A novel method of alkoxyamine homolysis activation via photochemical rearrangement.

We proposed the nitrone-oxaziridine rearrangement as a novel method for photochemical activation for the homolysis of alkoxyamine in nitroxide-mediated polymerization. The photoisomerization of the aldo-/ketonitrone-group into the oxaziridine one in 2,5-dihydroimidazole 3-oxide-based alkoxyamines was studied; the products of photolysis have been identified, and quantum yields were measured. Conversion of the nitrone group into the oxaziridine one was found to decrease the activation energy of alkoxyamine homolysis by ca. 10 kJ mol-1.

Antibiofilm activity of cell-free supernatants of vaginal isolates of Corynebacterium amycolatum against Pseudomonas aeruginosa and Klebsiella pneumoniae.

Biofilm formation is an important factor in the development of antibiotic resistance and chronic infection. In this study, we demonstrated that the cell-free supernatant of vaginal isolates of C. amycolatum caused a reduction in biofilm formation, destroyed the preformed biofilms, altered the cell surface properties and reduced the production of exopolysaccharides in clinical isolates of P. aeruginosa и Kl. pneumoniae. Microscopic observations showed that P. aeruginosa and Kl. pneumoniae biofilm formed small clusters scattered over the surface after treatment with cell-free supernatant of C. amycolatum ICIS 99, in contrast to the dense aggregates observed in controls, as well as the flat, scattered, and unstructured biofilm architecture after treatment of preformed biofilms cell-free supernatant. The cells were flat and relatively unstructured. Based on these results, we hypothesize that C. amycolatum likely produces secondary metabolites with antimicrobial activity and utilizes a similar mechanism of action to bacteriocins and/or biosurfactants. The data obtained open the prospect of studying the metabolic profile of the cell-free supernatant of C. amycolatum to understand the nature and mechanism of the detected antibacterial action and provide further support for the probiotic potential of C. amycolatum vaginal isolates.

The Kinetic Solvent Effect on 1,3-Dipolar Cycloaddition of 2,2,5,5-Tetramethyl-3-imidazoline-3-oxide-1-oxyl.

The use of 2,2,5,5-tetramethyl-3-imidazoline-3-oxide-1-oxyl (1) as a controlling agent in Nitroxide Mediated Polymerization allows for activation of alkoxyamine homolysis by 1,3-dipolar cycloaddition of a vinyl monomer [Edeleva et al. Chem. Commun. 2019, 55, 190-193]. Polymerization can be carried out in a medium with different polarity and hydrogen bonding capacity which affects the rate of 1,3-dipolar cycloaddition reaction. In the present study, the solvent effect on the rate of this reaction was investigated by the electron paramagnetic resonance and density functional theory for the six different dipolarophiles, e. g. styrene, n-butyl acrylate, acrylonitrile, methyl vinyl ketone, maleic anhydride, and N-phenyl maleimide. The rate of 1,3 dipolar cycloaddition of non-polar styrene was found to be slightly dependent on solvent, while one order of magnitude decrease in rate coefficient is observed for other dipolarophiles when going from hexane to methanol.

Genome sequence of Corynebacterium amycolatum ICIS 99 isolated from human vagina reveals safety and beneficial properties.

Corynebacterium amycolatum ICIS 99 was isolated from vaginal smears of healthy women and showed promising results in antimicrobial screenings. Here, we report the draft genome sequence of this strain and analyze its main features to assess its safety and useful properties. The genome is 2,532,503 bp long and contains 2186 CDSs with an average G + C content of 59.0%. Analyses of the ICIS 99 genome revealed the absence of true virulence factors. The genome contains genes involved in the synthesis of secondary metabolites and bacteriocins of the class sactipeptide. In the genome of ICIS 99, we identified a large number of genes responsible for adaptation and survival in the vaginal environment, including acid and oxidative stress resistance genes. The genomic information of ICIS 99 provides a basis for understanding the safety and useful properties of ICIS 99 and for considering it as a potential probiotic strain. The whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JAIUSU000000000.

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.

The Kinetics of 1,3-Dipolar Cycloaddition of Vinyl Monomers to 2,2,5,5-Tetramethyl-3-imidazoline-3-oxides.

In our previous work [Edeleva et al. Chem. Commun. 2019, 55, 190-193], we proposed a versatile approach to the activation of the homolysis of an aldonitrone group-containing alkoxyamine by 1,3-dipolar cycloaddition to a vinyl monomer. Both nitroxide- and alkoxyamine-containing aldonitrones were found to be capable of reacting with the activated alkenes. In the present study, the kinetics of these reactions with 11 different vinyl monomers were investigated using EPR and NMR spectroscopy, and apparent activation energies as well as pre-exponential factors were determined. The influence of monomer structure on the rate of the 1,3-dipolar cycloaddition is discussed. For the vinyl monomers typically used in nitroxide mediated polymerization (styrene, methyl methacrylate) the rate coefficient of cycloaddition to the nitroxide is around k(353 K) ∼4 ⋅ 10-4  L mol-1 s-1 , whereas for n-butyl acrylate and methyl vinyl ketone we observed the fastest cycloaddition reaction with k(353 K)=8 ⋅ 10-3 and 4 ⋅ 10-2  L mol-1 s-1 respectively.

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.

NMR and EPR Study of Homolysis of Diastereomeric Alkoxyamines.

Three alkoxyamines based on imidazoline radicals with a pyridine functional group-potential initiators of nitroxide-mediated, controlled radical polymerization-were synthesized. Electron Paramagnetic Resonance (EPR) measurements reveal biexponential kinetics for the thermolysis for diastereomeric alkoxyamines and monoexponential kinetics for an achiral alkoxyamine. For comparison, the thermolysis of all three alkoxyamines was studied by NMR in the presence of three different scavengers, namely tetramethylpiperidine-N-oxyl (TEMPO), thiophenol (PhSH), and ß-mercaptoethanol (BME), and detailed analysis of products was performed. NMR differentiates between N-inversion, epimerization, and homolysis reactions. The choice of scavenger is crucial for making a reliable and accurate estimate of the true homolysis rate constant.

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.

Dataset for transcriptome analysis of Salmonella enterica subsp. enterica serovar Typhimurium strain 14028S response to starvation.

Salmonella enterica is an ubiquitous pathogen throughout the world causing gastroenteritis in humans and animals. Survival of pathogenic bacteria in the external environment may be associated with the ability to overcome the stress caused by starvation. The bacterial response to starvation is well understood in laboratory cultures with a sufficiently high cell density. However, bacterial populations often have a small size when facing this challenge in natural biotopes. The aim of this work was to find out if there are differences in the transcriptomes of S. enterica depending on the factor of cell density during starvation. Here we present transcriptome data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S grown in carbon rich or carbon deficient medium with high or low cell density. These data will help identify genes involved in adaptation of low-density bacterial populations to starvation conditions.

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.

How intramolecular coordination bonding (ICB) controls the homolysis of the C-ON bond in alkoxyamines.

Because the C-ON bond homolysis rate constant k d is an essential parameter of alkoxyamine reactivity, it is especially important to tune k d without a major alteration of the structure of the molecule. Recently, several approaches have become known, e.g., protonation of functional groups and formation of metal complexes. In this paper, coordination reactions of [Zn(hfac)2(H2O)2] with a series of new SG1-based alkoxyamines affording complexes with different structures are presented. The k d values of the complexed forms of the alkoxyamines were compared to those of free and protonated ones to reveal the contribution of the electron-withdrawing property and structure stabilization. Together with previously published data, this work provides clues to the design of alkoxyamines that can be effectively activated upon coordination with metal ions. Furthermore, our results provide insight into the mechanism underlying the influence of complexation on the reactivity of alkoxyamines. This led us to describe different types of coordination: intramolecular in nitroxyl fragment, intramolecular in alkyl fragment, intramolecular between alkyl and nitroxyl fragment, and intermolecular one. All of them exhibit different trends which are dramatically altered by changes in conformation.

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.

Gut as a target for cadmium toxicity.

The primary objective of the present study was to review the impact of Cd exposure on gut microbiota and intestinal physiology, as well as to estimate whether gut may be considered as the target for Cd toxicity. The review is based on literature search in available databases. The existing data demonstrate that the impact of Cd on gut physiology is two-sided. First, Cd exposure induces a significant alteration of bacterial populations and their relative abundance in gut (increased Bacteroidetes-to-Firmicutes ratio), accompanied by increased lipopolysaccharide (LPS) production, reflecting changed metabolic activity of the intestinal microbiome. Second, in intestinal wall Cd exposure induces inflammatory response and cell damage including disruption of tight junctions, ultimately leading to increased gut permeability. Together with increased LPS production, impaired barrier function causes endotoxinemia and systemic inflammation. Hypothetically, Cd-induced increase gut permeability may also result in increased bacterial translocation. On the one hand, bacteriolysis may be associated with aggravation of endotoxemia. At the same time, together with Cd-induced impairment of macrophage inflammatory response, increased bacterial translocation may result in increased susceptibility to infections. Such a supposition is generally in agreement with the finding of higher susceptibility of Cd-exposed mice to infections. The changed microbiome metabolic activity and LPS-induced systemic inflammation may have a significant impact on target organs. The efficiency of probiotics in at least partial prevention of the local (intestinal) and systemic toxic effects of cadmium confirms the role of altered gut physiology in Cd toxicity. Therefore, probiotic treatment may be considered as the one of the strategies for prevention of Cd toxicity in parallel with chelation, antioxidant, and anti-inflammatory therapy.

Draft Genome Sequence of the Vaginal Isolate Corynebacterium amycolatum ICIS 9.

Corynebacterium amycolatum ICIS 9 was isolated from a vaginal smear of a healthy woman. Here, we report the draft genome sequence of C. amycolatum ICIS 9, which will be useful for further studies of specific genetic features of this strain and for understanding its probiotic properties.

Draft Genome Sequence of Corynebacterium amycolatum Strain ICIS 53 Isolated from a Female Urogenital Tract.

This report describes the draft genome sequence of Corynebacterium amycolatum strain ICIS 53, isolated from the reproductive tract of a healthy woman. The size of the genome was 2,460,257 bp (58.98% G+C content). Annotation revealed 2,173 coding sequences, including 2,076 proteins, 7 rRNA genes, and 53 tRNA genes.

Influence of zinc nanoparticles on survival of worms Eisenia fetida and taxonomic diversity of the gut microflora.

The study was conducted to examine the effect of zinc nanoparticles on survival of worms Eisenia fetida and composition of the gut microflora. Analysis of the survival data has shown that the introduction of high doses of the nanoparticles causes death of worms in the second group with 35 % mortality rate and activates protective mechanisms realized as mucous film. DNA from the worm guts was extracted and 16S metagenomic sequencing was fulfilled using MiSeq (Illumina). Regarding the gut microflora of worms in the control group, high diversity of microorganisms (303 OTUs) was noted. Most of those belong to the taxa Firmicutes (51.9 % of the total high-quality united reads), Proteobacteria (24.1 % of the total), and Actinobacteria (13.3 % of the total), which were represented by numerous species of gen. Clostridium (C. saccharobutylicum, C. saccharoperbutylacetonicum, C. beijerinckii), gen. Pseudomonas (P. hydrogenovora, P. aeruginosa, and P. putida), gen. Bacillus (B. megaterium, B. silvestris), gen. Cellulomonas (B. megaterium, B. silvestris), and other numerically smaller genera. Adding of zinc nanoparticles to the substrate decreased the diversity of bacteria (78 OTUs) as well as percentage of bacteria belonging to the taxon Firmicutes (-41.6 %) and increased the proportion of Proteobacteria due to growth in abundance of gen. Verminephrobacter (+46 %) and gen. Ochrobactrum (+19.5 %).