Analysis of polymorphism in Alu-incertional loci in the population of Tatar in Russia

The study of variability and diversity of the human genome in the population had a rapid development. The purpose of this paper is to compare the data on Alu-insertion polymorphism in the population of the Kazan and baptized Tatars, Russian Federation, as well as in the neighboring populations. The material for the genetic analysis was DNA collected from 192 unrelated individuals, representatives of Tatar nationality (96-Kazan Tatars and 96 - baptized Tatars), Russian Federation. Data on ethnicity was found out by the survey, blood sampling was carried out on a voluntary basis with signed informed consent. Alu-insertion polymorphism in the population of the Kazan and baptized Tatars, Russian Federation, as well as in the neighboring populations was analysed. © IDOSI Publications, 2013

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

© 2017 Galitskaya et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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) × 10 6 and (0.4±0.0) × 10 7 g -1 , and the Rhodospiralles and Lactobacialles orders dominated. Fungal communities had (2.9±0.0) ×10 5 and (6.1±0.2) ×10 5 ITS copies g -1 , and the Saccharomycetales order dominated. At the end of the thermophilic stage on the 30 th 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

Lessons from the Whole Exome Sequencing Effort in Populations of Russia and Tajikistan

© 2016, Springer Science+Business Media New York.In contrast with the traditional methods applied to assessment of population diversity, high-throughput sequencing technologies have a wider application in clinical practice with greater potential to find novel disease-causing variants for multifactorial disorders. Widely used test panels may not meet their goal to diagnose the patient’s condition with a full reliability since this method often does not take into account the population frequencies of analyzed genetic markers. Here, we analyzed 57 male individuals of five ethnic groups from Russia and Tajikistan using the whole exome sequencing technique (Ion AmpliSeq Exome), which resulted in detecting more than 299,000 single nucleotide polymorphisms. Samples formed clusters on the PCA plot according to the geographical location of the corresponding populations. Thereby, the methodology of whole-exome sequencing, in general, and the Ion AmpliSeq Exome panel, in particular, could be positively applied for the purposes of population genetics and for detection of the novel clinically relevant variants

High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1

© 2015 Suleimanova et al. Strain 3.5.1 was isolated from soils of the Republic of Tatarstan, Russia, on the basis of presence of a high phytate-degrading activity. Strains with such activities attract special interest because of its potential use as feed additives and natural manures. Strain 3.5.1 harbors a 99 % 16S rRNA nucleotide sequence similarity to different Pantoea species (P. vagans, P. ananatis, P. agglomerans, P. anthophila and Pantoea sp.) and exhibits unique biochemical properties that do not allow strain identification up to species. Moreover, the strain 3.5.1 shows a low ANI and MALDI-TOF Mass Spectrometry scores. Thus, it is likely that the strain 3.5.1 represents a new Pantoea species. Here, we present the genome sequence of Pantoea sp. strain 3.5.1. The 4,964,649 bp draft genome consists of 23 contigs with 4,556 protein-coding and 143 RNA genes. Genome sequencing and annotation revealed two phytase genes and putative regulatory genes controlling its activity

The mitochondrial gene order and CYTB gene evolution in insects

Over millions of years of evolution, the genomes of modern insects have accumulated a significant number of mutations, which often can lead up a blind alley when carrying out phylogenetic research. Genomic differences between some representatives belonging to the same family or group are often so great that they demand using nonconventional methods of the phylogenetic analysis. It is known that molecular evolution goes by the way of not only single nucleotide substitutions, but also by larger genomic reorganizations, such as insertion or deletion of large genome fragments, and even changing the order of genes. Mitochondrial DNA genes (mtDNA) are quite often used as markers for phylogenetic research into many organisms including arthropods, because mtDNA is multicopied, is inherited maternally, does not undergo recombination and accumulates mutations quickly enough (relative to the nuclear genome). To date, a large number of full nucleotide sequences of mitogenomes (thousands of organisms) has been deposited in public databases; however, their phylogenetic analysis has obstacles, especially for representatives of the insects (Insecta), whose evolution takes a considerable part of geological time. In this work we describe the application and a comparison of two ways of the phylogenetic analysis for different groups of insects. The first method uses the variability of the nucleotide sequence of mtDNA, and the second one analyses the order of genes in full mitochondrial genomes of insects that can be used as an additional marker in phylogenetic research into representatives of the order Hymenoptera

Genome sequences of Acholeplasma laidlawii strains differing in sensitivity to ciprofloxacin

© 2017 Medvedeva et al. Acholeplasma laidlawii is a well-suited model for study of the molecular basis of the adaptation of mollicutes to environmental conditions. Here we present the whole-genome sequences of four strains of A. laidlawii with differential sensitivity to ciprofloxacin

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

© 2017 The Authors 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

Characterization of Dysbiotic Changes of Skin Microbiota in Contact Sports Athletes

© 2017, Springer Science+Business Media New York.Contact sports athletes often suffer from various skin disorders (inflammatory diseases of bacterial and fungal origin, atopic dermatitis, psoriasis, etc.) resulting in long breaks in training which ruin athletic performance. Wrestling implies intense skin-to-skin contact that creates perfect conditions for transmission of the infectious agents. Following the standard rules of hygiene (showering and handwashing directly after each competition and training) does not exclude the possibility to get an infection from sparring partner. To characterize the skin microbial composition of wrestlers who do not have current manifestation of any skin disorders, the metagenomic analysis was performed. Absolute predominance of Bacillus genus in metagenomic profiles of wrestlers’ skin was observed in contrast with the existing literature data. Classic microbiological approaches allowed to detect hemolytic forms of microorganisms. Wrestlers’ skin appeared to be colonized with hemolytic bacilli, whereas the non-wrestler athletes did not have such bacteria on their skin. Such dysbiotic shifts in the microbial community may cause the emergence of skin diseases. Revealed properties could help to design highly effective antiseptics for the contact sports hygiene

Gut Microbiome Shotgun Sequencing in Assessment of Microbial Community Changes Associated with H. pylori Eradication Therapy

© 2016, Springer Science+Business Media New York.Disturbance of intestinal microbiota content and functions often results in different pathological conditions. Pharmacotherapy including antibiotics use is one of the factors leading to dysbiosis. To evaluate the influence of antibiotics use on intestinal microbiota metagenomic profiles of stool, samples of 74 patients before and after Helicobacter pylori—eradication therapy—were analyzed. Evaluation of taxonomic diversity changes based on Shannon index and Bray-Curtis metrics allows to range patients according to mild, moderate, and severe risk of disturbance of intestinal microbiota pathological conditions