1
|
Jiao JY, Abdugheni R, Zhang DF, Ahmed I, Ali M, Chuvochina M, Dedysh SN, Dong X, Göker M, Hedlund BP, Hugenholtz P, Jangid K, Liu SJ, Moore ERB, Narsing Rao MP, Oren A, Rossello-Mora R, Rekadwad BN, Salam N, Shu W, Sutcliffe IC, Teo WFA, Trujillo ME, Venter SN, Whitman WB, Zhao G, Li WJ. Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era. Natl Sci Rev 2024; 11:nwae168. [PMID: 39071100 PMCID: PMC11275469 DOI: 10.1093/nsr/nwae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 07/30/2024] Open
Abstract
Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.
Collapse
Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, China
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad 45500, Pakistan
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig D-38124, Germany
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Kamlesh Jangid
- Bioenergy Group, MACS Collection of Microorganisms, Agharkar Research Institute, Pune 411004, India
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Edward R B Moore
- Department of Infectious Disease, Institute for Biomedicine, and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40234, Sweden
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Talca 3460000, Chile
| | - Aharon Oren
- The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles 070190, Spain
| | - Bhagwan Narayan Rekadwad
- MicrobeAI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Nimaichand Salam
- National Agri-Food Biotechnology Institute, Knowledge City, Mohali 140306, India
| | - Wensheng Shu
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Iain C Sutcliffe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Wee Fei Aaron Teo
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca 37008, Spain
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Guoping Zhao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| |
Collapse
|
2
|
Lee SD, Yang HL, Kim IS. Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium. Front Microbiol 2023; 14:1299950. [PMID: 38164402 PMCID: PMC10757982 DOI: 10.3389/fmicb.2023.1299950] [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: 09/23/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the "Microbacterium agarici clade", with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.
Collapse
Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - Hong Lim Yang
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon, Republic of Korea
- BioPS Co., Ltd., Daejeon, Republic of Korea
| |
Collapse
|
3
|
Azizan A, Alfaro AC, Jaramillo D, Venter L, Young T, Frost E, Lee K, Van Nguyen T, Kitundu E, Archer SDJ, Ericson JA, Foxwell J, Quinn O, Ragg NLC. Pathogenicity and virulence of bacterial strains associated with summer mortality in marine mussels (Perna canaliculus). FEMS Microbiol Ecol 2022; 98:6855225. [PMID: 36449667 DOI: 10.1093/femsec/fiac140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/09/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
The occurrence of pathogenic bacteria has emerged as a plausible key component of summer mortalities in mussels. In the current research, four bacterial isolates retrieved from moribund Greenshell࣪ mussels, Perna canaliculus, from a previous summer mortality event, were tentatively identified as Vibrio and Photobacterium species using morpho-biochemical characterization and MALDI-TOF MS and confirmed as V. celticus, P. swingsii, P. rosenbergii, and P. proteolyticum using whole genome sequencing. These isolates were utilized in a laboratory challenge where mussels were injected with cell concentrations ranging from 105 to 109 CFU/mussel. Of the investigated isolates, P. swingsii induced the highest mortality. Additionally, results from quantitative polymerase chain reaction analysis, focusing on known virulence genes were detected in all isolates grown under laboratory conditions. Photobacterium rosenbergii and P. swingsii showed the highest expression levels of these virulence determinants. These results indicate that Photobacterium spp. could be a significant pathogen of P. canaliculus, with possible importance during summer mortality events. By implementing screening methods to detect and monitor Photobacterium concentrations in farmed mussel populations, a better understanding of the host-pathogen relationship can be obtained, aiding the development of a resilient industry in a changing environment.
Collapse
Affiliation(s)
- Awanis Azizan
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Diana Jaramillo
- Animal Health Laboratory, Ministry for Primary Industries, New Zealand PO Box 2526, Wellington 6140, New Zealand
| | - Leonie Venter
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.,Centre for Biomedical & Chemical Sciences, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Emily Frost
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Kevin Lee
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Thao Van Nguyen
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.,NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Eileen Kitundu
- Department of Food Sciences and Microbiology, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Stephen D J Archer
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Jessica A Ericson
- Aquaculture Department, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Jonathan Foxwell
- Animal Health Laboratory, Ministry for Primary Industries, New Zealand PO Box 2526, Wellington 6140, New Zealand
| | - Oliver Quinn
- Animal Health Laboratory, Ministry for Primary Industries, New Zealand PO Box 2526, Wellington 6140, New Zealand
| | - Norman L C Ragg
- Aquaculture Department, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| |
Collapse
|
4
|
Montero-Calasanz MDC, Yaramis A, Rohde M, Schumann P, Klenk HP, Meier-Kolthoff JP. Genotype-phenotype correlations within the Geodermatophilaceae. Front Microbiol 2022; 13:975365. [PMID: 36439792 PMCID: PMC9686282 DOI: 10.3389/fmicb.2022.975365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.
Collapse
Affiliation(s)
- Maria del Carmen Montero-Calasanz
- IFAPA Las Torres-Andalusian Institute of Agricultural and Fisheries Research and Training, Junta de Andalucía, Seville, Spain,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom,*Correspondence: Maria del Carmen Montero-Calasanz,
| | - Adnan Yaramis
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Manfred Rohde
- Central Facility for Microscopy, HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jan P. Meier-Kolthoff
- Department Bioinformatics and Databases, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|
5
|
de Azevedo GPR, Mattsson HK, Tonon LAC, Arruda T, Salazar V, Bielinski V, Chagas F, Tschoeke DA, Thompson CC, Thompson FL. Vibrio fluminensis sp. nov. isolated from the skin of Southern Atlantic sharpnose-pufferfish (Canthigaster figueiredoi). Arch Microbiol 2022; 204:664. [DOI: 10.1007/s00203-022-03266-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 11/28/2022]
|
6
|
Doyle DA, Smith PR, Lawson PA, Tanner RS. Clostridium muellerianum sp. nov., a carbon monoxide-oxidizing acetogen isolated from old hay. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005297] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An acid/alcohol-producing, Gram-stain-positive, obligately anaerobic, rod-shaped, non-motile, non-spore forming acetogen, designated as strain P21T, was isolated from old hay after enrichment with CO as the substrate. Spores not observed even after prolonged incubation (30 days). Phylogenetic analysis of the 16S rRNA gene sequence of strain P21T showed it was closely related to
Clostridium carboxidivorans
DSM 15243T (97.9%),
Clostridium scatologenes
DSM 757T (97.7 %) and
Clostridium drakei
DSM 12750T (97.7 %). The genome is 5.6 Mb and the G+C content is 29.4 mol%. Average nucleotide identity between strain P21T,
C. carboxidivorans
,
C. scatologenes
and
C. drakei
was 87.1, 86.4, 86.4 %, respectively. Strain P21T grew on CO:CO2, H2:CO2, l-arabinose, ribose, xylose, fructose, galactose, glucose, lactose, mannose, cellobiose, sucrose, cellulose, starch, pyruvate, choline, glutamate, histidine, serine, threonine and casamino acids. End products of metabolism were acetate, butyrate, caproate, ethanol and hexanol. Dominant cellular fatty acids (>10 %) were C16 : 0 (41.5 %), C16 : 1 ω7c/C16 : 1 ω6c (10.0 %), and a summed feature containing cyclo C17 : 1/C18 : 0 (17.3 %). Based on the phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain P21T represents a new species in the genus
Clostridium
, for which the name Clostridium muellerianum sp. nov. is proposed. The type strain is P21T (=DSM 111390T=NCIMB 15261T).
Collapse
Affiliation(s)
- D. Annie Doyle
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Parker R. Smith
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Ralph S. Tanner
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| |
Collapse
|
7
|
Hunter KC, Lawson PA, Dowd SE, McLaughlin RW. Clostridium chrysemydis sp. nov., isolated from the faecal material of a painted turtle. Int J Syst Evol Microbiol 2021; 71. [PMID: 34569920 DOI: 10.1099/ijsem.0.005023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strict anaerobic, Gram-stain-positive rod-shaped bacterium, designated PTT, was isolated from the faecal material of a painted turtle (Chrysemys picta). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to Clostridium sensu stricto with the highest sequence similarities to Clostridium moniliforme (97.4 %), Clostridium sardiniense (97.2 %) and the misclassified organism Eubacterium multiforme (97.1 %). The predominant cellular fatty acids of strain PTT were C14 : 0, C16 : 0 and an unidentified product with an equivalent chain length of 14.969. The G+C content determined from the genome was 28.8 mol%. The fermentation end products from glucose were acetate and butyrate with no alcohols detected and trace amounts of CO2 and H2 also detected; no respiratory quinones were detected. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus Clostridium for which the name Clostridium chrysemydis sp. nov. is proposed. The type strain is strain PTT (=CCUG 74180T=ATCC TSD-219T).
Collapse
Affiliation(s)
- Kathryn C Hunter
- General Studies, Gateway Technical College, Kenosha WI 53144, USA
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK 73019, USA
| | - Scot E Dowd
- MR DNA (Molecular Research LP), Shallowater, TX, USA
| | - R W McLaughlin
- General Studies, Gateway Technical College, Kenosha WI 53144, USA
| |
Collapse
|
8
|
Fotedar R, Sankaranarayanan K, Caldwell ME, Zeyara A, Al Malki A, Kaul R, Al Shamari H, Ali M, Al Marri M, Lawson PA. Reclassification of Facklamia ignava, Facklamia sourekii and Facklamia tabacinasalis as Falseniella ignava gen. nov., comb. nov., Hutsoniella sourekii gen. nov., comb. nov., and Ruoffia tabacinasalis gen. nov., comb. nov., and description of Ruoffia halotolerans sp. nov., isolated from hypersaline Inland Sea of Qatar. Antonie van Leeuwenhoek 2021; 114:1181-1193. [PMID: 34181136 DOI: 10.1007/s10482-021-01587-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/24/2021] [Indexed: 11/24/2022]
Abstract
A Gram-stain-positive, non-pigmented, coccus-shaped, facultatively anaerobic and α-hemolytic bacterium designated as INB8T was isolated from a hypersaline marine water sample collected at the Inland Sea of Qatar. The isolate was able to grow at 25-40 °C (optimum, 30 °C), at pH 5-11 and with 2-8% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain INB8T was placed within the family Aerococcaceae with the highest sequence similarity to Facklamia tabacinasalis CCUG 30090T (99.5%), followed by Facklamia hominis CCUG 36813T (93.9%), Facklamia sourekii Y17312T (93.8%), Facklamia ignava CCUG 37419T (93.6%), Facklamia miroungae CCUG 42728T (93.5%), Suicoccus acidiformans ZY16052T (93.5%), Facklamia languida CCUG 37842T (93.2%), Ignavigranum ruoffiae (93.1%), and Dolosicoccus paucivorans DSM 15742T (90.8%). Average nucleotide identity and digital DNA-DNA hybridization values between strain INB8T and F. tabacinasalis CCUG 30090T were determined to be 94.5% and 58.9% respectively, confirming strain INB8T represents a novel species. The major fatty acids were C14:0, C16:0, C18:0 and C18:1 ω9c. The G + C content of strain INB8T determined from the genome was 36.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic information, it is proposed that Facklamia tabacinasalis should be reclassified as Ruoffia tabacinasalis, Facklamia ignava be reclassified as Falseniella ignava, and Facklamia sourekii be reclassified Hutsoniella sourekii. It is further proposed that strain INB8T should be classified as a species of the genus Ruoffia for which the name Ruoffia halotolerans sp. nov. is proposed. The type strain is INB8T (= LMG 30291T = CCUG 70701T = QCC/B60/17T).
Collapse
Affiliation(s)
- Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, Qatar.
| | - Krithivasan Sankaranarayanan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA
| | - Matthew E Caldwell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Aisha Zeyara
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, Qatar
| | - Amina Al Malki
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, Qatar
| | - Ridhima Kaul
- Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Hamad Al Shamari
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, Qatar
| | - Mohammad Ali
- Equine Veterinary Medical Centre, A Member of Qatar Foundation, Al Rayan, Qatar
| | - Masoud Al Marri
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, Qatar
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| |
Collapse
|
9
|
Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov. Front Microbiol 2021; 12:683109. [PMID: 34248901 PMCID: PMC8267831 DOI: 10.3389/fmicb.2021.683109] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.
Collapse
Affiliation(s)
- Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University Singapore, Singapore, Singapore
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
10
|
Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. mSystems 2020; 5:5/5/e00491-20. [PMID: 32900868 PMCID: PMC7483508 DOI: 10.1128/msystems.00491-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Most studies proposing new strategies to manage and treat infections have been largely focused on identifying druggable targets that can inhibit a pathogen's growth when it is the single cause of infection. In vivo, however, infections can be caused by multiple species. This is important to take into account when attempting to develop or use current antibacterials since their efficacy can change significantly between single infections and coinfections. In this study, we used genome-scale metabolic models (GEMs) to interrogate the growth capabilities of Vibrio cholerae in single infections and coinfections with enterotoxigenic E. coli (ETEC), which cooccur in a large fraction of diarrheagenic patients. Coinfection model predictions showed that V. cholerae growth capabilities are enhanced in the presence of ETEC relative to V. cholerae single infection, through cross-fed metabolites made available to V. cholerae by ETEC. In vitro, cocultures of the two enteric pathogens further confirmed model predictions showing an increased growth of V. cholerae in coculture relative to V. cholerae single cultures while ETEC growth was suppressed. Dual RNAseq analysis of the cocultures also confirmed that the transcriptome of V. cholerae was distinct during coinfection compared to single-infection scenarios where processes related to metabolism were significantly perturbed. Further, in silico gene-knockout simulations uncovered discrepancies in gene essentiality for V. cholerae growth between single infections and coinfections. Integrative model-guided analysis thus identified druggable targets that would be critical for V. cholerae growth in both single infections and coinfections; thus, designing inhibitors against those targets would provide a broader spectrum of coverage against cholera infections. Gene essentiality is altered during polymicrobial infections. Nevertheless, most studies rely on single-species infections to assess pathogen gene essentiality. Here, we use genome-scale metabolic models (GEMs) to explore the effect of coinfection of the diarrheagenic pathogen Vibrio cholerae with another enteric pathogen, enterotoxigenic Escherichia coli (ETEC). Model predictions showed that V. cholerae metabolic capabilities were increased due to ample cross-feeding opportunities enabled by ETEC. This is in line with increased severity of cholera symptoms known to occur in patients with dual infections by the two pathogens. In vitro coculture systems confirmed that V. cholerae growth is enhanced in cocultures relative to single cultures. Further, expression levels of several V. cholerae metabolic genes were significantly perturbed as shown by dual RNA sequencing (RNAseq) analysis of its cocultures with different ETEC strains. A decrease in ETEC growth was also observed, probably mediated by nonmetabolic factors. Single gene essentiality analysis predicted conditionally independent genes that are essential for the pathogen’s growth in both single-infection and coinfection scenarios. Our results reveal growth differences that are of relevance to drug targeting and efficiency in polymicrobial infections. IMPORTANCE Most studies proposing new strategies to manage and treat infections have been largely focused on identifying druggable targets that can inhibit a pathogen's growth when it is the single cause of infection. In vivo, however, infections can be caused by multiple species. This is important to take into account when attempting to develop or use current antibacterials since their efficacy can change significantly between single infections and coinfections. In this study, we used genome-scale metabolic models (GEMs) to interrogate the growth capabilities of Vibrio cholerae in single infections and coinfections with enterotoxigenic E. coli (ETEC), which cooccur in a large fraction of diarrheagenic patients. Coinfection model predictions showed that V. cholerae growth capabilities are enhanced in the presence of ETEC relative to V. cholerae single infection, through cross-fed metabolites made available to V. cholerae by ETEC. In vitro, cocultures of the two enteric pathogens further confirmed model predictions showing an increased growth of V. cholerae in coculture relative to V. cholerae single cultures while ETEC growth was suppressed. Dual RNAseq analysis of the cocultures also confirmed that the transcriptome of V. cholerae was distinct during coinfection compared to single-infection scenarios where processes related to metabolism were significantly perturbed. Further, in silico gene-knockout simulations uncovered discrepancies in gene essentiality for V. cholerae growth between single infections and coinfections. Integrative model-guided analysis thus identified druggable targets that would be critical for V. cholerae growth in both single infections and coinfections; thus, designing inhibitors against those targets would provide a broader spectrum of coverage against cholera infections.
Collapse
|
11
|
Azevedo GPR, Mattsson HK, Lopes GR, Vidal L, Campeão M, Tonon LAC, Garcia GD, Tschoeke DA, Silva BS, Otsuki K, Gomez-Gil B, Swings J, Thompson FL, Thompson CC. Vibrio tetraodonis sp. nov.: genomic insights on the secondary metabolites repertoire. Arch Microbiol 2020; 203:399-404. [PMID: 32844278 DOI: 10.1007/s00203-020-02019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/30/2020] [Accepted: 08/08/2020] [Indexed: 11/26/2022]
Abstract
Description of a Gram-negative, motile, circular-shaped bacterial strain, designated A511T obtained from the skin of the pufferfish Sphoeroides spengleri (Family Tetraodontidae), collected in Arraial do Cabo, Brazil. Optimum growth occurs at 20-28 °C in the presence of 3% NaCl. The genome sequence of the novel isolate consisted of 4.36 Mb, 3,976 coding genes and G + C content of 42.5%. Genomic taxonomy analyses based on average amino acid (AAI), genome-to-genome-distance (GGDH) and phylogenetic reconstruction placed A511T (= CBAS 712T = CAIM 1939T) into a new species of the genus Vibrio (Vibrio tetraodonis sp. nov.). The genome of the novel species contains eight genes clusters (~ 183.9 Kbp in total) coding for different types of bioactive compounds that hint to several possible ecological roles in the pufferfish host.
Collapse
Affiliation(s)
- Gustavo P R Azevedo
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.
| | - Hannah K Mattsson
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Grasiele R Lopes
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Livia Vidal
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Mariana Campeão
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Luciane A Chimetto Tonon
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos, SP, CEP 13560-970, Brazil
| | - Gizele D Garcia
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
- Institute of Microbiology, Federal University of Rio de Janeiro, Macaé, RJ, Brazil
| | - Diogo A Tschoeke
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Bruno S Silva
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Koko Otsuki
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Bruno Gomez-Gil
- CIAD, AC. Mazatlan Unit for Aquaculture, AP 711, 82000, Mazatlan, Sinaloa, Mexico
| | - Jean Swings
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Fabiano L Thompson
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
| | - Cristiane C Thompson
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.
| |
Collapse
|
12
|
Fotedar R, Caldwell ME, Sankaranarayanan K, Al-Zeyara A, Al-Malki A, Kaul R, Al Marri M, Al-Shamari HS, Lawson PA. Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf. Int J Syst Evol Microbiol 2020; 70:4130-4138. [PMID: 32614761 DOI: 10.1099/ijsem.0.004256] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain B66T was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 6.5-8) and with 0-6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66T was affiliated with the family Alteromonadaceae, sharing the highest sequence similarities to the genera Alteromonas (93.7-95.4 %), Aestuariibacter (94.0-95.1 %), Agaribacter (93.3-93.7 %), Glaciecola (92.0-93.7 %), Marisendiminitalea (93.2-93.3 %) and Planctobacterium (92.9 %). In the phylogenetic trees, strain B66T demonstrated the novel organism formed a distinct lineage closely associated with Aestuariibacter and Planctobacterium. Major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c/iso-C15 : 0 2-OH and iso-C15 : 0 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66T is considered to represent a novel species and genus for which the name Ningiella ruwaisensis gen. nov., sp. nov., is proposed. The type strain is B66T (=QCC B003/17T=LMG 30288 T=CCUG 70703T).
Collapse
Affiliation(s)
- Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Matthew E Caldwell
- Department of Microbiology and Plant Biology, University of Oklahoma, OK 73019, USA
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, OK 73019, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, OK 73019, USA
| | - Aisha Al-Zeyara
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Ameena Al-Malki
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Ridhima Kaul
- Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Masoud Al Marri
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Hamad S Al-Shamari
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, Doha, State of Qatar
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, OK 73019, USA
| |
Collapse
|
13
|
Lawson PA, Patel NB, Mohammed A, Moore ERB, Lo AS, Sardi A, Davis JM, Doyle DA, Hui Y, Testerman T. Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov. Int J Syst Evol Microbiol 2020; 70:3639-3646. [PMID: 32501783 DOI: 10.1099/ijsem.0.004204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, microaerophilic, non-motile, rod-shaped bacterium strain designated PMP191FT, was isolated from a human peritoneal tumour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism formed a lineage within the family Chitinophagaceae that was distinct from members of the genus Pseudoflavitalea (95.1-95.2 % sequence similarity) and Pseudobacter ginsenosidimutans (94.4 % sequence similarity). The average nucleotide identity values between strain PMP191FT and Pseudoflavitalea rhizosphaerae T16R-265T and Pseudobacter ginsenosidimutans Gsoil 221T was 68.9 and 62.3% respectively. The only respiratory quinone of strain PMP191FT was MK-7 and the major fatty acids were iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine and some unidentified amino and glycolipids. The G+C content of strain PMP191FT calculated from the genome sequence was 43.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strain PMP191FT represents a novel species and genus for which the name Parapseudoflavitalea muciniphila gen. nov., sp. nov. is proposed. The type strain is PMP191FT (=DSM 104999T=ATCC BAA-2857T = CCUG 72691T). The phylogenetic analyses also revealed that Pseudobacter ginsenosidimutans shared over 98 % sequence similarly to members of the genus Pseudoflavitalea. However, the average nucleotide identity value between Pseudoflavitalea rhizosphaerae T16R-265T, the type species of the genus and Pseudobacter ginsenosidimutans Gsoil 221T was 86.8 %. Therefore, we also propose that Pseudobacter ginsenosidimutans be reclassified as Pseudoflavitalea ginsenosidimutans comb. nov.
Collapse
Affiliation(s)
- Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Nisha B Patel
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Ahmed Mohammed
- University of Baghdad School of Veterinary Medicine, Baghdad, Iraq.,Department of Pathology, Microbiology and Immunology, University of South Carolina, Columbia, SC, USA
| | - Edward R B Moore
- Culture Collection, Department of Clinical Bacteriology, University of Göteborg, S-41346 Göteborg, Sweden
| | | | - Armando Sardi
- Department of Surgical Oncology, Institute for Cancer Care at Mercy Medical Center, Baltimore, MD, USA
| | - Jeffrey M Davis
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - D Annie Doyle
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Yvonne Hui
- Department of Pathology, Microbiology and Immunology, University of South Carolina, Columbia, SC, USA
| | - Traci Testerman
- Department of Pathology, Microbiology and Immunology, University of South Carolina, Columbia, SC, USA
| |
Collapse
|
14
|
Tan L, Gómez-Betancur I, Guo S, Ge Y, Zhao J, Chen C, Wang N. Complete Genome of Vibrio neocaledonicus CGJ02-2, An active Compounds Producing Bacterium Isolated from South China Sea. Curr Microbiol 2020; 77:2665-2673. [PMID: 32458061 DOI: 10.1007/s00284-020-02047-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 05/20/2020] [Indexed: 11/30/2022]
Abstract
Strain CGJ02-2 was isolated from the coral reefs in South China sea and deposited in South China Sea Institute of Oceanology, Chinese Academy of Sciences. Active compounds including indole, ρ-hydroxybenzaldehyde were isolated from this strain. To explore the biosynthetic way of these compounds and search gene clusters, the complete genome of this strain was sequenced by Single Molecule, Real-Time (SMRT) technology. It was de novo assembled to two circular chromosomes of 3,400,283 bp with GC% 44.77 and 1,845,572 bp with GC% 44.59 respectively and classified as Vibrio alginolyticus. In silico phenotype features of Vibrio alginolyticus CGJ02-2 were also analyzed. The biosynthetic pathway of ρ-hydroxybenzaldehyde and indole in this strain were postulated. Gene clusters of four secondary metabolites including bacteriocin, ectoine, siderophore, arylpolyene were identified. This study provides helpful information for further utilizing Vibrio alginolyticus CGJ02-2 as a source of valuable bioactive compounds.
Collapse
Affiliation(s)
- Lin Tan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, Hainan, China.
| | - Isabel Gómez-Betancur
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, Hainan, China.,Programa de Ofidismo/Escorpionismo, Facultad de Ciencias Farmacéuticas Y Alimentarias, Universidad de Antioquia, 1226, Medellín, Colombia
| | - Suxia Guo
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, Hainan, China
| | - Yu Ge
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, Hainan, China
| | - Jianping Zhao
- School of Pharmacy, National Center for Natural Products Research, Thad Cochran Research Center, University of Mississippi, University, MS, 38677, USA
| | - Chang Chen
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
| | - Nan Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, Hainan, China
| |
Collapse
|
15
|
Genomic taxonomy of the Mediterranei clade of the genus Vibrio (Gammaproteobacteria). Antonie van Leeuwenhoek 2020; 113:851-859. [DOI: 10.1007/s10482-020-01396-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/16/2020] [Indexed: 11/26/2022]
|
16
|
Enterovibrio baiacu sp. nov. Curr Microbiol 2020; 77:154-157. [PMID: 31620811 DOI: 10.1007/s00284-019-01785-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 09/19/2019] [Accepted: 10/01/2019] [Indexed: 10/25/2022]
Abstract
We report here the novel species to encompass the isolate A649T (=CBAS 716T = CBRVS P1061T) obtained from viscera of the healthy pufferfish Sphoeroides spengleri (Family Tetraodontidae). Genomic taxonomy analysis demonstrates that the novel strain A649T had < 95% average amino acid identity/average nucleotide identity (AAI/ANI) and < 70% similarity of genome-to-genome distance (GGDH) towards its closest neighbors which places A649T into a new Enterovibrio species (Enterovibrio baiacu sp nov.). In silico phenotyping disclosed several features that may be used to differentiate related Enterovibrio species. The nearly complete genome assembly of strain A649T consisted of 5.4 Mbp and 4826 coding genes.
Collapse
|
17
|
Phytohalomonas tamaricis gen. nov., sp. nov., an endophytic bacterium isolated from Tamarix ramosissima roots growing in Kumtag desert. Arch Microbiol 2019; 202:143-151. [PMID: 31535159 DOI: 10.1007/s00203-019-01724-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/05/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
A gram-stain-negative, aerobic, non-spore-forming, rod-shaped, non-motile bacterium strain R4HLG17T was isolated from Tamarix ramosissima roots growing in Kumtag desert. The strain grew at salinities of 0-16% (w/v) NaCl (optimum 5-6%), pH 5-9 (optimum 7) and at 16-45 °C. Based on 16S rRNA gene sequence similarity, strain R4HLG17T belonged to the family Halomonadaceae and was most closely related to Halomonas lutea DSM 23508T(95.1%), followed by Halotalea alkalilenta AW-7T(94.8%), Salinicola acroporae S4-41T(94.8%), Salinicola halophilus CG4.1T(94.6%), and Larsenimonas salina M1-18T(94.4%). Multilocus sequence analysis (MLSA) based on the partial sequences of 16S rRNA, atpA, gyrB, rpoD, and secA genes indicated that the strain R4HLG17T formed an independent and monophyletic branch related to other genera of Halomonadaceae, supporting its placement as a new genus in this family. The draft genome of strain R4HLG17T was 3.6 Mb with a total G + C content of 55.1%. The average nucleotide identity to Halomonas lutea DSM 23508T was 83.5%. Q-9 was detected as the major respiratory quinone and summed feature 8 (C18:1ω7c/C18:1ω6c), summed feature 3 (C16:1ω7c/C16:1ω6c), and C16:0 as predominant cellular fatty acids. On the basis of chemotaxonomic, phylogenetic, and phenotypic evidence, strain R4HLG17T is concluded to represent a novel species of a new genus within Halomonadaceae, for which the name Phytohalomonas tamaricis gen. nov., sp. nov., is proposed. The type strain is R4HLG17T (=ACCC 19929T=KCTC 52415T).
Collapse
|
18
|
Halomonas coralii sp. nov. Isolated from Mussismilia braziliensis. Curr Microbiol 2019; 76:678-680. [DOI: 10.1007/s00284-019-01674-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/19/2019] [Indexed: 10/27/2022]
|
19
|
" Candidatus Colwellia aromaticivorans" sp. nov., " Candidatus Halocyntiibacter alkanivorans" sp. nov., and " Candidatus Ulvibacter alkanivorans" sp. nov. Genome Sequences. Microbiol Resour Announc 2019; 8:8/15/e00086-19. [PMID: 30975799 PMCID: PMC6460022 DOI: 10.1128/mra.00086-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Unplanned oil spills during offshore production are a serious problem for the industry and the marine environment. Here, we present the genome sequence analysis of three novel hydrocarbon-degrading bacteria, namely, “Candidatus Colwellia aromaticivorans” sp. Unplanned oil spills during offshore production are a serious problem for the industry and the marine environment. Here, we present the genome sequence analysis of three novel hydrocarbon-degrading bacteria, namely, “Candidatus Colwellia aromaticivorans” sp. nov., “Candidatus Halocyntiibacter alkanivorans” sp. nov., and “Candidatus Ulvibacter alkanivorans” sp. nov.
Collapse
|
20
|
Ina-Salwany MY, Al-Saari N, Mohamad A, Mursidi FA, Mohd-Aris A, Amal MNA, Kasai H, Mino S, Sawabe T, Zamri-Saad M. Vibriosis in Fish: A Review on Disease Development and Prevention. JOURNAL OF AQUATIC ANIMAL HEALTH 2019; 31:3-22. [PMID: 30246889 DOI: 10.1002/aah.10045] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/16/2018] [Indexed: 05/19/2023]
Abstract
Current growth in aquaculture production is parallel with the increasing number of disease outbreaks, which negatively affect the production, profitability, and sustainability of the global aquaculture industry. Vibriosis is among the most common diseases leading to massive mortality of cultured shrimp, fish, and shellfish in Asia. High incidence of vibriosis can occur in hatchery and grow-out facilities, but juveniles are more susceptible to the disease. Various factors, particularly the source of fish, environmental factors (including water quality and farm management), and the virulence factors of Vibrio, influence the occurrence of the disease. Affected fish show weariness, with necrosis of skin and appendages, leading to body malformation, slow growth, internal organ liquefaction, blindness, muscle opacity, and mortality. A combination of control measures, particularly a disease-free source of fish, biosecurity of the farm, improved water quality, and other preventive measures (e.g., vaccination) might be able to control the infection. Although some control measures are expensive and less practical, vaccination is effective, relatively cheap, and easily implemented. In this review, the latest knowledge on the pathogenesis and control of vibriosis, including vaccination, is discussed.
Collapse
Affiliation(s)
- M Y Ina-Salwany
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nurhidayu Al-Saari
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- International Institute for Halal Research and Training, International Islamic University Malaysia, KICT Building, Level 3, 53100, Gombak, Selangor, Malaysia
| | - Aslah Mohamad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Fathin-Amirah Mursidi
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Aslizah Mohd-Aris
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biology, School of Biology, Universiti Teknologi MARA, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia
| | - M N A Amal
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Hisae Kasai
- Laboratory of Fish Pathology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - M Zamri-Saad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| |
Collapse
|
21
|
Genome Sequences of
Vibrio maerlii
sp. nov. and
Vibrio rhodolitus
sp. nov., Isolated from Rhodoliths. Microbiol Resour Announc 2018; 7:MRA01039-18. [PMID: 30533792 PMCID: PMC6256479 DOI: 10.1128/mra.01039-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/17/2018] [Indexed: 11/20/2022] Open
Abstract
We report here the genome sequences of the novel isolates G62
T
and G98
T
from rhodoliths. The nearly complete genomes consisted of 4.7 Mbp (4,233 coding sequences [CDS]) for G62
T
and 4.5 Mbp (4,085 CDS) for G98
T
.
Collapse
|
22
|
Identification of VPA1327 (vopT) as a Novel Genetic Marker for Detecting Pathogenic Vibrio parahaemolyticus. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.2.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
23
|
Riesco R, Carro L, Román-Ponce B, Prieto C, Blom J, Klenk HP, Normand P, Trujillo ME. Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics. Front Microbiol 2018; 9:1360. [PMID: 29988535 PMCID: PMC6026663 DOI: 10.3389/fmicb.2018.01360] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/05/2018] [Indexed: 11/13/2022] Open
Abstract
The type isolates of species Micromonospora saelicesensis and Micromonospora noduli are Gram-stain positive actinobacteria that were originally isolated from nitrogen fixing nodules of the legumes Lupinus angustifolius and Pisum sativum, respectively. These two species are very closely related and questions arise as to whether they should be merged into a single species. To better delineate the relationship of M. saelicesensis and M. noduli, 10 strains isolated from plant tissue (nodules and leaves) and identified by their 16S rRNA gene sequences as either M. saelicensesis or M. noduli, based on a cut-off value of ≥99.5% were selected for whole-genome sequencing and compared with the type strains of M. saelicesensis Lupac 09T and M. noduli GUI43T using overall genome relatedness indices (OGRI) which included ANI, OrthoANI and digital DNA-DNA hybridization. Whole- and core-genome phylogenomic analyses were also carried out. These results were compared with the topologies of the 16S rRNA and gyrB gene phylogenies. Good correlation was found between all trees except for the 16S rRNA gene. Overall results also supported the current classification of M. saelicesensis and M. noduli as separate species. Especially useful was the core-genome phylogenetic analyses based on 92 genes and the dDDH results which were highly correlated. The importance of using more than one strain for a better definition of a species was also shown. A series of in vitro phenotypic assays performed at different times were compared with in silico predictions based on genomic data. In vitro phenotypic tests showed discrepancies among the independent studies, confirming the lack of reproducibility even when tests were performed in the same laboratory. On the other hand, the use of in silico predictions proved useful for defining a stable phenotype profile among the strains analyzed. These results provide a working framework for defining Micromonospora species at the genomic and phenotypic level.
Collapse
Affiliation(s)
- Raúl Riesco
- Departament of Microbiology and Genetics, Edificio Departamental, University of Salamanca, Salamanca, Spain
| | - Lorena Carro
- Departament of Microbiology and Genetics, Edificio Departamental, University of Salamanca, Salamanca, Spain
| | - Brenda Román-Ponce
- Departament of Microbiology and Genetics, Edificio Departamental, University of Salamanca, Salamanca, Spain
| | - Carlos Prieto
- Servicio de Bioinformática, NUCLEUS, Edificio I+D+i, University of Salamanca, Salamanca, Spain
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Philippe Normand
- Centre National de la Recherche Scientifique-UMR5557 Ecologie Microbienne, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Martha E Trujillo
- Departament of Microbiology and Genetics, Edificio Departamental, University of Salamanca, Salamanca, Spain
| |
Collapse
|
24
|
Coutinho FH, Gregoracci GB, Walter JM, Thompson CC, Thompson FL. Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses. Trends Microbiol 2018; 26:955-965. [PMID: 29937307 DOI: 10.1016/j.tim.2018.05.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 01/31/2023]
Abstract
Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus-host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.
Collapse
Affiliation(s)
- Felipe Hernandes Coutinho
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Evolutionary Genomics Group, Departamento de Produccíon Vegetal y Microbiología, Universidad Miguel Hernández (UMH), Alicante, Spain
| | | | - Juline Marta Walter
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Carneiro Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Federal Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| |
Collapse
|
25
|
Phyllobacterium zundukense sp. nov., a novel species of rhizobia isolated from root nodules of the legume species Oxytropis triphylla (Pall.) Pers. Int J Syst Evol Microbiol 2018; 68:1644-1651. [DOI: 10.1099/ijsem.0.002722] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
26
|
Menezes FGR, Barbosa WE, Vasconcelos LS, Rocha RS, Maggioni R, Sousa OV, Hofer E, Vieira RHSF. Genotypic assessment of a dichotomous key to identify Vibrio coralliilyticus, a coral pathogen. DISEASES OF AQUATIC ORGANISMS 2018; 128:87-92. [PMID: 29565257 DOI: 10.3354/dao03209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Vibrio coralliilyticus is a known pathogen to corals and larvae of bivalves. Its identification is made based on phenotypic and genotypic characters of isolated strains. To evaluate the efficiency of the phenotypic identification, 21 strains identified as V. coralliilyticus using a widely used dichotomous key were analyzed by qualitative PCR and sequencing of the 16S rDNA region. The results obtained by the behavioral test, amino acids usage, allow us to distinguish 3 A/L/O profiles: (1) A+/L-/O+; (2) A+/L+/O+; and (3) A-/L+/O+. In the genotypic tests, all strains tested positive with primers specific for the Vibrio genus. However, when primers were used for species identification, the results did not match those obtained with the dichotomous key chosen. The phenotypic characteristics taken into account to set apart V. coralliilyticus and other species were not proven to be efficient. More information about the morphological diversity of colonies and enzymatic activities should be considered in the formulation of phenotypic keys for V. coralliilyticus and related species.
Collapse
|
27
|
Nóbrega MS, Silva BS, Leomil L, Tschoeke DA, Campeão ME, Garcia GD, Dias GA, Vieira VV, Thompson CC, Thompson FL. Description of Alteromonas abrolhosensis sp. nov., isolated from sea water of Abrolhos Bank, Brazil. Antonie van Leeuwenhoek 2018; 111:1131-1138. [PMID: 29349565 DOI: 10.1007/s10482-018-1016-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/10/2018] [Indexed: 11/29/2022]
Abstract
Two Gram-negative, motile, aerobic bacteria isolated from waters of the Abrolhos Bank were classified through a whole genome-based taxonomy. Strains PEL67ET and PEL68C shared 99% 16S rRNA and dnaK sequence identity with Alteromonas marina SW-47T and Alteromonas macleodii ATCC 27126T. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), average amino acid identity (AAI) and average nucleotide identity (ANI) showed that PEL67ET and PEL68C had identity values between 33-36, 86-88 and 83-84%, and 85-86 and 83%, respectively, towards their close neighbors A. macleodii ATCC 27126T and A. marina SW-47T. The DNA G + C contents of PEL67ET and PEL68C were 44.5%. The phenotypic features that differentiate PEL67ET and PEL68C strains from their close neighbors were assimilation of galactose and activity of phosphatase, and lack of mannitol, maltose, acetate, xylose and glycerol assimilation and lack of lipase, α and β-glucosidase activity. The new species Alteromonas abrolhosensis is proposed. The type strain is PEL67ET (= CBAS 610T = CAIM 1925T).
Collapse
Affiliation(s)
- Maria S Nóbrega
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Bruno S Silva
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Diogo Antonio Tschoeke
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Mariana E Campeão
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Gizele D Garcia
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Graciela A Dias
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | | | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil. .,CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho 373. Sala 102, Bloco A, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil. .,SAGE-COPPE, Federal University of Rio de Janeiro, Rio De Janeiro, RJ, Brazil. .,CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho 373. Sala 102, Bloco A, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
| |
Collapse
|
28
|
Amin AR, Tanaka M, Al-saari N, Feng G, Mino S, Ogura Y, Hayashi T, Meirelles PM, Thompson FL, Gomez-Gil B, Sawabe T, Sawabe T. Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae, isolated from coral reef seawater off Ishigaki Island, Japan. Syst Appl Microbiol 2017. [DOI: 10.1016/j.syapm.2017.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
29
|
Machado H, Cardoso J, Giubergia S, Rapacki K, Gram L. FurIOS: A Web-Based Tool for Identification of Vibrionaceae Species Using the fur Gene. Front Microbiol 2017; 8:414. [PMID: 28348552 PMCID: PMC5346536 DOI: 10.3389/fmicb.2017.00414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/27/2017] [Indexed: 11/13/2022] Open
Abstract
Gene based methods for identification of species from the Vibrionaceae family have been developed during the last decades to address the limitations of the commonly used 16S rRNA gene phylogeny. Recently, we found that the ferric-uptake regulator gene (fur) can be used as a single identification marker providing species discrimination, consistent with multi-locus sequencing analyses and whole genome phylogenies. To allow for broader and easy use of this marker, we have developed an online prediction service that allows the identification of Vibrionaceae species based on their fur-sequence. The input is a DNA sequence that can be uploaded on the web service; the output is a table containing the strain identifier, e-value, and percentage of identity for each of the matches with rows colored in green for hits with high probability of being the same species. The service is available on the web at: http://www.cbs.dtu.dk/services/furIOS-1.0/. The fur-sequences can be derived either from genome sequences or from PCR-amplification of the genomic region encoding the fur gene. We have used 191 strains identified as Vibrionaceae based on 16S rRNA gene sequence to test the PCR method and the web service on a large dataset. We were able to classify 171 of 191 strains at the species level and 20 strains remained unclassified. Furthermore, the fur phylogenetics and subsequent in silico DNA-DNA hybridization demonstrated that two strains (ATCC 33789 and ZS-139) previously identified as Vibrio splendidus are more closely related to V. tasmaniensis and V. cyclitrophicus, respectively. FurIOS is an easy-to-use online service that allows the identification of bacteria from the Vibrionaceae family at the species level using the fur gene as a single marker. Its simplistic design and straightforward pipeline makes it suitable for any research environment, from academia to industry.
Collapse
Affiliation(s)
- Henrique Machado
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens LyngbyDenmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens LyngbyDenmark
| | - João Cardoso
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens LyngbyDenmark
| | - Sonia Giubergia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens LyngbyDenmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens LyngbyDenmark
| | - Kristoffer Rapacki
- Center for Biological Sequence Analysis, Department of Bioinformatics, Technical University of Denmark, Kongens LyngbyDenmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens LyngbyDenmark
| |
Collapse
|
30
|
Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade. Sci Rep 2017; 7:41394. [PMID: 28145490 PMCID: PMC5286417 DOI: 10.1038/srep41394] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 01/09/2023] Open
Abstract
The core of the Vibrio Harveyi clade contains V. harveyi, V. campbellii, V. owensii, V. jasicida, and V. rotiferianus. They are well recognized aquatic animal pathogens, but misclassification has been common due to similarities in their rDNA sequences and phenotypes. To better understand their evolutionary relationships and functional features, we sequenced a shrimp pathogen strain V. harveyi 1114GL, reclassified it as V. campbellii and compared this and 47 other sequenced Vibrio genomes in the Harveryi clade. A phylogeny based on 1,775 genes revealed that both V. owensii and V. jasicida were closer to V. campbellii than to V. harveyi and that V. campbellii strains can be divided into two distinct groups. Species-specific genes such as intimin and iron acquisition genes were identified in V. campbellii. In particular, the 1114GL strain contains two bacterial immunoglobulin-like genes for cell adhesion with 22 Big_2 domains that have been extensively reshuffled and are by far the most expanded among all species surveyed in this study. The 1114GL strain differed from ATCC BAA-1116 by ~9% at the synonymous sites, indicating high diversity within V. campbellii. Our study revealed the characteristics of V. campbellii in the Harveyi clade and the genetic basis for their wide-spread pathogenicity.
Collapse
|
31
|
Vibrio sonorensis sp. nov. isolated from a cultured oyster Crassostrea gigas. Antonie van Leeuwenhoek 2016; 109:1447-1455. [PMID: 27465217 DOI: 10.1007/s10482-016-0744-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/21/2016] [Indexed: 12/13/2022]
Abstract
Strain CAIM 1076T was isolated from a cultured oyster Crassostrea gigas in Puerto Peñasco, Sonora state, México. The strain was taxonomically characterised by means of a genomic approach, comprising 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), the DNA G+C content and whole genome analyses (ANI and GGDC), and by phenotypic characterisation. Strain CAIM 1076T was found to be catalase and oxidase positive, and cells were observed to be motile and facultative anaerobic. Analysis of the almost-complete 16S rRNA gene sequence placed this strain within the genus Vibrio; closely related species were Vibrio maritimus, Vibrio variabilis, Vibrio proteolyticus, and Vibrio nigripulchritudo with similarity values of 98.9, 98.5, 98.1, and 98.0 %, respectively. MLSA of six housekeeping genes (ftsZ, gapA, gyrB, recA, rpoA and topA) was performed with the closely related species. A draft genome sequence of strain CAIM 1076T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The genomic similarity values with V. maritimus were 71.6 % (ANIb), 85.1 % (ANIm) and a GGDC value of 20.3 ± 2.3 %; with V. variabilis the genomic similarities were 71.8 % (ANIb), 85.4 % (ANIm) and 20.0 ± 2.3 % (GGDC); with V. proteolyticus, 71.6 % (ANIb), 84.1 % (ANIm) and 18.8 ± 2.2 % (GGDC); and with V. nigripulchritudo, 70.8 % (ANIb), 84.9 % (ANIm) and 20.5 ± 2.3 % (GGDC). These ANI and GGDC values are below the thresholds for the delimitation of prokaryotic species, i.e., 95-96 and 70 %, respectively. Phenotypic characters also showed differences with the closely related species analysed. The results presented here support the description of a novel species, for which the name Vibrio sonorensis sp. nov. is proposed, with strain CAIM 1076T (=CECT 9100T, =DSM 102190T) as the type strain.
Collapse
|
32
|
Gao F, Al-Saari N, Rohul Amin AKM, Sato K, Mino S, Suda W, Oshima K, Hattori M, Ohkuma M, Hargreaves PI, Meirelles PM, Thompson FL, Thompson C, Gomez-Gil B, Sawabe T, Sawabe T. Vibrio ishigakensis sp. nov., in Halioticoli clade isolated from seawater in Okinawa coral reef area, Japan. Syst Appl Microbiol 2016; 39:330-5. [PMID: 27262360 DOI: 10.1016/j.syapm.2016.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 03/31/2016] [Accepted: 04/06/2016] [Indexed: 11/26/2022]
Abstract
Five novel strains showing non-motile, alginolytic, halophilic and fermentative features were isolated from seawater samples off Okinawa in coral reef areas. These strains were characterized by an advanced polyphasic taxonomy including genome based taxonomy using multilocus sequence analysis (MLSA) and in silico DNA-DNA similarity (in silico DDH). Phylogenetic analyses on the basis of 16S rRNA gene sequences revealed that the isolates could be assigned to the genus Vibrio, however they were not allocated into any distinct cluster with known Vibrionaceae species. MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the vibrios formed an outskirt branch of Halioticoli clade. The experimental DNA-DNA hybridization data revealed that the five strains were in the range of being defined as conspecific but separate from nine Halioticoli clade species. The G+C contents of the Vibrio ishigakensis strains were 47.3-49.1mol%. Both Amino Acid Identity and Average Nucleotide Identity of the strain C1(T) against Vibrio ezurae HDS1-1(T), Vibrio gallicus HT2-1(T), Vibrio halioticoli IAM 14596(T), Vibrio neonatus HDD3-1(T) and Vibrio superstes G3-29(T) showed less than 95% similarity. The genome-based taxonomic approach by means of in silico DDH values also supports the V. ishigakensis strains being distinct from the other known Halioticoli clade species. Sixteen traits (growth temperature range, DNase and lipase production, indole production, and assimilation of 10 carbon compounds) distinguished these strains from Halioticoli clade species. The names V. ishigakensis sp. nov. is proposed for the species of Halioticoli clade, with C1(T) as the type strain (JCM 19231(T)=LMG 28703(T)).
Collapse
Affiliation(s)
- Feng Gao
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Nurhidayu Al-Saari
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - A K M Rohul Amin
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Kazumichi Sato
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Wataru Suda
- Laboratory of Metagenomics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan; Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Kenshiro Oshima
- Laboratory of Metagenomics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Masahira Hattori
- Laboratory of Metagenomics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan; Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan
| | - Paulo Iiboshi Hargreaves
- Institute of Biology, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Pedro Milet Meirelles
- Institute of Biology, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Institute of Biology, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Thompson
- Institute of Biology, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno Gomez-Gil
- CIAD, AC Mazatlan Unit for Aquaculture and Environmental Management, AP 711 Mazatlán, Sinaloa, Mexico
| | - Toko Sawabe
- Department of Food and Nutrition, Hakodate Junior College, Hakodate, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
| |
Collapse
|
33
|
Thalassospira australica sp. nov. isolated from sea water. Antonie van Leeuwenhoek 2016; 109:1091-100. [DOI: 10.1007/s10482-016-0710-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
|
34
|
Pujalte MJ, Lucena T, Rodrigo-Torres L, La Mura A, Ruvira MA, Arahal DR. Grimontia celer sp. nov., from sea water. Int J Syst Evol Microbiol 2016; 66:2906-2909. [PMID: 27125858 DOI: 10.1099/ijsem.0.001119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Strain 96-237T, a Gram-reaction-negative, curved- to spiral-shaped motile bacterium, isolated from coastal marine water, was found to be related to species of the genus Grimontia by 16S rRNA gene sequence comparison, sharing 98.3 % similarity to Grimontia marina CECT 8713Tand 98.8 % to 'Grimontiaindica' AK16. Phenotypic analysis revealed that strain 96-237T is slightly halophilic, mesophilic and facultatively anaerobic, fermenting d-glucose, d-ribose, d-mannose, d-mannitol, maltose and sucrose. It was positive for oxidase and indole production and negative for arginine dihydrolase and lysine and ornithine decarboxylases. Its major fatty acids were C16 : 1ω7c/C16 : 1ω6c (SF3), C18 : 1ω7c and C16 : 0. Its DNA G+C content was 48.4 mol%. The strain was different at the species level from all other species of the genusGrimontia, with average nucleotide identity indices of 79.6 % to Grimontia. hollisae CECT 8713T, 87.8 % to G. marina CECT 5069T and 89.1 % to 'G. indica' AK16 genomes. Thus, the strain represents a novel species for which we propose the name Grimontia celer and 96-237T (=CECT 9029T =KCTC 42960T =LMG 29238T) as the type strain.
Collapse
Affiliation(s)
- María J Pujalte
- Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo, Universitat de València, Spain
| | - Teresa Lucena
- Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo, Universitat de València, Spain
| | - Lidia Rodrigo-Torres
- Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo, Universitat de València, Spain
| | - Alexandra La Mura
- Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo, Universitat de València, Spain
| | - María A Ruvira
- Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo, Universitat de València, Spain
| | - David R Arahal
- Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo, Universitat de València, Spain
| |
Collapse
|
35
|
Appolinario LR, Tschoeke DA, Rua CPJ, Venas T, Campeão ME, Amaral GRS, Leomil L, de Oliveira L, Vieira VV, Otsuki K, Swings J, Thompson FL, Thompson CC. Description of Endozoicomonas arenosclerae sp. nov. using a genomic taxonomy approach. Antonie van Leeuwenhoek 2016; 109:431-8. [PMID: 26786501 DOI: 10.1007/s10482-016-0649-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 01/11/2016] [Indexed: 11/28/2022]
Abstract
The taxonomic position of strains Ab112(T) (CBAS 572(T)) and Ab227_MC (CBAS 573) was evaluated by means of genomic taxonomy. These isolates represent the dominant flora cultured from the healthy marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro. Strains CBAS 572(T) and CBAS 573 shared >98 % 16S rRNA sequence identity with Endozoicomonas numazuensis and Endozoicomonas montiporae. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), amino acid identity (AAI) and average nucleotide identity (ANI) further showed that these strains had <70 %, at maximum 71.1 and 78 % of identity, respectively, to their closest neighbours E. numazuensis and E. montiporae. The DNA G+C content of CBAS 572(T) and CBAS 573 were 47.6 and 47.7 mol%, respectively. Phenotypic and chemotaxonomic features also allowed a separation from the type strains of their phylogenetic neighbours. Useful phenotypic features for discriminating CBAS 572(T) and CBAS 573 from E. numazuensis and E. montiporae species include C8 esterase, N-acetyl-β-glucosaminidase, citric acid, uridine and siderophore. The species Endozoicomonas arenosclerae sp. nov. is proposed to harbour the new isolates. The type strain is CBAS 572(T) (=Ab112(T)).
Collapse
Affiliation(s)
- Luciana R Appolinario
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Diogo A Tschoeke
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Cintia P J Rua
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Tainá Venas
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Mariana E Campeão
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Gilda R S Amaral
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Louisi de Oliveira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | | | - Koko Otsuki
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Jean Swings
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,Laboratory for Microbiology, Ghent University, Ghent, Belgium
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.
| |
Collapse
|
36
|
Al-saari N, Gao F, A.K.M. Rohul A, Sato K, Sato K, Mino S, Suda W, Oshima K, Hattori M, Ohkuma M, Meirelles PM, Thompson FL, Thompson C, A. Filho GM, Gomez-Gil B, Sawabe T, Sawabe T. Advanced Microbial Taxonomy Combined with Genome-Based-Approaches Reveals that Vibrio astriarenae sp. nov., an Agarolytic Marine Bacterium, Forms a New Clade in Vibrionaceae. PLoS One 2015; 10:e0136279. [PMID: 26313925 PMCID: PMC4551953 DOI: 10.1371/journal.pone.0136279] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 08/01/2015] [Indexed: 11/18/2022] Open
Abstract
Advances in genomic microbial taxonomy have opened the way to create a more universal and transparent concept of species but is still in a transitional stage towards becoming a defining robust criteria for describing new microbial species with minimum features obtained using both genome and classical polyphasic taxonomies. Here we performed advanced microbial taxonomies combined with both genome-based and classical approaches for new agarolytic vibrio isolates to describe not only a novel Vibrio species but also a member of a new Vibrio clade. Two novel vibrio strains (Vibrio astriarenae sp. nov. C7T and C20) showing agarolytic, halophilic and fermentative metabolic activity were isolated from a seawater sample collected in a coral reef in Okinawa. Intraspecific similarities of the isolates were identical in both sequences on the 16S rRNA and pyrH genes, but the closest relatives on the molecular phylogenetic trees on the basis of 16S rRNA and pyrH gene sequences were V. hangzhouensis JCM 15146T (97.8% similarity) and V. agarivorans CECT 5085T (97.3% similarity), respectively. Further multilocus sequence analysis (MLSA) on the basis of 8 protein coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) obtained by the genome sequences clearly showed the V. astriarenae strain C7T and C20 formed a distinct new clade protruded next to V. agarivorans CECT 5085T. The singleton V. agarivorans has never been included in previous MLSA of Vibrionaceae due to the lack of some gene sequences. Now the gene sequences are completed and analysis of 100 taxa in total provided a clear picture describing the association of V. agarivorans into pre-existing concatenated network tree and concluded its relationship to our vibrio strains. Experimental DNA-DNA hybridization (DDH) data showed that the strains C7T and C20 were conspecific but were separated from all of the other Vibrio species related on the basis of both 16S rRNA and pyrH gene phylogenies (e.g., V. agarivorans CECT 5085T, V. hangzhouensis JCM 15146T V. maritimus LMG 25439T, and V. variabilis LMG 25438T). In silico DDH data also supported the genomic relationship. The strains C7T also had less than 95% average amino acid identity (AAI) and average nucleotide identity (ANI) towards V. maritimus C210, V. variabilis C206, and V. mediterranei AK1T, V. brasiliensis LMG 20546T, V. orientalis ATCC 33934T, and V. sinaloensis DSM 21326. The name Vibrio astriarenae sp. nov. is proposed with C7 as the type strains. Both V. agarivorans CECT 5058T and V. astriarenae C7T are members of the newest clade of Vibrionaceae named Agarivorans.
Collapse
Affiliation(s)
- Nurhidayu Al-saari
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Minato-cho, Hakodate, Japan
- * E-mail:
| | - Feng Gao
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Minato-cho, Hakodate, Japan
| | - Amin A.K.M. Rohul
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Minato-cho, Hakodate, Japan
| | - Kazumichi Sato
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Minato-cho, Hakodate, Japan
| | - Keisuke Sato
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Minato-cho, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Minato-cho, Hakodate, Japan
| | - Wataru Suda
- Laboratory of Metagenomics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Kenshiro Oshima
- Laboratory of Metagenomics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Masahira Hattori
- Laboratory of Metagenomics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Ibaraki, Japan
| | - Pedro M. Meirelles
- Institute of Biology, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L. Thompson
- Institute of Biology, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Thompson
- Institute of Biology, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Bruno Gomez-Gil
- CIAD, AC Mazatlan Unit for Aquaculture and Environmental Management, Mazatlán, México
| | - Toko Sawabe
- Department of Food and Nutrition, Hakodate Junior College, Hakodate, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Minato-cho, Hakodate, Japan
| |
Collapse
|
37
|
Espinoza-Valles I, Vora GJ, Lin B, Leekitcharoenphon P, González-Castillo A, Ussery D, Høj L, Gomez-Gil B. Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792. MICROBIOLOGY-SGM 2015. [PMID: 26198743 DOI: 10.1099/mic.0.000141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Vibrio harveyi CAIM 1792 is a marine bacterial strain that causes mortality in farmed shrimp in north-west Mexico, and the identification of virulence genes in this strain is important for understanding its pathogenicity. The aim of this work was to compare the V. harveyi CAIM 1792 genome with related genome sequences to determine their phylogenic relationship and explore unique regions in silico that differentiate this strain from other V. harveyi strains. Twenty-one newly sequenced genomes were compared in silico against the CAIM 1792 genome at nucleotidic and predicted proteome levels. The proteome of CAIM 1792 had higher similarity to those of other V. harveyi strains (78%) than to those of the other closely related species Vibrio owensii (67%), Vibrio rotiferianus (63%) and Vibrio campbellii (59%). Pan-genome ORFans trees showed the best fit with the accepted phylogeny based on DNA-DNA hybridization and multi-locus sequence analysis of 11 concatenated housekeeping genes. SNP analysis clustered 34/38 genomes within their accepted species. The pangenomic and SNP trees showed that V. harveyi is the most conserved of the four species studied and V. campbellii may be divided into at least three subspecies, supported by intergenomic distance analysis. blastp atlases were created to identify unique regions among the genomes most related to V. harveyi CAIM 1792; these regions included genes encoding glycosyltransferases, specific type restriction modification systems and a transcriptional regulator, LysR, reported to be involved in virulence, metabolism, quorum sensing and motility.
Collapse
Affiliation(s)
| | - Gary J Vora
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Baochuan Lin
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Pimlapas Leekitcharoenphon
- National Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Dave Ussery
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.,Comparative Genomics group, Biosciences Division, Oak Ridge National Labs, Oak Ridge, Tennessee, USA
| | - Lone Høj
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Bruno Gomez-Gil
- CIAD A.C., Mazatlán Unit for Aquaculture, Mazatlán, Sinaloa, Mexico
| |
Collapse
|
38
|
González-Castillo A, Enciso-Ibarrra J, Bolán-Mejia MC, Balboa S, Lasa A, Romalde JL, Cabanillas-Beltrán H, Gomez-Gil B. Vibrio mexicanus sp. nov., isolated from a cultured oyster Crassostrea corteziensis. Antonie van Leeuwenhoek 2015; 108:355-64. [DOI: 10.1007/s10482-015-0488-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/19/2015] [Indexed: 11/24/2022]
|
39
|
Campbell-Sills H, El Khoury M, Favier M, Romano A, Biasioli F, Spano G, Sherman DJ, Bouchez O, Coton E, Coton M, Okada S, Tanaka N, Dols-Lafargue M, Lucas PM. Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines. Genome Biol Evol 2015; 7:1506-18. [PMID: 25977455 PMCID: PMC4494047 DOI: 10.1093/gbe/evv084] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oenococcus oeni is a lactic acid bacteria species encountered particularly in wine, where it achieves the malolactic fermentation. Molecular typing methods have previously revealed that the species is made of several genetic groups of strains, some being specific to certain types of wines, ciders or regions. Here, we describe 36 recently released O. oeni genomes and the phylogenomic analysis of these 36 plus 14 previously reported genomes. We also report three genome sequences of the sister species Oenococcus kitaharae that were used for phylogenomic reconstructions. Phylogenomic and population structure analyses performed revealed that the 50 O. oeni genomes delineate two major groups of 12 and 37 strains, respectively, named A and B, plus a putative group C, consisting of a single strain. A study on the orthologs and single nucleotide polymorphism contents of the genetic groups revealed that the domestication of some strains to products such as cider, wine, or champagne, is reflected at the genetic level. While group A strains proved to be predominant in wine and to form subgroups adapted to specific types of wine such as champagne, group B strains were found in wine and cider. The strain from putative group C was isolated from cider and genetically closer to group B strains. The results suggest that ancestral O. oeni strains were adapted to low-ethanol containing environments such as overripe fruits, and that they were domesticated to cider and wine, with group A strains being naturally selected in a process of further domestication to specific wines such as champagne.
Collapse
Affiliation(s)
- Hugo Campbell-Sills
- Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | | | - Marion Favier
- BioLaffort, Research Subsidiary of the Laffort group, Bordeaux, France
| | - Andrea Romano
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Franco Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giuseppe Spano
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Foggia, Italy
| | - David J Sherman
- INRIA, Univ. Bordeaux, Project team MAGNOME, Talence, France CNRS, Univ. Bordeaux, UMR 5800 LaBRI, Talence, France
| | - Olivier Bouchez
- INRA, UMR444, laboratoire de Génétique Cellulaire, Castanet-Tolosan, France GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Emmanuel Coton
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Monika Coton
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Sanae Okada
- NODAI Culture Collection Center, Tokyo University of Agriculture, Japan
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, Japan
| | - Marguerite Dols-Lafargue
- Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France Bordeaux INP, ISVV, EA 4577 Œnologie, Villenave d'ornon, France
| | - Patrick M Lucas
- Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France
| |
Collapse
|
40
|
Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME JOURNAL 2015; 9:2360-72. [PMID: 25848870 DOI: 10.1038/ismej.2015.45] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/07/2015] [Accepted: 02/26/2015] [Indexed: 01/19/2023]
Abstract
To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.
Collapse
Affiliation(s)
- Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | | | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Wendy Schackwitz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Qichao Tu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Grant M Zane
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Qiao Ma
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Yuanyuan Qu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Judy D Wall
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| |
Collapse
|
41
|
Hedlund BP, Dodsworth JA, Staley JT. The changing landscape of microbial biodiversity exploration and its implications for systematics. Syst Appl Microbiol 2015; 38:231-6. [PMID: 25921438 DOI: 10.1016/j.syapm.2015.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 12/31/2022]
Abstract
A vast diversity of Bacteria and Archaea exists in nature that has evaded axenic culture. Advancements in single-cell genomics, metagenomics, and molecular microbial ecology approaches provide ever-improving insight into the biology of this so-called "microbial dark matter"; however, due to the International Code of Nomenclature of Prokaryotes, yet-uncultivated microorganisms are not accommodated in formal taxonomy regardless of the quantity or quality of data. Meanwhile, efforts to calibrate the existing taxonomy with phylogenetic anchors and genomic data are increasingly robust. The current climate provides an exciting opportunity to leverage rapidly expanding single-cell genomics and metagenomics datasets to improve the taxonomy of Bacteria and Archaea. However, this opportunity must be weighted carefully in light of the strengths and limitations of these approaches. We propose to expand the definition of the Candidatus taxonomy to include taxa, from the phylum level to the species level, that are described genomically, particularly when genomic work is coupled with advanced molecular ecology approaches to probe metabolic functions in situ. This system would preserve the rigor and value of traditional microbial systematics while enabling growth of a provisional taxonomic structure to facilitate communication about "dark" lineages on the tree of life.
Collapse
Affiliation(s)
- Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA.
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - James T Staley
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
42
|
Amaral GRS, Campeão ME, Swings J, Thompson FL, Thompson CC. Finding diagnostic phenotypic features of Photobacterium in the genome sequences. Antonie van Leeuwenhoek 2015; 107:1351-8. [PMID: 25724129 DOI: 10.1007/s10482-015-0414-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/23/2015] [Indexed: 01/14/2023]
Abstract
Photobacterium species are ubiquitous in the aquatic environment and can be found in association with animal hosts including pathogenic and mutualistic associations. The traditional phenotypic characterization of Photobacterium is expensive, time-consuming and restricted to a limited number of features. An alternative is to infer phenotypic information directly from whole genome sequences. The present study evaluates the usefulness of whole genome sequences as a source of phenotypic information and compares diagnostic phenotypes of the Photobacterium species from the literature with the predicted phenotypes obtained from whole genome sequences. All genes coding for the specific proteins involved in metabolic pathways responsible for positive phenotypes of the seventeen diagnostic features were found in the majority of the Photobacterium genomes. In the Photobacterium species that were negative for a given phenotype, at least one or several genes involved in the respective biochemical pathways were absent.
Collapse
Affiliation(s)
- Gilda Rose S Amaral
- Laboratory for Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | | | | | | |
Collapse
|
43
|
The fur gene as a new phylogenetic marker for Vibrionaceae species identification. Appl Environ Microbiol 2015; 81:2745-52. [PMID: 25662978 DOI: 10.1128/aem.00058-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is one of the main phylogenetic species markers; however, it does not provide discrimination in the family Vibrionaceae, where other molecular techniques allow better interspecies resolution. Although multilocus sequence analysis (MLSA) has been used successfully in the identification of Vibrio species, the technique has several limitations. They include the fact that several locus amplifications and sequencing have to be performed, which still sometimes lead to doubtful identifications. Using an in silico approach based on genomes from 103 Vibrionaceae strains, we demonstrate here the high resolution of the fur gene in the identification of Vibrionaceae species and its usefulness as a phylogenetic marker. The fur gene showed within-species similarity higher than 95%, and the relationships inferred from its use were in agreement with those observed for 16S rRNA analysis and MLSA. Furthermore, we developed a fur PCR sequencing-based method that allowed identification of Vibrio species. The discovery of the phylogenetic power of the fur gene and the development of a PCR method that can be used in amplification and sequencing of the gene are of general interest whether for use alone or together with the previously suggested loci in an MLSA.
Collapse
|
44
|
Bull CT, Koike ST. Practical benefits of knowing the enemy: modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:157-80. [PMID: 26002289 DOI: 10.1146/annurev-phyto-080614-120122] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California's Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and bacterial taxonomy. Whole-genome sequence analysis needs to become adequately accessible, automated, and affordable in order to be used routinely for identification and epidemiology. The power of molecular tools in accurately identifying bacterial pathogenesis is therefore of value to the farmer, diagnostician, phytobacteriologist, and taxonomist.
Collapse
Affiliation(s)
- Carolee T Bull
- United States Department of Agriculture, Agricultural Research Service, Salinas, California 93905;
| | | |
Collapse
|
45
|
Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 2014; 197:359-70. [PMID: 25533848 DOI: 10.1007/s00203-014-1071-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/20/2022]
Abstract
Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.
Collapse
|
46
|
Mazel D, Colwell R, Klose K, Oliver J, Crumlish M, McDougald D, Bland MJ, Austin B. VIBRIO 2014 meeting report. Res Microbiol 2014; 165:857-64. [PMID: 25463383 DOI: 10.1016/j.resmic.2014.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 10/15/2014] [Accepted: 10/15/2014] [Indexed: 11/16/2022]
Affiliation(s)
- Didier Mazel
- Unité Plasticité du Génome bactérien and CNRS UMR 3525, Département de Génomes et Génétique, Institut Pasteur, Paris, France.
| | - Rita Colwell
- Maryland Pathogen Research Institute and Center of Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Karl Klose
- Department of Biology, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - James Oliver
- Department of Biology, University North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Mags Crumlish
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - Diane McDougald
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, The University of New South Wales, Sydney 2052, Australia
| | - Michael J Bland
- Unité Plasticité du Génome bactérien and CNRS UMR 3525, Département de Génomes et Génétique, Institut Pasteur, Paris, France
| | - Brian Austin
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| |
Collapse
|
47
|
Du J, Lai Q, Liu Y, Du Y, Liu X, Sun F, Shao Z. Idiomarina atlantica sp. nov., a marine bacterium isolated from the deep sea sediment of the North Atlantic Ocean. Antonie Van Leeuwenhoek 2014; 107:393-401. [DOI: 10.1007/s10482-014-0337-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 11/15/2014] [Indexed: 10/24/2022]
|
48
|
Bina XR, Wong EA, Bina TF, Bina JE. Construction of a tetracycline inducible expression vector and characterization of its use in Vibrio cholerae. Plasmid 2014; 76:87-94. [PMID: 25451701 DOI: 10.1016/j.plasmid.2014.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 10/14/2014] [Accepted: 10/20/2014] [Indexed: 01/08/2023]
Abstract
We report the construction of a tetracycline inducible expression vector that allows regulated gene expression in the enteric pathogen Vibrio cholerae. The expression vector, named pXB300, contains the tetracycline regulatory elements from Tn10, a multiple cloning site downstream of the tetA promoter and operator sequences, a ColE1 origin of replication, a β-lactamase resistance gene for positive selection, and the hok/sok addiction system for selection in the absence of antibiotic. The function of the tetracycline expression system was demonstrated by cloning lacZ under control of the tetA promoter and quantifying β-galactosidase expression in Escherichia coli and V. cholerae. The utility for pXB300 was documented by complementation of V. cholerae virulence mutants during growth under virulence inducing conditions. The results showed that pXB300 allowed high-level expression of recombinant genes with linear induction in response to the exogenous concentration of the inducer anhydrotetracycline. We further show that pXB300 was reliably maintained in V. cholerae during growth in the absence of antibiotic selection.
Collapse
Affiliation(s)
- X Renee Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Eileen A Wong
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Thomas F Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - James E Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| |
Collapse
|
49
|
Ecophysiological diversity of a novel member of the genus Alteromonas, and description of Alteromonas mediterranea sp. nov. Antonie van Leeuwenhoek 2014; 107:119-32. [DOI: 10.1007/s10482-014-0309-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
|
50
|
Ng HJ, López-Pérez M, Webb HK, Gomez D, Sawabe T, Ryan J, Vyssotski M, Bizet C, Malherbe F, Mikhailov VV, Crawford RJ, Ivanova EP. Marinobacter salarius sp. nov. and Marinobacter similis sp. nov., isolated from sea water. PLoS One 2014; 9:e106514. [PMID: 25198502 PMCID: PMC4157798 DOI: 10.1371/journal.pone.0106514] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/31/2014] [Indexed: 11/18/2022] Open
Abstract
Two non-pigmented, motile, Gram-negative marine bacteria designated R9SW1T and A3d10T were isolated from sea water samples collected from Chazhma Bay, Gulf of Peter the Great, Sea of Japan, Pacific Ocean, Russia and St. Kilda Beach, Port Phillip Bay, the Tasman Sea, Pacific Ocean, respectively. Both organisms were found to grow between 4 °C and 40 °C, between pH 6 to 9, and are moderately halophilic, tolerating up to 20% (w/v) NaCl. Both strains were found to be able to degrade Tween 40 and 80, but only strain R9SW1T was found to be able to degrade starch. The major fatty acids were characteristic for the genus Marinobacter including C16:0, C16:1ω7c, C18:1ω9c and C18:1ω7c. The G+C content of the DNA for strains R9SW1T and A3d10T were determined to be 57.1 mol% and 57.6 mol%, respectively. The two new strains share 97.6% of their 16S rRNA gene sequences, with 82.3% similarity in the average nucleotide identity (ANI), 19.8% similarity in the in silico genome-to-genome distance (GGD), 68.1% similarity in the average amino acid identity (AAI) of all conserved protein-coding genes, and 31 of the Karlin's genomic signature dissimilarity. A phylogenetic analysis showed that R9SW1T clusters with M. algicola DG893T sharing 99.40%, and A3d10T clusters with M. sediminum R65T sharing 99.53% of 16S rRNA gene sequence similarities. The results of the genomic and polyphasic taxonomic study, including genomic, genetic, phenotypic, chemotaxonomic and phylogenetic analyses based on the 16S rRNA, gyrB and rpoD gene sequence similarities, the analysis of the protein profiles generated using MALDI-TOF mass spectrometry, and DNA-DNA relatedness data, indicated that strains R9SW1T and A3d10(T) represent two novel species of the genus Marinobacter. The names Marinobacter salarius sp. nov., with the type strain R9SW1(T) ( = LMG 27497(T) = JCM 19399(T) = CIP 110588(T) = KMM 7502(T)) and Marinobacter similis sp. nov., with the type strain A3d10(T) ( = JCM 19398(T) = CIP 110589(T) = KMM 7501T), are proposed.
Collapse
Affiliation(s)
- Hooi Jun Ng
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | | | - Hayden K. Webb
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Daniela Gomez
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries, Hokkaido University, Minato-cho, Hakodate, Japan
| | - Jason Ryan
- Callaghan Innovation, Lower Hutt, Wellington, New Zealand
| | | | - Chantal Bizet
- Collection de 1’Institut Pasteur, Institut Pasteur, Paris, France
| | - François Malherbe
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Valery V. Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, Primorski Krai, Russian Federation
| | - Russell J. Crawford
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Elena P. Ivanova
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| |
Collapse
|