Draft Genome Sequences of Two Strains of Enterococcus lactis Showing High Potential as Cattle Probiotic Supplements.

Probiotic supplements are currently widely used in cattle feeding practices. However, knowledge regarding the genomic landscape of cattle probiotic microorganisms is relatively scarce and is based on analogies with human probiotics. Here, we report on the draft genome sequences of two Enterococcus lactis strains, VKPM B-4989 and VKPM B-4992, which were isolated from the rumen of a healthy calf and utilized as a probiotic additive.

Draft Genome Sequence of the Anoxygenic Phototrophic Bacterium Rhodoferax sp. Strain U11-2br, Isolated from a Mountain Lake on the Ulagan Plateau.

We report the draft genome sequence of an anoxygenic phototrophic bacterium, Rhodoferax sp. strain U11-2br, which was isolated from a freshwater mountain lake on the Ulagan Plateau (Altai, Russia). The assembly contains 4,514,979 bp, with a GC content of 59.9%.

Draft Genome Sequence of the Anoxygenic Phototrophic Bacterium Rhodomicrobium sp. Strain Az07, Isolated from a Brackish Canal.

Rhodomicrobium sp. strain Az07 was isolated from a brackish canal. The organism is more halotolerant than previously described species of the genus Rhodomicrobium. The Illumina MiSeq system was used to sequence the genome of the isolated strain. The assembly contains 3,291,400 bp, 106 contigs, and a GC content of 62.7%.

Draft De Novo Genome Assembly of Acinetobacter pittii Strain VKPM B-3780, a Prospective Multifunctional Bioremediation Agent.

Acinetobacter pittii strain VKPM B-3780 is a prospective degrader of oil and methanol, isolated from industrial wastewater. Here, we present the draft genome sequence of strain VKPM B-3780, obtained using Illumina sequencing of the fragment genomic library.

Draft Genome Sequence of Rhodococcus erythropolis VKPM Ac-1659, a Putative Oil-Degrading Strain Isolated from Polluted Soil in Siberia.

The draft genome sequence of Rhodococcus erythropolis VKPM Ac-1659, a putative oil-degrading strain, is reported. This genome sequence may provide better insights into the diversity and evolution of the genes responsible for hydrocarbon degradation in soil microorganisms.

Data on draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia).

The draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia) is presented. The complete genome assembly was of 2 713 207 bp with predicted completeness of 99.38%. Genome structural annotation revealed 2674 protein-coding genes, 127 pseudogenes and 77 RNA genes. Pangenome analysis of 7 currently available high quality Caldanaerobacter spp. genomes including 1523vc revealed 4673 gene clusters. Of them, 1130 clusters formed a core genome of genus Caldanaerobacter. Of the rest 3543 Caldanaerobacter pangenome genes, 385 were exclusively represented in 1523vc genome. 101 of 2801 Caldanaerobacter CDS were found to be encoding carbohydrate-active enzymes (CAZymes). The majority of CAZymes were predicted to be involved in degradation of beta-linked polysaccharides as chitin, cellulose and hemicelluloses, reflecting the metabolism of strain 1523vc, isolated on cellulose. 5 of 101 CAZyme genes were found to be unique for the strain 1523vc and belonged to GH23, GT56, GH15 and two CE9 family proteins. The draft genome of strain 1523vc was deposited at DBJ/EMBL/GenBank under the accessions JABEQB000000000, PRJNA629090 and SAMN14766777 for Genome, Bioproject and Biosample, respectively.

Draft genome sequence data of Bifidobacterium longum strain VKPM Ac-1636, a prospective probiotic isolated from human gut.

Data on the draft genome sequence of Bifidobacterium longumsubsp. longum strain Ac-1636 is presented in this report. This strain, isolated from the digestive tract of one-year old healthy infant, was deposited in the Russian National Collection of Industrial Microorganisms as a prospective candidate for development of probiotics and probiotic foods. The 2,321,741 bp draft genome consists of 73 scaffolds with N50 of 162,253 bp. Genome annotation revealed the presence of multiple determinants of probiotic properties of this strain. The draft genome sequence data of strainAc-1636 is available in DBJ/EMBL/GenBank under the accession nos. RZHL00000000, PRJNA511803 and SAMN10644101 for Genome, Bioproject and Biosample, respectively.

Data on draft genome sequence of Bacillus sp. strain VKPM B-3276 isolated from Culex pipiens larvae.

The draft genome sequence of Bacillus sp. VKPM B-3276, a mesophilic, gram-positive bacterium, isolated from dead Culex pipiens larvae is presented. This strain was deposited in the Russian National Collection of Industrial Microorganisms as a prospective candidate for development of new entomopathogenic agents. The genome of Bacillus sp. VKPM B-3276 was 6,126,346 bp in length with predicted completeness of 99.43%. Genome analysis identified 6518 protein-coding sequences and 111 RNAs genes. 13% (271) of the protein-coding genes were assigned to "Carbohydrates" subsystem category, according to RAST/SEED. Among them about 50 enzymes, responsible for chitin, peptidoglycan and related molecules decomposition, were found. The draft genome of strain VKPM B-3276 was deposited at DBJ/EMBL/GenBank under the accession nos. RZHM00000000, PRJNA511803 and SAMN10644103 for Genome, Bioproject and Biosample, respectively.

Decoupling between sulfate reduction and the anaerobic oxidation of methane in the shallow methane seep of the Black sea.

Methane seepages are widespread in the Black Sea. However, microbiological research has been carried out only at the continental shelf seeps. The present work dealt with coastal gas seepages of the Kalamit Bay (Black Sea). High-throughput 16S rRNA gene sequencing and radiotracer analysis (14С and 35S) were used to determine the composition of the microbial community and the rates of microbial sulfate reduction and methane oxidation. The phylum Proteobacteria, represented mainly by sulfate reducers of the class Deltaproteobacteria, was the predominant in sequence dataset. Bacteroidetes and Planctomycetes were other numerous phyla. Among archaea, the phylum Woesearchaeota and Marine Benthic Group B were predominant in the upper horizons. Relative abundance of Euryarchaeota of the families Methanomicrobiaceae and Methanosarcinaceae (including ANME-3 archaea) increased in deeper sediment layers. Sulfate reduction rate (up to 2.9 mmol/L × day) was considerably higher than the rate of anaerobic methane oxidation (up to 43.4 µmol/L × day), which indicated insignificant contribution of anaerobic methane oxidation to the total sulfide production.

The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner.

Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity. However, deletion of dps changed the profile of proteins in starved cells, SELEX screen revealed genomic regions preferentially bound in vitro and certain affinity of Dps for artificial branched molecules was detected by atomic force microscopy. Here we report a non-random distribution of Dps binding sites across the bacterial chromosome in exponentially growing cells and show their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. In the dps-null mutant we, therefore, observed a differentially altered expression of several targeted genes and found suppressed transcription from the dps promoter. In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA polymerase or, vice versa, competing with inhibitors to activate transcription.

[Induction of transcription through the scs insulator leads to abnormal development of Drosophila melanogaster].

A regulatory element named scs is one of the first insulators discovered in Drosophila, which was found on the boundary of the hsp70 domain. The 993-bp scs insulator contains two promoters at the ends and two polyadenylation signals located in the same orientation in the central part of the insulator. In the Drosophila transgenic lines, induction of a strong transcription through the scs insulator only in the direction that coincides with the direction of the two polyadenylation sites activity results in multiple phenotypic defects of the Drosophila development and embryonic lethality. A similar effect was not observed upon testing of other known Drosophila insulators.

The Use of Transcription Terminators to Generate Transgenic Lines of Chinese Hamster Ovary Cells (CHO) with Stable and High Level of Reporter Gene Expression.

Mammalian cell lines are widely used to produce recombinant proteins. Stable transgenic cell lines usually contain many insertions of the expression vector in one genomic region. Transcription through transgene can be one of the reasons for target gene repression after prolonged cultivation of cell lines. In the present work, we used the known transcription terminators from the SV40 virus, as well as the human ß- and γ-globin genes, to prevent transcription through transgene. The transcription terminators were shown to increase and stabilize the expression of the EGFP reporter gene in transgenic lines of Chinese hamster ovary (CHO) cells. Hence, transcription terminators can be used to create stable mammalian cells with a high and stable level of recombinant protein production.

Tepidisphaera mucosa gen. nov., sp. nov., a moderately thermophilic member of the class Phycisphaerae in the phylum Planctomycetes, and proposal of a new family, Tepidisphaeraceae fam. nov., and a new order, Tepidisphaerales ord. nov.

Three strains of facultatively aerobic, moderately thermophilic bacteria were isolated from terrestrial hot springs in Baikal Lake region and Kamchatka (Russia). Cells of the new isolates were cocci reproducing by binary fission. The temperature range for growth was between 20 and 56 °C and the pH range for growth from pH 4.5 to 8.5, with optimal growth at 47-50 °C and pH 7.0-7.5. The organisms were chemoheterotrophs preferring sugars and polysaccharides as growth substrates. 16S rRNA gene sequences of strains 2842, 2813 and 2918Kr were nearly identical (99.7-100 % similarity) and indicated that the strains belonged to the phylum Planctomycetes. The phylogenetically closest cultivated relatives were Algisphaera agarilytica 06SJR6-2(T) and Phycisphaera mikurensis FYK2301M01(T) with 16S rRNA gene sequence similarity values of 82.4 and 80.3 %, respectively. The novel strains differed from them by higher growth temperature, sensitivity to NaCl concentration above 3.0 % and by their cellular fatty acids profile. On the basis of phylogenetic and physiological data, strains 2842(T), 2813 and 2918Kr represent a novel genus and species for which we propose the name Tepidisphaera mucosa sp. nov. The type strain is 2842(T) ( = VKM B-2832(T) = JCM 19875(T)). We also propose that Tepidisphaera gen. nov. is the type genus of a novel family, Tepidisphaeraceae fam. nov. and a novel order, Tepidisphaerales ord. nov.

Mobilitalea sibirica gen. nov., sp. nov., a halotolerant polysaccharide-degrading bacterium.

A novel strictly anaerobic, halotolerant, organotrophic bacterium, strain P3M-3(T), was isolated from a microbial mat formed under the flow of hot water emerging from a 2775 m-deep well in Tomsk region (western Siberia, Russia). Cells of strain P3M-3(T) were straight and curved rods, 0.2-0.4 µm in width and 1.5-20 µm in length. Strain P3M-3(T) grew optimally at 37 °C, pH 7.0-7.5 and in a NaCl concentration of 15 g l(-1). Under optimum growth conditions, the doubling time was 1 h. The isolate was able to ferment a variety of mono-, di- and polysaccharides, including microcrystalline cellulose. Acetate, ethanol, H2 and CO2 were the main products of glucose fermentation. The DNA G+C content was 33.4 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain P3M-3(T) was a member of family Lachnospiraceae, whose representatives are also found in Clostridium cluster XIVa. 16S rRNA gene sequence similarity with Clostridium jejuense HY-35-12(T), the closest relative, was 93.9%. A novel genus and species, Mobilitalea sibirica gen. nov., sp. nov., are proposed based on phylogenetic analysis and physiological properties of the novel isolate. The type strain of the type species is P3M-3(T) ( = DSM 26468(T) = VKM B-2804(T)).

Complete Genomic Sequence of "Thermofilum adornatus" Strain 1910bT, a Hyperthermophilic Anaerobic Organotrophic Crenarchaeon.

The complete genomic sequence of a novel hyperthermophilic crenarchaeon, strain 1910b(T), was determined. The genome comprises a 1,750,259-bp circular chromosome containing single copies of 3 rRNA genes, 43 tRNA genes, and 1,896 protein-coding sequences. In silico genome-genome hybridization suggests the proposal of a novel species, "Thermofilum adornatus" strain 1910b(T).

Complete Genome Sequence of Salinarchaeum sp. Strain HArcht-Bsk1T, Isolated from Hypersaline Lake Baskunchak, Russia.

The complete genome sequence of a novel halophilic archaeon, Salinarchaeum sp. strain HArcht-Bsk1(T), was determined using next-generation sequencing. The genome comprises a 3,255,260-bp circular chromosome with a G+C content of 66.7%. Automatic annotation of the genome revealed a single rRNA operon, 45 tRNAs, and 3,013 protein-coding gene sequences.