研究者詳細 - 鈴木　治夫

論文 - 鈴木　治夫

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Inflammation-associated adherent-invasive Escherichia coli are enriched in pathways for use of propanediol and iron and M-cell translocation.

Dogan B, Suzuki H, Herlekar D, Sartor RB, Campbell BJ, Roberts CL, Stewart K, Scherl EJ, Araz Y, Bitar PP, Lefébure T, Chandler B, Schukken YH, Stanhope MJ, Simpson KW

Inflammatory bowel diseases （Inflammatory Bowel Diseases） 20 （ 11 ） 1919 - 32 2014年11月

研究論文（学術雑誌）, 査読有り, ISSN 1078-0998

Copyright © 2014 Crohn's & Colitis Foundation of America, Inc. Background: Perturbations of the intestinal microbiome, termed dysbiosis, are linked to intestinal inflammation. Isolation of adherent-invasive Escherichia coli (AIEC) from intestines of patients with Crohn's disease (CD), dogs with granulomatous colitis, and mice with acute ileitis suggests these bacteria share pathoadaptive virulence factors that promote inflammation. Methods: To identify genes associated with AIEC, we sequenced the genomes of phylogenetically diverse AIEC strains isolated from people with CD (4), dogs with granulomatous colitis (2), and mice with ileitis (2) and 1 non-AIEC strain from CD ileum and compared them with 38 genome sequences of E. coli and Shigella. We then determined the prevalence of AIEC-associated genes in 49 E. coli strains from patients with CD and controls and correlated genotype with invasion of intestinal epithelial cells, persistence within macrophages, AIEC pathotype, and growth in standardized conditions. Results: Genes encoding propanediol utilization (pdu operon) and iron acquisition (yersiniabactin, chu operon) were overrepresented in AIEC relative to nonpathogenic E. coli. PduC (propanediol dehydratase) was enriched in CD-derived AIEC, correlated with increased cellular invasion, and persistence in vitro and was increasingly expressed in fucose-containing media. Growth of AIEC required iron, and the presence of chuA (heme acquisition) correlated with persistence in macrophages. CD-associated AIEC with lpfA154 (long polar fimbriae) demonstrated increased invasion of epithelial cells and translocation across M cells. Conclusions: Our findings provide novel insights into the genetic basis of the AIEC pathotype, supporting the concept that AIEC are equipped to exploit and promote intestinal inflammation and reveal potential targets for intervention against AIEC and inflammation-associated dysbiosis.

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Draft genome sequences of three Holospora species (Holospora obtusa, Holospora undulata, and Holospora elegans), endonuclear symbiotic bacteria of the ciliate Paramecium caudatum.

Dohra H, Tanaka K, Suzuki T, Fujishima M, Suzuki H

FEMS microbiology letters （FEMS Microbiology Letters） 359 （ 1 ） 16 - 8 2014年10月

研究論文（学術雑誌）, 査読有り, ISSN 0378-1097

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Draft genome sequence of strain q-1, an iodide-oxidizing alphaproteobacterium isolated from natural gas brine water.

Ehara A, Suzuki H, Kanesaki Y, Yoshikawa H, Amachi S

Genome announcements （Genome Announcements） 2 （ 4 ） 2014年07月

研究論文（学術雑誌）, 査読有り

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Draft genome sequence of Gluconobacter thailandicus NBRC 3257.

Matsutani M, Suzuki H, Yakushi T, Matsushita K

Standards in genomic sciences （Standards in Genomic Sciences） 9 （ 3 ） 614 - 23 2014年06月

研究論文（学術雑誌）, 査読有り

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Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment.

Mendes-Soares H, Suzuki H, Hickey RJ, Forney LJ

Journal of bacteriology （Journal of Bacteriology） 196 （ 7 ） 1458 - 70 2014年04月

研究論文（学術雑誌）, 査読有り, ISSN 0021-9193

Lactobacilli are found in a wide variety of habitats. Four species, Lactobacillus crispatus, L. gasseri, L. iners, and L. jensenii, are common and abundant in the human vagina and absent from other habitats. These may be adapted to the vagina and possess characteristics enabling them to thrive in that environment. Furthermore, stable codominance of multiple Lactobacillus species in a single community is infrequently observed. Thus, it is possible that individual vaginal Lactobacillus species possess unique characteristics that confer to them host-specific competitive advantages. We performed comparative functional genomic analyses of representatives of 25 species of Lactobacillus, searching for habitat-specific traits in the genomes of the vaginal lactobacilli. We found that the genomes of the vaginal species were significantly smaller and had significantly lower GC content than those of the nonvaginal species. No protein families were found to be specific to the vaginal species analyzed, but some were either overor underrepresented relative to nonvaginal species. We also found that within the vaginal species, each genome coded for species- specific protein families. Our results suggest that even though the vaginal species show no general signatures of adaptation to the vaginal environment, each species has specific and perhaps unique ways of interacting with its environment, be it the host or other microbes in the community. These findings will serve as a foundation for further exploring the role of lactobacilli in the ecological dynamics of vaginal microbial communities and their ultimate impact on host health. © 2014, American Society for Microbiology.

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Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts.

Kodama Y, Suzuki H, Dohra H, Sugii M, Kitazume T, Yamaguchi K, Shigenobu S, Fujishima M

BMC genomics （BMC Genomics） 15 （ 1 ） 183 2014年03月

研究論文（学術雑誌）, 査読有り

Background: The ciliate Paramecium bursaria harbors several hundred cells of the green-alga Chlorella sp. in their cytoplasm. Irrespective of the mutual relation between P. bursaria and the symbiotic algae, both cells retain the ability to grow without the partner. They can easily reestablish endosymbiosis when put in contact with each other. Consequently, P. bursaria is an excellent model for studying cell-cell interaction and the evolution of eukaryotic cells through secondary endosymbiosis between different protists. Despite the importance of this organism, no genomic resources have been identified for P. bursaria to date. This investigation compared gene expressions through RNA-Seq analysis and de novo transcriptome assembly of symbiont-free and symbiont-bearing host cells.Results: To expedite the process of gene discovery related to the endosymbiosis, we have undertaken Illumina deep sequencing of mRNAs prepared from symbiont-bearing and symbiont-free P. bursaria cells. We assembled the reads de novo to build the transcriptome. Sequencing using Illumina HiSeq2000 platform yielded 232.3 million paired-end sequence reads. Clean reads filtered from the raw reads were assembled into 68,175 contig sequences. Of these, 10,557 representative sequences were retained after removing Chlorella sequences and lowly expressed sequences. Nearly 90% of these transcript sequences were annotated by similarity search against protein databases. We identified differentially expressed genes in the symbiont-bearing P. bursaria cells relative to the symbiont-free cells, including heat shock 70 kDa protein and glutathione S-transferase.Conclusions: This is the first reported comprehensive sequence resource of Paramecium - Chlorella endosymbiosis. Results provide some keys for the elucidation of secondary endosymbiosis in P. bursaria. We identified P. bursaria genes that are differentially expressed in symbiont-bearing and symbiont-free conditions. © 2014 Kodama et al.; licensee BioMed Central Ltd.

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Characterization of the heart transcriptome of the white shark (Carcharodon carcharias).

Richards VP, Suzuki H, Stanhope MJ, Shivji MS

BMC genomics （BMC Genomics） 14 （ 1 ） 697 2013年10月

研究論文（学術雑誌）, 査読有り

Background: The white shark (Carcharodon carcharias) is a globally distributed,apex predator possessing physical, physiological, and behavioral traits thathave garnered it significant public attention. In addition to interest inthe genetic basis of its form and function, as a representative of theoldest extant jawed vertebrate lineage, white sharks are also ofconservation concern due to their small population size and threat fromoverfishing. Despite this, surprisingly little is known about the biology ofwhite sharks, and genomic resources are unavailable. To address thisdeficit, we combined Roche-454 and Illumina sequencing technologies tocharacterize the first transciptome of any tissue for this species. Results: From white shark heart cDNA we generated 665,399 Roche 454 reads (medianlength 387-bp) that were assembled into 141,626 contigs (mean length503-bp). We also generated 78,566,588 Illumina reads, which we aligned tothe 454 contigs producing 105,014 454/Illumina consensus sequences. Tothese, we added 3,432 non-singleton 454 contigs. By comparing thesesequences to the UniProtKB/Swiss-Prot database we were able to annotate21,019 translated open reading frames (ORFs) of ≥ 20 amino acids. Ofthese, 19,277 were additionally assigned Gene Ontology (GO) functionalannotations. While acknowledging the limitations of our single tissuetranscriptome, Fisher tests showed the white shark transcriptome to besignificantly enriched for numerous metabolic GO terms compared to the zebrafish and human transcriptomes, with white shark showing more similarity tohuman than to zebra fish (i.e. fewer terms were significantly different). Wealso compared the transcriptome to other available elasmobranch sequences,for signatures of positive selection and identified several genes ofputative adaptive significance on the white shark lineage. The white sharktranscriptome also contained 8,404 microsatellites (dinucleotide,trinucleotide, or tetranucleotide motifs ≥ five perfect repeats).Detailed characterization of these microsatellites showed that ORFs withtrinucleotide repeats, were significantly enriched for transcriptionregulatory roles and that trinucleotide frequency within ORFs was lower thanfor a wide range of taxonomic groups including other vertebrates.Conclusion: The white shark heart transcriptome represents a valuable resource for futureelasmobranch functional and comparative genomic studies, as well as forpopulation and other biological studies vital for effective conservation ofthis globally vulnerable species. © 2013 Richards et al.; licensee BioMed Central Ltd.

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Draft Genome Sequence of Holospora undulata Strain HU1, a Micronucleus-Specific Symbiont of the Ciliate Paramecium caudatum.

Dohra H, Suzuki H, Suzuki T, Tanaka K, Fujishima M

Genome announcements （Genome Announcements） 1 （ 4 ） 2013年08月

研究論文（学術雑誌）, 査読有り

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Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43/6/78(T.).

Lin C, den Bakker HC, Suzuki H, Lefébure T, Ponnala L, Sun Q, Stanhope MJ, Wiedmann M, Duhamel GE

Genome announcements （Genome Announcements） 1 （ 1 ） 2013年01月

研究論文（学術雑誌）, 査読有り

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Functional bias of positively selected genes in Streptococcus genomes.

Suzuki H, Stanhope MJ

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases （Infection, Genetics and Evolution） 12 （ 2 ） 274 - 7 2012年03月

研究論文（学術雑誌）, 査読有り, ISSN 1567-1348

Rates of nonsynonymous substitution (dN) significantly higher than rates of synonymous substitution (dS) have been used as evidence of positive selection for the fixation of advantageous point mutations. It has been suggested that positive selection contributes to the evolution of virulence factors and certain functional categories in bacterial pathogens. The genus Streptococcus contains a number of important human and agricultural pathogens. Here we assessed positive selection across 13 Streptococcus species, and their relationship with virulence factors and functional categories. We found that known virulence genes were subject to positive selection pressure as much as other genes. After false discovery rate correction for multiple comparisons, no functional categories were significantly over- or under-represented in positively selected genes relative to other genes. Our results suggest that within the genus Streptococcus positive selection based on dN/dS ratios is not distributed with bias across biological functions. © 2012.

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Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae.

Suzuki H, Lefébure T, Bitar PP, Stanhope MJ

BMC genomics （BMC Genomics） 13 （ 1 ） 38 2012年01月

研究論文（学術雑誌）, 査読有り

Background: Staphylococcus belongs to the Gram-positive low G + C content group of the Firmicutes division of bacteria. Staphylococcus aureus is an important human and veterinary pathogen that causes a broad spectrum of diseases, and has developed important multidrug resistant forms such as methicillin-resistant S. aureus (MRSA). Staphylococcus simiae was isolated from South American squirrel monkeys in 2000, and is a coagulase-negative bacterium, closely related, and possibly the sister group, to S. aureus. Comparative genomic analyses of closely related bacteria with different phenotypes can provide information relevant to understanding adaptation to host environment and mechanisms of pathogenicity.Results: We determined a Roche/454 draft genome sequence for S. simiae and included it in comparative genomic analyses with 11 other Staphylococcus species including S. aureus. A genome based phylogeny of the genus confirms that S. simiae is the sister group to S. aureus and indicates that the most basal Staphylococcus lineage is Staphylococcus pseudintermedius, followed by Staphylococcus carnosus. Given the primary niche of these two latter taxa, compared to the other species in the genus, this phylogeny suggests that human adaptation evolved after the split of S. carnosus. The two coagulase-positive species (S. aureus and S. pseudintermedius) are not phylogenetically closest but share many virulence factors exclusively, suggesting that these genes were acquired by horizontal transfer. Enrichment in genes related to mobile elements such as prophage in S. aureus relative to S. simiae suggests that pathogenesis in the S. aureus group has developed by gene gain through horizontal transfer, after the split of S. aureus and S. simiae from their common ancestor.Conclusions: Comparative genomic analyses across 12 Staphylococcus species provide hypotheses about lineages in which human adaptation has taken place and contributions of horizontal transfer in pathogenesis. © 2012 Suzuki et al; licensee BioMed Central Ltd.

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Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution.

Suzuki H, Lefébure T, Hubisz MJ, Pavinski Bitar P, Lang P, Siepel A, Stanhope MJ

Genome biology and evolution （Genome Biology and Evolution） 3 （ 1 ） 168 - 85 2011年

研究論文（学術雑誌）, 査読有り

Comparative genomics of closely related bacterial species with different pathogenesis and host preference can provide a means of identifying the specifics of adaptive differences. Streptococcus dysgalactiae (SD) is comprised of two subspecies: S. dysgalactiae subsp. equisimilis is both a human commensal organism and a human pathogen, and S. dysgalactiae subsp. dysgalactiae is strictly an animal pathogen. Here, we present complete genome sequences for both taxa, with analyses involving other species of Streptococcus but focusing on adaptation in the SD species group. We found little evidence for enrichment in biochemical categories of genes carried by each SD strain, however, differences in the virulence gene repertoire were apparent. Some of the differences could be ascribed to prophage and integrative conjugative elements. We identified approximately 9% of the nonrecombinant core genome to be under positive selection, some of which involved known virulence factors in other bacteria. Analyses of proteomes by pooling data across genes, by biochemical category, clade, or branch, provided evidence for increased rates of evolution in several gene categories, as well as external branches of the tree. Promoters were primarily evolving under purifying selection but with certain categories of genes evolving faster. Many of these fast-evolving categories were the same as those associated with rapid evolution in proteins. Overall, these results suggest that adaptation to changing environments and new hosts in the SD species group has involved the acquisition of key virulence genes along with selection of orthologous protein-coding loci and operon promoters. © 2011 The Author(s).

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Predicting plasmid promiscuity based on genomic signature.

Suzuki H, Yano H, Brown CJ, Top EM

Journal of bacteriology （Journal of Bacteriology） 192 （ 22 ） 6045 - 55 2010年11月

研究論文（学術雑誌）, 査読有り, ISSN 0021-9193

Despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. Our goal was to infer this so-called evolutionary host range. The nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts' signature over time. Therefore, we examined whether the evolutionary host range of plasmids could be inferred by comparing their trinucleotide composition to that of all completely sequenced bacterial chromosomes. The diversity of candidate hosts was determined using taxonomic classification and genetic distance. The method was first tested using plasmids from six incompatibility (Inc) groups whose host ranges are generally thought to be narrow (IncF, IncH, and IncI) or broad (IncN, IncP, and IncW) and then applied to other plasmid groups. The evolutionary host range was found to be broad for IncP plasmids, narrow for IncF and IncI plasmids, and intermediate for IncH and IncN plasmids, which corresponds with their known host range. The IncW plasmids as well as several plasmids from the IncA/C, IncP, IncQ, IncU, and PromA groups have signatures that were not similar to any of the chromosomal signatures, raising the hypothesis that these plasmids have not been ameliorated in any host due to their promiscuous nature. The inferred evolutionary host range of IncA/C, IncP-9, and IncL/M plasmids requires further investigation. In this era of high-throughput sequencing, this genomic signature method is a useful tool for predicting the host range of novel mobile elements. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

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Comparative genomics of pAKD4, the prototype IncP-1delta plasmid with a complete backbone.

Sen D, Yano H, Suzuki H, Król JE, Rogers L, Brown CJ, Top EM

Plasmid （Plasmid） 63 （ 2 ） 98 - 107 2010年03月

研究論文（学術雑誌）, 査読有り, ISSN 0147-619X

Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1δ plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803. bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1δ plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer, and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1δ clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1δ backbone. We therefore propose it to be the prototype IncP-1δ plasmid. © 2009 Elsevier Inc.

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The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.

Zhou X, Hansmann MA, Davis CC, Suzuki H, Brown CJ, Schütte U, Pierson JD, Forney LJ

FEMS immunology and medical microbiology （FEMS Immunology and Medical Microbiology） 58 （ 2 ） 169 - 81 2010年03月

研究論文（学術雑誌）, 査読有り, ISSN 0928-8244

To determine whether different racial groups shared common types of vaginal microbiota, we characterized the composition and structure of vaginal bacterial communities in asymptomatic and apparently healthy Japanese women in Tokyo, Japan, and compared them with those of White and Black women from North America. The composition of vaginal communities was compared based on community profiles of terminal restriction fragments of 16S rRNA genes and phylogenetic analysis of cloned 16S rRNA gene sequences of the numerically dominant bacterial populations. The types of vaginal communities found in Japanese women were similar to those of Black and White women. As with White and Black women, most vaginal communities were dominated by lactobacilli, and only four species of Lactobacillus (Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus gasseri) were commonly found. Communities dominated by multiple species of lactobacilli were common in Japanese and White women, but rare in Black women. The incidence, in Japanese women, of vaginal communities with several non-Lactobacillus species at moderately high frequencies was intermediate between Black women and White women. The limited number of community types found among women in different ethnic groups suggests that host genetic factors, including the innate and adaptive immune systems, may be more important in determining the species composition of vaginal bacterial communities than are cultural and behavioral differences. © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept.

Lefébure T, Bitar PD, Suzuki H, Stanhope MJ

Genome biology and evolution （Genome Biology and Evolution） 2 （ 1 ） 646 - 55 2010年

研究論文（学術雑誌）, 査読有り

Defining bacterial species and understanding the relative cohesiveness of different components of their genomes remains a fundamental problem in microbiology. Bacterial species tend to be comprised of both a set of core and dispensable genes, with the sum of these two components forming the species pan-genome. The role of the core and dispensable genes in defining bacterial species and the question of whether pan-genomes are finite or infinite remain unclear. Here we demonstrate, through the analysis of 96 genome sequences derived from two closely related sympatric sister species of pathogenic bacteria (Campylobacter coli and C. jejuni), that their pan-genome is indeed finite and that there are unique and cohesive features to each of their genomes defining their genomic identity. The two species have a similar pan-genome size; however, C. coli has acquired a larger core genome and each species has evolved a number of species-specific core genes, possibly reflecting different adaptive strategies. Genome-wide assessment of the level of lateral gene transfer within and between the two sister species, as well as within the core and non-core genes, demonstrates a resistance to interspecies recombination in the core genome of the two species and therefore provides persuasive support for the core genome hypothesis for bacterial species. © The Author(s) 2010.

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Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index.

Arakawa K, Suzuki H, Tomita M

BMC genomics （BMC Genomics） 10 640 2009年12月

研究論文（学術雑誌）, 査読有り

Background: Due to their bi-directional replication machinery starting from a single finite origin, bacterial genomes show characteristic nucleotide compositional bias between the two replichores, which can be visualised through GC skew or (C-G)/(C+G). Although this polarisation is used for computational prediction of replication origins in many bacterial genomes, the degree of GC skew visibility varies widely among different species, necessitating a quantitative measurement of GC skew strength in order to provide confidence measures for GC skew-based predictions of replication origins.Results: Here we discuss a quantitative index for the measurement of GC skew strength, named the generalised GC skew index (gGCSI), which is applicable to genomes of any length, including bacterial chromosomes and plasmids. We demonstrate that gGCSI is independent of the window size and can thus be used to compare genomes with different sizes, such as bacterial chromosomes and plasmids. It can suggest the existence of different replication mechanisms in archaea and of rolling-circle replication in plasmids. Correlation of gGCSI values between plasmids and their corresponding host chromosomes suggests that within the same strain, these replicons have reproduced using the same replication machinery and thus exhibit similar strengths of replication strand skew.Conclusions: gGCSI can be applied to genomes of any length and thus allows comparative study of replication-related mutation and selection pressures in genomes of different lengths such as bacterial chromosomes and plasmids. Using gGCSI, we showed that replication-related mutation or selection pressure is similar for replicons with similar machinery. © 2009 Arakawa et al; licensee BioMed Central Ltd.

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Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids.

Van der Auwera GA, Król JE, Suzuki H, Foster B, Van Houdt R, Brown CJ, Mergeay M, Top EM

Antonie van Leeuwenhoek （Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology） 96 （ 2 ） 193 - 204 2009年08月

研究論文（学術雑誌）, 査読有り, ISSN 0003-6072

The self-transmissible, broad-host-range (BHR) plasmid pMOL98 was previously isolated from polluted soil using a triparental plasmid capture approach and shown to possess a replicon similar to that of the BHR plasmids pSB102 and pIPO2. Here, complete sequence analysis and comparative genomics reveal that the 55.5 kb nucleotide sequence of pMOL98 shows extensive sequence similarity and synteny with the BHR plasmid family that now includes pIPO2, pSB102, pTER331, and pMRAD02. They share a plasmid backbone comprising replication, partitioning and conjugative transfer functions. Comparison of the variable accessory regions of these plasmids shows that the majority of natural transposons, as well as the mini-transposon used to mark the plasmids, are inserted in the parA locus. The transposon unique to pMOL98 appears to have inserted from the chromosome of the recipient strain used in the plasmid capture procedure. This demonstrates the necessity for careful screening of plasmids and host chromosomes to avoid mis-interpretation of plasmid genome content. The presence of very similar BHR plasmids with different accessory genes in geographically distinct locations suggests an important role in horizontal gene exchange and bacterial adaptation for this recently defined plasmid group, which we propose to name "PromA". © Springer Science+Business Media B.V. 2009.

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Measure of synonymous codon usage diversity among genes in bacteria.

Suzuki H, Saito R, Tomita M

BMC bioinformatics （BMC Bioinformatics） 10 167 2009年06月

研究論文（学術雑誌）, 査読有り

Background: In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels among different genomes. Here, we introduce a mean dissimilarity-based index (Dmean) for quantifying the level of diversity in synonymous codon usage among all genes within a genome. Results: The application of Dmean to 268 bacterial genomes shows that in bacteria with extremely biased genomic G+C compositions there is little diversity in synonymous codon usage among genes. Furthermore, our findings contradict previous reports. For example, a low level of diversity in codon usage among genes has been reported for Helicobacter pylori, but based on Dmean, the diversity level of this species is higher than those of more than half of bacteria tested here. The discrepancies between our findings and previous reports are probably due to differences in the methods used for measuring codon usage diversity. Conclusion: We recommend that Dmean be used to measure the diversity level of codon usage among genes. This measure can be applied to other compositional features such as amino acid usage and dinucleotide relative abundance as a genomic signature. © 2009 Suzuki et al; licensee BioMed Central Ltd.

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Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes.

Suzuki H, Sota M, Brown CJ, Top EM

Nucleic acids research （Nucleic Acids Research） 36 （ 22 ） e147 2008年12月

研究論文（学術雑誌）, 査読有り, ISSN 0305-1048

Plasmids are ubiquitous mobile elements that serve as a pool of many host beneficial traits such as antibiotic resistance in bacterial communities. To understand the importance of plasmids in horizontal gene transfer, we need to gain insight into the 'evolutionary history' of these plasmids, i.e. the range of hosts in which they have evolved. Since extensive data support the proposal that foreign DNA acquires the host's nucleotide composition during long-term residence, comparison of nucleotide composition of plasmids and chromosomes could shed light on a plasmid's evolutionary history. The average absolute dinucleotide relative abundance difference, termed δ-distance, has been commonly used to measure differences in dinucleotide composition, or 'genomic signature', between bacterial chromosomes and plasmids. Here, we introduce the Mahalanobis distance, which takes into account the variance-covariance structure of the chromosome signatures. We demonstrate that the Mahalanobis distance is better than the δ-distance at measuring genomic signature differences between plasmids and chromosomes of potential hosts. We illustrate the usefulness of this metric for proposing candidate long-term hosts for plasmids, focusing on the virulence plasmids pXO1 from Bacillus anthracis, and pO157 from Escherichia coli O157:H7, as well as the broad host range multi-drug resistance plasmid pB10 from an unknown host. © 2008 The Author(s).

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