1
|
Lau NS, Heng WL, Miswan N, Azami NA, Furusawa G. Comparative Genomic Analyses of the Genus Photobacterium Illuminate Biosynthetic Gene Clusters Associated with Antagonism. Int J Mol Sci 2022; 23:ijms23179712. [PMID: 36077108 PMCID: PMC9456166 DOI: 10.3390/ijms23179712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Photobacterium is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. Photobacterium sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 Photobacterium strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with P. galatheae, forming a distinct clade with P. halotolerans, P. salinisoli, and P. arenosum. The core genome of Photobacterium was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA–DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against Vibrio spp. Intriguingly, clustering based on BGCs profiles grouped P. galatheae, P. halotolerans, P. salinisoli, P. arenosum, and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich Photobacterium strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.
Collapse
|
2
|
The Evolution of a Specialized, Highly Virulent Fish Pathogen through Gene Loss and Acquisition of Host-Specific Survival Mechanisms. Appl Environ Microbiol 2022; 88:e0022222. [PMID: 35862683 PMCID: PMC9317898 DOI: 10.1128/aem.00222-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Photobacterium damselae comprises two subspecies, P. damselae subsp. damselae and P. damselae subsp. piscicida, that contrast remarkably despite their taxonomic relationship. The former is opportunistic and free-living but can cause disease in compromised individuals from a broad diversity of taxa, while the latter is a highly specialized, primary fish pathogen. Here, we employ new closed curated genome assemblies from Australia to estimate the global phylogenetic structure of the species P. damselae. We identify genes responsible for the shift from an opportunist to a host-adapted fish pathogen, potentially via an arthropod vector as fish-to-fish transmission was not achieved in repeated cohabitation challenges despite high virulence for Seriola lalandi. Acquisition of ShdA adhesin and of thiol peroxidase may have allowed the environmental, generalist ancestor to colonize zooplankton and to occasionally enter in fish host sentinel cells. As dependence on the host has increased, P. damselae has lost nonessential genes, such as those related to nitrite and sulfite reduction, urea degradation, a type 6 secretion system (T6SS) and several toxin-antitoxin (TA) systems. Similar to the evolution of Yersinia pestis, the loss of urease may be the crucial event that allowed the pathogen to stably colonize zooplankton vectors. Acquisition of host-specific genes, such as those required to form a sialic acid capsule, was likely necessary for the emergent P. damselae subsp. piscicida to become a highly specialized, facultative intracellular fish pathogen. Processes that have shaped P. damselae subsp. piscicida from subsp. damselae are similar to those underlying evolution of Yersinia pestis from Y. pseudotuberculosis. IMPORTANCEPhotobacterium damselae subsp. damselae is a ubiquitous marine bacterium and opportunistic pathogen of compromised hosts of diverse taxa. In contrast, its sister subspecies P. damselae subsp. piscicida (Pdp) is highly virulent in fish. Pdp has evolved from a single subclade of Pdd through gene loss and acquisition. We show that fish-to-fish transmission does not occur in repeated infection models in the primary host, Seriola lalandi, and present genomic evidence for vector-borne transmission, potentially via zooplankton. The broad genomic changes from generalist Pdd to specialist Pdp parallel those of the environmental opportunist Yersinia pseudotuberculosis to vector-borne plague bacterium Y. pestis and demonstrate that evolutionary processes in bacterial pathogens are universal between the terrestrial and marine biosphere.
Collapse
|
3
|
Park SY, Kim IH, Yu HJ, Paik HR, Son JS, Kim JH. Complete genome sequence of serotype 3 Streptococcus suis INT-01, isolated from a domestic pig in Korea. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2021; 63:662-665. [PMID: 34189513 PMCID: PMC8203990 DOI: 10.5187/jast.2021.e47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 12/05/2022]
Abstract
Streptococcus suis is a major pig pathogen causing severe
economic losses to the swine industry. This study aimed to analyze the genome of
S. suis strain INT-01 isolated from a domestic pig in
Korea. We found that the genome of strain INT-01 contains 2,092,054 bp, with a
guanine (G) + cytosine (C) content of 41.3%, and the capsular polysaccharide
synthesis locus of this strain is almost identical to that of serotype 3
S. suis strain 4961 isolated from China, suggesting that
these isolates can be classified as serotype 3. Genomic analyses revealed that
strain INT-01 is an extracellular protein factor
(epf)−/ muraminidase-released protein
(mrp)+/ suilysin
(sly)−S. suis, which is the most prevalent genotype in Korea, and
several virulence-related genes associated with the pathogenicity of S.
suis were also detected. The genomic information of strain INT-01
may provide important insights into the development of control strategies
against S. suis infections in Korea.
Collapse
Affiliation(s)
- Seon Young Park
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.,Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Korea
| | | | | | | | | | - Ji Hyung Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| |
Collapse
|
4
|
Characterization of oral and cloacal microbial communities in cold-stunned Kemp's ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation. PLoS One 2021; 16:e0252086. [PMID: 34043685 PMCID: PMC8159006 DOI: 10.1371/journal.pone.0252086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
Microbial communities of animals play a role in health and disease, including immunocompromised conditions. In the northeastern United States, cold-stunning events often cause endangered Kemp's ridley turtles (Lepidochelys kempii) to become stranded on beaches in autumn. These sea turtles are admitted to rehabilitation facilities when rescued alive and are presumed immunocompromised secondary to hypothermia. To better understand the role that microbes play in the health of cold-stunned sea turtles, we characterized the oral and cloacal microbiome from Kemp's ridley turtles at multiple timepoints during rehabilitation, from admission to pre-release, by using Illumina sequencing to analyze the 16S rRNA gene. Microbial communities were distinct between body sites and among turtles that survived and those that died. We found that clinical parameters such as presence of pneumonia or values for various blood analytes did not correlate with oral or cloacal microbial community composition. We also investigated the effect of antibiotics on the microbiome during rehabilitation and prior to release and found that the type of antibiotic altered the microbial community composition, yet overall taxonomic diversity remained the same. The microbiome of cold-stunned Kemp's ridley turtles gradually changed through the course of rehabilitation with environment, antibiotics, and disease status all playing a role in those changes and ultimately the release status of the turtles.
Collapse
|
5
|
Kim SW, Han SJ, Lee YR, Kim BY, Park SC. First report of a Risso’s dolphin (
Grampus griseus
) stranded in Jeju Island, Republic of Korea: findings from necropsy, histopathology and microbiome analysis. VETERINARY RECORD CASE REPORTS 2019. [DOI: 10.1136/vetreccr-2019-000860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Sang Wha Kim
- College of Veterinary MedicineSeoul National UniversitySeoulKorea
| | - Se Jin Han
- College of Veterinary MedicineSeoul National UniversitySeoulKorea
| | | | - Byung Yeop Kim
- Department of Marine Industry and Maritime PoliceCollege of Ocean ScienceJeju National UniversityJeju‐doKorea
| | - Se Chang Park
- College of Veterinary MedicineSeoul National UniversitySeoulKorea
| |
Collapse
|
6
|
Yu Y, Zhang Z, Wang Y, Liao M, Rong X, Li B, Wang K, Chen J, Zhang H. Complete Genome Sequence of Photobacterium damselae Subsp. damselae Strain SSPD1601 Isolated from Deep-Sea Cage-Cultured Sebastes schlegelii with Septic Skin Ulcer. Int J Genomics 2019; 2019:4242653. [PMID: 31093490 PMCID: PMC6481104 DOI: 10.1155/2019/4242653] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/16/2019] [Accepted: 02/20/2019] [Indexed: 11/21/2022] Open
Abstract
Photobacterium damselae subsp. damselae (PDD) is a Gram-negative bacterium that can infect a variety of aquatic organisms and humans. Based on an epidemiological investigation conducted over the past 3 years, PDD is one of the most important pathogens causing septic skin ulcer in deep-sea cage-cultured Sebastes schlegelii in the Huang-Bohai Sea area and present throughout the year with high abundance. To further understand the pathogenicity of this species, the pathogenic properties and genome of PDD strain SSPD1601 were analyzed. The results revealed that PDD strain SSPD1601 is a rod-shaped cell with a single polar flagellum, and the clinical symptoms were replicated during artificial infection. The SSPD1601 genome consists of two chromosomes and two plasmids, totaling 4,252,294 bp with 3,751 coding sequences (CDSs), 196 tRNA genes, and 47 rRNA genes. Common virulence factors including flagellin, Fur, RstB, hcpA, OMPs, htpB-Hsp60, VasK, and vgrG were found in strain SSPD1601. Furthermore, SSPD1601 is a pPHDD1-negative strain containing the hemolysin gene hlyAch and three putative hemolysins (emrA, yoaF, and VPA0226), which are likely responsible for the pathogenicity of SSPD1601. The phylogenetic analysis revealed SSPD1601 to be most closely related to Phdp Wu-1. In addition, the antibiotic resistance phenotype indicated that SSPD1601 was not sensitive to ceftazidime, pipemidic, streptomycin, cefalexin, bacitracin, cefoperazone sodium, acetylspiramycin, clarithromycin, amikacin, gentamycin, kanamycin, oxacillin, ampicillin, and trimethoprim-sulfamethoxazole, but only the bacitracin resistance gene bacA was detected based on Antibiotic Resistance Genes Database. These results expand our understanding of PDD, setting the stage for further studies of its pathogenesis and disease prevention.
Collapse
Affiliation(s)
- Yongxiang Yu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao 266071, China
| | - Zheng Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yingeng Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Meijie Liao
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaojun Rong
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Bin Li
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao 266071, China
| | - Kai Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao 266071, China
| | - Jing Chen
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao 266071, China
| | - Hao Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao 266071, China
| |
Collapse
|
7
|
First report of the complete mitochondrial genome and phylogenetic analysis of Fraser’s dolphin Lagenodelphis hosei (Cetacea: Delphinidae). CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-017-0964-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
8
|
Park SY, Lim SR, Son JS, Kim HK, Yoon SW, Jeong DG, Lee MS, Lee JR, Lee DH, Kim JH. Complete Genome Sequence of Aeromonas rivipollensis KN-Mc-11N1, Isolated from a Wild Nutria (Myocastor coypus) in South Korea. Microbiol Resour Announc 2018; 7:e00907-18. [PMID: 30533878 PMCID: PMC6256423 DOI: 10.1128/mra.00907-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/06/2018] [Indexed: 11/20/2022] Open
Abstract
We report here the complete genome sequence of Aeromonas rivipollensis KN-Mc-11N1, which was isolated from a wild nutria (Myocastor coypus) in South Korea. Genomic analysis indicated that A. rivipollensis may have zoonotic potential similar to that of other aeromonads, and nutria could be one of the sources of transmission of zoonotic pathogens to humans.
Collapse
Affiliation(s)
- Seon Young Park
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Animal Science, College of Life Sciences, Pusan National University, Miryang, Republic of Korea
| | - Se Ra Lim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Bio-analytical Science Division, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jee Soo Son
- iNtRON Biotechnology, Inc., Seongnam, Republic of Korea
| | - Hye Kwon Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sun-Woo Yoon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Bio-analytical Science Division, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Dae Gwin Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Bio-analytical Science Division, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Moo-Seung Lee
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jung Ro Lee
- Division of Ecological Conservation Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Do-Hun Lee
- Division of Ecological Conservation Research, National Institute of Ecology, Seocheon, Republic of Korea
| | - Ji Hyung Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| |
Collapse
|
9
|
LEE K, KIM HK, PARK SK, SOHN H, CHO Y, CHOI YM, JEONG DG, KIM JH. First report of the occurrence and whole-genome characterization of Edwardsiella tarda in the false killer whale (Pseudorca crassidens). J Vet Med Sci 2018; 80:1041-1046. [PMID: 29695679 PMCID: PMC6021894 DOI: 10.1292/jvms.17-0590] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 04/16/2018] [Indexed: 01/22/2023] Open
Abstract
Although several Edwardsiella tarda infections have been reported, its pathogenic role in marine mammals has not been investigated at the genome level. We investigated the genome of E. tarda strain KC-Pc-HB1, isolated from the false killer whale (Pseudorca crassidens) found bycaught in South Korea. The obtained genome was similar to that of human pathogenic E. tarda strains, but distinct from other Edwardsiella species. Although type III and VI secretion systems, which are essential for the virulence of other Edwardsiella species, were absent, several virulence-related genes involved in the pathogenesis of E. tarda were found in the genome. These results provide important insights into the E. tarda infecting marine mammals and give valuable information on potential virulence factors in this pathogen.
Collapse
Affiliation(s)
- Kyunglee LEE
- Cetacean Research Institute (CRI), National Institute of
Fisheries Science (NIFS), Ulsan 44780, Republic of Korea
| | - Hye Kwon KIM
- Infectious Disease Research Center, Korea Research Institute
of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sung-Kyun PARK
- Infectious Disease Research Center, Korea Research Institute
of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Hawsun SOHN
- Cetacean Research Institute (CRI), National Institute of
Fisheries Science (NIFS), Ulsan 44780, Republic of Korea
| | - Yuna CHO
- Cetacean Research Institute (CRI), National Institute of
Fisheries Science (NIFS), Ulsan 44780, Republic of Korea
| | - Young-Min CHOI
- Cetacean Research Institute (CRI), National Institute of
Fisheries Science (NIFS), Ulsan 44780, Republic of Korea
| | - Dae Gwin JEONG
- Infectious Disease Research Center, Korea Research Institute
of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Ji Hyung KIM
- Infectious Disease Research Center, Korea Research Institute
of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| |
Collapse
|
10
|
Characterization of the complete mitochondrial genome of Stejneger’s beaked whale, Mesoplodon stejnegeri (Cetacea: Ziphiidae). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0943-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
11
|
Determination of the haplotype and complete mitochondrial genome of the leatherback turtle Dermochelys coriacea (Testudines: Dermochelyidae) found in the vicinity of Korea. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0905-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|