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Jiang C, Kasai H, Mino S, Romalde JL, Sawabe T. The pan‐genome of Splendidus clade species in the family
Vibrionaceae
: insights into evolution, adaptation, and pathogenicity. Environ Microbiol 2022; 24:4587-4606. [DOI: 10.1111/1462-2920.16209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
| | - Hisae Kasai
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
| | - Jesús L. Romalde
- Departamento de Microbiología y Parasitología, CRETUS & CIBUS‐Facultad de Biología. Universidade de Santiago de Compostela Spain
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
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Ancestral gene acquisition as the key to virulence potential in environmental Vibrio populations. ISME JOURNAL 2018; 12:2954-2966. [PMID: 30072747 PMCID: PMC6246604 DOI: 10.1038/s41396-018-0245-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 06/30/2018] [Accepted: 07/06/2018] [Indexed: 11/08/2022]
Abstract
Diseases of marine animals caused by bacteria of the genus Vibrio are on the rise worldwide. Understanding the eco-evolutionary dynamics of these infectious agents is important for predicting and managing these diseases. Yet, compared to Vibrio infecting humans, knowledge of their role as animal pathogens is scarce. Here we ask how widespread is virulence among ecologically differentiated Vibrio populations, and what is the nature and frequency of virulence genes within these populations? We use a combination of population genomics and molecular genetics to assay hundreds of Vibrio strains for their virulence in the oyster Crassostrea gigas, a unique animal model that allows high-throughput infection assays. We show that within the diverse Splendidus clade, virulence represents an ancestral trait but has been lost from several populations. Two loci are necessary for virulence, the first being widely distributed across the Splendidus clade and consisting of an exported conserved protein (R5.7). The second is a MARTX toxin cluster, which only occurs within V. splendidus and is for the first time associated with virulence in marine invertebrates. Varying frequencies of both loci among populations indicate different selective pressures and alternative ecological roles, based on which we suggest strategies for epidemiological surveys.
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Wei W, Xiong L, Ye YN, Du MZ, Gao YZ, Zhang KY, Jin YT, Yang Z, Wong PC, Lau SKP, Kan B, Zhu J, Woo PCY, Guo FB. Mutation Landscape of Base Substitutions, Duplications, and Deletions in the Representative Current Cholera Pandemic Strain. Genome Biol Evol 2018; 10:2072-2085. [PMID: 30060177 PMCID: PMC6105331 DOI: 10.1093/gbe/evy151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 01/03/2023] Open
Abstract
Pandemic cholera is a major concern for public health because of its high mortality and morbidity. Mutation accumulation (MA) experiments were performed on a representative strain of the current cholera pandemic. Although the base-pair substitution mutation rates in Vibrio cholerae (1.24 × 10-10 per site per generation for wild-type lines and 3.29 × 10-8 for mismatch repair deficient lines) are lower than that previously reported in other bacteria using MA analysis, we discovered specific high rates (8.31 × 10-8 site/generation for wild-type lines and 1.82 × 10-6 for mismatch repair deficient lines) of base duplication or deletion driven by large-scale copy number variations (CNVs). These duplication-deletions are located in two pathogenic islands, IMEX and the large integron island. Each element of these islands has discrepant rate in rapid integration and excision, which provides clues to the pandemicity evolution of V. cholerae. These results also suggest that large-scale structural variants such as CNVs can accumulate rapidly during short-term evolution. Mismatch repair deficient lines exhibit a significantly increased mutation rate in the larger chromosome (Chr1) at specific regions, and this pattern is not observed in wild-type lines. We propose that the high frequency of GATC sites in Chr1 improves the efficiency of MMR, resulting in similar rates of mutation in the wild-type condition. In addition, different mutation rates and spectra were observed in the MA lines under distinct growth conditions, including minimal media, rich media and antibiotic treatments.
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Affiliation(s)
- Wen Wei
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- School of Life Sciences, Chongqing University, China
| | - Lifeng Xiong
- Department of Microbiology, Research Centre of Infection and Immunology, State Key Laboratory of Emerging Infectious Diseases, and Carol Yu Centre for Infection, The University of Hong Kong, China
| | - Yuan-Nong Ye
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- Bioinformatics and Biomedical Bigdata Mining Laboratory, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Meng-Ze Du
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yi-Zhou Gao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Kai-Yue Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan-Ting Jin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Po-Chun Wong
- Department of Microbiology, Research Centre of Infection and Immunology, State Key Laboratory of Emerging Infectious Diseases, and Carol Yu Centre for Infection, The University of Hong Kong, China
| | - Susanna K P Lau
- Department of Microbiology, Research Centre of Infection and Immunology, State Key Laboratory of Emerging Infectious Diseases, and Carol Yu Centre for Infection, The University of Hong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, China
| | - Biao Kan
- National Institute for Communicable Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
| | - Jun Zhu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Patrick C Y Woo
- Department of Microbiology, Research Centre of Infection and Immunology, State Key Laboratory of Emerging Infectious Diseases, and Carol Yu Centre for Infection, The University of Hong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, China
| | - Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
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Characterization of N-Acyl Homoserine Lactones in Vibrio tasmaniensis LGP32 by a Biosensor-Based UHPLC-HRMS/MS Method. SENSORS 2017; 17:s17040906. [PMID: 28425948 PMCID: PMC5426830 DOI: 10.3390/s17040906] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 04/14/2017] [Accepted: 04/17/2017] [Indexed: 12/13/2022]
Abstract
Since the discovery of quorum sensing (QS) in the 1970s, many studies have demonstrated that Vibrio species coordinate activities such as biofilm formation, virulence, pathogenesis, and bioluminescence, through a large group of molecules called N-acyl homoserine lactones (AHLs). However, despite the extensive knowledge on the involved molecules and the biological processes controlled by QS in a few selected Vibrio strains, less is known about the overall diversity of AHLs produced by a broader range of environmental strains. To investigate the prevalence of QS capability of Vibrio environmental strains we analyzed 87 Vibrio spp. strains from the Banyuls Bacterial Culture Collection (WDCM911) for their ability to produce AHLs. This screening was based on three biosensors, which cover a large spectrum of AHLs, and revealed that only 9% of the screened isolates produced AHLs in the defined experimental conditions. Among these AHL-producing strains, Vibrio tasmaniensis LGP32 is a well-known pathogen of bivalves. We further analyzed the diversity of AHLs produced by this strain using a sensitive bioguided UHPLC-HRMS/MS approach (Ultra-High-Performance Liquid Chromatography followed by High-Resolution tandem Mass Spectrometry) and we identified C10-HSL, OH-C12-HSL, oxo-C12-HSL and C14:1-HSL as QS molecules. This is the first report that documents the production of AHL by Vibrio tasmaniensis LGP32.
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Dillon MM, Sung W, Sebra R, Lynch M, Cooper VS. Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri. Mol Biol Evol 2016; 34:93-109. [PMID: 27744412 PMCID: PMC5854121 DOI: 10.1093/molbev/msw224] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of two Vibrio species, the low-%GC squid symbiont V. fischeri and the pathogen V. cholerae, collected under conditions that greatly minimize the efficiency of natural selection. In apparent contrast to their high diversity in nature, both wild-type V. fischeri and V. cholerae have among the lowest rates for base-substitution mutations (bpsms) and insertion-deletion mutations (indels) that have been measured, below 10-3/genome/generation. Vibrio fischeri and V. cholerae have distinct mutation spectra, but both are AT-biased and produce a surprising number of multi-nucleotide indels. Furthermore, the loss of a functional MMR system caused the mutation spectra of these species to converge, implying that the MMR system itself contributes to species-specific mutation patterns. Bpsm and indel rates varied among genome regions, but do not explain the more rapid evolutionary rates of genes on chromosome 2, which likely result from weaker purifying selection. More generally, the very low mutation rates of Vibrio species correlate inversely with their immense population sizes and suggest that selection may not only have maximized replication fidelity but also optimized other polygenic traits relative to the constraints of genetic drift.
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Affiliation(s)
- Marcus M Dillon
- Microbiology Graduate Program, University of New Hampshire, Durham, NH
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, Charlotte, NC.,Department of Biology, Indiana University, Bloomington, IN
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN
| | - Vaughn S Cooper
- Microbiology Graduate Program, University of New Hampshire, Durham, NH .,Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Sawabe T, Ogura Y, Matsumura Y, Feng G, Amin AR, Mino S, Nakagawa S, Sawabe T, Kumar R, Fukui Y, Satomi M, Matsushima R, Thompson FL, Gomez-Gil B, Christen R, Maruyama F, Kurokawa K, Hayashi T. Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Front Microbiol 2013; 4:414. [PMID: 24409173 PMCID: PMC3873509 DOI: 10.3389/fmicb.2013.00414] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/16/2013] [Indexed: 12/13/2022] Open
Abstract
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
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Affiliation(s)
- Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Yoshitoshi Ogura
- Division of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki Miyazaki, Japan
| | - Yuta Matsumura
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Gao Feng
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Akm Rohul Amin
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Satoshi Nakagawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Toko Sawabe
- Department of Food and Nutrition, Hakodate Junior College Hakodate, Japan
| | - Ramesh Kumar
- National Institute for Interdisciplinary Science and Technology (CSIR) Kerala, India
| | - Yohei Fukui
- National Research Institute of Fisheries Science, Fisheries Research Agency Yokohama, Japan
| | - Masataka Satomi
- National Research Institute of Fisheries Science, Fisheries Research Agency Yokohama, Japan
| | - Ryoji Matsushima
- National Research Institute of Fisheries Science, Fisheries Research Agency Yokohama, Japan
| | - Fabiano L Thompson
- Department of Genetics, Center of Health Sciences, Federal University of Rio de Janeiro (UFRS) Rio de Janeiro, Brazil
| | | | - Richard Christen
- CNRS UMR 7138, Systématique-Adaptation-Evolution Nice, France ; Systématique-Adaptation-Evolution, Université de Nice-Sophia Antipolis Nice, France
| | - Fumito Maruyama
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University Tokyo, Japan
| | - Ken Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology Tokyo, Japan
| | - Tetsuya Hayashi
- Division of Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki Miyazaki, Japan
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Okabe S, Oshiki M, Kamagata Y, Yamaguchi N, Toyofuku M, Yawata Y, Tashiro Y, Nomura N, Ohta H, Ohkuma M, Hiraishi A, Minamisawa K. A great leap forward in microbial ecology. Microbes Environ 2011; 25:230-40. [PMID: 21576878 DOI: 10.1264/jsme2.me10178] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.
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Affiliation(s)
- Satoshi Okabe
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060–8628, Japan.
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Nakamura H, Narihiro T, Tsuruoka N, Mochimaru H, Matsumoto R, Tanabe Y, Hagiya K, Ikeba K, Maruyama A, Hanada S. Evaluation of the aflatoxin biosynthetic genes for identification of the Aspergillus section Flavi. Microbes Environ 2011; 26:367-9. [PMID: 21791886 DOI: 10.1264/jsme2.me11201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several fungi in the Aspergillus section Flavi have been widely used for fermentative food production, while some related species in the section are known to produce mycotoxin(s) that causes mycotic diseases. Common evolutionary markers, such as rRNA gene sequences and their internal transcribed spacers, cannot differentiate these non-aflatoxin-producing species from aflatoxin producers. Multilocus sequence analysis (MLSA) based on four aflatoxin biosynthetic genes encoding aflR, aflT, norA, and vbs, which are more variable nucleotide sequences than rRNA genes, can distinguish safe koji molds, A. oryzae and A. sojae, from aflatoxin-producing strains, A. flavus, A. toxicarius and A. parasiticus.
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Affiliation(s)
- Hitomi Nakamura
- International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
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Thompson FL, Neto AA, Santos EDO, Izutsu K, Iida T. Effect of N-acetyl-D-glucosamine on gene expression in Vibrio parahaemolyticus. Microbes Environ 2011; 26:61-6. [PMID: 21487204 DOI: 10.1264/jsme2.me10152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyzed the effect of N-acetyl-D-glucosamine (GlcNAc) on gene expression in the marine bacterium Vibrio parahaemolyticus. The total number of genes whose expression was induced and repressed genes in the presence of GlcNAc was 81 and 55, respectively. The induced genes encoded a variety of products, including proteins related to energy metabolism (e.g. GlcNAc and chitin utilization), transport, central metabolism and chemotaxis, hypothetical proteins, mannose-sensitive hemagglutinin pilus (MSHA), and a PilA protein, whereas the repressed genes encoded mainly hypothetical proteins. GlcNAc appears to influence directly or indirectly a variety of cellular processes, including energy metabolism, chitin utilization, competence, biofilm formation and pathogenicity. GlcNAc, one of the most abundant aminosugars in the oceans, is used by V. parahaemolyticus as an energy source and affects the cellular functioning of this marine bacterium.
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Affiliation(s)
- Fabiano L Thompson
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Brazil.
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