Data on gut metagenomes of the patients with Helicobacter pylori infection before and after the antibiotic therapy

Complete Genome Sequence of Stenotrophomonas rhizophila KC1, a Quorum Sensing-Producing Algicidal Bacterium Isolated from Mangrove Kandelia candel

This paper describes the isolation of an algicidal strain, Stenotrophomonas rhizophila KC1, from mangrove (Kandelia candel) and its genome, which was sequenced using next-generation sequencing technology. The genome is 5.93 Mb with a G+C content of 63.17%. A total of 3,352 functional proteins were assigned according to Kyoto Encyclopedia of Genes and Genomes categories. A total of 11,586 protein-coding genes, 73 transfer RNA genes, and 17 ribosomal RNA genes were obtained. In silico genome annotation protocols identified 83 putative quorum sensing (QS) genes, and the algicidal potential of KC1 was related with the QS genes (for example LuxI-LuxR genes). Collectively, these data suggest that KC1 may be an antialgal bacterium whose behavior can be modulated by QS signaling. The annotated genome sequence of this strain may represent a valuable tool for studying algae-bacteria interactions and developing microbe-based methods for controlling harmful algae.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy

The human gut microbiome plays an important role both in health and disease. Use of antibiotics can alter gut microbiota composition, which can lead to various deleterious events. Here we report a whole genome sequencing metagenomic/genomic study of the intestinal microbiota changes caused by Helicobacter pylori (HP) eradication therapy. Using approaches for metagenomic data analysis we revealed a statistically significant decrease in alpha-diversity and relative abundance of Bifidobacterium adolescentis due to HP eradication therapy, while the relative abundance of Enterococcus faecium increased. We have detected changes in general metagenome resistome profiles as well: after HP eradication therapy, the ermB, CFX group, and tetQ genes were overrepresented, while tetO and tetW genes were underrepresented. We have confirmed these results with genome-resolved metagenomic approaches. MAG (metagenome-assembled genomes) abundance profiles have changed dramatically after HP eradication therapy. Focusing on ermB gene conferring resistance to macrolides, which were included in the HP eradication therapy scheme, we have shown a connection between antibiotic resistance genes (ARGs) and some overrepresented MAGs. Moreover, some E. faecium strains isolated from stool samples obtained after HP eradication have manifested greater antibiotic resistance in vitro in comparison to other isolates, as well as the higher number of ARGs conferring resistance to macrolides and tetracyclines.

[Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes]

The constant increase of antibiotic-resistant strains of bacteria is caused by extensive uses of antibiotics in medicine and animal breeding. It was suggested that the gut microbiota serves as a reservoir for antibiotics resistance genes that can be carried from symbiotic bacteria to pathogenic ones, in particular, as a result of transduction. In the current study, we have searched for antibiotics resistance genes that are located inside prophages in human gut microbiota using PHASTER prophage predicting tool and CARD antibiotics resistance database. After analysing metagenomic assemblies of eight samples of antibiotic treated patients, lsaE, mdfA and cpxR/cpxA genes were identified inside prophages. The abovementioned genes confer resistance to antimicrobial peptides, pleuromutilin, lincomycins, streptogramins and multidrug resistance. Three (0.46%) of 659 putative prophages predicted in metagenomic assemblies contained antibiotics resistance genes in their sequences.

The data of genomic and phenotypic profiles of the N-acyl homoserine lactone-producing algicidal bacterium Stenotrophomonas rhizophila GA1

Herein, an algicidal strain, Stenotrophomonas rhizophila GA1, was isolated from a marine dinoflagellate and its genome was sequenced using next-generation sequencing technology. The genome size of S. rhizophila GA1 was determined to be 5.92 Mb with a G+C content of 62.39%, comprising eight scaffolds of 67 contigs. A total of 4579 functional proteins were assigned according to COG categories. In silico genome annotation protocols identified multiple putative LuxI-like genes located in the upstream position at contig 4. The thin-layer chromatography analysis showed that three kinds of acyl homoserine lactone (AHL) signals could be produced by S. rhizophila GA1. This work describes an algicidal bacterium capable of generating AHL molecules for its ecological adaptation. The annotated genome sequence of this strain may represent a valuable tool for studying algae-bacterium interactions and developing microbial methods to control harmful algae. The genome scaffolds generated are available in the National Center Biotechnology Information (NCBI) BioProject with accession number PRJNA485554.

Draft genomes of Enterococcus faecium strains isolated from human feces before and after eradication therapy against Helicobacter pylori

The abundance of Enterococci in the human intestinal microbiota environment is usually < 0.1% of the total bacterial fraction. The multiple resistance to antibiotics of the opportunistic Enterococcus spp. is alarming for the world medical community because of their high prevalence among clinically significant strains of microorganisms. Enterococci are able to collect different mobile genetic elements and transmit resistance to antibiotics to wide range of Gram-positive and Gram-negative species of microorganisms, including the transmission of vancomycin resistance to methicillin-resistant strains of Staphylococcus aureus. The number of infections caused by antibiotics resistant strains of Enterococcus spp. is increasing. Here we present a draft genomes of Enterococcus faecium strains. These strains were isolated from human feces before and after (1 month) Helicobacter pylori eradication therapy. The samples were subject to whole-genome sequencing using Illumina HiSeq. 2500 platform. The data is available at NCBI https://www.ncbi.nlm.nih.gov/bioproject/PRJNA412824.

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.