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1.
Arch Microbiol ; 2020 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-33284382

RESUMO

Strain CECT 9734 T, a Gram-negative, aerobic, chemoorganotrophic bacterium, motile by polar flagella, was isolated from cultured European seabass, Dicenthrarchus labrax, in Spain. It grows from 5 to 42 ºC, 6-9 pH and 1-12% total salinity. Major cellular fatty acids are C15:0 iso, summed feature 9 (C17:1 iso w9c/C16:0 10-methyl) and C17:0 iso. The genome size is 2.5 Mbp and G + C content is 49.5 mol%. Comparative analysis of the 16S rRNA gene sequence shows that the strain is a member of Pseudidiomarina, with highest similarities with Pseudidiomarina halophila (97.0%) and Pseudidiomarina salinarum (96.9%). Phylogenomic tree based on UBCG program shows P. halophila as its closest relative. ANI and in-silico DDH with other Pseudidiomarina spp. are lower than 87 and 20%, respectively, suggesting that strain CECT 9734 T represents a new species, for which we propose the name Pseudidiomarina piscicola sp. nov. and CECT 9734 T (= LUBLD50 7aT = LMG 31044 T) as type strain.

2.
Nucleic Acids Res ; 2020 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-33119759

RESUMO

Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.

3.
BMC Microbiol ; 20(1): 207, 2020 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-32660423

RESUMO

BACKGROUND: Isolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection contains isolates from both photic (817) and aphotic layers (744), including the mesopelagic (362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. We described the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along different depths. RESULTS: The partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing all photic, mesopelagic, and bathypelagic isolates sequences retrieved from different stations, 37% of them were 100% identical. This percentage increased up to 59% when mesopelagic and bathypelagic strains were grouped as the aphotic dataset and compared to the photic dataset of isolates, indicating the ubiquity of some bacterial isolates along different ocean depths. Finally, we isolated three strains that represent a new species, and the genome comparison and phenotypic characterization of two of these strains (ISS653 and ISS1889) concluded that they belong to a new species within the genus Mesonia. CONCLUSIONS: Overall, this study highlights the relevance of culture-dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of the culturable marine bacteria as part of the total marine microbial diversity.

4.
Curr Microbiol ; 77(9): 2031-2041, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32594222

RESUMO

Strain SB0023/3 T, isolated from spores of the arbuscular mycorrhizal fungus Glomus iranicum var. tenuihypharum, was analysed to determine whether it represents a new species. It was studied for its applicability in the field of agriculture to reduce the input of nitrogen fertilizers. Comparative analysis of the 16S rRNA gene sequence shows the strain to be affiliated to the genus Methylobacterium, the closest similarities (98.7%) being shared with Methylobacterium dankookense. Further phylogenomic analysis through Up-to-date Bacterial Core Gene (UBCG) confirmed Methylobacterium dankookense as its closest relative. Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (DDH) were lower than 92% and 44%, respectively, of the values shown by its phylogenetic relatives. Its genome had an approximate length of 6.05 Mb and the G + C content of the genome was 70.1 mol%. The main cellular fatty acid was Summed Feature 8 (C18:1ω7c and/or C18:1ω6c). It is a Gram-staining-negative, pink-pigmented, strictly aerobic and facultative methylotroph; it grows at 28 ºC and can grow at up to 3% salinity in the presence of sodium chloride. All the data collected support the naming of a novel species to accommodate the strain SB0023/3 T, for which the name Methylobacterium symbioticum sp. nov. is proposed. The type strain is SB0023/3 T (=CECT 9862 T =PYCC 8351 T).

5.
Int J Syst Evol Microbiol ; 70(7): 4329-4338, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32589567

RESUMO

Strain ISS653T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1-15 % NaCl) and mesophilic (4-37 °C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15 : 0, iso-C15 : 0 2-OH, and iso-C17 : 0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2 %), Salegentibacter mishustinae (93.1 %) and Mesonia mobilis (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81 % AAI; 78.9 % ANI), M. phycicola (76 % AAI; 76.3 % ANI), Mesonia maritima (72 % AAI, 74.9 % ANI), Mesonia hippocampi (64 % AAI, 70.8 % ANI) and Mesonia algae (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653T in a clade with species of the genus Mesonia. We conclude that strain ISS653T represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653T (=CECT 9532T=LMG 31236T) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans.


Assuntos
Flavobacteriaceae/classificação , Filogenia , Água do Mar/microbiologia , Oceano Atlântico , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Oceano Pacífico , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados
6.
Int J Syst Evol Microbiol ; 70(2): 1231-1239, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31793854

RESUMO

Strain ISS155T, isolated from surface Mediterranean seawater, has cells that are Gram-reaction-negative, motile, strictly aerobic chemoorganotrophic, oxidase-positive, unable to reduce nitrate to nitrite, and able to grow with cellulose as the sole carbon and energy source. It is mesophilic, neutrophilic, slightly halophilic and has a requirement for sodium and magnesium ions. Its 16S rRNA gene sequence places the strain among members of Cellvibrionaceae, in the Gammaproteobacteria, with Agarilytica rhodophyticola 017T as closest relative (94.3 % similarity). Its major cellular fatty acids are C18 : 1, C16 : 0 and C16 : 1; major phospholipids are phosphatidyl glycerol, phosphatidyl ethanolamine and an unidentified lipid, and the major respiratory quinone is Q8. The genome size is 6.09 Mbp and G+C content is 45.2 mol%. A phylogenomic analysis using UBCG merges strain ISS155T in a clade with A. rhodophyticola, Teredinibacter turnerae, Saccharophagus degradans and Agaribacterium haliotis type strain genomes, all of them possessing a varied array of carbohydrate-active enzymes and the potential for polysaccharide degradation. Average amino acid identity indexes determined against available Cellvibrionaceae type strain genomes show that strain ISS155T is related to them by values lower than 60 %, with a maximum of 58 % to A. rhodophyticola 017T and 57 % to T. turnerae T7902T and S. degradans 2-40T. These results, together with the low 16S rRNA gene sequence similarities and differences in phenotypic profiles, indicate that strain ISS155T represents a new genus and species in Cellvibrionaceae, for which we propose the name Thalassocella blandensis gen. nov., sp. nov., and strain ISS155T (=CECT 9533T=LMG 31237T) as the type strain.


Assuntos
Phyllobacteriaceae/classificação , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Mar Mediterrâneo , Fosfolipídeos/química , Phyllobacteriaceae/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
7.
Int J Syst Evol Microbiol ; 69(11): 3405-3413, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31373895

RESUMO

Strain CECT 7735T, a marine Gram-reaction negative, aerobic, non-motile bacterium, was isolated from coastal seawater in Valencia, Spain. Strain CECT 7735T is chemoorganotrophic, mesophilic, slightly halophilic, grows at 15-28 °C but not at 4 or 37 °C, requires seawater for growth and grows up to 6 % salinity. The major cellular fatty acid is summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The G+C content of the genome is 55.7 mol%. Comparative analysis of the 16S rRNA gene sequence shows the strain is affiliated to the family Rhodobacteraceae, in the class Alphaproteobacteria, with highest similarities to Phaeobacter species (97.0-97.5 %), Shimia species (96.5-97.3 %) and Pseudopelagicola gijangensis (96.5 %). Further phylogenomic analysis through the up-to-date-bacterial core gene (UBCG) set showed P. gijangensis to be its closest relative. Average nucleotide identity and in silico DNA-DNA hybridization values are lower than 85 and 21 %, respectively, with its phylogenetic relatives, suggesting that strain CECT 7735T represents a new species. The average amino acid identity value was over 70 % with the genome of the type strain of P. gijangensis and with all those of Shimia species. These values, together with UBCG set trees, suggest that the new species and P. gijangensisbelong to the same genus and that Pseudopelagicola should be reclassified as a Shimia species. We conclude that strain CECT 7735T represents a new species in the genus Shimia, for which we propose the name Shimiathalassica sp. nov. In addition, Pseudopelagicola gijangensis is reclassified as Shimiagijangensis comb. nov. From the same phylogenomic study, it can be concluded that Thalassobius activus should be reclassified in the genus Cognatishimia as Cognatishimiaactiva comb. nov.


Assuntos
Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha
8.
Int J Syst Evol Microbiol ; 68(8): 2515-2522, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29944092

RESUMO

Strain CECT 5091T, an aerobic, marine, Gram-reaction- and Gram-stain-negative, chemoheterotrophic bacterium was isolated from oysters harvested off the Spanish Mediterranean coast. Analysis of the 16S rRNA gene sequence placed the strain within the genus Ruegeria, in the family Rhodobacteraceae, with 16S rRNA gene similarities of 98.7, 98.7 and 98.4 % to Ruegeria conchae, Ruegeria atlanticaand Ruegeria arenilitoris, respectively. Average nucleotide identities (ANI) and in silico DNA-DNA hybridization (DDH) were determined, comparing the genome sequence of CECT 5091T with those of the type strains of 12 species of the genus Ruegeria: the values obtained were always below the thresholds (95-96 % ANI, 70 % in silico DDH) used to define genomic species, proving that CECT 5091T represents a novel species of the genus Ruegeria. The strain was slightly halophilic and mesophilic, with optimum growth at 26 °C, pH 7.0 and 3 % salinity, it required sodium and magnesium ions for growth and was able to reduce nitrate to dinitrogen. Carbon sources for growth include some carbohydrates (d-ribose, d-glucose, l-rhamnose, N-acetyl-d-glucosamine) and multiple organic acids and amino acids. The major cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), representing 70 % of the total fatty acids. Carbon monoxide oxidation, cyanophycin synthetic ability and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine production are predicted from genome annotation, while bacteriochlorophyll a production was absent. The DNA G+C content of the genome was 56.7 mol%. We propose the name Ruegeriadenitrificans sp. nov. and strain CECT 5091T (=5OM10T=LMG 29896T) as the type strain for the novel species.


Assuntos
Ostreidae/microbiologia , Filogenia , Rhodobacteraceae/classificação , Animais , Proteínas de Bactérias/biossíntese , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Mar Mediterrâneo , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Rhodobacteraceae/genética , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Espanha
9.
Syst Appl Microbiol ; 41(5): 444-451, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29804705

RESUMO

Three strains, H01100409BT, H01100413B, and H27100402HT, were isolated from several internal organs of diseased redbanded seabream (Pagrus auriga) reared in Andalusia (Southern Spain). All strains were studied by phenotypic, including chemotaxonomy, and genomic characteristics. Phylogenetic analysis based on concatenated sequences of six housekeeping genes (gyrB, ftsZ, topA, mreB, gapA, and 16S rRNA) supported the inclusion of the strains within the clade Phosphoreum of the genus Photobacterium, and two of the strains (H27100402HT and H01100409BT) formed a tight group separated from the closest species P. aquimaris. Genomic analyses, including average nucleotide identity (ANIb and ANIm) and DNA-DNA hybridization (DDH), clearly separated strains H27100402HT and H01100409BT from the other species within the clade Phosphoreum with values below the thresholds for species delineation. The chemotaxonomic features (including FAME analysis and MALDI-TOF-MS) of H27100402HT and H01100409BT strains confirmed their differentiation from the related taxa. The results demonstrated that strain H01100413B was classified as P. aquimaris and the strains H27100402HT and H01100409BT represented a new species each in the genus Photobacterium, for which we propose the names Photobacterium malacitanum sp. nov., type strain H27100402HT (=CECT 9190T=LMG 29992T), and Photobacterium andalusiense sp. nov., type strain H01100409BT (=CECT 9192T=LMG 29994T).


Assuntos
Doenças dos Peixes/microbiologia , Photobacterium/classificação , Photobacterium/fisiologia , Filogenia , Animais , Composição de Bases , DNA Bacteriano/genética , Doenças dos Peixes/epidemiologia , Pesqueiros , Genes Bacterianos/genética , Genoma Bacteriano/genética , Fenótipo , Photobacterium/química , Photobacterium/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA/veterinária , Espanha/epidemiologia , Especificidade da Espécie , Vitamina K 2/análogos & derivados , Vitamina K 2/química
10.
Int J Syst Evol Microbiol ; 67(9): 3506-3512, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28857026

RESUMO

Two bacterial strains, EAod9T and SMJ21T, isolated from salt-marsh plants, were determined to be related to species of the genus Vibriofrom from 16S rRNA sequence comparisons. Their closest phylogenetic relatives are members of the Gazogenes clade, Vibrio mangrovi and Vibrio rhizosphaerae , which show the greatest similarity to the SMJ21TrRNA sequence (97.3 and 97.1 %, respectively), while EAod9T had less than 97.0 % similarity to any other species of the genus Vibrio. Both strains share the basic characteristics of the genus Vibrio, as they are Gram-stain negative, motile, slightly halophilic, facultatively anaerobic bacteria. In addition, they are oxidase-negative and unable to grow on TCBS Agar; they grow between 15 to 26 °C, pH 6 to 8 and in up to 10 % (w/v) total salinity. They produce indol, are positive in the Voges-Proskauer test and are negative for arginine dihydrolase, lysine and ornithine decarboxylases. Strain SMJ21T is aerogenic and red-pigmented, due to prodigiosin production, while strain EAod9T ferments glucose without gas and is not pigmented. The major cellular fatty acids of both novel strains were C16 : 1ω7c/C16 : 1ω6c and C16 : 0. WGSobtained for both strains, along with the other five members of the clade, allowed the determination of ANI indexes and in silico estimations of DDH values, which confirmed that the two strains represent two novel species of the genus Vibrio: Vibriopalustris sp. nov. (with EAod9T=CECT 9027T=LMG 29724T as the proposed type strain) and Vibrio spartinae sp. nov. (with SMJ21T=CECT 9026T=LMG 29723T as the proposed type strain).


Assuntos
Amaranthaceae/microbiologia , Filogenia , Poaceae/microbiologia , Vibrio/classificação , Áreas Alagadas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Pigmentação , RNA Ribossômico 16S/genética , Plantas Tolerantes a Sal/microbiologia , Análise de Sequência de DNA , Espanha , Vibrio/genética , Vibrio/isolamento & purificação
11.
Int J Syst Evol Microbiol ; 67(11): 4518-4525, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28933324

RESUMO

Three bacterial strains were isolated from liver and spleen of diseased farmed redbanded seabream (Pagrus auriga) in south-west Spain. Their partial 16S rRNA gene sequences clustered within those of the genus Photobacterium, showing high similarity (98.6-99.3 %) to the type strains of Photobacterium iliopiscarium, P. piscicola, P. kishitanii, P. aquimaris and P. phosphoreum. Multilocus sequence analysis using six housekeeping genes (gapA, topA, mreB, ftsZ, gyrB and 16S rRNA) confirmed the new strains as forming an independent branch with a bootstrap value of 100, likely to represent a novel species. To confirm this, we used whole genome sequencing and genomic analysis (ANIb, ANIm and in silico DNA-DNA hybridization) obtaining values well below the thresholds for species delineation. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strains from related taxa. Cells were Gram-stain-negative, motile bacilli, chemo-organotrophic and facultatively anaerobic. They fermented glucose, as well as galactose and d-mannose, without production of gas. Oxidase and catalase were positive. The predominant cellular fatty acids were C16 : 1ω7c/C16 : 1ω6c and C16  :  0. The predominant respiratory quinone (Q-8) and major polar lipids (phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol) were inferred from annotated genes in the genome of strain H01100410BT, which had a G+C content of 38.6 mol%. The results obtained demonstrate that the three strains represent a novel species, for which the name Photobacterium toruni sp. nov. is proposed. The type strain is H01100410BT (=CECT 9189T=LMG 29991T).


Assuntos
Photobacterium/classificação , Filogenia , Dourada/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Photobacterium/genética , Photobacterium/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha , Vitamina K 2/análogos & derivados , Vitamina K 2/química
12.
Int J Syst Evol Microbiol ; 67(6): 1669-1671, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28150577

RESUMO

The synonymy between Vibrio hemicentrotiKim et al. 2013 and Vibrio splendidus(Beijerinck 1900) Baumann et al. 1981 was suggested after a recent multilocus sequence analysis of the Splendidus clade, which included the type strains of both species. To clarify their status, we have determined genomic indexes from whole genome sequences of strains V. hemicentroti CECT 8714T and V. splendidus NCCB 53037T. Average Nucleotide Identities of 96.0-96.7 % and an in silico DNA-DNA hybridization value of 70.2 %, as well as similarity levels of selected housekeeping gene sequences support the consideration of V.hemicentroti as a later heterotypic synonym of V. splendidus.


Assuntos
Filogenia , Vibrio/classificação , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Análise de Sequência de DNA , Vibrio/genética
13.
Front Microbiol ; 8: 2645, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29375512

RESUMO

A taxogenomic study was conducted to describe two new Thalassobius species and to analyze the internal consistency of the genus Thalassobius along with Shimia and Thalassococcus. Strains CECT 5113T, CECT 5114, CECT 5118T, and CECT 5120 were isolated from coastal Mediterranean seawater, Spain. Cells were Gram-negative, non- motile coccobacilli, aerobic chemoorganotrophs, with an optimum temperature of 26°C and salinity of 3.5-5%. Major cellular fatty acids of strains CECT 5113T and CECT 5114 were C18 : 1 ω7c/ω6c and C10 : 0 3OH, G+C content was 54.4-54.5 mol% and were able to utilize propionate, L-threonine, L- arginine, and L-aspartate as carbon sources. They exhibited 98.3% 16S rRNA gene sequence similarity, 75.0-75.1 ANIb and 19.5-20.9 digital DDH to type strain of their closest species, Thalassobius maritimus. Based on these data, strains CECT 5113T and CECT 5114 are recognized as a new species, for which the name Thalassobius activus is proposed, with strain CECT 5113T (=LMG 29900T) as type strain. Strains CECT 5118T and CECT 5120 were found to constitute another new species, with major cellular fatty acids C18 : 1 ω7c/ω6c and C18 : 1 ω7c 11-methyl and a G+C content of 59.8 mol%; they were not able to utilize propionate, L-threonine, L- arginine or L-aspartate. Their closest species was Thalassobius mediterraneus, with values of 99.6% 16S rRNA gene sequence similarity, 79.1% ANIb and 23.2% digital DDH compared to the type strain, CECT 5383T. The name Thalassobius autumnalis is proposed for this second new species, with strain CECT 5118T (=LMG 29904T) as type strain. To better determine the phylogenetic relationship of the two new species, we submitted 12 genomes representing species of Thalassobius, Shimia, and Thalassoccocus, to a phylogenomic analysis based on 54 single protein-encoding genes (BCG54). The resulting phylogenomic tree did not agree with the current genera classification, as Thalassobius was divided in three clades, Thalassobius sensu stricto (T. mediterraneus, T. autumnalis sp. nov., and T. gelatinovorus), Thalassobius aestuarii plus the three Shimia spp (S. marina, S. haliotis, and Shimia sp. SK013) and finally, Thalasobius maritimus plus T. activus sp. nov. Thalassococcus halodurans remained apart from the two genera. Phenotypic inferences from explored genomes are presented.

14.
Int J Syst Evol Microbiol ; 66(12): 5544-5549, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27902199

RESUMO

A novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121T, was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to Marinomonas dokdonensis and other Marinomonas species (96.3 and 93.3-95.7 % sequence similarities, respectively), within the family Oceanospirillaceae. Strain MED121T was included into a whole-genome sequencing study and, subsequently, it was characterized using a polyphasic taxonomic approach. It was found to be oxidase and catalase positive, its cells are cocci to short rods, it does not ferment carbohydrates and does not reduce nitrate to nitrite or gas and it requires at least 2.5 % (w/v) marine salts and tolerates up to 7 % (w/v) salts. Its major cellular fatty acids in order of abundance are C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c, C16 : 0 and C10 : 0 3-OH. Its genome had an approximate length of 5.1 million bases and a DNA G+C content equal to 40.9 mol%. Analysis of the annotated genes reveals the capacity for the synthesis of ubiquinone 8 (Q8) and the polar lipids phosphatidylglycerol and phosphatidylethanolamine, in agreement with other members of the genus. All the data collected supported the creation of a novel species to accommodate this bacterium, for which the name Marinomonas blandensis sp. nov. is proposed. The type strain is MED121T (=CECT 7076T=LMG 29722T).


Assuntos
Marinomonas/classificação , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Marinomonas/genética , Marinomonas/isolamento & purificação , Mar Mediterrâneo , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
15.
Syst Appl Microbiol ; 39(6): 361-9, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27238556

RESUMO

A multilocus sequence analysis was undertaken in order to redefine the Splendidus clade of the genus Vibrio, a large group of species containing several pathogenic members that affect fish and shellfish, and are difficult to identify through both phenotypic and genotypic approaches. The study included analysis of partial sequences of recA, gyrB, mreB, rpoD and pyrH genes, as well as the 16S rRNA gene. Seventeen type strain species were included that were complemented with other reference strains and a collection of isolates tentatively identified as members of this clade, as well as a set of other Vibrio species. The clade was well defined and stable in all analyses, and was confirmed to contain V. celticus, V. atlanticus, V. artabrorum, V. toranzoniae and V. hemicentroti, in addition to the twelve previously recognized species. While some species were well-defined members (e.g. Vibrio cyclitrophicus, V. chagasii) others formed tight groups that were related by sequence similarities and lineage topology, which suggested a synonymy among their members, particularly the V. splendidus-V. hemicentroti pair. Most of the isolates were related to two major groups: the V. celticus-V. crassostreae-V. gigantis subclade that contained all isolates from oysters sampled in the cold season, and V. chagasii that included oyster isolates from warm months. This suggested a sharp seasonal occurrence for these species. None of the single genes were able to mimic the resolving power of the five-gene MLSA and none worked well for the identification of the whole group of species in the clade.


Assuntos
Técnicas de Tipagem Bacteriana , Doenças dos Peixes/microbiologia , Peixes/microbiologia , Tipagem de Sequências Multilocus , Ostreidae/microbiologia , Frutos do Mar/microbiologia , Vibrio/classificação , Vibrio/genética , Animais , Sequência de Bases , DNA Girase/genética , DNA Bacteriano/genética , RNA Polimerases Dirigidas por DNA/genética , Filogenia , RNA Ribossômico 16S/genética , Recombinases Rec A/genética , Estações do Ano , Análise de Sequência de DNA , Fator sigma/genética , Transferases/genética , Vibrio/isolamento & purificação
16.
Int J Syst Evol Microbiol ; 66(8): 2906-2909, 2016 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-27125858

RESUMO

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.


Assuntos
Filogenia , Água do Mar/microbiologia , Vibrionaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha , Vibrionaceae/genética , Vibrionaceae/isolamento & purificação
17.
Int J Syst Evol Microbiol ; 66(4): 1686-1691, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26821806

RESUMO

Two strains of Gram-stain-negative, chemo-organotrophic, aerobic and halophilic gammaproteobacteria, isolated from within the stem and roots of Spartina maritima in salt marshes from the south Atlantic Spanish coast, were found to represent a novel species in the genus Marinomonas through phylogenetic analysis of their 16S rRNA genes and phenotypic characterization. 16S rRNA gene sequences of the two strains shared < 96.2% similarity with other Marinomonas species, with Marimonas alcarazii being the most similar in sequence. They required sodium ions for growth, were able to thrive at low (4 °C) temperatures and at salinities of 12-15%, were unable to hydrolyse any tested macromolecule except casein, and grew with different monosaccharides, disaccharides, sugar alcohols, organic acids and amino acids. The novel species differed from other Marinomonas species in the use of several sole carbon sources, its temperature and salinity ranges for growth, ion requirements and cellular fatty acid composition, which included C16:0, C16:1 and C18:1 as major components and C10:0 3-OH, C12:0 and C12:0 3-OH as minor components. The name Marinomonas spartinae sp. nov. is proposed, with SMJ19T (=CECT 8886T=KCTC 42958T) as the type strain.


Assuntos
Marinomonas/classificação , Filogenia , Poaceae/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Endófitos/classificação , Endófitos/genética , Endófitos/isolamento & purificação , Ácidos Graxos/química , Marinomonas/genética , Marinomonas/isolamento & purificação , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Raízes de Plantas/microbiologia , Caules de Planta/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha , Áreas Alagadas
18.
Syst Appl Microbiol ; 38(3): 169-75, 2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25861826

RESUMO

A Multilocus Sequence Analysis (MLSA) was performed on members of the Scophthalmi clade in the genus Vibrio, including type and reference strains of the species V. scophthalmi, V. ichthyoenteri, and 39 strains phenotypically identified as Vibrio ichthyoenteri-like, with the aim of better defining boundaries between these two closely related, fish-associated species. The type strain of V. ponticus, recently added to the clade Scophthalmi, was also included. The study was based on partial sequences of the protein-coding housekeeping genes rpoD, mreB, recA, ftsZ, and gyrB, and the 16S rRNA. While the 16S rRNA gene-based trees were unable to pull apart members of V. scophthalmi or V. ichthyoenteri, both the other individual gene trees and the trees obtained from the five-genes concatenated sequences were able to consistently differentiate four subclades within the main clade, corresponding to the bona fide V. scophthalmi, V. ichthyoenteri, and two small ones that may represent a new species each. The best genes to differentiate V. scophthalmi from V. ichthyoenteri were rpoD, recA, and mreB. Vibrio ponticus failed to associate to the clade in the MLSA and in most single gene trees for which it should not be considered part of it. In this study we also confirm using genomic indexes that V. ichthyoenteri and V. scophthalmi are two separate species.


Assuntos
Vibrio/classificação , Vibrio/genética , Animais , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Peixes/microbiologia , Genes Essenciais , Dados de Sequência Molecular , Tipagem de Sequências Multilocus , Filogenia , RNA Ribossômico 16S/genética , Homologia de Sequência , Vibrio/isolamento & purificação
19.
Genome Announc ; 3(2)2015 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-25767236

RESUMO

Vibrio renopiscarius DCR 1-4-2(T) (CECT 8603(T)) and DCR 1-4-12 (CECT 8604) were isolated from healthy gilthead sea bream (Sparus aurata) from Mediterranean fish farms (Castellón, Spain). Their draft genome sequences (30 and 44 contigs, respectively) have 4.3 Mbp and a G+C content of 45.2 mol% and contain almost 3,700 protein-encoding genes.

20.
Int J Syst Evol Microbiol ; 65(Pt 6): 1941-1945, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25795068

RESUMO

Two strains of Gram-negative, facultatively anaerobic, slightly halophilic bacteria, isolated from healthy gilthead sea bream (Sparus aurata) cultured in Spanish Mediterranean fish farms, were different from their closest relatives, Vibrio scophthalmi and V. ichthyoenteri, by phenotypic, phylogenetic and genomic standards. The strains were negative for decarboxylase tests and lacked extracellular hydrolytic activities, but were able to ferment d-mannitol, sucrose, cellobiose and d-gluconate, among other carbohydrates. The major cellular fatty acids were C16:1 and C16:0, in agreement with other species of the genus Vibrio. Their 16S rRNA gene sequences were 98.4 and 97.2 % similar to those of the type strains of V. scophthalmi and V. ichthyoenteri, and the similarities using other housekeeping genes (ftsZ, rpoD, recA, mreB and gyrB) and indices of genomic resemblance (average nucleotide identity and estimated DNA-DNA hybridization) between the isolates and those type strains were clearly below intraspecific levels, supporting the recognition of the strains as members of a separate novel species. Thus, we propose the name Vibrio renipiscarius sp. nov., with DCR 1-4-2T ( = CECT 8603T = KCTC 42287T) as the type strain.


Assuntos
Filogenia , Dourada/microbiologia , Vibrio/classificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha , Vibrio/genética , Vibrio/isolamento & purificação
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