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.

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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.

A b s t r a c tMicroorganisms which inhabit gut play great role in providing with nutrients, antibiotics, hormones and vitamins necessary for poultry health and performance. Therefore study of gut microbiome changes during ontogenesis seems to be essential. The structure of gut microflora in poultry embryos is of particular interest and debated because of very few publications on the problem. Despite embryo intestine is commonly considered sterile there are several reports on gut colonization by microorganisms in embryos during ontogenesis. Using T-RFLP (Terminal Restriction Fragment Length Polymorphism) analysis to generate a fingerprint of a microbial community we compared gut flora in chick embryos on days 6 and 17 to those in 26-day, 150-day and 300-day old Hisex White layers. Unlike accepted view, a high biodiversity was seen in embryo gut with Enterobacteriaceae (Escherichia coli mainly) predominated. Clostridia, Bacteroides, Negativicutes, Actinomycetales, Bifidocteriales were also found in contrast to earlier reports of their presence only in chicks at hatching and in adult poultry gut. Moreover, in the embryo gut we found the causal agents of dangerous animal disease, Burkholderia sp., Pseudomonas sp., Salmonella sp., Klebsiella sp. and Rickettsiales bacteria. Interestingly, the embryo gut biodiversity on day 6 was higher as compared to day 17 (75±2.75 phylotypes vs 30±1.20 phylotypes). In the layers aged 26, 150 and 300 days the diversity was much higher (over 175±8.12 phylotypes) as compared to embryos due to new members involved into gut bacterial community. Moreover, the poultry aged 300 days was lower both in the total diversity and in the percentage of unidentified microorganisms when compared to 26-day and 150-day old hens. In the adults, the predominating microbial taxa changed, in particular, Clostridia and Negativicutes became more abundant whereas Bacillales and Bifidobacteriales were depressed. Our findings indicate gut colonization by Lactobacilales and pathogenic Listeria sp., Pantoea sp., Enterobacter sp., Mycoplasma sp., Acinetobacter sp., Pasteurellaceae, Campylobacteraceae, Fusobacteria which occurred during ontogenesis. Thus the gut microbiome formation starts in embryo which is important for hatching and growing healthy poultry.