Eugenia A. Boulygina

Genomic and proteomic profiles of Acholeplasma laidlawii strains differing in sensitivity to ciprofloxacin.

As a result of comparative analysis of complete genomes as well as cell and vesicular proteomes of A. laidlawii strains differing in sensitivity to ciprofloxacin, it was first shown that the mycoplasma resistance to the antibiotic is associated with the reorganization of genomic and proteomic profiles, which concerns many genes and proteins involved in fundamental cellular processes and realization of bacterial virulence.

Genome Sequences of Acholeplasma laidlawii Strains with Increased Resistance to Tetracycline and Melittin

ABSTRACT Acholeplasma laidlawii is a well-suited model for studying the molecular basis for adapting mollicutes to environmental conditions. Here, we present the whole-genome sequences of two strains of A. laidlawii with increased resistance to tetracycline and melittin.

Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing

Composting is viewed as one of the primary methods to treat organic wastes. Co-composting may improve the efficiency of this treatment by establishing the most suitable conditions for decomposers than those present in the individual wastes. Given that bacteria and fungi are the driving agents of composting, information about the composition of their communities and dynamics during composting may improve reproducibility, performance and quality of the final compost as well as help to evaluate the potential human health risk and the choice of the most appropriate application procedure. In this study, the co-composting of mixtures containing two similar components (organic fraction of municipal solid waste and sawdust polluted by oil) and one discriminate component (sewage sludges of different origin) were investigated. Bacterial and fungal community successions in the two mixtures were analyzed during the composting process by determining the change in their structural dynamics using qPCR and 454 pyrosequencing methods in a lab experiment for a period of 270 days. During the initial composting stage, the number of 16S bacterial copies was (3.0±0.2) x 106 and (0.4±0.0) x 107 g-1, and the Rhodospiralles and Lactobacialles orders dominated. Fungal communities had (2.9±0.0) x105 and (6.1±0.2) x105 ITS copies g-1, and the Saccharomycetales order dominated. At the end of the thermophilic stage on the 30th day of composting, bacterial and fungal communities underwent significant changes: dominants changed and their relative abundance decreased. Typical compost residents included Flavobacteriales, Chitinophagaceae and Bacterioidetes for bacteria and Microascaceae, Dothideomycetes, Eurotiomycetes, Sordariomycetes, and Agaricomycetes for fungi. During the later composting stages, the dominating taxa of both bacterial and fungal communities remained, while their relative abundance decreased. In accordance with the change in the dominating OTUs, it was concluded that the dynamics of the bacterial and fungal communities were not similar. Analysis by non-metric multidimensional scaling (NMDS) revealed that the bacterial communities of the two composts became progressively more similar; a similar trend was followed by the fungal community.

The Influence of Helicobacter Pylori Eradication Therapy on Intestinal Microbiota

H. pylori eradication therapy including antibiotics as well as H. pylori itself can influence the normal intestinal microbiota content. The aim of the study was to describe the gut microbiota composition in H. pylori-positive and H. pylori-negative patients as well as the influence of eradication therapy on gut microbiota. 198 stool samples were taken for analysis: 74 samples from H. pylori-positive patients before eradication therapy, 74 from the same patients after eradication, 50 from H. pylori-negative patients (control group). Total DNA was isolated from the stool samples and subjected to whole-genome sequencing on SOLiD 5500 Wildfire platform. Intestinal microbiota was evaluated based on number of species, qualitative composition, Shannon diversity index and Bray-Curtis metrics. Results. Bacterial community was quite similar in all groups: Bacteroides, Prevotella, Eubacterium, Roseburia, Faecalibacterium and Clostridium genera were predominant in all samples. The spread in variations of the prevailing Firmicutes and Bacteroides phyla was wider after the treatment than in control samples. In about half of patients eradication therapy led to the decrease of both the number of species and the Shannon index indicating a decrease in the overall bacterial diversity with a possible predominance of individual species. Eradication therapy resulted in the reduction of the relative representation of Bifidobacterium, Collinsella, Coprococcus genera, accompanied with the increase of Clostridium, Bacteroides, Coprobacillus and Flavonifractor genera. Evaluation of taxonomic diversity changes based on Shannon index and Bray-Curtis metrics allows to differentiate patients into the groups with mild, moderate and severe changes. In 82% of cases mild and moderate changes in microbial community content were found increased level of Bacteroides genus, decreasing levels of Bifidobacterium and Eubacterium genus, simultaneously. Escherichia genus had the increased abundance in the majority of patients with severe microbial shifts after eradication therapy. Changes in the composition of intestinal microbiota after H. pylori eradication therapy depend mostly on the initial content of the intestinal microbiota: the closer initial microbial state of H. pylori-positive patients to the control samples is, the milder changes could be detected after eradication therapy. Gene-centric analysis of the functional composition in paired samples taken before and after therapy showed an increase of the relative abundance of genes conferring antibiotic resistance. Conclusions. Evaluation of intestinal microflora content prior to treatment can probably predict the incidence of side effects related to changes in microbial composition. This work was financially supported by the Ministry of Education and Science of Russian Federation (agreement #14.575.21.0076, ID RFMEFI575I4X0076).

Shotgun metagenomic data on the human stool samples to characterize shifts of the gut microbial profile after the Helicobacter pylori eradication therapy

The shotgun sequencing data presented in this report are related to the research article named “Gut microbiome shotgun sequencing in assessment of microbial community changes associated with H. pylori eradication therapy” (Khusnutdinova et al., 2016) [1]. Typically, the H. pylori eradication protocol includes a prolonged two-week use of the broad-spectrum antibiotics. The presented data on the whole-genome sequencing of the total DNA from stool samples of patients before the start of the eradication, immediately after eradication and several weeks after the end of treatment could help to profile the gut microbiota both taxonomically and functionally. The presented data together with those described in Glushchenko et al. (2017) [2] allow researchers to characterize the metagenomic profiles in which the use of antibiotics could result in dramatic changes in the intestinal microbiota composition. We perform 15 gut metagenomes from 5 patients with H. pylori infection, obtained through the shotgun sequencing on the SOLiD 5500 W platform. Raw reads are deposited in the ENA under project ID PRJEB21338.

Draft Genome Sequence of Bacillus ginsengihumi Strain M2.11 with Phytase Activity.

ABSTRACT This paper announces the genome sequence of Bacillus ginsengihumi strain M2.11, which has been characterized as a strain which produces the enzyme with the ability to degrade phytase. The genome of the strain M2.11 is 3.7 Mb and harbors 3,082 coding sequences.

Draft Genome Sequence of Agreia bicolorata Strain AC-1804, a Producer of Large Amounts of Carotenoid Pigments, Isolated from Narrow Reed Grass Infected by the Phytoparasitic Nematode

ABSTRACT Here, we report the draft genome sequence of Agreia bicolorata strain AC-1804, isolated from narrow reed grass galls induced by a plant-parasitic nematode which is able to produce large amounts of carotenoid pigments. The draft genome sequence of 3,919,485 bp provides a resource for carotenoid pathway research.