研究者詳細 - 鈴木　治夫

論文 - 鈴木　治夫

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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

© 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

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

© 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

© 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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Identification of novel Legionella genes required for endosymbiosis in Paramecium based on comparative genome analysis with Holospora spp.

Watanabe K, Suzuki H, Nishida T, Mishima M, Tachibana M, Fujishima M, Shimizu T, Watarai M

FEMS microbiology ecology （FEMS microbiology ecology） 94 （ 11 ） 2018年11月

研究論文（学術雑誌）, 査読有り, ISSN 0168-6496

The relationship between Legionella and protist hosts has a huge impact when considering the infectious risk in humans because it facilitates the long-term replication and survival of Legionella in the environment. The ciliate Paramecium is considered to be a protist host for Legionella in natural environments, but the details of their endosymbiosis are largely unknown. In this study, we determined candidate Legionella pneumophila genes that are likely to be involved in the establishment of endosymbiosis in Paramecium caudatum by comparing the genomes of Legionella spp. and Holospora spp. that are obligate endosymbiotic bacteria in Paramecium spp. Among the candidate genes, each single deletion mutant for five genes (lpg0492, lpg0522, lpg0523, lpg2141 and lpg2398) failed to establish endosymbiosis in P. caudatum despite showing intracellular growth in human macrophages. The mutants exhibited no characteristic changes in terms of their morphology, multiplication rate or capacity for modulating the phagosomes in which they were contained, but their resistance to lysozyme decreased significantly. This study provides insights into novel factors required by L. pneumophila for endosymbiosis in P. caudatum, and suggests that endosymbiotic organisms within conspecific hosts may have shared genes related to effective endosymbiosis establishment.

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Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago

Ohta T., Kawashima T., Shinozaki N., Dobashi A., Hiraoka S., Hoshino T., Kanno K., Kataoka T., Kawashima S., Matsui M., Nemoto W., Nishijima S., Suganuma N., Suzuki H., Taguchi Y., Takenaka Y., Tanigawa Y., Tsuneyoshi M., Yoshitake K., Sato Y., Yamashita R., Arakawa K., Iwasaki W.

Journal of Plant Research （Journal of Plant Research） 131 （ 4 ） 709 - 717 2018年07月

研究論文（学術雑誌）, 査読有り, ISSN 09189440

© 2018, The Botanical Society of Japan and Springer Japan KK, part of Springer Nature. Recent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are isolated from the external environment until the bud opens and only then can the petal surface accumulate environmental DNA. Here, we performed a crowdsourced experiment, the “Ohanami Project”, to obtain environmental DNA samples from petal surfaces of Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago during spring 2015. C. × yedoensis is the most popular garden cherry species in Japan and clones of this cultivar bloom simultaneously every spring. Data collection spanned almost every prefecture and totaled 577 DNA samples from 149 collaborators. Preliminary amplicon-sequencing analysis showed the rapid attachment of environmental DNA onto the petal surfaces. Notably, we found DNA of other common plant species in samples obtained from a wide distribution; this DNA likely originated from the pollen of the Japanese cedar. Our analysis supports our belief that petal surfaces after blossoming are a promising target to reveal the dynamics of environmental DNA in nature. The success of our experiment also shows that crowdsourced environmental DNA analyses have considerable value in ecological studies.

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Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes

Cornejo O., Hickey R., Suzuki H., Forney L.

Evolutionary Applications （Evolutionary Applications） 11 （ 3 ） 312 - 324 2018年03月

研究論文（学術雑誌）, 査読有り, ISSN 17524563

© 2017 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd Gardnerella vaginalis has long been associated with bacterial vaginosis, a condition that increases the risk of women to preterm birth, sexually transmitted infections, and other adverse sequelae. However, G. vaginalis is also commonly found in healthy asymptomatic women of all ages. This raises the question if genetic differences among strains might distinguish potentially pathogenic from commensal strains. To disentangle the diversity of G. vaginalis, we invoked the concept of ecotypes—lineages of genetically and ecologically distinct strains within a named species—to better understand their evolutionary history and identify functional characteristics. We compared the genomes of G. vaginalis to six species in the closely related Bifidobacterium genus and found that G. vaginalis has a large accessory genome relative to Bifidobacterium, including many unique genes possibly involved in metabolism, drug resistance, and virulence. We then performed a comparative genomic analysis of 35 strains of G. vaginalis to infer a phylogeny based on the combined analysis of the core genome, using nucleotide substitution models, and the accessory genome, using gene gain/loss models. With the inferred tree topology, we performed comparisons of functional gene content among lineages that diverged at varying depths in the phylogeny and found significant differences in the representation of genes putatively involved in pathogenicity. Our functional enrichment analysis suggests that some lineages of G. vaginalis may possess enhanced pathogenic capabilities, including genes involved in mucus degradation like sialidases, while others may be commensal strains, lacking many of these pathogenic capabilities. The combined phylogenetic evidence and functional enrichment analysis allowed us to identify distinct ecotypes that have evolved in G. vaginalis as the result of the differential gene gain/loss for specific functions, including the capability to cause disease. We finally discuss how this analysis framework could be used to gain insight into the etiology of bacterial vaginosis and improve diagnosis.

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Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan.

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

Journal of genomics 6 122 - 126 2018年

研究論文（学術雑誌）, 査読有り

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Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan.

Suzuki H, Tomita M, Tsai PJ, Ko WC, Hung YP, Huang IH, Chen JW

Gut pathogens （Gut Pathogens） 9 （ 1 ） 70 2017年

研究論文（学術雑誌）, 査読有り

© 2017 The Author(s). Background: Clostridium difficile is a Gram-positive anaerobe and the leading cause of antibiotic-associated diarrhea worldwide. The emergence of ribotype 027 (RT027) strains is associated with increased incidence of infection and mortality. To further understand the relationship between C. difficile NCKUH-21, a RT027 strain isolated from a patient in Taiwan, and other RT027 strains, we performed whole-genome shotgun sequencing on NCKUH-21 and comparative genomic analyses. Results: The genome size, G+C content, and gene number for the NCKUH-21 strain were determined to be similar to those for other C. difficile strains. The core genome phylogeny indicated that the five RT027 strains R20291, CD196, NCKUH-21, BI1, and 2007855 formed a clade. A pathogenicity locus, tcdR-tcdB-tcdE-orf-tcdA-tcdC, was conserved in the genome. A genomic region highly similar to the Clostridium phage $$\upvarphi$$ φ CD38-2 was present in the NCKUH-21 strain but absent in the other RT027 strains and designated as the prophage $$\upvarphi$$ φ NCKUH-21. The prophage $$\upvarphi$$ φ NCKUH-21 genes were significantly higher in G+C content than the other genes in the NCKUH-21 genome, indicating that the prophage does not match the base composition of the host genome. Conclusions: This is the first whole-genome analysis of a RT027 C. difficile strain isolated from Taiwan. Due to the high identity with $$\upvarphi$$ φ CD38-2, the prophage identified in the NCKUH-21 genome has the potential to regulate toxin production. These results provide important information for understanding the pathogenicity of RT027 C. difficile in Taiwan.

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Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan.

Yuliana T, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S

Journal of genomics 5 51 - 53 2017年

研究論文（学術雑誌）, 査読有り

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Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment.

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

Genome announcements （Genome Announcements） 4 （ 5 ） 2016年10月

研究論文（学術雑誌）, 査読有り

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Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria.

Useh NM, Ngbede EO, Akange N, Thomas M, Foley A, Keena MC, Nelson E, Christopher-Hennings J, Tomita M, Suzuki H, Scaria J

Genome announcements （Genome Announcements） 4 （ 3 ） 2016年05月

研究論文（学術雑誌）, 査読有り

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Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia.

Suzuki H, Dapper AL, Jackson CE, Lee H, Pejaver V, Doak TG, Lynch M, Preer JR Jr

Genome announcements （Genome Announcements） 3 （ 6 ） 2015年11月

研究論文（学術雑誌）, 査読有り

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Analysis of amino acid and codon usage in Paramecium bursaria.

Dohra H, Fujishima M, Suzuki H

FEBS letters （FEBS Letters） 589 （ 20 Pt B ） 3113 - 8 2015年10月

研究論文（学術雑誌）, 査読有り, ISSN 0014-5793

© 2015 Federation of European Biochemical Societies. The ciliate Paramecium bursaria harbors the green-alga Chlorella symbionts. We reassembled the P. bursaria transcriptome to minimize falsely fused transcripts, and investigated amino acid and codon usage using the transcriptome data. Surface proteins preferentially use smaller amino acid residues like cysteine. Unusual synonymous codon and amino acid usage in highly expressed genes can reflect a balance between translational selection and other factors. A correlation of gene expression level with synonymous codon or amino acid usage is emphasized in genes down-regulated in symbiont-bearing cells compared to symbiont-free cells. Our results imply that the selection is associated with P. bursaria-Chlorella symbiosis.

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Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preference.

Scaria J, Suzuki H, Ptak CP, Chen JW, Zhu Y, Guo XK, Chang YF

BMC genomics （BMC Genomics） 16 （ 1 ） 448 2015年06月

研究論文（学術雑誌）, 査読有り

© 2015 Scaria et al. Background: Clostridium difficile and C. sordellii are two anaerobic, spore forming, gram positive pathogens with a broad host range and the ability to cause lethal infections. Despite strong similarities between the two Clostridial strains, differences in their host tissue preference place C. difficile infections in the gastrointestinal tract and C. sordellii infections in soft tissues. Results: In this study, to improve our understanding of C. sordellii and C. difficile virulence and pathogenesis, we have performed a comparative genomic and phenomic analysis of the two. The global phenomes of C. difficile and C. sordellii were compared using Biolog Phenotype microarrays. When compared to C. difficile, C. sordellii was found to better utilize more complex sources of carbon and nitrogen, including peptides. Phenotype microarray comparison also revealed that C. sordellii was better able to grow in acidic pH conditions. Using next generation sequencing technology, we determined the draft genome of C. sordellii strain 8483 and performed comparative genome analysis with C. difficile and other Clostridial genomes. Comparative genome analysis revealed the presence of several enzymes, including the urease gene cluster, specific to the C. sordellii genome that confer the ability of expanded peptide utilization and survival in acidic pH. Conclusions: The identified phenotypes of C. sordellii might be important in causing wound and vaginal infections respectively. Proteins involved in the metabolic differences between C. sordellii and C. difficile should be targets for further studies aimed at understanding C. difficile and C. sordellii infection site specificity and pathogenesis.