Evaluating the phytotoxicological effects of bulk and nano forms of zinc oxide on cellular respiration-related indices and differential gene expression in Hordeum vulgare L.

The increasing use of nanoparticles is driving the growth of research on their effects on living organisms. However, studies on the effects of nanoparticles on cellular respiration are still limited. The remodeling of cellular-respiration-related indices in plants induced by zinc oxide nanoparticles (nnZnO) and its bulk form (blZnO) was investigated for the first time. For this purpose, barley (Hordeum vulgare L.) seedlings were grown hydroponically for one week with the addition of test compounds at concentrations of 0, 0.3, 2, and 10 mg mL-1. The results showed that a low concentration (0.3 mg mL-1) of blZnO did not cause significant changes in the respiration efficiency, ATP content, and total reactive oxygen species (ROS) content in leaf tissues. Moreover, a dose of 0.3 mg mL-1 nnZnO increased respiration efficiency in both leaves (17 %) and roots (38 %). Under the influence of blZnO and nnZnO at medium (2 mg mL-1) and high (10 mg mL-1) concentrations, a dose-dependent decrease in respiration efficiency from 28 % to 87 % was observed. Moreover, the negative effect was greater under the influence of nnZnO. The gene transcription of the subunits of the mitochondria electron transport chain (ETC) changed mainly only under the influence of nnZnO in high concentration. Expression of the ATPase subunit gene, atp1, increased slightly (by 36 %) in leaf tissue under the influence of medium and high concentrations of test compounds, whereas in the root tissues, the atp1 mRNA level decreased significantly (1.6-2.9 times) in all treatments. A dramatic decrease (1.5-2.4 times) in ATP content was also detected in the roots. Against the background of overexpression of the AOX1d1 gene, an isoform of alternative oxidase (AOX), the total ROS content in leaves decreased (with the exception of 10 mg mL-1 nnZnO). However, in the roots, where the pressure of the stress factor is higher, there was a significant increase in ROS levels, with a maximum six-fold increase under 10 mg mL-1 nnZnO. A significant decrease in transcript levels of the pentose phosphate pathway and glycolytic enzymes was also shown in the root tissues compared to leaves. Thus, the disruption of oxidative phosphorylation leads to a decrease in ATP synthesis and an increase in ROS production; concomitantly reducing the efficiency of cellular respiration.

Unexpected ubiquity of heart-shaped scale morphotype in Centroplasthelida (Haptista): Ancestral trait or multiple acquisitions?

Centrohelids (Haptista: Centroplasthelida) are axopodial protists with a remarkable diversity of external siliceous scale morphologies. It is believed that the last common ancestor of centrohelids had a double layer of siliceous scales composed of plate scales closer to a cell surface and spine scales radiating outwards. The characteristic morphotype of spine scales with a heart-shaped base was once believed to be a unique feature of the genus Choanocystis, as it was defined by Siemensma and Roijackers (1988). Further research revealed that this morphology is present in different and sometimes distantly related lineages: Ozanamiidae, Meringosphaeridae, and Marophryidae. Here, we report the fourth clade, Pterocystidae, which is also revealed to contain representatives having this phenotype. Cernunnos gen. nov. is erected here to place Cernunnos uralica sp. nov., Cernunnos arctica sp. nov., Cernunnos america sp. nov., and Cernunnos antarctica Tikhonenkov et Mylnikov, 2010, Gerasimova comb. nov. C. uralica was studied with scanning electron microscopy and SSU rDNA sequencing. Molecular phylogenetic analysis placed it into marine environmental clade P within Pterocystida. The ubiquity of spine scales with heart-shaped bases could be an example of parallel evolution, but taking into account the considerable similarity it is likely an ancestral trait, acquired from the last common ancestor of centrohelids.

Physiological and Biochemical Responses of Solanum lycopersicum L. to Benzo[a]pyrene Contaminated Soils.

Benzo[a]pyrene (BaP) is noted as one of the main cancer-causing pollutants in human beings and may damage the development of crop plants. The present work was designed to explore more insights into the toxic effects of BaP on Solanum lycopersicum L. at various doses (20, 40, and 60 MPC) spiked in Haplic Chernozem. A dose-dependent response in phytotoxicity were noted, especially in the biomass of the roots and shoots, at doses of 40 and 60 MPC BaP and the accumulation of BaP in S. lycopersicum tissues. Physiological and biochemical response indices were severely damaged based on applied doses of BaP. During the histochemical analysis of the localization of superoxide in the leaves of S. lycopersicum, formazan spots were detected in the area near the leaf's veins. The results of a significant increase in malondialdehyde (MDA) from 2.7 to 5.1 times, proline 1.12- to 2.62-folds, however, a decrease in catalase (CAT) activity was recorded by 1.8 to 1.1 times. The activity of superoxide dismutase (SOD) increased from 1.4 to 2, peroxidase (PRX) from 2.3 to 5.25, ascorbate peroxidase (APOX) by 5.8 to 11.5, glutathione peroxidase (GP) from 3.8 to 7 times, respectively. The structure of the tissues of the roots and leaves of S. lycopersicum in the variants with BaP changed depending on the dose: it increased the intercellular space, cortical layer, and the epidermis, and the structure of the leaf tissues became looser.

Postbiotics versus probiotics in early-onset colorectal cancer.

Probiotics and postbiotics mechanisms of action and applications in early-onset colorectal cancer (EOCRC) prevention and treatment have significant importance but are a matter of debate and controversy. Therefore, in this review, we aimed to define the probiotics concept, advantages and limitations in comparison to postbiotics, and proposed mechanisms of anti-tumor action in EOCRC prevention and treatment of postbiotics. Biotics (probiotics, prebiotics, and postbiotics) could confer the health benefit by affecting the host gut microbiota directly and indirectly. The main mechanisms of action of probiotics in exerting anticancer features include immune system regulation, inhibition of cancer cell propagation, gut dysbiosis restoration, anticancer agents' production, gut barrier function renovation, and cancer-promoting agents' reduction. Postbiotics are suggested to have different mechanisms of action to restore eubiosis against EOCRC, including modulation of gut microbiota composition, gut microbial metabolites regulation, and intestinal barrier function improvement via different features such as immunomodulatory, anti-inflammatory, antioxidant, and anti-proliferative properties. A better understanding of postbiotics challenges and mechanism of action in therapeutic applications will allow us to sketch accurate trials in order to use postbiotics as bio-therapeutics in EOCRC.

Trichococcus shcherbakoviae subsp. psychrophilus subsp. nov., a psychrotolerant facultative anaerobe isolated from a cold spring.

A psychrotolerant facultative anaerobe, strain SKBGT, was isolated from the bottom sediments of the cold mineral spring Buxichen (Buryatia, Russia). Gram-positive non-motile cocci with a diameter of 1.75-2.5 µm were observed singly or in long chains. Cells grew in the temperature range from ̶ 5-35 °C. Growth was observed within the pH range of 7.0-9.5, with the optimum growth at pH 7.6 and at a NaCl concentration from 0-1.0 % (optimum 0.1 % (w/v)). Strain SKBGT was a chemoorganoheterotroph that used sugars and some organic acids as substrates. The predominant fatty acids in cell walls were С16:1ω9, С18:1ω9, and С16 : 0. The 16S rRNA gene sequence of strain SKBGT shared high similarity (>99 %) with those of the type strains of the genus Trichococcus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKBGT and Trichococcus shcherbakoviae ArtT (=DSM 107162T=VKM B-3260T) were 70.1 and 95.4 %, respectively. The genomic DNA G+C content of strain SKBGT was 47.1 mol%. Compared with the type strain of T. shcherbakoviae, the new strain was characterized by a temperature optimum for growth (10 °C) significantly lower than that of T. shcherbakoviae DSM 107162T (20-30 °C). Based on phenotypic and genomic characteristics, the isolate SKBGT was classified as T. shcherbakoviae subsp. psychrophilus subsp. nov. The type strain is SKBGT (=VKM B-3241Т=JCM 33326T).

Cappable-Seq Reveals Specific Patterns of Metabolism and Virulence for Salmonella Typhimurium Intracellular Survival within Acanthamoeba castellanii.

The bacterial pathogen Salmonella enterica, which causes enteritis, has a broad host range and extensive environmental longevity. In water and soil, Salmonella interacts with protozoa and multiplies inside their phagosomes. Although this relationship resembles that between Salmonella and mammalian phagocytes, the interaction mechanisms and bacterial genes involved are unclear. Here, we characterized global gene expression patterns of S. enterica serovar Typhimurium within Acanthamoeba castellanii at the early stage of infection by Cappable-Seq. Gene expression features of S. Typhimurium within A. castellanii were presented with downregulation of glycolysis-related, and upregulation of glyoxylate cycle-related genes. Expression of Salmonella Pathogenicity Island-1 (SPI-1), chemotaxis system, and flagellar apparatus genes was upregulated. Furthermore, expression of genes mediating oxidative stress response and iron uptake was upregulated within A. castellanii as well as within mammalian phagocytes. Hence, global S. Typhimurium gene expression patterns within A. castellanii help better understand the molecular mechanisms of Salmonella adaptation to an amoeba cell and intracellular persistence in protozoa inhabiting water and soil ecosystems.

Multiple Euryhaline Lineages of Centrohelids (Haptista: Centroplasthelida) in Inland Saline Waters Revealed with Metabarcoding.

The diversity of centrohelids in inland saline waters was studied with metabarcoding for the first time. The fragment of V6-V7 regions of 18S rDNA was sequenced with newly designed primers. Obtained OTUs were identified with molecular phylogenetic analysis and comparison of the signatures in 39es9 hairpin of V7. The obtained data included some OTUs, which could be attributed to four described species, but the majority belonged to previously established or novel environmental clades. Along with some presumably marine/brackish clades and freshwater/low salinity (0-2 ppt) clades, seven presumable species demonstrating broad (from 1-2 up to 78 ppt) salinity tolerance were detected. A number of OTUs belonged to Raphidocystis contractilis, which is known from three independent findings in brackish habitats only. Thus, it was assumed that this species is stenohaline and specifically adapted to salinity 5-15 ppt. The high level of salinity tolerance was suggested for centrohelids before based on morphology, which was used to justify their cosmopolitan distribution. Later these views were criticized based on environmental sequencing, but the results of the current survey indicate, that at least some species are present at salinities from almost freshwater (1-2 ppt) to twice oceanic (78 ppt) and are presumably capable of overcoming oceanic salinity barriers for their distribution.

Pinjata ruminata gen. et sp. n.-A New Member of Centrohelid Family Yogsothothidae (Haptista: Centroplasthelida) from the Brackish River.

A new genus and species of centrohelid heliozoan Pinjata ruminata from the Tuzlukkol' River (Orenburg Region of Russia) and Gor'koe Lake (Chelyabinsk Region of Russia) is studied with light- and electron microscopy. Pinjata ruminata has two types of plate scales, partially running up the sides of the axopodia. Inner plate scales (3.2-4.9 × 1.5-2.6 µm) are flat, ovate-oblong and have a broad axial thickening and a thin electron-dense border. Outer plate scales (4.2-6.7 × 1.5-3.0 µm) are concave, elongated, of irregular shape, often curved, and broadened towards one end. Roundish depressions are forming two rows on both sides of the narrow axial thickening. The cells are attached to the substratum. Molecular phylogenetic analysis based on the SSU rDNA robustly placed P. ruminata in the family Yogsothothidae. This position is confirmed with the presence of five panacanthocystid increase regions. The morphology of the new genus is in a good accordance with diagnosis of the family. The status of a genus "Heteroraphidiophrys" is discussed. Other potential findings of Pinjata from literature are analyzed. Pinjata represents the third lineage of centrohelids, characterized with the presence of only tangentially oriented plate scales. The halophilic nature of Yogsothothidae is suggested.

High-Throughput Sequencing of the 16S rRNA Gene as a Survey to Analyze the Microbiomes of Free-Living Ciliates Paramecium.

Ciliates are the largest group of ubiquitous aquatic bacterivorous protists, and many species are easily cultivated. However, only few studies reported prokaryotic communities naturally associated with ciliate cells. Herein, we analyzed the microbiome composition of several strains of Paramecium (Ciliophora) originating from different locations and belonging to two morpho-species by high-throughput sequencing (HTS) of the 16S rRNA gene. Possible reasons of HTS results bias were addressed comparing DNA libraries obtained using different primers and different number of ciliate cells. Microbiomes associated with ciliates and their environments were always significantly different by prokaryotic taxonomic composition and bacterial richness. There were also pronounced differences between Paramecium strains. Interestingly, potentially pathogenic bacteria were revealed in Paramecium microbiomes.

Oral microbiomes in children with asthma and dental caries.

OBJECTIVE: Recently, a significant association between dental caries and the severity of bronchial asthma in children has been revealed. This finding indicates a possible relationship between the oral microbiome and the pathogenesis of asthma. The purpose of our study was to estimate differences in the dental plaque microbiota of asthmatic children with and without dental caries by 16S rDNA sequencing. MATERIAL AND METHODS: Dental plaque samples were obtained with a spoon excavator from the occlusal surface of one deciduous tooth (the second mandibular left molar in caries-free children and the most affected tooth in caries-affected children). Total DNA was extracted from dental plaque. DNA libraries were analysed by 16S rRNA gene sequencing on the MiSeq (Illumina) platform. RESULTS: There were no significant differences in the composition of bacterial communities from both caries-affected and caries-free children with asthma. The "caries-enriched" genus was Veillonella (Veillonellaceae, Selenomonadales, Negativicutes). Relative abundance of Neisseria was significantly higher in caries-free children with asthma (p < 0.05). CONCLUSIONS: The most significant difference in compared bacterial communities was a higher relative abundance of Veillonella in caries-affected plaques that suggests its involvement in pathogenesis of caries. Potential respiratory pathogens are present in oral cavity of both caries-affected and caries-free asthmatic children.

A New Species of Centrohelid Heliozoan Acanthocystis amura n. sp. Isolated From Two Remote Locations in Russia.

A new species of centrohelid heliozoan Acanthocystis amura from the Amur River, the Far East of Russia was studied with light- and electron microscopy. Acanthocystis amura has simple oval plate scales (1.2-2.6 × 1.0-1.8 µm) with an axial thickening and a thin border as well as two types of spine scales. The spine scales of type 1 were 1.3-4.8 µm long and had four small hooks on their tips. The spine scales of type 2 were shorter, 1.0-3.6 µm long and had four teeth at the distal end. The morphology of A. amura resembles that of Acanthocystis quadrifurca. They both have similar spine scales but their plate scales are completely different. Acanthocystis valdiviense differs from the new species in absence of hook-bearing scales. Molecular phylogeny based on 18S rDNA consistently placed A. amura into Acanthocystis nichollsi/Acanthocystis costata clade, but relationships between those three species were not resolved. Morphology of another centrohelid strain from another location (the South Urals) has been compared with that of the original strain and few minor differences in size characteristics of the scales have been revealed.

Circulating levels of proinflammatory mediators as potential biomarkers of post-traumatic knee osteoarthritis development.

BACKGROUND: The identification of biomarkers of post-traumatic osteoarthritis (PTOA) progression is of clinical importance. The aims of this study were: (1) to assess the abilities of various soluble proinflammatory mediators in plasma to distinguish patients with knee PTOA from controls; (2) to determine the correlations between the mediators in plasma and those mediators in synovial fluid (SF); and (3) to explore the associations of the mediators with radiographic PTOA severity. MATERIALS AND METHODS: The concentrations of IL-1ß, IL-6, IL-18, TNFα, and leptin were measured using ELISA. Nitric oxide was determined as nitrite/nitrate (NO x ) using the Griess reaction. RESULTS: We included 171 subjects (134 PTOA patients and 37 controls) and excluded patients with rheumatoid arthritis or gout. The ROC curve of plasma NO x had the highest AUC, a specificity of 100%, and a sensitivity of 84.4%. The combination of IL-6 and leptin proved to be the most discriminatory, with an AUC value of 0.933, a specificity of 96.7%, and a sensitivity of 85.7%. The levels of NO x , IL-6, IL-18, and leptin in plasma were significantly correlated with their levels in SF. Leptin levels in both plasma (p = 0.036) and SF (p = 0.041) and the synovial IL-18 level (p = 0.045) were correlated with the Kellgren-Lawrence (KL) grade. Early-stage PTOA (KL 1-2) was associated with a high concentration of IL-1ß in plasma before and after (OR 6.235, 95% CI 1.362 to 28.552, p = 0.018) adjusting for age, gender, and BMI. CONCLUSIONS: Circulating NO x level and a combination of IL-6 and leptin permitted the strongest discrimination of patients with PTOA from controls. PTOA severity was correlated with leptin levels in plasma and SF and with the synovial IL-18 level. Early PTOA was associated with the circulating level of IL-1ß. LEVEL OF EVIDENCE: III (case-control study).

Genome Characterization and Probiotic Potential of Corynebacterium amycolatum Human Vaginal Isolates.

The vaginal microbiome of healthy women contains nondiphtheria corynebacteria. The role and functions of nondiphtheria corynebacteria in the vaginal biotope are still under study. We sequenced and analysed the genomes of three vaginal C. amycolatum strains isolated from healthy women. Previous studies have shown that these strains produced metabolites that significantly increased the antagonistic activity of peroxide-producing lactic acid bacteria against pathogenic and opportunistic microorganisms and had strong antimicrobial activity against opportunistic pathogens. Analysis of the C. amycolatum genomes revealed the genes responsible for adaptation and survival in the vaginal environment, including acid and oxidative stress resistance genes. The genes responsible for the production of H2O2 and the synthesis of secondary metabolites, essential amino acids and vitamins were identified. A cluster of genes encoding the synthesis of bacteriocin was revealed in one of the annotated genomes. The obtained results allow us to consider the studied strains as potential probiotics that are capable of preventing the growth of pathogenic microorganisms and supporting colonisation resistance in the vaginal biotope.

Zinc Oxide Nanoparticles: Physiological and Biochemical Responses in Barley (Hordeum vulgare L.).

This work aimed to study the toxic implications of zinc oxide nanoparticles (ZnO NPs) on the physio-biochemical responses of spring barley (Hordeum sativum L.). The experiments were designed in a hydroponic system, and H. sativum was treated with two concentrations of ZnO NPs, namely 300 and 2000 mg/L. The findings demonstrated that ZnO NPs prevent the growth of H. sativum through the modulation of the degree of oxidative stress and the metabolism of antioxidant enzymes. The results showed increased malondialdehyde (MDA) by 1.17- and 1.69-fold, proline by 1.03- and 1.09-fold, and catalase (CAT) by 1.4- and 1.6-fold in shoots for ZnO NPs at 300 and 2000 mg/L, respectively. The activity of superoxide dismutase (SOD) increased by 2 and 3.3 times, ascorbate peroxidase (APOX) by 1.2 and 1.3 times, glutathione-s-transferase (GST) by 1.2 and 2.5 times, and glutathione reductase (GR) by 1.8 and 1.3 times in roots at 300 and 2000 mg/L, respectively. However, the level of δ-aminolevulinic acid (ALA) decreased by 1.4 and 1.3 times in roots and by 1.1 times in both treatments (nano-300 and nano-2000), respectively, indicating changes in the chlorophyll metabolic pathway. The outcomes can be utilized to create a plan of action for plants to withstand the stress brought on by the presence of NPs.

Effects of ZnO nanoparticles and its bulk form on growth, antioxidant defense system and expression of oxidative stress related genes in Hordeum vulgare L.

A comparative analysis of physio-biochemical indices and transcriptional activity of oxidative stress genes in barley (Hordeum vulgare L.) seedlings after 7-days exposure to bulk- and nano-ZnO (300 and 2000 mg/L) was carried out. A dose-dependent reduction in the length and weight of roots and shoots, as well as a significant accumulation of Zn in plant parts, was shown. Alterations in the shape and size of organelles, cytoplasmic vacuolization, and chloroplast and mitochondrial disorganization were also revealed. These processes are particularly pronounced when H. vulgare is exposed to the higher concentrations of nano-ZnO. The study of the antioxidant defense system revealed mainly an increase in the level of reduced glutathione and the activities of superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and glutathione S-transferase (GST). The increases in activity, by 4-fold and 3-fold, was found for glutathione transferase in the roots when exposed to 2000 mg/L bulk- and nano-ZnO, respectively. The study of transcriptional activity demonstrated that in the roots under the influence of bulk- and nano-ZnO, along with Mn-SOD, Fe-SOD is highly expressed, mainly associated with the protection of chloroplasts. Analysis of the Cat 1 and Cat 2 gene expression showed that the main contribution to the increase in catalase activity in treated H. vulgare is made by the CAT-1 isozyme. Generally, in response to the impact of the studied ZnO forms, the antioxidant defense system is activated in H. vulgare, which effectively prevents the progression of oxidative stress in early stages of plant ontogenesis. Nevertheless, with constant exposure to bulk- and nano-ZnO at high concentrations, such activation leads to a depletion of the plant's energy resources, which negatively affects its growth and development. The results obtained could be useful in predicting the risks associated with the further transfer of nano-ZnO to the environment.

Macrophage Phenotype in Combination with Tumor Microbiome Composition Predicts RCC Patients' Survival: A Pilot Study.

The identification of new prognostic markers of renal cell carcinoma (RCC) is an urgent problem in oncourology. To investigate the potential prognostic significance of tumor microbiome and stromal inflammatory markers, we studied a cohort of 66 patients with RCC (23 clear cell RCC, 19 papillary RCC and 24 chromophobe RCC). The microbiome was analyzed in tumor and normal tissue by 16S rRNA amplicon sequencing. Characterization of the tumor stroma was performed using immunohistochemistry. A significant difference in alpha diversity was demonstrated between normal kidney tissue and all types of RCC. Further, we demonstrated that the bacterial burden was higher in adjacent normal tissue than in a tumor. For the first time, we demonstrated a significant correlation between bacterial burden and the content of PU.1+ macrophages and CD66b+ neutrophils in kidney tumors. Tumors with high content of PU.1+ cells and CD66b+ cells in the stroma were characterized by a lower bacterial burden. In the tumors with high bacterial burden, the number of PU.1+ cells and CD66b+ was associated with a poor prognosis. The identified associations indicate the great prognostic potential of a combined tumor microbiome and stromal cell analysis.

Prognostic Significance of the Microbiome and Stromal Cells Phenotype in Esophagus Squamous Cell Carcinoma.

Esophageal cancer is one of the most aggressive malignant neoplasms, with low survival rates and limited treatment options. In this study we analyzed the microbiome composition and the phenotype of inflammatory tumor infiltrate in squamous cell carcinoma of esophagus (ESCC) and examined possible relationships between them and their prognostic significance. We found that the predominant phyla of microorganisms found in both tumors and adjacent normal tissues were Firmicutes, Proteobacteria, Actinobacteria, Gemmatimonadetes and Bacteroidetes. We established that only bacteria of the genus Staphylococcus differ between tumors and normal tissues. We found a significant correlation between bacterial burden and the phenotype of the tumor stroma. Namely, a group of tumors characterized by a high expression of CD206 (r = -0.3976, p = 0.0056) in the stroma and iNOS (r = -0.2953, p = 0.0439) in tumor cells is characterized by a higher bacterial burden. Further, we established that in the group with a high content of CD206+ macrophages, there is also a predominance of gram-positive bacteria over gram-negative ones. We found that gram-positive bacterial burden is associated with disease prognosis in ESCC showing high content of CD206+ macrophages. In conclusion we established that the tumor microbiome, can be prognostically significant for ESCC when combined with other stromal markers.

Transcriptomic data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S treated with novobiocin.

In enteric bacteria, DNA supercoiling is highly responsive to environmental conditions. Host specific features of environment serve as cues for the expression of genes required for colonization of host niches via changing supercoiling [1]. It has been shown that substitution at position 87 of GyrA of Salmonella enterica str. SL1344 influences global supercoiling and results in an altered transcriptome with increased expression of stress response pathways [2]. Aminocoumarin antibiotics, such as novobiocin, can be used to relax supercoiling and alter the expression of supercoiling-sensitive genes. Meanwhile, Salmonella enterica demonstrates a significant resistance to this antibiotic and relatively small variability of supercoiling in response to the growth phase, osmotic pressure, and novobiocin treatment. Here we present for the first time transcriptome data of Salmonella enterica subsp. Enterica serovar Typhimurium str. 14028S grown in the presence of novobiocin. These data will help identify genes involved in novobiocin resistance and adaptation processes associated with torsion perturbations in S. enterica. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP239815) and have been assigned BioProject accession PRJNA599397.

Data on rumen and faeces microbiota profiles of Yakutian and Kalmyk cattle revealed by high-throughput sequencing of 16S rRNA gene amplicons.

It is known that the rumen microbiome directly or indirectly contributes to animal production, and may be a prospective target for mitigation of greenhouse gas emissions [1]. At the same time, feed types and components of diet can influence the composition of the rumen microbiome [2,3]. Fluctuations in the composition of the digestive tract microbiota can alter the development, health, and productivity of cattle [4]. Many studies of cattle microbiomes have focussed on the rumen microbiota, whereas the faecal microbiota has received less attention [5], [6], [7]. Therefore, the features of the faecal and the ruminal microbiomes in different cattle breeds are yet to be studied. Here, we provided 16S rRNA gene amplicon data of the ruminal and the faecal microbiomes from Yakutian and Kalmyk cattle living in the Republic of Sakha, Yakutia, Russia. Total DNA was extracted from 13 faecal and 13 ruminal samples, and DNA libraries were prepared and sequenced on an Illumina MiSeq platform. Paired-end raw reads were processed, and final operational taxonomic units (OTUs) were assigned to the respective prokaryotic taxa using the RDP (Ribosomal Database Project) database. Analysis of the microbiome composition at the phylum level revealed very similar faecal microbiota between the introduced Kalmyk breed and the indigenous Yakutian breed, whereas the ruminal microbiomes of these breeds differed substantially in terms of relative abundance of some prokaryotic phyla. We believe that the data obtained may provide new insights into the dynamics of the ruminal and the faecal microbiota of cattle as well as disclose breed-specific features of ruminal microbiomes. Besides, these data will contribute to our understanding of the ruminal microbiome structure and function, and might be useful for the management of cattle feeding and ruminal methane production.

Data on draft genome sequence of stenotrophomonas sp. SAM-B isolated from a mineral cold spring located in Tyva, southern Siberia.

Stenotrophomonas sp. SAM-B was isolated from Uzharlyg Mineral Cold Spring, Samagaltay Settlement, Republic of Tyva (Southern Siberia), Russian Federation. A whole genome sequencing of Stenotrophomonas sp. SAM-B was performed using an Illumina MiSeq platform. The resulting draft genome contains 4,253,956 bp with 66.48% GC-content and 71 contigs; the longest contig contains 968,648 bp, and the N50 has a length of 401,736 bp. The genome includes 3816 protein-coding genes, among which 23 are responsible for protein degradation, 65 are associated with stress response, and 31 are associated with virulence, disease, and defense, including beta-lactamase and resistance to fluoroquinolones. The genome data on the SAM-B strain provides fundamental knowledge that would allow a better understanding of the microorganisms inhabiting cold water environments. Moreover, the results of the genome annotation indicated that diverse metabolic pathways are encoded in the genome of the SAM-B strain and that it has biotechnological potential. The draft genome sequence of Stenotrophomonas sp. SAM-B has been deposited in DDBJ/ENA/GenBank under the accession number JABBXB000000000; the accession number of the genome sequence referred to in this paper is JABBXB010000000.