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Asif M, Li-Qun Z, Zeng Q, Atiq M, Ahmad K, Tariq A, Al-Ansari N, Blom J, Fenske L, Alodaini HA, Hatamleh AA. Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism. Comput Struct Biotechnol J 2023; 21:4647-4662. [PMID: 37841331 PMCID: PMC10568305 DOI: 10.1016/j.csbj.2023.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.
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Affiliation(s)
- Muhammad Asif
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhang Li-Qun
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Muhammad Atiq
- Department of Plant Pathology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khalil Ahmad
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Aqil Tariq
- Department of Wildlife, Fisheries, and Aquaculture, College of Forest Resources, Mississippi State, University, MS 39762-9690, USA
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Linda Fenske
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Hissah Abdulrahman Alodaini
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Okubo T, Toyoda A, Fukuhara K, Uchiyama I, Harigaya Y, Kuroiwa M, Suzuki T, Murakami Y, Suwa Y, Takami H. The physiological potential of anammox bacteria as revealed by their core genome structure. DNA Res 2021; 28:6046978. [PMID: 33367889 PMCID: PMC7814187 DOI: 10.1093/dnares/dsaa028] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/04/2020] [Indexed: 01/25/2023] Open
Abstract
We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2− reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. Kuenenia stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologues. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least five paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH2OH by self-production for anammox metabolism.
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Affiliation(s)
- Takashi Okubo
- Marine Microbiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Kohei Fukuhara
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8585, Japan
| | - Yuhki Harigaya
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Megumi Kuroiwa
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Takuma Suzuki
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Yuka Murakami
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Yuichi Suwa
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Hideto Takami
- Marine Microbiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan
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3
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Uchiyama I, Mihara M, Nishide H, Chiba H, Kato M. MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons. Nucleic Acids Res 2020; 47:D382-D389. [PMID: 30462302 PMCID: PMC6324027 DOI: 10.1093/nar/gky1054] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/03/2018] [Indexed: 01/20/2023] Open
Abstract
The Microbial Genome Database for Comparative Analysis (MBGD) is a database for comparative genomics based on comprehensive orthology analysis of bacteria, archaea and unicellular eukaryotes. MBGD now contains 6318 genomes. To utilize the database for both closely related and distantly related genomes, MBGD previously provided two types of ortholog tables: the standard ortholog table containing one representative genome from each genus covering the entire taxonomic range and the taxon specific ortholog tables for each taxon. However, this approach has a drawback in that the standard ortholog table contains only genes that are conserved in the representative genomes. To address this problem, we developed a stepwise procedure to construct ortholog tables hierarchically in a bottom-up manner. By using this approach, the new standard ortholog table now covers the entire gene repertoire stored in MBGD. In addition, we have enhanced several functionalities, including rapid and flexible keyword searching, profile-based sequence searching for orthology assignment to a user query sequence, and displaying a phylogenetic tree of each taxon based on the concatenated core gene sequences. For integrative database searching, the core data in MBGD are represented in Resource Description Framework (RDF) and a SPARQL interface is provided to search them. MBGD is available at http://mbgd.genome.ad.jp/.
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Affiliation(s)
- Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Motohiro Mihara
- Dynacom Co., Ltd. 5-1-27, Onoedori, Chuo-ku, Kobe, Hyogo 651-0088, Japan
| | - Hiroyo Nishide
- Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Hirokazu Chiba
- Database Center for Life Science, Research Organization of Information and Systems 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Masaki Kato
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
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Takami H, Toyoda A, Uchiyama I, Itoh T, Takaki Y, Arai W, Nishi S, Kawai M, Shin-Ya K, Ikeda H. Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1. DNA Res 2018; 24:169-177. [PMID: 28065880 PMCID: PMC5397603 DOI: 10.1093/dnares/dsw055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/19/2016] [Indexed: 11/13/2022] Open
Abstract
Lysobacter enzymogenes M497-1 is a producer of commercialized achromopeptidase and is expected to harbour genes encoding various other antimicrobial enzymes. Here, we present the complete sequence of the genome of M497-1 and the expression profiles of the genes for various antimicrobial enzymes. Of the 117 peptidase-encoding genes found in the 6.1-Mb genome of M497-1, 15 genes (aside from the gene encoding the achromopeptidase) were expressed at a level higher than that of the average ribosomal protein genes in the 24-h culture. Thus, the strain was found more valuable than hitherto considered. In addition, M497-1 harbours 98 genes involved in the biosynthesis of various natural products, 16 of which are M497-1-specific across 4 Lysobacter species. A gene cluster starting at LEN_2603 through LEN_2673 among the 98 genes closely resembled the lysobactin biosynthesis gene cluster of Lysobacter sp. ATCC 53042. It is likely that M497-1 may produce lysobactin or related antibacterial compounds. Furthermore, comparative genomic analysis of M497-1 and four other Lysobacter species revealed that their core genome structure comprises 3,737 orthologous groups. Our findings are expected to advance further biotechnological application of Lysobacter spp. as a promising source of natural bioactive compounds.
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Affiliation(s)
- Hideto Takami
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Yoshihiro Takaki
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Wataru Arai
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Shinro Nishi
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Mikihiko Kawai
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, Sagamihara, Kanagawa, Japan
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Oliver A, Kay M, Cooper KK. Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC Genomics 2018; 19:310. [PMID: 29716534 PMCID: PMC5930826 DOI: 10.1186/s12864-018-4635-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 03/28/2018] [Indexed: 12/31/2022] Open
Abstract
Background Cocci-shaped Sporosarcina strains are currently one of the few known cocci-shaped spore-forming bacteria, yet we know very little about the genomics. The goal of this study is to utilize comparative genomics to investigate the diversity of cocci-shaped Sporosarcina strains that differ in their geographical isolation and show different nutritional requirements. Results For this study, we sequenced 28 genomes of cocci-shaped Sporosarcina strains isolated from 13 different locations around the world. We generated the first six complete genomes and methylomes utilizing PacBio sequencing, and an additional 22 draft genomes using Illumina sequencing. Genomic analysis revealed that cocci-shaped Sporosarcina strains contained an average genome of 3.3 Mb comprised of 3222 CDS, 54 tRNAs and 6 rRNAs, while only two strains contained plasmids. The cocci-shaped Sporosarcina genome on average contained 2.3 prophages and 15.6 IS elements, while methylome analysis supported the diversity of these strains as only one of 31 methylation motifs were shared under identical growth conditions. Analysis with a 90% identity cut-off revealed 221 core genes or ~ 7% of the genome, while a 30% identity cut-off generated a pan-genome of 8610 genes. The phylogenetic relationship of the cocci-shaped Sporosarcina strains based on either core genes, accessory genes or spore-related genes consistently resulted in the 29 strains being divided into eight clades. Conclusions This study begins to unravel the phylogenetic relationship of cocci-shaped Sporosarcina strains, and the comparative genomics of these strains supports identification of several new species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4635-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Oliver
- Department of Biology, California State University Northridge, Northridge, CA, USA.,Present Address: Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Matthew Kay
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA.
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Uchiyama I. Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG. Methods Mol Biol 2018; 1611:147-168. [PMID: 28451978 DOI: 10.1007/978-1-4939-7015-5_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Comparative genomics is becoming an essential approach for identification of genes associated with a specific function or phenotype. Here, we introduce the microbial genome database for comparative analysis (MBGD), which is a comprehensive ortholog database among the microbial genomes available so far. MBGD contains several precomputed ortholog tables including the standard ortholog table covering the entire taxonomic range and taxon-specific ortholog tables for various major taxa. In addition, MBGD allows the users to create an ortholog table within any specified set of genomes through dynamic calculations. In particular, MBGD has a "My MBGD" mode where users can upload their original genome sequences and incorporate them into orthology analysis. The created ortholog table can serve as the basis for various comparative analyses. Here, we describe the use of MBGD and briefly explain how to utilize the orthology information during comparative genome analysis in combination with the stand-alone comparative genomics software RECOG, focusing on the application to comparison of closely related microbial genomes.
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Affiliation(s)
- Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
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Hayatsu M, Tago K, Uchiyama I, Toyoda A, Wang Y, Shimomura Y, Okubo T, Kurisu F, Hirono Y, Nonaka K, Akiyama H, Itoh T, Takami H. An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil. ISME JOURNAL 2017; 11:1130-1141. [PMID: 28072419 DOI: 10.1038/ismej.2016.191] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 11/16/2016] [Accepted: 11/19/2016] [Indexed: 12/22/2022]
Abstract
Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates. Whereas all known gammaproteobacterial AOB (γ-AOB) species, which have been isolated from marine and saline aquatic environments, are halophiles, TAO100 is not phenotypically halophilic. Thus, TAO100 represents the first soil-originated and non-halophilic γ-AOB. The TAO100 genome is considerably smaller than those of other γ-AOB and lacks several genes associated with salt tolerance which are unnecessary for survival in soil. The ammonia monooxygenase subunit A gene of TAO100 and its transcript are higher in abundance than those of ammonia-oxidizing archaea and betaproteobacterial AOB in the strongly acidic soil. These results indicate that TAO100 plays an important role in the nitrification of acidic soils. Based on these results, we propose TAO100 as a novel species of a new genus, Candidatus Nitrosoglobus terrae.
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Affiliation(s)
- Masahito Hayatsu
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Kanako Tago
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Ikuo Uchiyama
- National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yong Wang
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yumi Shimomura
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takashi Okubo
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yuhei Hirono
- Institute of Fruit Tree and Tea Science, NARO, Shimada, Shizuoka, Japan
| | - Kunihiko Nonaka
- Institute of Fruit Tree and Tea Science, NARO, Shimada, Shizuoka, Japan
| | - Hiroko Akiyama
- Institute of Agro-Environmental Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology,Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Hideto Takami
- Yokohama Institute, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan
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8
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Uchiyama I, Albritton J, Fukuyo M, Kojima KK, Yahara K, Kobayashi I. A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands. PLoS One 2016; 11:e0159419. [PMID: 27504980 PMCID: PMC4978471 DOI: 10.1371/journal.pone.0159419] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/01/2016] [Indexed: 01/03/2023] Open
Abstract
Genomes of a given bacterial species can show great variation in gene content and thus systematic analysis of the entire gene repertoire, termed the pan-genome, is important for understanding bacterial intra-species diversity, population genetics, and evolution. Here, we analyzed the pan-genome from 30 completely sequenced strains of the human gastric pathogen Helicobacter pylori belonging to various phylogeographic groups, focusing on 991 accessory (not fully conserved) orthologous groups (OGs). We developed a method to evaluate the mobility of genes within a genome, using the gene order in the syntenically conserved regions as a reference, and classified the 991 accessory OGs into five classes: Core, Stable, Intermediate, Mobile, and Unique. Phylogenetic networks based on the gene content of Core and Stable classes are highly congruent with that created from the concatenated alignment of fully conserved core genes, in contrast to those of Intermediate and Mobile classes, which show quite different topologies. By clustering the accessory OGs on the basis of phylogenetic pattern similarity and chromosomal proximity, we identified 60 co-occurring gene clusters (CGCs). In addition to known genomic islands, including cag pathogenicity island, bacteriophages, and integrating conjugative elements, we identified some novel ones. One island encodes TerY-phosphorylation triad, which includes the eukaryote-type protein kinase/phosphatase gene pair, and components of type VII secretion system. Another one contains a reverse-transcriptase homolog, which may be involved in the defense against phage infection through altruistic suicide. Many of the CGCs contained restriction-modification (RM) genes. Different RM systems sometimes occupied the same (orthologous) locus in the strains. We anticipate that our method will facilitate pan-genome studies in general and help identify novel genomic islands in various bacterial species.
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Affiliation(s)
- Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- * E-mail:
| | - Jacob Albritton
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Masaki Fukuyo
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Kenji K. Kojima
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Sciences, the University of Tokyo, Minato-ku, Tokyo, Japan
- Genetic Information Research Institute, Los Altos, California, United States of America
| | - Koji Yahara
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Biostatistics Center, Kurume University, Kurume, Fukuoka, Japan
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Sciences, the University of Tokyo, Minato-ku, Tokyo, Japan
- Tohoku University, Graduate School of Life Sciences, Sendai, Japan
- Kyorin University, Faculty of Medicine, Mitaka, Japan
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Hiramatsu K, Ito T, Tsubakishita S, Sasaki T, Takeuchi F, Morimoto Y, Katayama Y, Matsuo M, Kuwahara-Arai K, Hishinuma T, Baba T. Genomic Basis for Methicillin Resistance in Staphylococcus aureus. Infect Chemother 2013; 45:117-36. [PMID: 24265961 PMCID: PMC3780952 DOI: 10.3947/ic.2013.45.2.117] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Indexed: 12/31/2022] Open
Abstract
Since the discovery of the first strain in 1961 in England, MRSA, the most notorious multidrug-resistant hospital pathogen, has spread all over the world. MRSA repeatedly turned down the challenges by number of chemotherapeutics, the fruits of modern organic chemistry. Now, we are in short of effective therapeutic agents against MRSA prevailing among immuno-compromised patients in the hospital. On top of this, we recently became aware of the rise of diverse clones of MRSA, some of which have increased pathogenic potential compared to the classical hospital-associated MRSA, and the others from veterinary sources. They increased rapidly in the community, and started menacing otherwise healthy individuals by causing unexpected acute infection. This review is intended to provide a whole picture of MRSA based on its genetic makeup as a versatile pathogen and our tenacious colonizer.
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Affiliation(s)
- Keiichi Hiramatsu
- Department of Bacteriology, Juntendo University, Tokyo, Japan
- Research Center for Infection Control Science, Juntendo University, Tokyo, Japan
| | - Teruyo Ito
- Department of Bacteriology, Juntendo University, Tokyo, Japan
| | - Sae Tsubakishita
- Department of Veterinary Science, Rakuno Gakuen University, Hokkaido, Japan
| | | | | | - Yuh Morimoto
- Department of Bacteriology, Juntendo University, Tokyo, Japan
- Research Center for Infection Control Science, Juntendo University, Tokyo, Japan
| | - Yuki Katayama
- Department of Bacteriology, Juntendo University, Tokyo, Japan
| | - Miki Matsuo
- Department of Bacteriology, Juntendo University, Tokyo, Japan
| | | | - Tomomi Hishinuma
- Department of Bacteriology, Juntendo University, Tokyo, Japan
- Research Center for Infection Control Science, Juntendo University, Tokyo, Japan
| | - Tadashi Baba
- Department of Bacteriology, Juntendo University, Tokyo, Japan
- Research Center for Infection Control Science, Juntendo University, Tokyo, Japan
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10
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Yahara K, Furuta Y, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I. Chromosome painting in silico in a bacterial species reveals fine population structure. Mol Biol Evol 2013; 30:1454-64. [PMID: 23505045 PMCID: PMC3649679 DOI: 10.1093/molbev/mst055] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify population structure have limitations in analyzing haplotypes and recombination across the genome. Recently, a method of chromosome painting in silico has been developed to overcome these shortcomings and has been applied to multiple human genome sequences. This method detects the genome-wide transfer of DNA sequence chunks through homologous recombination. Here, we apply it to the frequently recombining bacterial species Helicobacter pylori that has infected Homo sapiens since their birth in Africa and shows wide phylogeographic divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa, Japan, that we recently sequenced. The newer method revealed a finer population structure than revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic network analysis of the core genome. Novel subgroups were found in Europe, Amerind, and East Asia groups. Examination of genetic flux showed some singleton strains to be hybrids of subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of Asia. We expect this approach to further our understanding of intraspecific bacterial evolution by revealing population structure at a finer scale.
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Affiliation(s)
- Koji Yahara
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Kenshiro Oshima
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Masaru Yoshida
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
| | - Takeshi Azuma
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
| | - Masahira Hattori
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
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11
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Takami H, Taniguchi T, Moriya Y, Kuwahara T, Kanehisa M, Goto S. Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics 2012; 13:699. [PMID: 23234305 PMCID: PMC3541978 DOI: 10.1186/1471-2164-13-699] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 12/06/2012] [Indexed: 11/11/2022] Open
Abstract
Background One of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments. However, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules. Results Distribution of the completion ratio of the KEGG functional modules in 768 prokaryotic species varied greatly with the kind of module, and all modules primarily fell into 4 patterns (universal, restricted, diversified and non-prokaryotic modules), indicating the universal and unique nature of each module, and also the versatility of the KEGG Orthology (KO) identifiers mapped to each one. The module completion ratio in 8 phenotypically different bacilli revealed that some modules were shared only in phenotypically similar species. Metagenomes of human gut microbiomes from 13 healthy individuals previously determined by the Sanger method were analyzed based on the module completion ratio. Results led to new discoveries in the nutritional preferences of gut microbes, believed to be one of the mutualistic representations of gut microbiomes to avoid nutritional competition with the host. Conclusions The method developed in this study could characterize the functionome harbored in genomes and metagenomes. As this method also provided taxonomical information from KEGG modules as well as the gene hosts constructing the modules, interpretation of completion profiles was simplified and we could identify the complementarity between biochemical functions in human hosts and the nutritional preferences in human gut microbiomes. Thus, our method has the potential to be a powerful tool for comparative functional analysis in genomics and metagenomics, able to target unknown environments containing various uncultivable microbes within unidentified phyla.
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Affiliation(s)
- Hideto Takami
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, 237-0061, Japan.
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12
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Uchiyama I, Mihara M, Nishide H, Chiba H. MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. Nucleic Acids Res 2012; 41:D631-5. [PMID: 23118485 PMCID: PMC3531178 DOI: 10.1093/nar/gks1006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.
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Affiliation(s)
- Ikuo Uchiyama
- Laboratory of Genome Informatics, Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.
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13
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Yahara K, Kawai M, Furuta Y, Takahashi N, Handa N, Tsuru T, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I. Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species. Genome Biol Evol 2012; 4:628-40. [PMID: 22534164 PMCID: PMC3381677 DOI: 10.1093/gbe/evs043] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2012] [Indexed: 12/11/2022] Open
Abstract
The nature of a species remains a fundamental and controversial question. The era of genome/metagenome sequencing has intensified the debate in prokaryotes because of extensive horizontal gene transfer. In this study, we conducted a genome-wide survey of outcrossing homologous recombination in the highly sexual bacterial species Helicobacter pylori. We conducted multiple genome alignment and analyzed the entire data set of one-to-one orthologous genes for its global strains. We detected mosaic structures due to repeated recombination events and discordant phylogenies throughout the genomes of this species. Most of these genes including the "core" set of genes and horizontally transferred genes showed at least one recombination event. Taking into account the relationship between the nucleotide diversity and the minimum number of recombination events per nucleotide, we evaluated the recombination rate in every gene. The rate appears constant across the genome, but genes with a particularly high or low recombination rate were detected. Interestingly, genes with high recombination included those for DNA transformation and for basic cellular functions, such as biosynthesis and metabolism. Several highly divergent genes with a high recombination rate included those for host interaction, such as outer membrane proteins and lipopolysaccharide synthesis. These results provide a global picture of genome-wide distribution of outcrossing homologous recombination in a bacterial species for the first time, to our knowledge, and illustrate how a species can be shaped by mutual homologous recombination.
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Affiliation(s)
- Koji Yahara
- Division of Biostatistics, Graduate School of Medicine, Kurume University, Fukuoka, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Mikihiko Kawai
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
- Laboratory of Genome Informatics, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Yoshikazu Furuta
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Noriko Takahashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Naofumi Handa
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Takeshi Tsuru
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - Kenshiro Oshima
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Masaru Yoshida
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuo-ku, Hyogo, Japan
| | - Takeshi Azuma
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuo-ku, Hyogo, Japan
| | - Masahira Hattori
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Japan
- Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan
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14
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Capes MD, DasSarma P, DasSarma S. The core and unique proteins of haloarchaea. BMC Genomics 2012; 13:39. [PMID: 22272718 PMCID: PMC3287961 DOI: 10.1186/1471-2164-13-39] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/24/2012] [Indexed: 11/10/2022] Open
Abstract
Background Since the first genome of a halophilic archaeon was sequenced in 2000, biologists have been advancing the understanding of genomic characteristics that allow for survival in the harsh natural environments of these organisms. An increase in protein acidity and GC-bias in the genome have been implicated as factors in tolerance to extreme salinity, desiccation, and high solar radiation. However, few previous attempts have been made to identify novel genes that would permit survival in such extreme conditions. Results With the recent release of several new complete haloarchaeal genome sequences, we have conducted a comprehensive comparative genomic analysis focusing on the identification of unique haloarchaeal conserved proteins that likely play key roles in environmental adaptation. Using bioinformatic methods, we have clustered 31,312 predicted proteins from nine haloarchaeal genomes into 4,455 haloarchaeal orthologous groups (HOGs). We assigned likely functions by association with established COG and KOG databases in NCBI. After identifying homologs in four additional haloarchaeal genomes, we determined that there were 784 core haloarchaeal protein clusters (cHOGs), of which 83 clusters were found primarily in haloarchaea. Further analysis found that 55 clusters were truly unique (tucHOGs) to haloarchaea and qualify as signature proteins while 28 were nearly unique (nucHOGs), the vast majority of which were coded for on the haloarchaeal chromosomes. Of the signature proteins, only one example with any predicted function, Ral, involved in desiccation/radiation tolerance in Halobacterium sp. NRC-1, was identified. Among the core clusters, 33% was predicted to function in metabolism, 25% in information transfer and storage, 10% in cell processes and signaling, and 22% belong to poorly characterized or general function groups. Conclusion Our studies have established conserved groups of nearly 800 protein clusters present in all haloarchaea, with a subset of 55 which are predicted to be accessory proteins that may be critical or essential for success in an extreme environment. These studies support core and signature genes and proteins as valuable concepts for understanding phylogenetic and phenotypic characteristics of coherent groups of organisms.
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Affiliation(s)
- Melinda D Capes
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland, 701 East Pratt Street, Baltimore, MD 21202 USA
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15
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Kawai M, Furuta Y, Yahara K, Tsuru T, Oshima K, Handa N, Takahashi N, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I. Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes. BMC Microbiol 2011; 11:104. [PMID: 21575176 PMCID: PMC3120642 DOI: 10.1186/1471-2180-11-104] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 05/16/2011] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The genome of Helicobacter pylori, an oncogenic bacterium in the human stomach, rapidly evolves and shows wide geographical divergence. The high incidence of stomach cancer in East Asia might be related to bacterial genotype. We used newly developed comparative methods to follow the evolution of East Asian H. pylori genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains. RESULTS A phylogenetic tree of concatenated well-defined core genes supported divergence of the East Asian lineage (hspEAsia; Japanese and Korean) from the European lineage ancestor, and then from the Amerind lineage ancestor. Phylogenetic profiling revealed a large difference in the repertoire of outer membrane proteins (including oipA, hopMN, babABC, sabAB and vacA-2) through gene loss, gain, and mutation. All known functions associated with molybdenum, a rare element essential to nearly all organisms that catalyzes two-electron-transfer oxidation-reduction reactions, appeared to be inactivated. Two pathways linking acetyl~CoA and acetate appeared intact in some Japanese strains. Phylogenetic analysis revealed greater divergence between the East Asian (hspEAsia) and the European (hpEurope) genomes in proteins in host interaction, specifically virulence factors (tipα), outer membrane proteins, and lipopolysaccharide synthesis (human Lewis antigen mimicry) enzymes. Divergence was also seen in proteins in electron transfer and translation fidelity (miaA, tilS), a DNA recombinase/exonuclease that recognizes genome identity (addA), and DNA/RNA hybrid nucleases (rnhAB). Positively selected amino acid changes between hspEAsia and hpEurope were mapped to products of cagA, vacA, homC (outer membrane protein), sotB (sugar transport), and a translation fidelity factor (miaA). Large divergence was seen in genes related to antibiotics: frxA (metronidazole resistance), def (peptide deformylase, drug target), and ftsA (actin-like, drug target). CONCLUSIONS These results demonstrate dramatic genome evolution within a species, especially in likely host interaction genes. The East Asian strains appear to differ greatly from the European strains in electron transfer and redox reactions. These findings also suggest a model of adaptive evolution through proteome diversification and selection through modulation of translational fidelity. The results define H. pylori East Asian lineages and provide essential information for understanding their pathogenesis and designing drugs and therapies that target them.
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Affiliation(s)
- Mikihiko Kawai
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
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16
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Valas RE, Bourne PE. Save the tree of life or get lost in the woods. Biol Direct 2010; 5:44. [PMID: 20594329 PMCID: PMC2910001 DOI: 10.1186/1745-6150-5-44] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 07/01/2010] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The wealth of prokaryotic genomic data available has revealed that the histories of many genes are inconsistent, leading some to question the value of the tree of life hypothesis. It has been argued that a tree-like representation requires suppressing too much information, and that a more pluralistic approach is necessary for understanding prokaryotic evolution. We argue that trees may still be a useful representation for evolutionary histories in light of new data. RESULTS Genomic data alone can be highly misleading when trying to resolve the tree of life. We present evidence from protein abundance data sets that genomic conservation greatly underestimates functional conservation. Function follows more of a tree-like structure than genetic material, even in the presence of horizontal transfer. We argue that the tree of cells must be incorporated into any new synthesis in order to place horizontal transfers into their proper selective context. We also discuss the role data sources other than primary sequence can play in resolving the tree of cells. CONCLUSIONS The tree of life is alive, but not well. Construction of the tree of cells has been viewed as the end goal of the study of evolution, where in reality we need to consider it more of a starting point. We propose a duality where we must consider variation of genetic material in terms of networks and selection of cellular function in terms of trees. Otherwise one gets lost in the woods of neutral evolution.
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Affiliation(s)
- Ruben E Valas
- Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Philip E Bourne
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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17
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Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins. BMC Genomics 2010; 11:369. [PMID: 20537180 PMCID: PMC2890568 DOI: 10.1186/1471-2164-11-369] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 06/10/2010] [Indexed: 11/17/2022] Open
Abstract
Background Species of the family Vibrionaceae are ubiquitous in marine environments. Several of these species are important pathogens of humans and marine species. Evidence indicates that genetic exchange plays an important role in the emergence of new pathogenic strains within this family. Data from the sequenced genomes of strains in this family could show how the genes encoded by all these strains, known as the pangenome, are distributed. Information about the core, accessory and panproteome of this family can show how, for example, genes encoding virulence-associated proteins are distributed and help us understand how virulence emerges. Results We deduced the complete set of orthologs for eleven strains from this family. The core proteome consists of 1,882 orthologous groups, which is 28% of the 6,629 orthologous groups in this family. There were 4,411 accessory orthologous groups (i.e., proteins that occurred in from 2 to 10 proteomes) and 5,584 unique proteins (encoded once on only one of the eleven genomes). Proteins that have been associated with virulence in V. cholerae were widely distributed across the eleven genomes, but the majority was found only on the genomes of the two V. cholerae strains examined. Conclusions The proteomes are reflective of the differing evolutionary trajectories followed by different strains to similar phenotypes. The composition of the proteomes supports the notion that genetic exchange among species of the Vibrionaceae is widespread and that this exchange aids these species in adapting to their environments.
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18
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Alcaraz LD, Moreno-Hagelsieb G, Eguiarte LE, Souza V, Herrera-Estrella L, Olmedo G. Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC Genomics 2010; 11:332. [PMID: 20504335 PMCID: PMC2890564 DOI: 10.1186/1471-2164-11-332] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 05/26/2010] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus evolutionary relationships. By distinguishing between core and pan-genome, we determined the evolutionary and functional relationships of known Bacillus. RESULTS Our analysis is based upon twenty complete and draft Bacillus genomes, including a newly sequenced Bacillus isolate from an aquatic environment that we report for the first time here. Using a core genome, we were able to determine the phylogeny of known Bacilli, including aquatic strains whose position in the phylogenetic tree could not be unambiguously determined in the past. Using the pan-genome from the sequenced Bacillus, we identified functional differences, such as carbohydrate utilization and genes involved in signal transduction, which distinguished the taxonomic groups. We also assessed the genetic architecture of the defining traits of Bacillus, such as sporulation and competence, and showed that less than one third of the B. subtilis genes are conserved across other Bacilli. Most variation was shown to occur in genes that are needed to respond to environmental cues, suggesting that Bacilli have genetically specialized to allow for the occupation of diverse habitats and niches. CONCLUSIONS The aquatic Bacilli are defined here for the first time as a group through the phylogenetic analysis of 814 genes that comprise the core genome. Our data distinguished between genomic components, especially core vs. pan-genome to provide insight into phylogeny and function that would otherwise be difficult to achieve. A phylogeny may mask the diversity of functions, which we tried to uncover in our approach. The diversity of sporulation and competence genes across the Bacilli was unexpected based on previous studies of the B. subtilis model alone. The challenge of uncovering the novelties and variations among genes of the non-subtilis groups still remains. This task will be best accomplished by directing efforts toward understanding phylogenetic groups with similar ecological niches.
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Affiliation(s)
- Luis David Alcaraz
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN Campus Guanajuato, Guanajuato, México.
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Lefébure T, Stanhope MJ. Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res 2009; 19:1224-32. [PMID: 19304960 DOI: 10.1101/gr.089250.108] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human and animal enteric pathogens, with genome sequence data available for eight species. We estimate the Campylobacter core genome at 647 genes, with 92.5% of the nonrecombinant core genome loci under positive selection in at least one lineage and the same gene frequently under positive selection in multiple lineages. Tests are provided that reject recombination, saturation, and variation in codon usage bias as factors contributing to this high level of selection. We suggest this genome-wide adaptive evolution may result from a Red Queen macroevolutionary dynamic, in which species are involved in competition for resources within the mammalian and/or vertebrate gastrointestinal tract. Much reduced levels of positive selection evident in Streptococcus, as reported by the authors in an earlier work, may be a consequence of these taxa inhabiting less species-rich habitats, and more unique niches. Despite many common loci under positive selection in multiple Campylobacter lineages, we found no evidence for molecular adaptive convergence at the level of the same or adjacent codons, or even protein domains. Taken collectively, these results describe the diversification of a bacterial genus that involves pervasive natural selection pressure across virtually the entire genome, with this adaptation occurring in different ways in different lineages, despite the species tendency toward a common gastrointestinal habitat.
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Affiliation(s)
- Tristan Lefébure
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
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20
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Complete genome sequence of Macrococcus caseolyticus strain JCSCS5402, [corrected] reflecting the ancestral genome of the human-pathogenic staphylococci. J Bacteriol 2008; 191:1180-90. [PMID: 19074389 DOI: 10.1128/jb.01058-08] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We isolated the methicillin-resistant Macrococcus caseolyticus strain JCSC5402 from animal meat in a supermarket and determined its whole-genome nucleotide sequence. This is the first report on the genome analysis of a macrococcal species that is evolutionarily closely related to the human pathogens Staphylococcus aureus and Bacillus anthracis. The essential biological pathways of M. caseolyticus are similar to those of staphylococci. However, the species has a small chromosome (2.1 MB) and lacks many sugar and amino acid metabolism pathways and a plethora of virulence genes that are present in S. aureus. On the other hand, M. caseolyticus possesses a series of oxidative phosphorylation machineries that are closely related to those in the family Bacillaceae. We also discovered a probable primordial form of a Macrococcus methicillin resistance gene complex, mecIRAm, on one of the eight plasmids harbored by the M. caseolyticus strain. This is the first finding of a plasmid-encoding methicillin resistance gene. Macrococcus is considered to reflect the genome of ancestral bacteria before the speciation of staphylococcal species and may be closely associated with the origin of the methicillin resistance gene complex of the notorious human pathogen methicillin-resistant S. aureus.
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