Tag: MGEs

Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis

Whole genome sequencing and analysis To understand the mechanisms underlying the biological control capability of bacterial pathogens, the complete genome of MEP218 was sequenced, assembled, and deposited in the GenBank database under the accession number CP042864.2. The genome of MEP218 consists of a single circular chromosome of 3,944,892 bp with a…

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total 30,851 single-cell genomes, 51 metagenomes, and 1,544 metagenome-assembled genomes from the human oral/gut microbiota

README This is the large single amplified genome calatog (bbsag20) corresponding to the publication below: Title: “Single Amplified Genome Catalog Reveals the Dynamics of Mobilome and Resistome in the Human Microbiome” (preprint: 10.1101/2023.12.06.570492) Authors: Tetsuro Kawano-Sugaya, Koji Arikawa, Tatsuya Saeki, Taruho Endoh, Kazuma Kamata, Ayumi Matsuhashi, and Masahito Hosokawa Research…

Continue Reading total 30,851 single-cell genomes, 51 metagenomes, and 1,544 metagenome-assembled genomes from the human oral/gut microbiota

NERSC Collaborations Help Illuminate Earth’s Biodiversity

Oct. 26, 2023 — How do we know who’s in our world? Genomics researchers study and map the genomes of all kinds of genetic entities, from the blue whale all the way down to mobile genetic elements (MGEs), which have genetic material but are not considered living. But many organisms…

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Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen

V. cholerae in Yemen in 2018 and 2019 The National Centre of Public Health Laboratories (NCPHL) in Sana’a, the capital city of Yemen, received 6,311 and 3,225 clinical samples from suspected cholera patients in 2018 and 2019, respectively (Supplementary Table 1). Of these, 2,204 (35%) and 2,171 (67%) were confirmed…

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Characterization of the pig lower respiratory tract antibiotic resistome

Composition and distribution of ARGs in the pig lower respiratory tract microbiome Using 745 metagenome data of the lower respiratory tract microbiome from 675 experimental pigs across five populations, we constructed a swine respiratory microbial gene catalog containing 10,337,194 non-redundant genes. Of these, 1228 open reading frames (ORFs) were identified…

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Potential new function of CRISPR-Cas system discovered

Illustration of the newly proposed functionality of CRISPR–Cas systems within Ca. Altiarchaea. a, Viral targeting: CRISPR–Cas system targets the genomes of MGEs that infect the cell (current state of knowledge). b, Targeting of episymbiont: CRISPR–Cas system targets the genome of the episymbiont Ca. Huberiarchaeum to defend against the parasite. c,…

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Pig manure treatment strategies for mitigating the spread of antibiotic resistance

Manure treatment The long-term goal of manure management is to remove environmental contaminants: disposing of the high volume of waste, using its value to improve soil fertility, and ensuring biosecurity. Hence, it was necessary to study the physicochemical properties of both treated and untreated manure. Composted pig manure has an…

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Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly

doi: 10.1021/acs.est.3c01980. Online ahead of print. Affiliations Expand Affiliations 1 School of Environment, Tsinghua University, Beijing 100084, China. 2 State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China. 3 Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163,…

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Mountain Gravity Energy Storage (MGES) Market Forecast

Whole Genome Sequencing (WGS) Market Mountain Gravity Energy Storage (MGES) Market (2023) Report provides an in-depth summary of Mountain Gravity Energy Storage (MGES) Market Status as well as Product Specification, Technology Development, and Key Manufacturers. The Report Gives Detail Analysis on Market concern Like Mountain Gravity Energy Storage (MGES) Market…

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Whole strains vs MGEs in short and longterm transmission of ESBL genes between healthcare and community settings in Uganda

ESBL carriage Of the 1556 samples analyzed, 81.9% (1275) yielded suspected ESBL producing bacteria. The antimicrobial susceptibility testing of the obtained isolates showed that many of the strains were resistant to critical cephalosporin and carbapenem antimicrobials such as Cefepime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem and Imipenem in both healthcare and community…

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Translation-dependent downregulation of Cas12a mRNA by an anti-CRISPR protein

Abstract Bacteria have evolved multiple defense systems, including CRISPR-Cas, to cleave the DNA of phage and mobile genetic elements (MGE). In turn, phage have evolved anti-CRISPR (Acr) proteins that use novel and co-opted mechanisms to block DNA binding or cleavage. Here, we report that an anti-CRISPR (AcrVA2) unexpectedly inhibits Cas12a…

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Antibiotics | Free Full-Text | Whole Genome Sequencing and Phenotypic Analysis of Antibiotic Resistance in Filifactor alocis Isolates

1. Introduction Filifactor alocis is an obligate anaerobic, non-sporeforming, Gram-positive rod [1,2]. This microorganism was first described in 1985 after being isolated from patients with periodontitis or gingivitis [3]. However, it was not until the early to mid-2000s, with the improvement of molecular identification techniques, when F. alocis was first…

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Genomic characteristics of ESBL-producing E. coli in China

Introduction Currently, the emergence of bacterial resistance poses a significant challenge to public health worldwide. With the widespread use of antimicrobial agents in recent years, the isolation of multidrug-resistant Escherichia coli has increased yearly, particularly among Extended Spectrum β-lactamases (ESBLs) producing strains, which can cause not only multi-site infections but…

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Persistence of Antibiotic Resistance from Animal Agricultural Effluents to Surface Water Revealed by Genome-Centric Metagenomics

Author links open overlay panelJin Ju Kim a 1, Hoon Je Seong a b 1, Timothy A. Johnson c, Chang-Jun Cha a, Woo Jun Sul a, Jong-Chan Chae d Show more doi.org/10.1016/j.jhazmat.2023.131761Get rights and content ABSTRACT Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming…

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Comparative resistome, virulome and mobilome analysis of metagenomes from wild and farm animals

Resumo:  Although (in the context of bacterial infections) the goal of antibiotic use is to combat and eliminate pathogenic bacteria, hundreds of non-pathogenic bacterial species are also affected when antibiotics are administrated. This results in a selection of bacteria resistant to the class of antibiotic applied. Additionally, with the ability…

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Genome-based surveillance offers new hope in the fight against healthcare-associated infections

Large volumes of high-quality data can be created by high-throughput bacterial genomic sequencing. Simultaneous developments in sequencing technology and bioinformatics have made it easier to use genomics to analyze outbreaks and conduct broader public health surveillance.  A recent Microbial Genomics study considers major healthcare-associated pathogens and discusses both current and future public…

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Phenotypic and Genetic Analysis of KPC-49

Introduction The worldwide dissemination of carbapenem-resistant Enterobacteriaceae (CRE), particularly carbapenem-resistant K. pneumoniae (CRKP), poses a significant risk to public health. CRKP can cause various infections, such as urinary tract infections, bloodstream infections, and pneumonia, leading to high morbidity and mortality.1 Prevention and control of K. pneumoniae infection are becoming more…

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Population-level impacts of antibiotic usage on the human gut microbiome

A comprehensive catalogue of ARGs from the human microbiome We created a catalogue of ARGs across both the human microbiome and reference genomes by locating open reading frames (ORFs) on metagenomic assemblies from 8972 human microbiome samples spanning gut (7589), oral cavity (746), skin (380), airway (118), nasal cavity (55),…

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Metagenome sequencing to unveil the occurrence and distribution of antibiotic resistome and in a wastewater treatment plant

The emergence and persistence of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs) has aroused growing public concern for its risk to human health and ecological safety. Moreover, heavy metals concentrated in sewage and sludge could potentially favour co-selection of ARGs and heavy metal resistance genes (HMRGs). In this…

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How do we know that the AMR genes/ MGEs in the contig sequence is on plasmid or Chromosome?

How do we know that the AMR genes/ MGEs in the contig sequence is on plasmid or Chromosome? 0 Hi everyone, I have a set of bacterial contigs genomes generated by Spades assembler. I am trying to find the method for identifying whether the contig sequence is a plasmid or…

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Epidemiology of Clostridioides difficile infection

Introduction Clostridioides difficile (C. difficile) is an anaerobic, gram-positive, spore-forming bacillus and important pathogen of antimicrobial-associated diarrhea and nosocomial diarrhea in humans.1 Clostridioides difficile infection (CDI) can progress from self-resolving diarrhea to colitis, life-threatening pseudomembranous colitis and toxic megacolon, and death.2,3 CDI is a toxin-mediated disease, and the major virulence…

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Single-cell delineation of lineage and genetic identity in the mouse brain

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

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MGEs analysis in metagenomic data by ACLAME data base

MGEs analysis in metagenomic data by ACLAME data base 0 Hello everyone. I want to analyze MGEs from metagenomic data and i already trimmed adaptors sequences by scythe and trimmomatic and got my clipped fasta file. I want to analyze MGEs by ACLAME database. For that i need your guideline…

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A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

Abstract Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICE) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanism such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of…

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