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

Adaptation to Antimicrobials and Pathogenicity in Mycoplasmas: Development of Ciprofloxacin-Resistance and Evolution of Virulence in Acholeplasma laidlawii

Abstract: For the first time it was shown that the development of resistance to ciprofloxacin in vitro in Acholeplasma laidlawii, a mycoplasma which is widely spread in nature and which is the main contaminant of cell cultures and vaccines, is associated with diverse pathways of virulence evolution: virulome and virulence differ significantly between ciprofloxacin-resistant strains, including those with the same level of antimicrobial resistance

Characterization of gut contractility and microbiota in patients with severe chronic constipation

© 2020 Yarullina 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. Chronic constipation (CC) is one of the most common gastrointestinal disorders worldwide. Its pathogenesis, however, remains largely unclear. The purpose of the present work was to gain an insight into the role of contractility and microbiota in the etiology of CC. To this end, we studied spontaneous and evoked contractile activity of descending colon segments from patients that have undergone surgery for refractory forms of CC. The juxta-mucosal microbiota of these colon samples were characterized with culture-based and 16S rRNA sequencing techniques. In patients with CC the spontaneous colonic motility remained unchanged compared to the control group without dysfunction of intestinal motility. Moreover, contractions induced by potassium chloride and carbachol were increased in both circular and longitudinal colonic muscle strips, thus indicating preservation of contractile apparatus and increased sensitivity to cholinergic nerve stimulation in the constipated intestine. In the test group, the gut microbiota composition was assessed as being typically human, with four dominant bacterial phyla, namely Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, as well as usual representation of the most prevalent gut bacterial genera. Yet, significant inter-individual differences were revealed. The phylogenetic diversity of gut microbiota was not affected by age, sex, or colonic anatomy (dolichocolon, megacolon). The abundance of butyrate-producing genera Roseburia, Coprococcus, and Faecalibacterium was low, whereas conventional probiotic genera Lactobacillus and Bifidobacteria were not decreased in the gut microbiomes of the constipated patients. As evidenced by our study, specific microbial biomarkers for constipation state are absent. The results point to a probable role played by the overall gut microbiota at the functional level. To our knowledge, this is the first comprehensive characterization of CC pathogenesis, finding lack of disruption of motor activity of colonic smooth muscle cells and insufficiency of particular members of gut microbiota usually implicated in CC

Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment

© 2020, Springer-Verlag GmbH Germany, part of Springer Nature. The success of members of the genus Rhodococcus in colonizing arid rocky environments is owed in part to desiccation tolerance and an ability to extract iron through the secretion and uptake of siderophores. Here, we report a comprehensive genomic and taxonomic analysis of Rhodococcus qingshengii strain S10 isolated from eathered serpentine rock at the arid Khalilovsky massif, Russia. Sequence comparisons of whole genomes and of selected marker genes clearly showed strain S10 to belong to the R. qingshengii species. Four prophage sequences within the R. qingshengii S10 genome were identified, one of which encodes for a putative siderophore-interacting protein. Among the ten non-ribosomal peptides synthase (NRPS) clusters identified in the strain S10 genome, two show high homology to those responsible for siderophore synthesis. Phenotypic analyses demonstrated that R. qingshengii S10 secretes siderophores and possesses adaptive features (tolerance of up to 8% NaCl and pH 9) that should enable survival in its native habitat within dry serpentine rock

Diversity and adaptations of escherichia coli strains: Exploring the intestinal community in crohn’s disease patients and healthy individuals

Crohn’s disease (CD) is characterized by a chronic, progressive inflammation across the gastrointestinal tract with a series of exacerbations and remissions. A significant factor in the CD pathogenesis is an imbalance in gut microbiota composition, particularly the prevalence of Escherichia coli. In the present study, the genomes of sixty-three E. coli strains from the gut of patients with CD and healthy subjects were sequenced. In addition, eighteen E. coli-like metagenomeassembled genomes (MAGs) were reconstructed from the shotgun-metagenome sequencing data of fecal samples. The comparative analysis revealed the similarity of E. coli genomes regardless of the origin of the strain. The strains exhibited similar genetic patterns of virulence, antibiotic resistance, and bacteriocin-producing systems. The study showed antagonistic activity of E. coli strains and the metabolic features needed for their successful competition in the human gut environment. These observations suggest complex bacterial interactions within the gut which may affect the host and cause intestinal damage

Therapeutic Potential of Pharmacological Targeting NLRP3 Inflammasome Complex in Cancer

Introduction: Dysregulation of NLRP3 inflammasome complex formation can promote chronic inflammation by increased release of IL-1β. However, the effect of NLRP3 complex formation on tumor progression remains controversial. Therefore, we sought to determine the effect of NLRP3 modulation on the growth of the different types of cancer cells, derived from lung, breast, and prostate cancers as well as neuroblastoma and glioblastoma in-vitro. Method: The effect of Caspase 1 inhibitor (VX765) and combination of LPS/Nigericin on NLRP3 inflammasome activity was analyzed in A549 (lung cancer), MCF-7 (breast cancer), PC3 (prostate cancer), SH-SY5Y (neuroblastoma), and U138MG (glioblastoma) cells. Human fibroblasts were used as control cells. The effect of VX765 and LPS/Nigericin on NLRP3 expression was analyzed using western blot, while IL-1β and IL-18 secretion was detected by ELISA. Tumor cell viability and progression were determined using Annexin V, cell proliferation assay, LDH assay, sphere formation assay, transmission electron microscopy, and a multiplex cytokine assay. Also, angiogenesis was investigated by a tube formation assay. VEGF and MMPs secretion were detected by ELISA and a multiplex assay, respectively. Statistical analysis was done using one-way ANOVA with Tukey’s analyses and Kruskal–Wallis one-way analysis of variance. Results: LPS/Nigericin increased NRLP3 protein expression as well as IL-1β and IL-18 secretion in PC3 and U138MG cells compared to A549, MCF7, SH-SY5Y cells, and fibroblasts. In contrast, MIF expression was commonly found upregulated in A549, PC3, SH-SY5Y, and U138MG cells and fibroblasts after Nigericin treatment. Nigericin and a combination of LPS/Nigericin decreased the cell viability and proliferation. Also, LPS/Nigericin significantly increased tumorsphere size in PC3 and U138MG cells. In contrast, the sphere size was reduced in MCF7 and SH-SY5Y cells treated with LPS/Nigericin, while no effect was detected in A549 cells. VX765 increased secretion of CCL24 in A549, MCF7, PC3, and fibroblasts as well as CCL11 and CCL26 in SH-SY5Y cells. Also, VX765 significantly increased the production of VEGF and MMPs and stimulated angiogenesis in all tumor cell lines. Discussion: Our data suggest that NLRP3 activation using Nigericin could be a novel therapeutic approach to control the growth of tumors producing a low level of IL-1β and IL-18

The Effect of Helicobacter pylori Eradication on Human Microbiota: Metagenome Analysis of the Human Gut Microbiome

A total of 152 stool samples from 76 patients with symptoms of gastrointestinal diseases have been analyzed using metagenomic shotgun sequencing technology to assess the effect of Helicobacter pylori eradication therapy on Bifidobacterium, Lactobacillus, Escherichia, and Clostridium genera. The relative abundance of bacteria representing these genera in the intestinal microflora of patients before and after antibiotic therapy has been evaluated. It has been shown that the therapy did not have any critical effect in the majority of cases on the number of Lactobacillus, Escherichia and Clostridium genera in the microbial community. Their abundance varied within 0.5% in 76.5%, 51.3%, and 55.2% of patients, respectively. The Bifidobacterium genus has been found to be more susceptible to antibiotics (their number decreased significantly in 60.5% of cases). However, 9.2% of patients have shown the opposite effect. Thus, the obtained data demonstrate that Helicobacter pylori eradication therapy does not have uniform effects on the key members of human intestinal microbiota. This fact should be taken into account when predicting the risks of side effects of antibiotics

Characteristics of the colonic microbiome in patients with different obesity phenotypes (The original article)

Introduction. The concept of heterogeneity in obesity depending on the risk of developing cardiometabolic complications has garnered attention in recent decades, since not everyone with obesity goes on to develop metabolic dysfunction. The aim of the work is to study specific characteristics of colonic microbial communities in patients with different obesity phenotypes and in healthy individuals by employing metagenomics methods. Materials and methods. A total of 265 individuals (44 men and 221 women; mean age 47.1 ± 4.8 years) were enrolled in the study. They were further divided into clinical groups: Healthy normal-weight individuals (n = 129); patients with obesity (n = 136), including metabolically healthy obesity (n = 40) and metabolically unhealthy obesity (n = 55). Quantitative and qualitative assessment of the intestinal microbiome was based on metagenomic analysis. Fecal samples were used to isolate DNA and perform sequencing of the variable v3-v4 region of the 16S rRNA gene. Results. The study revealed statistically significant (p < 0.05) differences between quantitative and qualitative variables in studied phylotypes of colonic microorganisms in healthy individuals without obesity and in patients with different obesity phenotypes. Discussion. Patients with obesity had higher levels of Bacteroidetes, Proteobacteria and lower levels of Actinobacteria, Firmicutes, TM7 (Saccharibacteria), Fusobacteria, and more frequently detected phyla Tenericutes, Planctomycetes and Lentisphaerae compared to healthy individuals. Metabolically healthy obese patients had more rarely detected phylum Lentisphaerae in their colonic microbiome, increased numbers of Firmicutes and reduced numbers of Bacteroidetes compared to metabolically unhealthy obese patients. Conclusion. The findings demonstrate alterations in the colonic microbiome in patients with different obesity phenotypes

Inflammatory Bowel Disease-Associated Changes in the Gut: Focus on Kazan Patients

Background: Several studies have highlighted the role of host-microbiome interactions in the pathogenesis of inflammatory bowel disease (IBD), resulting in an increasing amount of data mainly focusing on Western patients. Because of the increasing prevalence of IBD in newly industrialized countries such as those in Asia, the Middle East, and South America, there is mounting interest in elucidating the gut microbiota of these populations. We present a comprehensive analysis of several IBD-related biomarkers and gut microbiota profiles and functions of a unique population of patients with IBD and healthy patients from Kazan (Republic of Tatarstan, Russia). Methods: Blood and fecal IBD biomarkers, serum cytokines, and fecal short-chain fatty acid (SCFA) content were profiled. Finally, fecal microbiota composition was analyzed by 16S and whole-genome shotgun sequencing. Results: Fecal microbiota whole-genome sequencing confirmed the presence of classic IBD dysbiotic features at the phylum level, with increased abundance of Proteobacteria, Actinobacteria, and Fusobacteria and decreased abundance of Firmicutes, Bacteroidetes, and Verrucomicrobia. At the genus level, the abundance of both fermentative (SCFA-producing and hydrogen (H2)-releasing) and hydrogenotrophic (H2-consuming) microbes was affected in patients with IBD. This imbalance was confirmed by the decreased abundance of SCFA species in the feces of patients with IBD and the change in anaerobic index, which mirrors the redox status of the intestine. Conclusions: Our analyses highlighted how IBD-related dysbiotic microbiota - which are generally mainly linked to SCFA imbalance - may affect other important metabolic pathways, such as H2 metabolism, that are critical for host physiology and disease development