Takuji Yamada
A5034753115- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Metabolomics and Mass Spectrometry Studies
- Colorectal Cancer Screening and Detection
- Gastric Cancer Management and Outcomes
- Diet and metabolism studies
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Clostridium difficile and Clostridium perfringens research
- Bacteriophages and microbial interactions
- Gastrointestinal Tumor Research and Treatment
- Metastasis and carcinoma case studies
- Nosocomial Infections in ICU
- Otolaryngology and Infectious Diseases
- Liver Disease Diagnosis and Treatment
- Nutritional Studies and Diet
- Gastrointestinal motility and disorders
- Renal Diseases and Glomerulopathies
- Insect symbiosis and bacterial influences
- Aquaculture disease management and microbiota
- Dialysis and Renal Disease Management
- Dysphagia Assessment and Management
- Machine Learning in Bioinformatics
Tokyo Institute of Technology
2016-2025
Shanghai Institute for Science of Science
2024-2025
SynZyme Technologies (United States)
2025
Life Science Institute
2025
Okinawa Institute of Science and Technology Graduate University
2024
Institute of Science Tokyo
2024
Metacomp Technologies (United States)
2024
Juntendo University
2024
Nagoya City University
2021-2023
Tokyo Women's Medical University
2011-2022
To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe Illumina-based metagenomic sequencing, assembly characterization 3.3 million non-redundant microbial genes, derived from 576.7 gigabases sequence, faecal samples 124 European individuals. The gene set, ∼150 times larger than complement, contains an overwhelming majority prevalent (more frequent) genes cohort probably includes a large proportion intestinal...
We describe the draft genome of microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count a consequence an elevated rate duplication resulting in tandem clusters. More than third Daphnia's genes have no detectable homologs any other available proteome, most amplified families are specific to lineage. coexpansion interacting within metabolic pathways suggests that maintenance duplicated not random, analysis expression under different...
Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing samples identify taxonomic markers that distinguished CRC patients from tumor-free controls a study population 156 participants. Accuracy detection was similar standard occult blood test (FOBT) when both approaches were combined, sensitivity improved >...
The colonization of land by plants was a key event in the evolution life. Here we report draft genome sequence filamentous terrestrial alga Klebsormidium flaccidum (Division Charophyta, Order Klebsormidiales) to elucidate early transition step from aquatic algae plants. Comparison with that other and demonstrate K. acquired many genes specific We indeed produces several plant hormones homologues some signalling intermediates required for hormone actions higher also encodes primitive system...
KEGG Atlas is a new graphical interface to the suite of databases, especially systems information in PATHWAY and BRITE databases.It currently consists single global map an associated viewer for metabolism, covering about 120 metabolic pathway maps 10 hierarchies.The allows user navigate zoom under Ajax technology.The mapping high-throughput experimental data onto main use Atlas.In metabolism map, node (circle) chemical compound edge (line) set reactions linked Orthology (KO) entries enzyme...
Simply Mycoplasma The bacterium pneumoniae , a human pathogen, has genome of reduced size and is one the simplest organisms that can reproduce outside host cells. As such, it represents an excellent model organism in which to attempt systems-level understanding its biological organization. Now three papers provide comprehensive quantitative analysis proteome, metabolic network, transcriptome M. (see Perspective by Ochman Raghavan ). Anticipating what might be possible future for more complex...
Background: It is increasingly recognized that gut microbiota play a pivotal role in the development of atherosclerotic cardiovascular disease. Previously, we have reported abundance genus Bacteroides lower patients with coronary artery disease (CAD) than without CAD risk factors or healthy volunteers. However, it remains unclear which and how specific bacteria contribute to progression atherosclerosis. Methods: We recruited controls factors. then compared microbial composition using 16S...
Simply Mycoplasma The bacterium pneumoniae , a human pathogen, has genome of reduced size and is one the simplest organisms that can reproduce outside host cells. As such, it represents an excellent model organism in which to attempt systems-level understanding its biological organization. Now three papers provide comprehensive quantitative analysis proteome, metabolic network, transcriptome M. (see Perspective by Ochman Raghavan ). Anticipating what might be possible future for more complex...
Recent studies have demonstrated that gut microbiota development influences infants' health and subsequent host physiology. However, the factors shaping of remain poorly understood, mechanisms through which these affect metabolite profiles not been extensively investigated. Here we analyse 27 infants during first month life. We find three distinct clusters transition towards Bifidobacteriaceae-dominant microbiota. observe considerable differences in human milk oligosaccharide utilization...
Simply Mycoplasma The bacterium pneumoniae , a human pathogen, has genome of reduced size and is one the simplest organisms that can reproduce outside host cells. As such, it represents an excellent model organism in which to attempt systems-level understanding its biological organization. Now three papers provide comprehensive quantitative analysis proteome, metabolic network, transcriptome M. (see Perspective by Ochman Raghavan ). Anticipating what might be possible future for more complex...
iPath2.0 is a web-based tool (http://pathways.embl.de) for the visualization and analysis of cellular pathways. Its primary map summarizes metabolism in biological systems as annotated to date. Nodes correspond various chemical compounds edges represent series enzymatic reactions. In two other maps, provides an overview secondary metabolite biosynthesis hand-picked selection important regulatory pathways functional modules, allowing more general protein functions genome or metagenome....
iPath3.0 (http://pathways.embl.de) is a web-application for the visualization and analysis of cellular pathways. It freely available open to everyone. Currently it based on four KEGG global maps, which summarize up 158 traditional pathway 192 modules other metabolic elements into one connected manually curated network. Users can fully customize these networks interactively explore them through its redesigned, fast lightweight interface, highlights general trends in multi-omics data. also...
Objectives: The pathophysiological mechanism of abdominal aortic aneurysm (AAA) remains unclear. We previously reported that Bifidobacterium adolescentis levels were reduced in the feces patients with AAA by 16S ribosomal ribonucleic acid (RNA) gene sequencing. In this study, we increased number cases and conducted metagenomic analyses to examine bacterial genes associated pathophysiology AAA. Methods: For gut microbiota data, from 55 52 no history AAA, lower extremity artery disease, or...
Recently, approaches have been developed to sample the genetic content of heterogeneous environments (metagenomics). However, by what means these sequences link distinct environmental conditions with specific biological processes is not well understood. Thus, a major challenge how usage particular pathways and subnetworks reflects adaptation microbial communities across habitats—i.e., network dynamics relates features. Previous research has treated as discrete, somewhat simplified classes...