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Ahn S, Choi DHS, Weerawongwiwat V, Kim JH, Sukhoom A, Kim W. Aquibaculum arenosum gen. nov., sp. nov., a novel member of the family Rhodovibrionaceae, isolated from sea sand. Int J Syst Evol Microbiol 2024; 74:006458. [PMID: 38995165 PMCID: PMC11316597 DOI: 10.1099/ijsem.0.006458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 07/02/2024] [Indexed: 07/13/2024] Open
Abstract
A Gram-negative, non-motile, and creamy-white coloured bacterium, designated CAU 1616T, was isolated from sea sand collected at Ayajin Beach, Goseong-gun, Republic of Korea. The bacterium was found to grow optimally at 37 °C, pH 8.0-8.5, and with 1-5 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain CAU 1616T within the order Rhodospirillales. The highest 16S rRNA gene sequence similarity was to Fodinicurvata fenggangensis YIM D812T (94.1 %), Fodinicurvata sediminis YIM D82T (93.7 %), Fodinicurvata halophila BA45ALT (93.6 %) and Algihabitans albus HHTR 118T (92.3 %). Comparing strain CAU 1616T with closely related species (Fodinicurvata fenggangensis YIM D812T and Fodinicurvata sediminis YIM D82T), the average nucleotide identity based on blast+ values were 69.7-69.8 %, the average amino acid identity values were 61.3-61.4 %, and the digital DNA-DNA hybridization values were 18.4-18.5 %. The assembled draft genome of strain CAU 1616T had 29 contigs with an N50 value of 385.8 kbp, a total length of 3 490 371 bp, and a DNA G+C content of 65.1 mol%. The predominant cellular fatty acids were C18 : 1 2-OH, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The major respiratory quinone was Q-10. Based on phenotypic, phylogenetic, and chemotaxonomic evidence, strain CAU 1616T represents a novel genus in the family Rhodovibrionaceae, for which the name Aquibaculum arenosum gen. nov., sp. nov. is proposed. The type strain is CAU 1616T (=KCTC 82428T=MCCC 1K06089T).
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Affiliation(s)
- Soyeon Ahn
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - David Hyung-Sun Choi
- Faculty of Arts and Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
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2
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Ahn S, Weerawongwiwat V, Lee Y, Choi DHS, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W. Description of Roseibium sediminicola sp. nov. Isolated from Sediment of a Tidal Flat on the Yellow Sea Coast. Curr Microbiol 2024; 81:150. [PMID: 38647555 DOI: 10.1007/s00284-024-03681-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/29/2024] [Indexed: 04/25/2024]
Abstract
A Gram-stain-negative, aerobic, rod-shaped, motile, flagellated bacterial strain, designated as CAU 1639T, was isolated from the tidal flat sediment on the Yellow Sea in the Republic of Korea. Growth of the isolate was observed at 20-37 °C, at pH 5.0-10.5 and with 0-7% (w/v) NaCl. The genomic DNA G + C content was 60.8%. Phylogenetic analysis, grounded on 16S rRNA gene sequencing, revealed that strain CAU 1639T was closely related to species within the genus Roseibium. It shared the highest similarity with Roseibium album CECT 5095T, followed by Roseibium aggregatum IAM 12614T and Roseibium salinum Cs25T, with 16S rRNA gene sequence similarity ranging from 98.0-98.4%. It was observed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values ranged between 72.5-79.5 and 20.0-22.9%, respectively. The polyphasic taxonomic analysis reveals that strain CAU 1639T represents a novel species in the genus Roseibium with the proposed name Roseibium sediminicola sp. nov. The type strain is CAU 1639T (= KCTC 82430T = MCCC 1K06081T).
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Affiliation(s)
- Soyeon Ahn
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Yunjeong Lee
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - David Hyung-Sun Choi
- Faculty of Arts and Science, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Jung-Hoon Yoon
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jung-Sook Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea.
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Filippova IP, Makhutova ON, Guseynova VE, Gladyshev MI. Fatty Acid Profiles of Some Siberian Bryophytes and Prospects of Their Use in Chemotaxonomy. Biomolecules 2023; 13:biom13050840. [PMID: 37238711 DOI: 10.3390/biom13050840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/09/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
The composition of fatty acids (FAs) in gametophyte samples of 20 Siberian bryophyte species from four orders of mosses and four orders of liverworts collected in relatively cold months (April and/or October) was examined. FA profiles were obtained using gas chromatography. Thirty-seven FAs were found, from 12:0 to 26:0; they included mono-, polyunsaturated (PUFAs) and rare FAs, such as 22:5n-3 and two acetylenic FAs, 6a,9,12-18:3 and 6a,9,12,15-18:4 (dicranin). Acetylenic FAs were found in all examined species of the Bryales and Dicranales orders, dicranin being the predominant FA. The role of particular PUFAs in mosses and liverworts is discussed. Multivariate discriminant analysis (MDA) was performed to determine whether FAs can be used in the chemotaxonomy of bryophytes. Based on the MDA results, FA composition is related to the taxonomic status of species. Thus, several individual FAs were identified as chemotaxonomic markers at the level of bryophyte orders. These were 18:3n-3; 18:4n-3; 6a,9,12-18:3; 6a,9,12,15-18:4; 20:4n-3 and EPA in mosses and 16:3n-3; 16:2n-6; 18:2n-6; 18:3n-3 and EPA in liverworts. These findings indicate that further research into bryophyte FA profiles can shed light on phylogenetic relationships within this group of plants and the evolution of their metabolic pathways.
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Affiliation(s)
- Irina P Filippova
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodny av., Krasnoyarsk 660041, Russia
| | - Olesia N Makhutova
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodny av., Krasnoyarsk 660041, Russia
- Institute of Biophysics, Krasnoyarsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Valeriya E Guseynova
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodny av., Krasnoyarsk 660041, Russia
| | - Michail I Gladyshev
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodny av., Krasnoyarsk 660041, Russia
- Institute of Biophysics, Krasnoyarsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
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4
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Tsertou MI, Triga A, Droubogiannis S, Kokkari C, Anasi G, Katharios P. Isolation and characterization of a novel Tenacibaculum species and a corresponding bacteriophage from a Mediterranean fish hatchery: Description of Tenacibaculum larymnensis sp. nov. and Tenacibaculum phage Larrie. Front Microbiol 2023; 14:1078669. [PMID: 36925475 PMCID: PMC10013915 DOI: 10.3389/fmicb.2023.1078669] [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: 11/01/2022] [Accepted: 01/30/2023] [Indexed: 03/08/2023] Open
Abstract
Tenacibaculum larymnensis sp. nov., a novel species of the Tenacibaculum genus was isolated from a commercial fish hatchery in Greece. The novel species is phylogenetically close to T. discolor and was biochemically and genetically characterized. The genome of T. larymnensis has 3.66 Mbps length, 31.83% GC content and the genomic analysis demonstrated that it harbors a wide enzymatic repertoire suggestive of increased degrading capacity but also several virulence factors including hemolysins, secretion systems, transporters, siderophores, pili and extracellular proteins. Using the novel strain, a virulent bacteriophage designated as Tenacibaculum phage Larrie was isolated and characterized. Larrie is a novel Siphovirus with relatively large genome, 77.5 kbps with 111 ORFs, a GC content of 33.7% and an exclusively lytic lifestyle. The new phage-host system can serve as an efficient model to study microbial interactions in the aquatic environment which contribute to the nutrient cycling.
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Affiliation(s)
- Maria Ioanna Tsertou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Stavros Droubogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Constantina Kokkari
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | | | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
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5
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Guan Y, Li Z, Kim MJ, Lee JY, Choe H, Park SH, Kang SW, Lee J, Lee JH, Kim HB, Lee JH, Kim E, Lee MK. Olsenella intestinalis sp. nov., isolated from cow feces. Arch Microbiol 2022; 204:384. [PMID: 35689096 DOI: 10.1007/s00203-022-03017-2] [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: 04/08/2022] [Accepted: 05/22/2022] [Indexed: 11/02/2022]
Abstract
A Gram-stain-negative, anaerobic, non-motile, rod-shaped bacterium, designated as BGYT1T, was isolated from the feces of a cow in Andong, Republic of Korea. It was studied using a polyphasic method to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BGYT1T formed a lineage within the genus Olsenella and was most closely related to O. umbonate KCTC 15140T (98.2%). The complete genome sequence of strain BGYT1T was 2,476,083 bp long with a G + C content of 66.9 mol% and contained 1835 genes and 8 contigs. The N50 value was 604,117 bp. There were 50 tRNAs, 6 rRNAs (5S, 16S, 23S), 1778 CDSs and 2 BGCs and 1 tmRNA. The values for ANI (76.8%), AAI (67.3%), and dDDH (22.2%) compared to the closest related species were all below the threshold for bacterial species delineation. In addition, genes encoding the cell wall degrading enzymes such as chitinases, β-1,3 glucanases, and proteases were also detected. The strain was able to grow at pH 6.0-8.0 (optimum, pH 7.0), in the presence of 0.5-1.5% NaCl (optimum, 0.5%, w/v) and at the temperature range of 35-40 °C (optimum, 35 °C). The predominant fatty acids were C16:0 DMA (20.2%), C16:0 (20.2%), C18:0 (10.5%) and C18:1 cis 9 (17.0%). The polar lipids consisted of an unidentified phospholipid, four unidentified glycolipids and three unidentified lipids. Based on its phenotypic analyses, phylogenetic and physiological characteristics, strain BGYT1T represented a novel species within the genus Olsenella, for which the name Olsenella intestinalis sp. nov. is proposed. The type strain is BGYT1T (= KCTC 25379T = GDMCC 1.3011T).
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Affiliation(s)
- Yong Guan
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.,Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Zhun Li
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Min-Ju Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jae-Young Lee
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Hanna Choe
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seung-Hwan Park
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Se Won Kang
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jiyoung Lee
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Ju Huck Lee
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan, 31116, South Korea
| | - Ju-Hoon Lee
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eunju Kim
- Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Mi-Kyung Lee
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.
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6
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Guan Y, Jiang Y, Kim YM, Yu SY, Choi SH, Choe H, Li Z, Lee MK. Pseudophaeobacter flagellatus sp. nov., isolated from coastal water. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile, rod-shaped novel bacterial strain, designated as MA21411-1T, was isolated from the Korean coast. The colonies were white-yellow-coloured, smooth, convex and entire, spherical and 1.0–1.8 mm in diameter. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MA21411-1T is closely related to species of the genus
Pseudophaeobacter
. The 16S rRNA gene sequence similarities between strain MA21411-1T and
Pseudophaeobacter arcticus
DSM 23566T,
Phaeobacter porticola
DSM 103148T and
Pseudophaeobacter leonis
DSM 25627T were 98.31, 97.80 and 97.28 %, respectively. Strain MA21411-1T has a draft genome size of 4 294 042 bp, annotated with 4125 protein-coding genes, and 53 tRNA, three rRNA and one tmRNA genes. The genomic DNA G+C content was 59.2 mol%. Comparative genome analysis revealed that the average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values among strain MA21411-1T and other related species were below the cut-off levels of 95, 70 and 95.5 %, respectively. The growth temperature range for growth was 15–28 °C (optimum, 25 °C), pH range was 6.0–9.0 (optimum, pH 6.0), and salt tolerance range was 0.5–4 % (optimum 0.5 %). Ubiquinone-10 was the sole quinone present in MA21411-1T and all three closely related strains. The major cellular fatty acid (>10 %) of the strain was summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c). The polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and four unidentified polar lipids. Based on the phylogenetic tree, as well as phenotypic, chemotaxonomic and genomic features, strain MA21411-1T represents a novel species of the genus
Pseudophaeobacter
, for which the name Pseudophaeobacter flagellatus sp. nov. is proposed. The type strain is MA21411-1T (=KCTC 92095T=GDMCC 1.2988T).
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Affiliation(s)
- Yong Guan
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Yue Jiang
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Young-Min Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seung Yeob Yu
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Seung-Hyeon Choi
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Hanna Choe
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Zhun Li
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Mi-Kyung Lee
- Biological Resource Center, Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
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Evaluating the Bacterial Diversity from the Southwest Coast of India Using Fatty Acid Methyl Ester Profiles. Curr Microbiol 2021; 78:649-658. [PMID: 33392676 DOI: 10.1007/s00284-020-02315-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
The fatty acid composition of bacterial isolates remains stable under standardized culture conditions, which makes it a useful taxonomic marker. The present study aims to characterize the diversity and quantity of fatty acid methyl esters (FAME) profiles of cultivable bacterial isolates collected along the southwest coast of India. Based on the similarity indices (range > 0.3-0.7) of the FAME profiles, the isolates were aggregated into 10 families, 11 genera and 19 species of cultured isolates. The following classes of bacteria were found: Bacilli, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Actinobacteria, which also included a few pathogens such as Pseudomonas, Staphylococcus and Bacillus sp. The hydroxyl FAMEs 2-hydroxydodecanoic acid (C12:0 2OH), 2-hydroxypentadecanoic acid (C15:0 2OH),3-hydroxy 14-methylpentadecanoic acid (C16:0iso 3OH), 3 hydroxy hexadecenoic acid (C16:0 3OH) and 3-hydroxy 15-methylhexadecanoic acid (C17:0iso 3OH), as well as the unsaturated FAMEs (11Z)-11-hexadecenoic acid (C16:1 ɷ5c), were exclusively associated with the isolates from Mangalore samples. Similarly, FAMEs 2-hydroxydecanoic acid (C10:0 2OH), 9-methyldecanoic acid (C11:0iso), undecanoic acid (C11:0), tridecanoic acid (C13:0), 10-methylhexadecanoic acid (C16:0 10-CH3) and (7Z)-7-hexadecenoic acid (C16:1 ɷ9c) occurred only in the isolates from Trivandrum samples. However, the isolates from Goa did not possess a signature FAME profile. The reproducibility of the GC-MIDI bacterial identification system was evaluated using 16S rRNA gene sequencing techniques for selected isolates.
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Nowlan JP, Lumsden JS, Russell S. Advancements in Characterizing Tenacibaculum Infections in Canada. Pathogens 2020; 9:pathogens9121029. [PMID: 33302445 PMCID: PMC7763822 DOI: 10.3390/pathogens9121029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Tenacibaculum is a genus of gram negative, marine, filamentous bacteria, associated with the presence of disease (tenacibaculosis) at aquaculture sites worldwide; however, infections induced by this genus are poorly characterized. Documents regarding the genus Tenacibaculum and close relatives were compiled for a literature review, concentrating on ecology, identification, and impacts of potentially pathogenic species, with a focus on Atlantic salmon in Canada. Tenacibaculum species likely have a cosmopolitan distribution, but local distributions around aquaculture sites are unknown. Eight species of Tenacibaculum are currently believed to be related to numerous mortality events of fishes and few mortality events in bivalves. The clinical signs in fishes often include epidermal ulcers, atypical behaviors, and mortality. Clinical signs in bivalves often include gross ulcers and discoloration of tissues. The observed disease may differ based on the host, isolate, transmission route, and local environmental conditions. Species-specific identification techniques are limited; high sequence similarities using conventional genes (16S rDNA) indicate that new genes should be investigated. Annotating full genomes, next-generation sequencing, multilocus sequence analysis/typing (MLSA/MLST), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF), and fatty acid methylesters (FAME) profiles could be further explored for identification purposes. However, each aforementioned technique has disadvantages. Since tenacibaculosis has been observed world-wide in fishes and other eukaryotes, and the disease has substantial economic impacts, continued research is needed.
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Affiliation(s)
- Joseph P. Nowlan
- Department of Pathobiology, University of Guelph, Guelph, OT N1G 2W1, Canada;
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada;
- Correspondence:
| | - John S. Lumsden
- Department of Pathobiology, University of Guelph, Guelph, OT N1G 2W1, Canada;
| | - Spencer Russell
- Center for Innovation in Fish Health, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada;
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Genetic diversity and population structure of Tenacibaculum maritimum, a serious bacterial pathogen of marine fish: from genome comparisons to high throughput MALDI-TOF typing. Vet Res 2020; 51:60. [PMID: 32381115 PMCID: PMC7204230 DOI: 10.1186/s13567-020-00782-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/08/2020] [Indexed: 01/08/2023] Open
Abstract
Tenacibaculum maritimum is responsible for tenacibaculosis, a devastating marine fish disease. This filamentous bacterium displays a very broad host range and a worldwide geographical distribution. We analyzed and compared the genomes of 25 T. maritimum strains, including 22 newly draft-sequenced genomes from isolates selected based on available MLST data, geographical origin and host fish. The genome size (~3.356 Mb in average) of all strains is very similar. The core genome is composed of 2116 protein-coding genes accounting for ~75% of the genes in each genome. These conserved regions harbor a moderate level of nucleotide diversity (~0.0071 bp-1) whose analysis reveals an important contribution of recombination (r/m ≥ 7) in the evolutionary process of this cohesive species that appears subdivided into several subgroups. Association trends between these subgroups and specific geographical origin or ecological niche remains to be clarified. We also evaluated the potential of MALDI-TOF-MS to assess the variability between T. maritimum isolates. Using genome sequence data, several detected mass peaks were assigned to ribosomal proteins. Additionally, variations corresponding to single or multiple amino acid changes in several ribosomal proteins explaining the detected mass shifts were identified. By combining nine polymorphic biomarker ions, we identified combinations referred to as MALDI-Types (MTs). By investigating 131 bacterial isolates retrieved from a variety of isolation sources, we identified twenty MALDI-Types as well as four MALDI-Groups (MGs). We propose this MALDI-TOF-MS Multi Peak Shift Typing scheme as a cheap, fast and an accurate method for screening T. maritimum isolates for large-scale epidemiological surveys.
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Insights into the microbiome of farmed Asian sea bass (Lates calcarifer) with symptoms of tenacibaculosis and description of Tenacibaculum singaporense sp. nov. Antonie van Leeuwenhoek 2020; 113:737-752. [PMID: 32080799 DOI: 10.1007/s10482-020-01391-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/03/2020] [Indexed: 12/26/2022]
Abstract
Outbreaks of diseases in farmed fish remain a recurring problem despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease in tropical aquaculture of the South-East Asian region is tenacibaculosis, which is attributed to members of the genus Tenacibaculum (family Flavobacteriaceae, phylum Bacteroidetes), most notably Tenacibaculum maritimum. The impact of tenacibaculosis on the fish microbiota remains poorly understood. In this study, we analysed the microbiota of different tissues of commercially reared Asian seabass (Lates calcarifer) that showed symptoms of tenacibaculosis and compared the microbial communities to those of healthy and experimentally infected fish that were exposed to diseased farmed fish. The relative abundance of Tenacibaculum species in experimentally infected fish was significantly lower than in commercially reared diseased fish and revealed a higher prevalence of different Tenacibaculum species. One isolated strain, TLL-A2T, shares 98.7% 16S rRNA gene identity with Tenacibaculum mesophilum DSM 13764T. The genome of strain TLL-A2T was sequenced and compared to that of T. mesophilum DSM 13764T. Analysis of average nucleotide identity and comparative genome analysis revealed only 92% identity between T. mesophilum DSM 13764T and strain TLL-A2T and differences between the two strains in predicted carbohydrate activating enzymes respectively. Phenotypic comparison between strain TLL-A2T and T. mesophilum DSM 13764T indicated additional differences, such as growth response at different salt concentrations. Based on molecular and phenotypic differences, strain TLL-A2T (=DSM 106434T, KCTC 62393T) is proposed as the type strain of Tenacibaculum singaporense sp. nov.
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Yu SY, Kim JS, Oh BS, Park SH, Kang SW, Park JE, Choi SH, Han KI, Lee KC, Eom MK, Suh MK, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JS, Lee JH. Bacteroides faecalis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2019; 69:3824-3829. [PMID: 31511127 DOI: 10.1099/ijsem.0.003690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative and strictly anaerobic bacterial strain, designated KGMB02408T, was isolated from faeces of a healthy human in the Republic of Korea. The isolate was characterized as non-motile, non-spore-forming and rod-shaped (variable in length). The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KGMB02408T belonged to the genus Bacteroides and was most closely related to Bacteroides faecichinchillae JCM 17102T (=KCTC 15666T; 96.5 %). Based on its whole-genome sequence, the DNA G+C content of the isolate was 39.5 mol%. The average nucleotide identity value between strain KGMB02408T and related species, B. faecichinchillae JCM 17102T, was 93.8 %. The major cellular fatty acids (>10 %) of the isolate were anteiso-C15 : 0, iso-C17 : 0-OH, summed feature 11 (iso-C17 : 0-OH and/or C18 : 2 DMA) and C16 : 0. Menaquinone-8 (28.6 %) and menaquinone-10 (47.1 %) were detected as the major respiratory quinones in the isolate. The major end products of glucose fermentation produced by strain KGMB02408T were lactic acid, acetic acid and formic acid. Based on its phylogenetic, phenotypic and chemotaxonomic characteristics, strain KGMB02408T represents a novel species of the genus Bacteroides in the family Bacteroidaceae. The type strain is KGMB02408T (=KCTC 15687T=DSM 107828T).
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Affiliation(s)
- Seung Yeob Yu
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Byeong Seob Oh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Jam-Eon Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Seung-Hyeon Choi
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Kook-Il Han
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Dong Ho Lee
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-gil, Bundang-Gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Hyuk Yoon
- Seoul National University Bundang Hospital, 82 Gumi-ro, 173 Beon-gil, Bundang-Gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Byung-Yong Kim
- ChunLab, Inc., 2477 Nambusunhwan-ro, Seocho-gu, Republic of Korea
| | - Seung-Jo Yang
- ChunLab, Inc., 2477 Nambusunhwan-ro, Seocho-gu, Republic of Korea
| | - Jung-Sook Lee
- University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.,Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
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Identification and typing of fish pathogenic species of the genus Tenacibaculum. Appl Microbiol Biotechnol 2018; 102:9973-9989. [DOI: 10.1007/s00253-018-9370-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 02/07/2023]
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13
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Comparison of serological and molecular typing methods for epidemiological investigation of Tenacibaculum species pathogenic for fish. Appl Microbiol Biotechnol 2018; 102:2779-2789. [PMID: 29453634 DOI: 10.1007/s00253-018-8825-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/16/2018] [Accepted: 01/20/2018] [Indexed: 02/04/2023]
Abstract
In the present study, the potential of serological methods, the repetitive extragenic palindromic PCR (REP-PCR) and the enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) for the typing of the species Tenacibaculum maritimum, Tenacibaculum soleae and Tenacibaculum discolor was evaluated. Moreover, molecular and proteomic techniques were used to assess variability among strains belonging to different serotypes, as well as isolated from different host species and geographical areas. Slide agglutination and dot-blot assays demonstrated the lack of immunological relationships among Tenacibaculum species analyzed. The serotype O1 was predominant within T. maritimum isolates regardless of the fish species or geographical area. Two serotypes were distinguished within T. soleae isolates and at least one within T. discolor strains. Species- and strain-specific profiles were obtained from the analysis of T. maritimum, T. soleae and T. discolor by REP-PCR and ERIC-PCR, demonstrating their potential as diagnostic tools. The genotyping analysis using both techniques showed genetic variability among the strains of each fish pathogenic Tenacibaculum species analysed. However, Tenacibaculum strains isolated from different host species or geographical areas or belonging to different serotypes produced REP and ERIC profiles with high similarity. Analysis by MALDI-TOF-MS of the T. maritimum strains could not detect any serotype-identifying biomarkers. Serotype-specific mass peaks were found for the serotypes O1 and O2 of T. soleae and for the serotype O1 of T. discolor. However, no relationships between the proteomic profiles and the source of isolation of the strains were obtained for any of the Tenacibaculum species analysed in this study.
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14
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Apablaza P, Frisch K, Brevik ØJ, Småge SB, Vallestad C, Duesund H, Mendoza J, Nylund A. Primary Isolation and Characterization of Tenacibaculum maritimum from Chilean Atlantic Salmon Mortalities Associated with a Pseudochattonella spp. Algal Bloom. JOURNAL OF AQUATIC ANIMAL HEALTH 2017; 29:143-149. [PMID: 28613984 DOI: 10.1080/08997659.2017.1339643] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
This study presents the first isolation of Tenacibaculum maritimum from farmed Atlantic Salmon Salmo salar in Chile. The isolate, designated T. maritimum Ch-2402, was isolated from gills of Atlantic Salmon at a farm located in region X, Los Lagos, Chile, during the harmful algal bloom caused by Pseudochattonella spp. in February 2016. The algal bloom is reported to have caused 40,000 metric tons of mortality in this salmon farming area. The bacterium T. maritimum, which causes tenacibaculosis, is recognized as an important pathogen of marine fish worldwide. Genetic, phylogenetic, and phenotypic characterizations were used to describe the T. maritimum Ch-2402 isolate. The isolate was similar to the type strain of T. maritimum but was genetically unique. Tenacibaculum dicentrarchi isolates were also recovered during sampling from the same farm. Based on the fact that T. maritimum has been shown to cause disease in Atlantic Salmon in other regions, the presence of this bacterium poses a potential risk of disease to fish in the Chilean aquaculture industry. Received November 6, 2016; accepted May 29, 2017.
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Affiliation(s)
- Patricia Apablaza
- a Fish Disease Research Group, Department of Biology , University of Bergen , Thormøhlensgate 55, Bergen N-5020 , Norway
- b Cermaq Group AS , Dronning Eufemias Gate 16, Post Office Box 144, Sentrum , Oslo N-0102 , Norway
| | - Kathleen Frisch
- a Fish Disease Research Group, Department of Biology , University of Bergen , Thormøhlensgate 55, Bergen N-5020 , Norway
- b Cermaq Group AS , Dronning Eufemias Gate 16, Post Office Box 144, Sentrum , Oslo N-0102 , Norway
| | - Øyvind Jakobsen Brevik
- b Cermaq Group AS , Dronning Eufemias Gate 16, Post Office Box 144, Sentrum , Oslo N-0102 , Norway
| | - Sverre Bang Småge
- a Fish Disease Research Group, Department of Biology , University of Bergen , Thormøhlensgate 55, Bergen N-5020 , Norway
- b Cermaq Group AS , Dronning Eufemias Gate 16, Post Office Box 144, Sentrum , Oslo N-0102 , Norway
| | - Camilla Vallestad
- a Fish Disease Research Group, Department of Biology , University of Bergen , Thormøhlensgate 55, Bergen N-5020 , Norway
| | - Henrik Duesund
- b Cermaq Group AS , Dronning Eufemias Gate 16, Post Office Box 144, Sentrum , Oslo N-0102 , Norway
| | - Julio Mendoza
- c Cermaq Chile , Diego Portales 2000, Piso 10, Puerto Montt , Chile
| | - Are Nylund
- a Fish Disease Research Group, Department of Biology , University of Bergen , Thormøhlensgate 55, Bergen N-5020 , Norway
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15
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Fernández-Álvarez C, Torres-Corral Y, Saltos-Rosero N, Santos Y. MALDI-TOF mass spectrometry for rapid differentiation of Tenacibaculum species pathogenic for fish. Appl Microbiol Biotechnol 2017; 101:5377-5390. [DOI: 10.1007/s00253-017-8324-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/29/2017] [Accepted: 04/29/2017] [Indexed: 11/24/2022]
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16
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Faílde LD, Bermúdez R, Losada AP, Riaza A, Santos Y, Quiroga MI. Immunohistochemical diagnosis of tenacibaculosis in paraffin-embedded tissues of Senegalese sole Solea senegalensis Kaup, 1858. JOURNAL OF FISH DISEASES 2014; 37:959-968. [PMID: 24274927 DOI: 10.1111/jfd.12199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/17/2013] [Accepted: 09/20/2013] [Indexed: 06/02/2023]
Abstract
A sensitive and specific immunohistochemical technique was developed to improve the diagnosis of tenacibaculosis and to better understand its pathogenesis. Senegalese sole Solea senegalensis Kaup, 1858 were inoculated subcutaneously with a bacterial suspension of Tenacibaculum maritimum, and samples were taken at different hours post-inoculation. Sections from different organs were used as positive controls. In addition, a total of 128 field samples from different organs collected from tenacibaculosis outbreaks were used. Tenacibaculum maritimum antigens were detected in several organs of experimentally infected Senegalese sole and in at least one of the tissues from fish suffering from natural tenacibaculosis previously confirmed by culture and PCR-based methods. In fish collected during outbreaks, a strong positive reaction was detected in ulcerative skin areas. Moreover, bacterial antigen was identified inside scale pockets and in sites of the skin with mild lesion. In kidney and spleen, evident immunostaining of bacterial antigen was detected in both naturally and experimentally infected fish. Besides, the presence of T. maritimum in the intestinal tract without associated histological changes suggests that this organ may act as a reservoir for T. maritimum. The results of this study confirm the usefulness of IHC for the diagnosis of tenacibaculosis in paraffin-embedded tissues.
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Affiliation(s)
- L D Faílde
- Departamento de Ciencias Clínicas Veterinarias, Universidad de Santiago de Compostela, Lugo, Spain
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17
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Das S, Dash HR, Mangwani N, Chakraborty J, Kumari S. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Methods 2014; 103:80-100. [PMID: 24886836 DOI: 10.1016/j.mimet.2014.05.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 12/29/2022]
Abstract
The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.
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Affiliation(s)
- Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
| | - Hirak R Dash
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Neelam Mangwani
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Supriya Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
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18
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Avendaño-Herrera R, Balboa S, Castro N, González-Contreras A, Magariños B, Fernández J, Toranzo AE, Romalde JL. Comparative polyphasic characterization of Streptococcus phocae strains with different host origin and description of the subspecies Streptococcus phocae subsp. salmonis subsp. nov. Int J Syst Evol Microbiol 2014; 64:1775-1781. [PMID: 24573159 DOI: 10.1099/ijs.0.056978-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic study was undertaken to clarify the taxonomic position of Streptococcus phocae strains isolated from Atlantic salmon (Salmo salar) cage-farmed in Chile. Four salmon and three seal isolates showed minor differences in the SDS-PAGE protein analysis. Thus, a major protein band present in the salmon isolates, of approximately 22.4 kDa, was absent in the pinniped strains, regardless of the growth media employed. In addition, the pinniped strains showed protein bands with molecular masses of 71.5 and 14.2 kDa, when grown on trypticase soy agar supplemented with 1% NaCl, or 25.6 kDa, when grown on Columbia blood agar, not present in the Atlantic salmon strains. A high similarity in the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS spectra of the strains was observed, although some minor peaks were absent in the fish isolates. Fatty acid methyl esters from isolates with different host origin significantly (P<0.05) differed in the content of C16:0, C17:0, C18:1ω9c, C20:4ω6,9,12,15c and summed features 3, 5 and 8. The salmon isolates formed a separate cluster in the phylogenetic analysis of housekeeping genes, separately or as concatenated sequences. Sequence divergences among salmon and seal strains were in the range of inter-subspecies differentiation for groEL (2.5%), gyrB (1.8%), recN (2.1%), rpoB (1.7%) and sodA (2.0%) genes. DNA-DNA hybridization results confirmed those of sequencing, showing reassociation values between seal and salmon strains close to the borderline of species definition. Differences in growth at low temperatures and in the haemolytic capacities were also observed between both groups of isolates. On the basis of all these results, the salmon isolates represent a novel subspecies of S. phocae, for which the name Streptococcus phocae subsp. salmonis subsp. nov. is proposed. The type strain is C-4T (=CECT 7921T=DSM 24768T). The subspecies Streptococcus phocae subsp. phocae subsp. nov. is automatically created. An emended description of S. phocae is also provided.
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Affiliation(s)
- Ruben Avendaño-Herrera
- Interdisciplinary Center for Aquaculture Research (INCAR), O'Higgins 1695, Concepción, Chile.,Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola Facultad de Ciencias Biológicas, Universidad Andrés Bello, Viña del Mar, Chile
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Spain
| | - Nuria Castro
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Spain
| | - Alberto González-Contreras
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola Facultad de Ciencias Biológicas, Universidad Andrés Bello, Viña del Mar, Chile
| | - Beatriz Magariños
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Spain
| | - Jorge Fernández
- Laboratorio de Genética Molecular, Instituto de Salud Pública, Chile
| | - Alicia E Toranzo
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Spain
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Johnson WR, Torralba M, Fair PA, Bossart GD, Nelson KE, Morris PJ. Novel diversity of bacterial communities associated with bottlenose dolphin upper respiratory tracts. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:555-562. [PMID: 23765934 DOI: 10.1111/j.1758-2229.2009.00080.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Respiratory illness is thought to be most the common cause of death in both wild and captive populations of bottlenose dolphins (Tursiops truncatus). The suspected pathogens that have been isolated from diseased animals have also been isolated from healthy individuals, suggesting they may be part of the normal flora. Our current understanding of the bacteria associated with the upper respiratory tract (URT) of bottlenose dolphins is based exclusively upon culture-based isolation and identification. Because < 1% of naturally occurring bacteria are culturable, a substantial fraction of the bacterial community associated with the dolphin URT remains to be described. The dolphin URT microbiota revealed by sequencing of bacterial 16S rDNA exhibits almost no overlap with the taxa indicated in culture-based studies. The most abundant sequences in our libraries were similar among all of our study animals and shared the greatest homology to sequences of bacteria belonging to the genera Cardiobacterium, Suttonella, Psychrobacter, Tenacibaculum, Fluviicola and Flavobacterium; however, they were sufficiently different from database sequences from both cultured and uncultured organisms to suggest they represent novel genera and species. Our findings also demonstrate the dominance of three of the four bacterial phyla that dominate other mammalian microbiomes, including those of humans, and show tremendous diversity at the species/strain level, suggesting tight coevolution of the dolphin host and its URT bacterial community.
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Affiliation(s)
- Wesley R Johnson
- Department of Biology, College of Charleston, Charleston, SC 29401, USA. Hollings Marine Laboratory, 331 Ft. Johnson Rd., Charleston, SC 29412, USA. J. Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA. Center for Coastal Environmental Health and Biomolecular Research, NOAA National Ocean Service, 219 Fort Johnson Rd. Charleston, SC 29412, USA. Georgia Aquarium, 225 Baker St., NW, Atlanta, GA 30313, USA
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Saini V, Raghuvanshi S, Talwar GP, Ahmed N, Khurana JP, Hasnain SE, Tyagi AK, Tyagi AK. Polyphasic taxonomic analysis establishes Mycobacterium indicus pranii as a distinct species. PLoS One 2009; 4:e6263. [PMID: 19606228 PMCID: PMC2707620 DOI: 10.1371/journal.pone.0006263] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 06/09/2009] [Indexed: 02/07/2023] Open
Abstract
Background Mycobacterium indicus pranii (MIP), popularly known as Mw, is a cultivable, non-pathogenic organism, which, based on its growth and metabolic properties, is classified in Runyon Group IV along with M. fortuitum, M. smegmatis and M. vaccae. The novelty of this bacterium was accredited to its immunological ability to undergo antigen driven blast transformation of leukocytes and delayed hypersensitivity skin test in leprosy patients, a disease endemic in the Indian sub-continent. Consequently, MIP has been extensively evaluated for its biochemical and immunological properties leading to its usage as an immunomodulator in leprosy and tuberculosis patients. However, owing to advances in sequencing and culture techniques, the citing of new strains with almost 100% similarity in the sequences of marker genes like 16S rRNA, has compromised the identity of MIP as a novel species. Hence, to define its precise taxonomic position, we have carried out polyphasic taxonomic studies on MIP that integrate its phenotypic, chemotaxonomic and molecular phylogenetic attributes. Methodology/Principal Findings The comparative analysis of 16S rRNA sequence of MIP by using BLAST algorithm at NCBI (nr database) revealed a similarity of ≥99% with M. intracellulare, M. arosiense, M. chimaera, M. seoulense, M. avium subsp. hominissuis, M. avium subsp. paratuberculosis and M. bohemicum. Further analysis with other widely used markers like rpoB and hsp65 could resolve the phylogenetic relationship between MIP and other closely related mycobacteria apart from M. intracellulare and M. chimaera, which shares ≥99% similarity with corresponding MIP orthologues. Molecular phylogenetic analysis, based on the concatenation of candidate orthologues of 16S rRNA, hsp65 and rpoB, also substantiated its distinctiveness from all the related organisms used in the analysis excluding M. intracellulare and M. chimaera with which it exhibited a close proximity. This necessitated further analysis of MIP with more sensitive and segregating parameters to ascertain its precise taxonomic position as a new species. The analysis of MIP and its comparison with other mycobacterial reference strains based on cellular and biochemical features, growth characteristics and chemotaxonomic studies like FAME profiling confirmed that MIP is uniquely endowed with diverse metabolic attributes that effectively distinguishes it from all the closely related mycobacteria including M. intracellulare and M. chimaera. Conclusion The results presented in this study coupled with the non-pathogenic nature and different biochemical and immunomodulatory properties of MIP affirm it as a distinct species belonging to M. avium complex (MAC). It is further proposed to use an earlier suggested name Mycobacterium indicus pranii for this newly established mycobacterial species. This study also exemplifies the growing need for a uniform, consensus based broader polyphasic frame work for the purpose of taxonomy and speciation, particularly in the genus Mycobacterium.
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Affiliation(s)
- Vikram Saini
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Niyaz Ahmed
- Pathogen Biology Laboratory, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Jitendra P. Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Seyed E. Hasnain
- Institute of Life Sciences, University of Hyderabad, Hyderabad, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Akhilesh K. Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Anil K. Tyagi
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
- * E-mail:
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Lee YS, Baik KS, Park SY, Kim EM, Lee DH, Kahng HY, Jeon CO, Jung JS. Tenacibaculum crassostreae sp. nov., isolated from the Pacific oyster, Crassostrea gigas. Int J Syst Evol Microbiol 2009; 59:1609-14. [PMID: 19542127 DOI: 10.1099/ijs.0.006866-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rod-shaped, yellow-pigmented, aerobic, Gram-negative bacterium, designated strain JO-1(T), was isolated from an apparently healthy Pacific oyster, Crassostrea gigas, collected at Wan Island, Korea. It grew at 15-37 degrees C (optimum 30 degrees C) only in the presence of sea salts. Strain JO-1(T) hydrolysed casein, Tween 80 and starch. The major fatty acids were iso-C(15 : 0) (23.8 %), summed feature 3 (comprising C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH; 14.5 %) and iso-C(15 : 1) G (14.1 %). Analysis of the 16S rRNA gene sequence indicated that strain JO-1(T) was a member of the genus Tenacibaculum in the family Flavobacteriaceae, with sequence similarity of 94.6-97.8 % to the type strains of recognized members of the genus. The G+C content of the genomic DNA was 31.4 mol%. DNA-DNA relatedness levels between strain JO-1(T) and the five closest relatives, Tenacibaculum litoreum KCCM 42115(T), T. lutimaris KCTC 12302(T), T. aestuarii KCTC 12569(T), T. mesophilum DSM 13764(T) and T. adriaticum JCM 14633(T), were less than 28 %. Phylogenetic analyses and differences in physiological and biochemical characteristics suggested that strain JO-1(T) (=KCTC 22329(T) =JCM 15428(T)) should be classified as the type strain of a novel species within the genus Tenacibaculum, for which the name Tenacibaculum crassostreae sp. nov. is proposed.
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Affiliation(s)
- Young Sun Lee
- Department of Biology, Sunchon National University, Suncheon 540-742, Republic of Korea
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Towards large-scale FAME-based bacterial species identification using machine learning techniques. Syst Appl Microbiol 2009; 32:163-76. [PMID: 19237256 DOI: 10.1016/j.syapm.2009.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 01/07/2009] [Accepted: 01/21/2009] [Indexed: 10/21/2022]
Abstract
In the last decade, bacterial taxonomy witnessed a huge expansion. The swift pace of bacterial species (re-)definitions has a serious impact on the accuracy and completeness of first-line identification methods. Consequently, back-end identification libraries need to be synchronized with the List of Prokaryotic names with Standing in Nomenclature. In this study, we focus on bacterial fatty acid methyl ester (FAME) profiling as a broadly used first-line identification method. From the BAME@LMG database, we have selected FAME profiles of individual strains belonging to the genera Bacillus, Paenibacillus and Pseudomonas. Only those profiles resulting from standard growth conditions have been retained. The corresponding data set covers 74, 44 and 95 validly published bacterial species, respectively, represented by 961, 378 and 1673 standard FAME profiles. Through the application of machine learning techniques in a supervised strategy, different computational models have been built for genus and species identification. Three techniques have been considered: artificial neural networks, random forests and support vector machines. Nearly perfect identification has been achieved at genus level. Notwithstanding the known limited discriminative power of FAME analysis for species identification, the computational models have resulted in good species identification results for the three genera. For Bacillus, Paenibacillus and Pseudomonas, random forests have resulted in sensitivity values, respectively, 0.847, 0.901 and 0.708. The random forests models outperform those of the other machine learning techniques. Moreover, our machine learning approach also outperformed the Sherlock MIS (MIDI Inc., Newark, DE, USA). These results show that machine learning proves very useful for FAME-based bacterial species identification. Besides good bacterial identification at species level, speed and ease of taxonomic synchronization are major advantages of this computational species identification strategy.
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