Comparative Genome Analysis of Uropathogenic Morganella morganii Strains

Morganella morganii is an opportunistic bacterial pathogen shown to cause a wide range of clinical and community-acquired infections. This study was aimed at sequencing and comparing the genomes of three M. morganii strains isolated from the urine samples of patients with community-acquired urinary tract infections. Draft genome sequencing was conducted using the Illumina HiSeq platform. The genomes of MM 1, MM 4, and MM 190 strains have a size of 3.82–3.97 Mb and a GC content of 50.9–51%. Protein-coding sequences (CDS) represent 96.1% of the genomes, RNAs are encoded by 2.7% of genes and pseudogenes account for 1.2% of the genomes. The pan-genome containes 4,038 CDS, of which 3,279 represent core genes. Six to ten prophages and 21–33 genomic islands were identified in the genomes of MM 1, MM 4, and MM 190. More than 30 genes encode capsular biosynthesis proteins, an average of 60 genes encode motility and chemotaxis proteins, and about 70 genes are associated with fimbrial biogenesis and adhesion. We determined that all strains contained urease gene cluster ureABCEFGD and had a urease activity. Both MM 4 and MM 190 strains are capable of hemolysis and their activity correlates well with a cytotoxicity level on T-24 bladder carcinoma cells. These activities were associated with expression of RTX toxin gene hlyA, which was introduced into the genomes by a phage similar to Salmonella phage 118970_sal4

Effect of the total fraction of

Intestinal microbes play a key role in the energy metabolism of broiler chickens, participate in the development of the gastrointestinal tract, including the regulation of intestinal epithelial proliferation, vitamin synthesis and ion absorption, fermentation of carbohydrates and proteins, biotransformation of bile acids, protection from pathogens and modulation of the immune system. Metagenomic analysis of the gastrointestinal microbiota allows to find approaches to improve the growth and productivity of chickens by introducing a diet based on beneficial bacterial strains or their secondary metabolites. In this paper, we studied the effect of the total fraction of Bacillus subtilis GM5 lipopeptides on the growth parameters and formation of bacterial communities in the caecum of cross Cobb 500 broiler chickens. It was found that the addition of bacillary lipopeptides to the feed resulted in an increase in chicken weight by 12.7% and a decrease in feed conversion by 6.36% compared to the control (P < 0.05). It was also shown that the introduction of a feed additive in the form of a lipopeptide fraction modulates the structure of the bacterial microbiota of the caecum of chickens. Thus, the proportion of classes Bacteroidia, Negativicutes, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Synergistia in the caecal microbiota of chickens of the experimental group increases, and the proportion of Clostridia, Methanobacteria decreases in comparison with the control

Effect of

The objective of the study was to determine the effect of adding protease obtained from the Bacillus pumilus 3-19 strain to the diet of Hubboard broiler chickens on the growth indicators of poultry and the composition of the cecum microbiota of broiler chickens. As a result of metagenomic analysis of 16S rRNA genes in the contents of the cecum of chickens, it was shown that the control and experimental groups formed two separate clusters, which indicates differences in microbial communities in these two groups. Analysis of alpha diversity showed an increase in species richness in the group of chickens that received protease as a feed additive. On day 35, both groups were dominated by bacterium of Firmicutes (21.13 — 49.01%) and Bacteroidetes (37.68 — 67.72%) groups. It was shown that in the group of chickens receiving protease as a feed additive, the average daily gain in live weight was higher than in the control group by 0.5 kg (P < 0.05). The introduction of protease resulted in an increased F/B ratio, which was positively correlated with chicken body weight. Thus, the addition of B. pumilus 3-19 protease to broiler feed leads to improved feed intake and digestibility, which is of great importance for reducing the cost of the final product. The use of protease regulates the cecum microbiota of broiler chickens and increases microbial diversity on 35 day of chicken growth

Comparative Genome Analysis of Two Bacillus pumilus Strains Producing High Level of Extracellular Hydrolases

Whole-genome sequencing of a soil isolate Bacillus pumilus, strain 7P, and its streptomycin-resistant derivative, B. pumilus 3-19, showed genome sizes of 3,609,117 bp and 3,609,444 bp, respectively. Annotation of the genome showed 3794 CDS (3204 with predicted function) and 3746 CDS (3173 with predicted function) in the genome of strains 7P and 3-19, respectively. In the genomes of both strains, the prophage regions Bp1 and Bp2 were identified. These include 52 ORF of prophage proteins in the Bp1 region and 38 prophages ORF in the Bp2 region. Interestingly, more than 50% of Bp1 prophage proteins are similar to the proteins of the phi105 in B. subtilis. The DNA region of Bp2 has 15% similarity to the DNA of the Brevibacillus Jimmer phage. Degradome analysis of the genome of both strains revealed 148 proteases of various classes. These include 60 serine proteases, 48 metalloproteases, 26 cysteine proteases, 4 aspartate proteases, 2 asparagine proteases, 3 threonine proteases, and 2 unclassified proteases. Likewise, three inhibitors of proteolytic enzymes were found. Comparative analysis of variants in the genomes of strains 7P and 3-19 showed the presence of 81 nucleotide variants in the genome 3-19. Among them, the missense mutations in the rpsL, comA, spo0F genes and in the upstream region of the srlR gene were revealed. These nucleotide polymorphisms may have affected the streptomycin resistance and overproduction of extracellular hydrolases of the 3-19 strain. Finally, a plasmid DNA was found in strain 7P, which is lost in its derivative, strain 3-19. This plasmid contains five coding DNA sequencing (CDS), two regulatory proteins and three hypothetical proteins

Non-Isothermal Decomposition as Efficient and Simple Synthesis Method of NiO/C Nanoparticles for Asymmetric Supercapacitors

A series of NiO/C nanocomposites with NiO concentrations ranging from 10 to 90 wt% was synthesized using a simple and efficient two-step method based on non-isothermal decomposition of Nickel(II) bis(acetylacetonate). X-ray diffraction (XRD) measurements of these NiO/C nanocomposites demonstrate the presence of β-NiO. NiO/C nanocomposites are composed of spherical particles distributed over the carbon support surface. The average diameter of nickel oxide spheres increases with the NiO content and are estimated as 36, 50 and 205 nm for nanocomposites with 10, 50 and 80 wt% NiO concentrations, respectively. In turn, each NiO sphere contains several nickel oxide nanoparticles, whose average sizes are 7–8 nm. According to the tests performed using a three-electrode cell, specific capacitance (SC) of NiO/C nanocomposites increases from 200 to 400 F/g as the NiO content achieves a maximum of 60 wt% concentration, after which the SC decreases. The study of the NiO/C composite showing the highest SC in three- and two-electrode cells reveals that its SC remains almost unchanged while increasing the current density, and the sample demonstrates excellent cycling stability properties. Finally, NiO/C (60% NiO) composites are shown to be promising materials for charging quartz clocks with a power rating of 1.5 V (30 min)

Non-Isothermal Decomposition as Efficient and Simple Synthesis Method of NiO/C Nanoparticles for Asymmetric Supercapacitors

A series of NiO/C nanocomposites with NiO concentrations ranging from 10 to 90 wt% was synthesized using a simple and efficient two-step method based on non-isothermal decomposition of Nickel(II) bis(acetylacetonate). X-ray diffraction (XRD) measurements of these NiO/C nanocomposites demonstrate the presence of &beta;-NiO. NiO/C nanocomposites are composed of spherical particles distributed over the carbon support surface. The average diameter of nickel oxide spheres increases with the NiO content and are estimated as 36, 50 and 205 nm for nanocomposites with 10, 50 and 80 wt% NiO concentrations, respectively. In turn, each NiO sphere contains several nickel oxide nanoparticles, whose average sizes are 7&ndash;8 nm. According to the tests performed using a three-electrode cell, specific capacitance (SC) of NiO/C nanocomposites increases from 200 to 400 F/g as the NiO content achieves a maximum of 60 wt% concentration, after which the SC decreases. The study of the NiO/C composite showing the highest SC in three- and two-electrode cells reveals that its SC remains almost unchanged while increasing the current density, and the sample demonstrates excellent cycling stability properties. Finally, NiO/C (60% NiO) composites are shown to be promising materials for charging quartz clocks with a power rating of 1.5 V (30 min)

Synthesis of Co3O4/CoOOH via electrochemical dispersion using a pulse alternating current method for lithium-ion batteries and supercapacitors

International audienc

Draft genome sequence data of Lysinibacillus fusiformis strain GM, isolated from potato phyllosphere as a potential probiotic

Here we present the morphological and physiological properties of isolated Lysinibacillus fusiformis strain GM, its draft genome sequence as well as annotation and analysis of its genome. Initial analysis of MALDI-TOF mass spectrometry, 16S rRNA gene analysis and in silico DNA-DNA hybridization revealed that the strain belongs to the species Lysinibacillus fusiformis. The 4,678,122 bp draft genome consist of 17 scaffolds encoding 4588 proteins and 137 RNAs. Annotation of the genome sequence revealed cellulase and protease encoding genes, genes of adhesion proteins and putative genes responsible for the biosynthesis of antimicrobial metabolites. The Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number NTMQ00000000.1 (https://www.ncbi.nlm.nih.gov/nuccore/NZ_NTMQ00000000.1). Keywords: Lysinibacillus fusiformis, Probiotic, Cellulase, Illumina MiSeq, In silico DNA-DNA hybridizatio

The <i>SDHD</i>:p.H102R Variant Is Frequent in Russian Patients with Head and Neck Paragangliomas and Associated with Loss of 11p15.5 Region and Hypermethylation of H19-DMR

Head and neck paragangliomas (HNPGLs) are rare neuroendocrine neoplasms derived from the parasympathetic paraganglia of the head and neck. At least 30% of HNPGLs are linked to germline mutations, predominantly in SDHx genes. In this study, we analyzed an extended cohort of Russian patients with HNPGLs using whole-exome sequencing and found a highly frequent missense variant p.H102R in the SDHD gene. We determined this variant in 34% of the SDHD mutation carriers. This variant was associated with somatic loss of the gene wild-type allele. Data from the B allele frequency method and microsatellite and microdeletion analysis indicated evident LOH at the 11p15.5 region and potential loss of the whole of chromosome 11. We found hypermethylation of H19-DMR in all tumors, whereas differential methylation of KvDMR was mostly retained. These findings do not support the paternal transmission of SDHD:p.H102R but are in agreement with the Hensen model. Using targeted sequencing, we also studied the variant frequency in a control cohort; we found SDHD:p.H102R in 1.9% of cases, allowing us to classify this variant as pathogenic. The immunohistochemistry of SDHB showed that the SDHD:p.H102R mutation, even in combination with wild-type allele loss, does not always lead to SDH deficiency. The obtained results demonstrate the frequent variant associated with HNPGLs in a Russian population and support its pathogenicity. Our findings help with understanding the mechanism of tumorigenesis and are also important for the development of cost-effective genetic screening programs