higher whereas the Campylobacter sp. number was 3.00 times lower and the family Enterobacteriaceae number was 1.44 times lower as compared to the control chicks. Yeast probiotic resulted in positive effect on cellulolytic Clostridia microorganisms but also led to rise of Campylobacter sp., Pasteurella sp. and Mycoplasma sp. counts. Poultry growth rate and productivity were influenced positively by both probiotics. The highest growth rate, weight gain, digestibility coefficient and vitamin A, E, B 2 and carotinoid accumulation in liver were characteristic of the chickens from group III. Yeast probiotic promoted feed consumption. Chemical composition of pectoral and leg muscles of the chicks fed with probiotics remained unchanged.

Rangifer tarandus (reindeer)-is actively bred in the northern regions of different countries. Therefore, an urgent task is to deepen information about the features of reindeer adaptations. Rumen symbiotic microorganisms play an important role in the life of Rangifer tarandus, allowing animals to efficiently use scarce nutrient resources of the tundra and forest-tundra. The microbial community of the reindeer rumen, as well as its age-related changes, are the least studied compared to other ruminants. The comparative analysis results of rumen bacterial community composition of calf (4 months), young animals (1-2 years) and adults (3-6 years) Rangifer tarandus of the Russian Arctic are presented for the first time. The reindeer ruminal bacterial community composition was analyzed in the laboratory of the 'BIOTROF+' Ltd by T-RFLP method. In the ontogenesis, significant changes in the microorganism representation were noticed, the greatest of which was noted in microorganism involved in carbohydrate fermentation. The content of cellulolytic Clostridia and the acid-utilizing species of the Negativicutes (P<0.05) decreased with age, but bacteria with the amylo-and cellulosolytic properties of the phylum Bacteroidetes increased (P<0.05). A wide range of microorganisms which traditionally belong to the pathogens of various animals and humans diseases was revealed. With age, a tendency to increase the number of pathogens, including the bacteria of the families Campylobacteraceae, Burkholderiaceae, phylum Fusobacteria, and the genus Staphylococcus was noticed. The greatest percent of opportunistic microorganisms, including phylum Actinobacteria and the family Enterobacteriaceae, were detected in young animals.

Background The key natural area of Russian reindeer (Rangifer tarandus, Nenets breed) is arctic zones, with severe climatic conditions and scarce feed resources, especially in the cold winter season. The adaptation of reindeer to these conditions is associated not only with the genetic potential of the animal itself. The rumen microbiome provides significant assistance in adapting animals to difficult conditions by participating in the fiber digestion. The aim of our study is to investigate the taxonomy and predicted metabolic pathways of the ruminal microbiota (RM) during the winter–spring (WS) and summer–autumn (SA) seasons, in calves and adult reindeer inhabiting the natural pastures of the Yamalo-Nenetsky Autonomous District of the Russian Federation. Methods The RM in reindeer was studied using the Next Generation Sequencing method with the MiSeq (Illumina, San Diego, CA, USA) platform. Reconstruction and prediction of functional profiles of the metagenome, gene families, and enzymes were performed using the software package PICRUSt2 (v.2.3.0). Results The nutritional value of WS and SA diets significantly differed. Crude fiber content in the WS diet was higher by 22.4% (p < 0.05), compared to SA, indicating possibly poorer digestibility and necessity of the adaptation of the RM to this seasonal change. A total of 22 bacterial superphyla and phyla were found in the rumen, superphylum Bacteroidota and phylum Firmicutes being the dominating taxa (up to 48.1% ± 4.30% and 46.1% ± 4.80%, respectively); while only two archaeal phyla presented as minor communities (no more then 0.54% ± 0.14% totally). The percentages of the dominating taxa were not affected by age or season. However, significant changes in certain minor communities were found, with seasonal changes being more significant than age-related ones. The percentage of phylum Actinobacteriota significantly increased (19.3-fold) in SA, compared to WS (p = 0.02) in adults, and the percentage of phylum Cyanobacteria increased up to seven-fold (p = 0.002) in adults and calves. Seasonal changes in RM can improve the ability of reindeer to withstand the seasons characterized by a low availability of nutrients. The PICRUSt2 results revealed 257 predicted metabolic pathways in RM: 41 pathways were significantly (p < 0.05) influenced by season and/or age, including the processes of synthesis of vitamins, volatile fatty acids, and pigments; metabolism of protein, lipids, and energy; pathogenesis, methanogenesis, butanediol to pyruvate biosynthesis, cell wall biosynthesis, degradation of neurotransmitters, lactic acid fermentation, and biosynthesis of nucleic acids. A large part of these changeable pathways (13 of 41) was related to the synthesis of vitamin K homologues. Conclusion The results obtained improve our knowledge on the structure and possible metabolic pathways of the RM in reindeer, in relation to seasonal changes.

The lack of lysine in the diet of pigs negatively affects appetite, weight gain, metabolism and immunity of animals. Most feeds for pigs are deficient in lysine. Synthetic amino acids, as feed additives, make feeds significantly more expensive. In this regards, the biologcs based on microbial producers able to synthetize lysine in the gastrointestinal tract of animals are promising. However, common producers of lysine, Brevibacterium lactofermentum, Escherichia coli and the genus Corynebacterium, are conditionally pathogenic as a causal agents of opportunistic infections. In the present study, we first examined the changes in intestinal bacterial community and the productive performance in Large White pigs («Novgorod bacon», Novgorod Province) under the influence a lysine producing strain Lactobacillus plantarum L-211 (JSC «Bioreactor», Moscow). Taxonomic composition of microorganisms was determined by T-RFLP (terminal restriction fragment length polymorphism) analysis. For surveillance we used two groups of pigs from 28-to 84-day age, fed with the basic diet (n = 715, group 1, control) and the same diet supplemented with L. plantarum L-211 at the dose not less than 10 9 CFU per animal added to water (n = 657, group 2). Microbial community in the pigs' large intestine was taxonomically divers and included a number of unidentified phylotypes. Here, the predominating bacteria were representatives of the phylum Firmicutes, including mainly Clostridia possessing cellulolytic and amylolytic properties, as well as the members of order Negativicutes able to ferment acids. The phyla Proteobacteria, Bacteroidetes, Actinobacteria and Fusobacteria were less abundant. The counts of genus Lactobacillus was lower than previously assumed, moreover, there was a complete absence of enterococci and bifidobacteria, which are usually attributed to the autochthonous microbiota of the large intestine of animals and birds. Lysine synthesizing strain L. plantarum L-211 had a high probiotic effect resulting in a significant increase in the counts of genera Lactobacillus (2.94-fold, P < 0.01) and Bacillus (3.29fold, P < 0.01), of phylum Bacteroidetes (5.29-fold, P < 0.01), and class Clostridia (2.05-fold, P < 0.01), whereas the proportions of pathogens from Staphylococcus genus and Сampylobacteriaceae family were below the T-RFLP sensitivity, and the family Pasteurellaceae decreased in number 1.41-fold (P < 0.05). Both the survival and the average daily weight gain (P < 0.05) in pigs, as influenced by the probiotic strain L. plantarum L-211, were higher. L. plantarum L-211 also improved feed conversion efficiency as compared to the control pigs.

Practice of layer poultry farming and commercial egg production relies on the optimal use and improvement of the welfare and genetically determined functional abilities of laying hens, their efficient intake of feed and its components, adaptation to housing conditions and resistance to infectious diseases including salmonellosis. Previous studies were focussed on relationships of chicken performance and resistance with the expression profiles of individual genes involved in metabolic processes and immune system, or with genetic markers that can be closely associated with these processes in chickens. In this study, mathematical models of coherent changes in laying hens were developed for the expression of eight genes involved in immunity and metabolism, on the one hand, and biochemical and immunological blood parameters, on the other hand, in response to Salmonella infection and administration of a phytobiotic Intebio. The proposed modelling approach can be a further basis for an in-depth research of the relationship between the gene expression, functional state and welfare of poultry, impact of pathogenic microorganisms and use of immunomodulatory drugs. HIGHLIGHTS Improved egg production and resistance rely on hens' potential in gene expression and metabolism. We developed mathematical models for coherent responses of hens' gene expression and blood indices to Salmonella infection and phytobiotic intake. This approach can be used for further studying relationship between gene expression, functional state, impact of pathogens and antimicrobial drugs.