A5047403424- Bacteriophages and microbial interactions
- Bacillus and Francisella bacterial research
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Helicobacter pylori-related gastroenterology studies
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Antibiotic Resistance in Bacteria
- Cancer-related gene regulation
- Legume Nitrogen Fixing Symbiosis
- Skin and Cellular Biology Research
- CRISPR and Genetic Engineering
- Viral gastroenteritis research and epidemiology
- Reproductive tract infections research
- Transgenic Plants and Applications
- Plant Pathogenic Bacteria Studies
- DNA Repair Mechanisms
- Antimicrobial Resistance in Staphylococcus
- Pharmaceutical and Antibiotic Environmental Impacts
- Monoclonal and Polyclonal Antibodies Research
- Escherichia coli research studies
- Evolution and Genetic Dynamics
- Microbial infections and disease research
- Galectins and Cancer Biology
Hokkaido University
1992-2024
Toyota Central Research and Development Laboratories (Japan)
2023-2024
Osaka City General Hospital
2024
Osaka Prefectural Medical Center
2024
Massachusetts Institute of Technology
2015-2022
The University of Tokyo
2010-2020
National Institute of Infectious Diseases
2019
Medscape
2019
Jichi Medical University
2019
Tokyo University of Agriculture
2018
Abstract There is a need for large-scale, longitudinal studies to determine the mechanisms by which gut microbiome and its interactions with host affect human health disease. Current methods profiling typically utilize next-generation sequencing applications that are expensive, slow, complex. Here, we present synthetic biology platform affordable, on-demand, simple analysis of samples using RNA toehold switch sensors in paper-based, cell-free reactions. We demonstrate species-specific...
Abstract Background The genome of Helicobacter pylori , an oncogenic bacterium in the human stomach, rapidly evolves and shows wide geographical divergence. high incidence stomach cancer East Asia might be related to bacterial genotype. We used newly developed comparative methods follow evolution Asian H. genomes using 20 complete sequences from Japanese, Korean, Amerind, European, West African strains. Results A phylogenetic tree concatenated well-defined core genes supported divergence...
Epigenetic modifications such as DNA methylation have large effects on gene expression and genome maintenance. Helicobacter pylori, a human gastric pathogen, has number of methyltransferase genes, with different strains having unique repertoires. Previous comparisons suggested that these methyltransferases often change sequence specificity through domain movement--the movement between within genes coding sequences target recognition domains. Using single-molecule real-time sequencing...
Elucidating the ecological and biological identity of extrachromosomal mobile genetic elements (eMGEs), such as plasmids bacteriophages, in human gut remains challenging due to their high complexity diversity. Here, we show efficient identification eMGEs complete circular or linear contigs from PacBio long-read metagenomic data. De novo assembly long reads 12 faecal samples generated 82 eMGE (2.5~666.7-kb), which were classified 71 11 including 58 novel six genomes five diverse crAssphages...
β-Lactam antibiotics disrupt the assembly of peptidoglycan (PG) within bacterial cell wall by inhibiting enzymatic activity penicillin-binding proteins (PBPs). It was recently shown that β-lactam treatment initializes a futile cycle PG synthesis and degradation, highlighting major gaps in our understanding lethal effects PBP inhibition antibiotics. Here, we assess downstream metabolic consequences Escherichia coli with mecillinam show lethality from PBP2 is specific consequence toxic shifts...
Increased antimicrobial resistance (AMR) among bacteria underscores the need to strengthen AMR surveillance and promote data-based prescribing. To evaluate trends associations between usage (AMU) AMR, we explored a dataset of 34,672 bacterial isolates collected 2015 2020 from clinical samples at University Teaching Hospital (UTH) in Lusaka, Zambia. The most frequently isolated species were Escherichia coli (4,986/34,672; 14.4%), Staphylococcus aureus (3,941/34,672; 11.4%), Klebsiella...
Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify have limitations in analyzing haplotypes recombination across the genome. Recently, a method of chromosome painting silico has been developed overcome these shortcomings applied multiple human genome sequences. This detects genome-wide transfer DNA sequence chunks through homologous recombination. Here, we apply it frequently recombining bacterial species...
The mobility of restriction-modification (RM) gene complexes and their association with genome rearrangements is a subject active investigation.Here we conducted systematic comparisons context analysis on fully sequenced prokaryotic genomes to detect RMlinked rearrangements.RM genes were frequently found be linked mobility-related such as integrase transposase homologs.They flanked by direct inverted repeats at significantly high frequency.Insertion long target duplication was observed for...
The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. blaCTX-M genes, encoding ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that blaCTX-M-harboring strains often exhibit multidrug resistance (MDR), it important to investigate the association between chromosomally integrated and presence additional antimicrobial (AMR) identify relevant genetic elements.A total...
The birth and death of genes is central to adaptive evolution, yet the underlying genome dynamics remain elusive. availability closely related complete sequences helps follow changes in gene contents clarify their relationship overall organization. Helicobacter pylori , bacteria our stomach, are known for extreme plasticity through mutation recombination will make a good target such an analysis. In comparing sequences, we found that gain loss (loci) outer membrane proteins, which mediate...
Downstream metabolic events can contribute to the lethality of drugs or agents that interact with a primary cellular target. In bacteria, production reactive oxygen species (ROS) has been associated lethal effects variety stresses including bactericidal antibiotics, but relative contribution this oxidative component cell death depends on factors. Experimental evidence suggested unresolvable DNA problems caused by incorporation oxidized nucleotides into nascent followed incomplete base...
A protein function is carried out by a specific domain localized at position. In the present study, we report that, within gene, amino acid sequence can move between certain position and another This was discovered when sequences of restriction-modification systems bacterial species Helicobacter pylori were compared. specificity subunit Type I systems, DNA recognition mediated target 1 (TRD1) TRD2. To our surprise, several are shared TRD1 TRD2 genes (alleles) same locus (chromosomal...
Helicobacter pylori is a gastric pathogen that infects half the human population and causes gastritis, ulcers, cancer. The cagA gene product major virulence factor associated with It injected into epithelial cells, undergoes phosphorylation by host cell kinases, perturbs signaling pathways. CagA known for its geographical, structural, functional diversity in C-terminal half, where an EPIYA host-interacting motif repeated. Western version of carries segment types A, B, C, while East Asian D...
Ribosomal RNA (rRNA) genes, essential to all forms of life, have been viewed as highly conserved and evolutionarily stable, partly because very little is known about their natural variations. Here, we explored large-scale variations rRNA genes through bioinformatic analyses available complete bacterial genomic sequences with an emphasis on formation mechanisms biological significance. Interestingly, found genomes in which no 16S harbor the core anti-Shine-Dalgarno sequence (5'-CCTCC-3')....
There have been no reports on the presence of tissue renin-angiotensin system in human heart, although angiotensinogen has described animal heart.To determine whether is synthesized we examined messenger RNA (mRNA) synthesis autopsy hearts by using ribonuclease protection assay. As a result, mRNA was detected atrial muscle, muscles conduction system, and left ventricular wall. In wall, expression more prominent subendocardial than midcardial or epicardial muscles. Using monoclonal antibody...
The nature of a species remains fundamental and controversial question. era genome/metagenome sequencing has intensified the debate in prokaryotes because extensive horizontal gene transfer. In this study, we conducted genome-wide survey outcrossing homologous recombination highly sexual bacterial Helicobacter pylori. We multiple genome alignment analyzed entire data set one-to-one orthologous genes for its global strains. detected mosaic structures due to repeated events discordant...
Helicobacter pylori, a bacterial pathogen that can infect human stomach causing gastritis, ulcers and cancer, is known to have high degree of genome/epigenome diversity as the result mutation recombination. The bacteria often in childhood persist for life host. One reasons rapid evolution H. pylori it changes its genome drastically adaptation new To investigate microevolution genome, we undertook whole sequencing same or very similar sequence type multi-locus typing (MLST) with seven genes...
DNA methylation is one of the best studied epigenetic modifications observed in prokaryotes as well eukaryotes. It affects nearby gene expression. Most reactions are catalyzed by a methyltransferase, modification enzyme restriction-modification (RM) system. Its target recognition domain (TRD) recognizes specific sequence for methylation. In this commentary, we review recent evidence movement TRDs between non-orthologous genes and within gene. These movements likely mediated recombination...
Comparisons of proteins show that they evolve through the movement domains. However, in many cases, underlying mechanisms remain unclear. Here, we observed movements DNA recognition domains between non-orthologous within a prokaryote genome. Restriction–modification (RM) systems, consisting sequence-specific methyltransferase and restriction enzyme, contribute to maintenance/evolution genomes/epigenomes. RM systems limit horizontal gene transfer but are themselves mobile. We compared Type...
Abstract Bacillus cereus is associated with foodborne illnesses characterized by vomiting and diarrhea. Although some B. strains that cause severe extraintestinal infections nosocomial are recognized as serious public health threats in healthcare settings, the genetic backgrounds of causing such remain unknown. By conducting pulsed-field gel electrophoresis multilocus sequence typing, we found a novel type (ST), newly registered ST1420, was dominant ST isolated from cases occurred 3...
Multidrug-resistant (MDR) Escherichia coli in food animals such as chickens is an emerging public health concern Zambia. Additionally, the country's high demand for poultry products necessitates further investigation into link between and human MDR E. coli. Twenty cefotaxime-resistant isolates collected from Lusaka, Zambia, were screened multidrug resistance sequenced on MiSeq MinION platforms. Genomes assembled de novo compared with 36 previously reported inpatients at University Teaching...
Decoding of closely related genomes is now revealing the process population evolution. In bacteria, divergence appears associated with a unique set sequence-specific epigenetic DNA methylation systems, often within restriction-modification (RM) systems. They might define gene expression pattern and limit genetic flux between lineages in divergence. We addressed contribution systems to diversification panmictic bacterial species, Helicobacter pylori, which shows an interconnected structure...