Laser microdissection of pisum sativum l. Nodules followed by rna‐seq analysis revealed crucial transcriptomic changes during infected cell differentiation

Garden pea (Pisum sativum L.) is a globally important legume crop. Like other legumes, it forms beneficial symbiotic interactions with the soil bacteria rhizobia, gaining the ability to fix at-mospheric nitrogen. In pea nodules, the meristem is long‐lasting and results in the formation of several histological zones that implicate a notable differentiation of infected host cells. However, the fine transcriptional changes that accompany differentiation are still unknown. In this study, using laser microdissection followed by RNA‐seq analysis, we performed transcriptomic profiling in the early infection zone, late infection zone, and nitrogen fixation zone of 11‐day‐old nodules of pea wild‐type line SGE. As a result, a list of functional groups of differentially expressed genes (DEGs) in different nodule histological zones and a list of genes with the most prominent expression changes during nodule development were obtained. Their analyses demonstrated that the highest amount of DEGs was associated with the nitrogen fixation zone. Among well‐known genes controlling nodule development, we revealed genes that can be novel players throughout nodule for-mation. The characterized genes in pea were compared with those previously described in other legumes and their possible functions in nodule development are discussed

Transcriptomic data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S treated with novobiocin

© 2020 The Authors In enteric bacteria, DNA supercoiling is highly responsive to environmental conditions. Host specific features of environment serve as cues for the expression of genes required for colonization of host niches via changing supercoiling [1]. It has been shown that substitution at position 87 of GyrA of Salmonella enterica str. SL1344 influences global supercoiling and results in an altered transcriptome with increased expression of stress response pathways [2]. Aminocoumarin antibiotics, such as novobiocin, can be used to relax supercoiling and alter the expression of supercoiling-sensitive genes. Meanwhile, Salmonella enterica demonstrates a significant resistance to this antibiotic and relatively small variability of supercoiling in response to the growth phase, osmotic pressure, and novobiocin treatment. Here we present for the first time transcriptome data of Salmonella enterica subsp. Enterica serovar Typhimurium str. 14028S grown in the presence of novobiocin. These data will help identify genes involved in novobiocin resistance and adaptation processes associated with torsion perturbations in S. enterica. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP239815) and have been assigned BioProject accession PRJNA599397

Dataset for transcriptome analysis of abscisic acid degrading bacterium Novosphingobium sp. P6W

© 2019 The Author(s) Plant growth-promoting rhizobacteria (PGPR) improve plant productivity and stress resistance. The mechanisms involved in plant-microbe interactions include the modulation of plant hormone status. The Novosphingobium sp. strain P6W was previously described as the bacterium capable of abscisic acid (ABA) degradation, and its inoculation decreased ABA concentrations in planta. The metabolic pathway for the ABA degradation in bacteria is still unknown. Here we present transcriptome data of Novosphingobium sp. P6W grown in the medium supplemented with ABA or fructose as the carbon source. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP189498) and have been assigned BioProject accession PRJNA529223

Structure and genetics of the O-antigen of Enterobacter cloacae K7 containing di-N-acetylpseudaminic acid

The O-antigen (O-polysaccharide) is an essential component of lipopolysaccharide on the surface of Gram-negative bacteria and plays an important role in interaction with host organisms. In this study, we investigated the chemical structure and characterized the gene cluster of Enterobacter cloacae K7 O-antigen. As judged by sugar analyses along with NMR spectroscopy data, E. cloacae K7 antigen has a tetrasaccharide O-unit with the following structure: →8)-β-Psep5Ac7Ac-(2 → 2)-β-L-Rhap-(1 → 4)-α-L-Rhap-(1 → 3)-α-D-Galp-(1→ The O-antigen gene cluster of E. cloacae K7 between conserved genes galF and gnd was sequenced. Most genes necessary for the O-antigen synthesis were found in the cluster and their functions were tentatively assigned by comparison with sequences in the available databases

Whole genome sequence data of Lactobacillus fermentum HFD1, the producer of antibacterial peptides

© 2020 The Author(s) Here we report the whole genome sequence of Lactobacillus fermentum HFD1 strain, the producer of antibacterial peptides. The genome consists of one circular chromosome with 2101878 bp in length and GC-content of 51.8%, and includes linear DNA with 5386 bp in length with 100% identity to bacteriophage phiX174. The analysis of the genome has revealed 2049 genes encoding for proteins including 867 proteins without known function and 70 genes encoding for RNAs (10 rRNAs, 59 tRNAs and 1 tmRNA). Putative genes responsible for the biosynthesis of 4 antimicrobial peptides were identified. The NCBI Bioproject has been deposited at NCBI under the accession number PRJNA615901 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA615901/) and consist of full annotated genome and raw sequence data

Data on the genome analysis of the probiotic strain Bacillus subtilis GM5

In the present study, we report data on the draft genome sequence of a lipopeptide producing rhizospheric Bacillus subtilis GM5 isolate. The genome consists of 4,271,280 bp with a GC-pair content of 43.3%. A total of 4518 genes including 75 tRNA genes, 3 operons coding for rRNA genes and 56 pseudogenes were annotated. Gene clusters responsible for the biosynthesis of secondary metabolites were validated. Six of the thirty-three clusters identified in the genome code for antimicrobial non-ribosomal peptides synthesis. The Whole Genome Shotgun project of B. subtilis GM5 has been deposited in the NCBI database under the accession number NZ_NKJH00000000 (https://www.ncbi.nlm.nih.gov/nuccore/NZ_NKJH00000000.1). Keywords: Bacillus subtilis, Analysis and assembly of the genome, Antimicrobial lipopeptide

Rational strategy for studying microbiome of the ocular surface of people using hard contact lenses by method of 16s rrna gene metabarcoding

© 2020, Media Sphera Publishing Group. All rights reserved. The study is based on the hypothesis that high taxonomic diversity of bacteria detectable on the eye surface by molecular genetic methods is attributed to the high level of its contamination by skin microflora. Such contamination would make it problematic to identify the fractions of real ocular surface microbiome, which remains behind the one-percent cut-off threshold adopted in the metagenomic analysis. Hard contact lenses for long-wearing act as a physical filter preventing DNA contamination from random microorganisms, and at the same time providing adhesion to the living cells of bacteria and fungi. To confirm this assumption, a detailed analysis of references was carried out, supplemented by original laboratory research. Material and methods. The analysis included 16 hard contact lenses obtained from 11 patients with impaired refraction (myopia). Additionally, conjunctival mucosa scrapings were collected from 42 patients. Samples were cross-analyzed by 16S rRNA gene se-quencing using 454 GS Junior (Ion Torrent) and Illumina MiSeq platforms. Results. Results obtained by the Illumina platform (analysis of the V3-V4 variable region of the 16S rRNA gene) showed better con-vergence with the data of culture tests reported in the literature. The major microorganism groups found were: Acinetobacter (39%), Gluconacetobacter (10.8%), Propionibacterium (9.3%), Corynebacterium (9.3%), Staphylococcus (7.2%), Streptococcus (7%), Pseudomonas (4.1%), Micrococcus (3.3%), Yersinia (3%), Chondromyces (2.4%), Serratia (2.3%), and Bacillus (2.1%). Analysis of the samples obtained directly from the mucosa revealed dominance of typical skin-associated microorganisms. Conclusion. The present study proposes a contamination-reduction algorithm for microbiological testing of the ocular surface using hard contact lenses for prolonged wearing as a carrier for microbial DNA

Comparison of the Microbiota and Inorganic Anion Content in the Saliva of Patients with Gastroesophageal Reflux Disease and Gastroesophageal Reflux Disease-Free Individuals

© 2020 Elvira E. Ziganshina et al. The oral cavity is one of the most complex microbial environments; however, the complex nature of the salivary microbiota and the level of inorganic anions in the saliva of subjects with and without gastroesophageal reflux disease (GERD) are poorly understood. The primary goals of this pilot research were to assess differences in salivary bacterial community composition and inorganic anion concentrations between patients with GERD and GERD-free people. Thus, the salivary microbiota within both groups was dominated by these genera: Streptococcus, Prevotella, Porphyromonas, Veillonella, Neisseria, Haemophilus, Fusobacterium, Rothia, and Leptotrichia. However, the relative abundances of the genera Actinomyces, Atopobium, Stomatobaculum, Ruminococcaceae_[G-2], Veillonella, and Leptotrichia were significantly higher in the saliva samples of patients with GERD, while the genera Porphyromonas, Gemella, Peptostreptococcus, and Neisseria were less abundant in this group. The concentrations of chloride, phosphate, and sulphate ions in the human saliva varied among all subjects and sampling time. These results broaden our knowledge of the salivary microbial community composition and chemistry of saliva of patients with GERD and GERD-free individuals

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

© 2020 The Author(s) 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

Complete Genome Sequence of Lactobacillus hilgardii LMG 7934, Carrying the Gene Encoding for the Novel PII-Like Protein PotN

© 2020, Springer Science+Business Media, LLC, part of Springer Nature. Lactic acid bacteria are widespread in various ecological niches with the excess of nutrients and have reduced capabilities to adapt to starvation. Among more than 280 Lactobacillus species known to the date, only five, including Lactobacillus hilgardii, carry in their genome the gene encoding for PII-like protein, one of the central regulators of cellular metabolism generally responding to energy- and carbon–nitrogen status in many free-living Bacteria, Archaea and in plant chloroplasts. In contrast to the classical PII encoding genes, in L. hilgardii genome the gene for PII homologue is located within the potABCD operon, encoding the ABC transporter for polyamines. Based on the unique genetic context and low sequence identity with genes of any other so-far characterized PII subfamilies, we termed this gene potN (Pot-protein, Nucleotide-binding). The second specific feature of L. hilgardii genome is that many genes encoding the proteins with similar function are present in two copies, while with low mutual identity. Thus, L. hilgardii LMG 7934 genome carries two genes of glutamine synthetase with 55% identity. One gene is located within classical glnRA operon with the gene of GlnR-like transcriptional regulator, while the second is monocistronic. Together with the relative large genome of L. hilgardii as compared to other Lactobacilli (2.771.862 bp vs ~ 2.2 Mbp in median), these data suggest significant re-arrangements of the genome and a wider range of adaptive capabilities of L. hilgardii in comparison to other bacteria of the genus Lactobacillus