慶應義塾研究者情報データベース

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• The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium.

  Yano H, Suzuki H, Maruyama F, Iwamoto T

  BMC genomics （BMC Genomics）  20 （ 1 ） 752 2019年10月

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  © 2019 The Author(s). Background: The rapid identification of lineage remains a challenge in the genotyping of clinical isolates of recombinogenic pathogens. The chromosome of Mycobacterium avium subsp. hominissuis (MAH), an agent of Mycobacterium avium complex (MAC) lung disease, is often mosaic and is composed of chromosomal segments originating from different lineages. This makes it difficult to infer the MAH lineage in a simple experimental set-up. To overcome this difficulty, we sought to identify chromosomal marker genes containing lineage-specific alleles by genome data mining. Results: We conducted genetic population structure analysis, phylogenetic analysis, and a survey of historical recombination using data from 125 global MAH isolates. Six MAH lineages (EA1, EA2, SC1, SC2, SC3, and SC4) were identified in the current dataset. One P-450 gene (locus-tag MAH-0788/MAV-0940) in the recombination-cold region was found to have multiple alleles that could discriminate five lineages. By combining the information about allele type from one additional gene, the six MAH lineages as well as other M. avium subspecies were distinguishable. A recombination-cold region of 116 kb contains an insertion hotspot and is flanked by a mammalian cell-entry protein operon where allelic variants have previously been reported to occur. Hence, we speculate that the acquisition of lineage-or strain-specific insertions has introduced homology breaks in the chromosome, thereby reducing the chance of interlineage recombination. Conclusions: The allele types of the newly identified marker genes can be used to predict major lineages of M. avium. The single nucleotide polymorphism typing approach targeting multiallelic loci in recombination-cold regions will facilitate the epidemiological study of MAC, and may also be useful for equivalent studies of other nontuberculous mycobacteria potentially carrying mosaic genomes.

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• Large-scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life.

  Saito M, Sato A, Nagata S, Tamaki S, Tomita M, Suzuki H, Kanai A

  Genome biology and evolution 2019年09月

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• Genomic analysis of Pseudomonas sp. Strain SCT, an iodate-reducing bacterium isolated from marine sediment, reveals a possible use for bioremediation

  Harada M., Ito K., Nakajima N., Yamamura S., Tomita M., Suzuki H., Amachi S.

  G3: Genes, Genomes, Genetics （G3: Genes, Genomes, Genetics）  9 （ 5 ） 1321 - 1329 2019年05月

  研究論文（学術雑誌）, 査読有り

  　概要を見る

  Copyright © 2019 Harada et al. Strain SCT is an iodate-reducing bacterium isolated from marine sediment in Kanagawa Prefecture, Japan. In this study, we determined the draft genome sequence of strain SCT and compared it to complete genome sequences of other closely related bacteria, including Pseudomonas stutzeri. A phylogeny inferred from concatenation of core genes revealed that strain SCT was closely related to marine isolates of P. stutzeri. Genes present in the SCT genome but absent from the other analyzed P. stutzeri genomes comprised clusters corresponding to putative prophage regions and possible operons. They included pil genes, which encode type IV pili for natural transformation; the mer operon, which encodes resistance systems for mercury; and the pst operon, which encodes a Pi-specific transport system for phosphate uptake. We found that strain SCT had more prophage-like genes than the other P. stutzeri strains and that the majority (70%) of them were SCT strain-specific. These genes, encoded on distinct prophage regions, may have been acquired after branching from a common ancestor following independent phage transfer events. Thus, the genome sequence of Pseudomonas sp. strain SCT can provide detailed insights into its metabolic potential and the evolution of genetic elements associated with its unique phenotype.

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• Comparative genomics of Bacteria commonly identified in the built environment

  Merino N., Zhang S., Tomita M., Suzuki H.

  BMC Genomics （BMC Genomics）  20 （ 1 ） 92 2019年01月

  研究論文（学術雑誌）, 査読有り

  　概要を見る

  © 2019 The Author(s). Background: The microbial community of the built environment (BE) can impact the lives of people and has been studied for a variety of indoor, outdoor, underground, and extreme locations. Thus far, these microorganisms have mainly been investigated by culture-based methods or amplicon sequencing. However, both methods have limitations, complicating multi-study comparisons and limiting the knowledge gained regarding in-situ microbial lifestyles. A greater understanding of BE microorganisms can be achieved through basic information derived from the complete genome. Here, we investigate the level of diversity and genomic features (genome size, GC content, replication strand skew, and codon usage bias) from complete genomes of bacteria commonly identified in the BE, providing a first step towards understanding these bacterial lifestyles. Results: Here, we selected bacterial genera commonly identified in the BE (or "Common BE genomes") and compared them against other prokaryotic genera ("Other genomes"). The "Common BE genomes" were identified in various climates and in indoor, outdoor, underground, or extreme built environments. The diversity level of the 16S rRNA varied greatly between genera. The genome size, GC content and GC skew strength of the "Common BE genomes" were statistically larger than those of the "Other genomes" but were not practically significant. In contrast, the strength of selected codon usage bias (S value) was statistically higher with a large effect size in the "Common BE genomes" compared to the "Other genomes." Conclusion: Of the four genomic features tested, the S value could play a more important role in understanding the lifestyles of bacteria living in the BE. This parameter could be indicative of bacterial growth rates, gene expression, and other factors, potentially affected by BE growth conditions (e.g., temperature, humidity, and nutrients). However, further experimental evidence, species-level BE studies, and classification by BE location is needed to define the relationship between genomic features and the lifestyles of BE bacteria more robustly.

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• Reconsidering plasmid maintenance factors for computational plasmid design

  Yano H., Shintani M., Tomita M., Suzuki H., Oshima T.

  Computational and Structural Biotechnology Journal （Computational and Structural Biotechnology Journal）  17   70 - 81 2019年01月

  研究論文（学術雑誌）, 査読有り

  　概要を見る

  © 2018 The Authors Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.

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• 都市環境における微生物群集の多様性とダイナミクス

  鈴木, 治夫

  学事振興資金研究成果実績報告書 （慶應義塾大学）  2019年

• 都市環境における微生物群集の多様性とダイナミクス

  鈴木, 治夫

  学事振興資金研究成果実績報告書 （慶應義塾大学）  2018年

• 都市環境における微生物群集の多様性とダイナミクス

  鈴木, 治夫

  学事振興資金研究成果実績報告書 （慶應義塾大学）  2017年

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• 大阪・関西万博とアジア競技大会における都市環境マイクロバイオームの変動調査

  2025年04月

  -

  2029年03月

  鈴木 治夫, 基盤研究(B), 補助金,  研究代表者

• 2020年東京オリンピック前後の都市マイクロバイオームの変動調査

  2020年04月

  -

  2023年03月

  文部科学省・日本学術振興会, 科学研究費助成事業, 鈴木 治夫, 基盤研究(C), 補助金,  研究代表者

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• 研究会Ｂ

  2026年度

• 卒業プロジェクト２

  2026年度

• アカデミックプロジェクト（先端生命科学Ｂ）

  2026年度

• 環境情報学

  2026年度

• バイオインフォマティクスのデータサイエンス

  2026年度

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