Publications by authors named "David R Arahal"

66 Publications

Genome Sequence of Bifidobacterium breve INIA P734 (CECT 8178), a Strain Isolated from Human Breast Milk.

Microbiol Resour Announc 2021 Jan 7;10(1). Epub 2021 Jan 7.

Departamento Tecnología de Alimentos, INIA, Madrid, Spain.

The draft genome sequence of INIA P734, a strain shared by mother and child, is reported. It consists of 50 contigs, with 2,391,925 bp, 2,099 genes, and a G+C content of 58.8%. The genome analysis revealed the absence of antibiotic resistance and pathogenicity-related genes.
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http://dx.doi.org/10.1128/MRA.00871-20DOI Listing
January 2021

Preparing a revision of the International Code of Nomenclature of Prokaryotes.

Int J Syst Evol Microbiol 2021 Jan 10;71(1). Epub 2020 Dec 10.

Department of Infectious Disease, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, P.O. Box 7193, SE-402 34 Göteborg, Sweden.

The Editorial Board of the International Code of Nomenclature of Prokaryotes here explains the proposed procedure towards the production of the next revision of the Prokaryotic Code, to include public discussion of a draft version, to be prepared by the editors, followed by balloting of the members of the International Committee on Systematics of Prokaryotes.
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http://dx.doi.org/10.1099/ijsem.0.004598DOI Listing
January 2021

Pseudidiomarina piscicola sp. nov., isolated from cultured European seabass, Dicenthrarchus labrax.

Arch Microbiol 2021 May 7;203(4):1293-1298. Epub 2020 Dec 7.

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, València, Spain.

Strain CECT 9734, 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 C iso, summed feature 9 (C iso w9c/C 10-methyl) and C 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 represents a new species, for which we propose the name Pseudidiomarina piscicola sp. nov. and CECT 9734 (= LUBLD50 7a = LMG 31044) as type strain.
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http://dx.doi.org/10.1007/s00203-020-02131-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8055624PMC
May 2021

gcType: a high-quality type strain genome database for microbial phylogenetic and functional research.

Nucleic Acids Res 2021 01;49(D1):D694-D705

Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

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/.
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http://dx.doi.org/10.1093/nar/gkaa957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778895PMC
January 2021

Opinions 100, 101 and 102.

Authors:
David R Arahal

Int J Syst Evol Microbiol 2020 Sep 19;70(9):5177-5181. Epub 2020 Aug 19.

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain.

The International Committee on Systematics of Prokaryotes has formally made final decisions, taking into account the conclusions of the Judicial Commission, on three pending Requests for an Opinion, thereby allowing the corresponding Opinions to be issued. According to Opinion 100, the request for the recognition of strain A1-86 (=DSM 17629=NCIMB 14373) as the neotype strain of (Hauduroy 1937) Prévot 1938 (Approved Lists 1980) is denied, ruling that a neotype does not need to be designated for because strain VPI 0990 (=ATCC 33656=CIP 105953) is considered to be a duplicate isolate of the same strain as VPI 0989 (=ATCC 25578) and may serve as its nomenclatural type. Opinion 101 approves the request that strain ATCC 25946 (=DSM 14877) serves as the type strain of instead of strain ATCC 25944, formally correcting the Approved Lists of Bacterial Names. Opinion 102 concludes that strain Cc m8 (=DSM 14697=CIP 109128=JCM 12621) is an established neotype strain for the species , replacing the designated type strain Windsor M271, and that strain Mx s8 (=DSM 14675=JCM 12634) is an established neotype strain for the species , replacing the designated type strain Windsor M78, with some additional considerations about the nature of the type material replaced and about the name () .
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http://dx.doi.org/10.1099/ijsem.0.004390DOI Listing
September 2020

Methylobacterium symbioticum sp. nov., a new species isolated from spores of Glomus iranicum var. tenuihypharum.

Curr Microbiol 2020 Sep 27;77(9):2031-2041. Epub 2020 Jun 27.

Symborg SL, Murcia, Spain.

Strain SB0023/3, 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 (Cω7c and/or Cω6c). 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, for which the name Methylobacterium symbioticum sp. nov. is proposed. The type strain is SB0023/3 (=CECT 9862 =PYCC 8351).
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http://dx.doi.org/10.1007/s00284-020-02101-4DOI Listing
September 2020

sp. nov., isolated from oceans during the oceans expedition, with a preference for mesopelagic waters.

Int J Syst Evol Microbiol 2020 Jul;70(7):4329-4338

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain.

Strain ISS653, 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-C, iso-C 2-OH, and iso-C 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 with the type strains of (93.2 %), (93.1 %) and (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with (81 % AAI; 78.9 % ANI), (76 % AAI; 76.3 % ANI), (72 % AAI, 74.9 % ANI), (64 % AAI, 70.8 % ANI) and (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653 in a clade with species of the genus . We conclude that strain ISS653 represents a novel species of the genus for which we propose the name sp. nov., and strain ISS653 (=CECT 9532=LMG 31236) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the 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.
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http://dx.doi.org/10.1099/ijsem.0.004296DOI Listing
July 2020

Genome-based analyses reveal a synonymy among Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996, Ventosa . 2004, Xu . 2007 and Cui . 2007. Emended description of Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996.

Int J Syst Evol Microbiol 2020 Mar;70(3):1698-1705

Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.

A comparative taxonomic study of , , and was carried out using different approaches, 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), phylogenomic analysis based on the comparison of the core genome, orthologous average nucleotide identity (OrthoANI), Genome-to-Genome Distance Calculator (GGDC), synteny plots and polar lipid profile (PLP). The MLSA study, using the five concatenated housekeeping genes , , , and ', and the phylogenomic analysis based on 1347 core translated gene sequences obtained from their genomes showed that JCM 9100, JCM 10247, JCM 13916 and JCM 13561 formed a robust cluster, clearly separated from the rest of species of the genus . The OrthoANI and digital DDH values, calculated by the GGDC, showed percentages among JCM 9100, JCM 10247, JCM 13916 and JCM 13561 that ranged from 98.1 to 97.5 %, and 84.0 to 78.0 %, respectively, while these values among those strains and the type strains of their most related species of were equal or lower than 90.8 and 41.2 %, respectively. Moreover, degree of synteny across the four genomes was very high, especially between the genomes of JCM 13561 and JCM 13916. In addition, the PLP is quite similar among the four strains studied, showing a common pattern typical of the neutrophilic species of the genus . Overall, these data show that , , and constitute a single species. Thus, the latter three should be considered as later, heterotypic synonyms of based on the rules for priority of names. We propose an emended description of , including the features of , and .
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http://dx.doi.org/10.1099/ijsem.0.003956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7386789PMC
March 2020

Opinions 97, 98 and 99.

Authors:
David R Arahal

Int J Syst Evol Microbiol 2020 Feb;70(2):1439-1440

Judicial Commission of the International Committee on Systematics of Prokaryotes, Chair.

The International Committee on Systematics of Prokaryotes has formally endorsed the conclusions of the Judicial Commission on three pending Requests for an Opinion, thereby allowing the corresponding Opinions to be issued. According to Opinion 97, the request for the conservation of the name is denied, allowing the continued use of the correction . Opinions 98 and 99 conclude that in the absence of associated authentic type material, the names and , respectively, are not validly published.
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http://dx.doi.org/10.1099/ijsem.0.003921DOI Listing
February 2020

gen. nov., sp. nov., a novel member of the family .

Int J Syst Evol Microbiol 2020 Feb;70(2):1231-1239

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain.

Strain ISS155, 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 , in the , with 017 as closest relative (94.3 % similarity). Its major cellular fatty acids are C, C and C; 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 ISS155 in a clade with , , and 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 type strain genomes show that strain ISS155 is related to them by values lower than 60 %, with a maximum of 58 % to 017 and 57 % to T7902 and 2-40. These results, together with the low 16S rRNA gene sequence similarities and differences in phenotypic profiles, indicate that strain ISS155 represents a new genus and species in , for which we propose the name gen. nov., sp. nov., and strain ISS155 (=CECT 9533=LMG 31237) as the type strain.
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http://dx.doi.org/10.1099/ijsem.0.003906DOI Listing
February 2020

Genomic Insights Into Five Strains of With Biotechnological Potential Isolated From , a Traditional Maize-Based Fermented Beverage From Northwestern Argentina.

Front Microbiol 2019 25;10:2232. Epub 2019 Sep 25.

Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain.

Lactic acid bacteria (LAB) are indigenous microorganisms that have been involved in food fermentations throughout history to preserve food and also to give special characteristics to them. The traditional fermented foods that are still being elaborated in indigenous populations around the world are a potential source of LAB with important biotechnological properties and/or beneficial to health. In a previous work, LAB biodiversity associated with , a traditional maize-based fermented beverage from Northwestern Argentina, was studied, both by culture dependent and independent methods. From that study, 392 isolates were recovered, mostly members of and . Biotechnological characterization of representative isolates led to the selection of five strains belonging to the species for their ability to produce vitamin B2 (riboflavin) and vitamin B9 (folates), their antimicrobial properties and antibiotics susceptibility. In this work, we present the Whole Genome Sequences (WGS) of these five strains that have been deposited in the Spanish Type Culture Collection: M5MA1 (= CECT 8962), M9MM1 (= CECT 8963), M9MM4 (= CECT 8964), M9MG6 (= CECT 8965), and M9Y2 (= CECT 8966), and a detailed description of their characterization, through a genomic approach, analyzing the genes responsible for these biotechnological properties, making a comparative study of the five genomes and reporting the aspects related to food safety, in accordance with the recommendations of the European Food Safety Authority (EFSA FEEDAP Panel, 2018) aiming at their use in the design of functional foods. The analysis unveiled, for the five strains, the complete set of genes for folate and riboflavin biosynthesis, the absence of pathogenic factors, the presence of CRISPR and genes, phage sequences, insertion elements and an aminoglycosides resistance gene, , whose resistance could not be proved phenotypically in any strain. Genomic comparisons showed that strain CECT 8962 was significantly different in terms of genetic content and allowed the identification of carbohydrates metabolism and membrane transport related genes as the main components of the unique and accessory genome.
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http://dx.doi.org/10.3389/fmicb.2019.02232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773835PMC
September 2019

sp. nov., and reclassification of as comb. nov., and as comb. nov.

Int J Syst Evol Microbiol 2019 Nov;69(11):3405-3413

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain.

Strain CECT 7735, a marine Gram-reaction negative, aerobic, non-motile bacterium, was isolated from coastal seawater in Valencia, Spain. Strain CECT 7735 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 (Cω7 and/or Cω6). 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 , in the class , with highest similarities to species (97.0-97.5 %), species (96.5-97.3 %) and (96.5 %). Further phylogenomic analysis through the up-to-date-bacterial core gene (UBCG) set showed to be its closest relative. Average nucleotide identity and DNA-DNA hybridization values are lower than 85 and 21 %, respectively, with its phylogenetic relatives, suggesting that strain CECT 7735 represents a new species. The average amino acid identity value was over 70 % with the genome of the type strain of and with all those of species. These values, together with UBCG set trees, suggest that the new species and belong to the same genus and that should be reclassified as a species. We conclude that strain CECT 7735 represents a new species in the genus , for which we propose the name sp. nov. In addition, is reclassified as comb. nov. From the same phylogenomic study, it can be concluded that should be reclassified in the genus as comb. nov.
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http://dx.doi.org/10.1099/ijsem.0.003629DOI Listing
November 2019

Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis.

Int J Syst Evol Microbiol 2018 Aug 26;68(8):2515-2522. Epub 2018 Jun 26.

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain.

Strain CECT 5091, 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 5091 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 5091 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 5091 (=5OM10=LMG 29896) as the type strain for the novel species.
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http://dx.doi.org/10.1099/ijsem.0.002867DOI Listing
August 2018

Roseivivax atlanticus (Li, Lai, Liu, Sun and Shao, 2015) is a later heterotypic synonym of Roseivivax marinus (Dai, Shi, Gao, Liu and Zhang, 2014).

Int J Syst Evol Microbiol 2018 Aug 22;68(8):2650-2652. Epub 2018 Jun 22.

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain.

The genomes of the type strains of Roseivivax atlanticusand Roseivivax marinus(Rhodobacteraceae, Alphaproteobacteria), were analysed to determine their respective Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization (DDH) values. These species were proposed and effectively published relatively closely in time (February and August 2014, respectively) and so not taking account of the other. The intergenomic relatedness between both type strains, 97.0-97.4 % ANI and 82.8 % in silico DDH, confirm that they represent members of the same genomic species. This conclusion is also supported at the phenotypic level. Since the nameRoseovarius marinuswas validly published earlier, R. atlanticus (Validation List 161, IJSEM 65, 1-4. 2015) should be considered a later heterotypic synonym of R. marinus(Dai, Shi, Gao, Liu and Zhang, 2014), in application of the priority rule.
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http://dx.doi.org/10.1099/ijsem.0.002893DOI Listing
August 2018

Photobacterium malacitanum sp. nov., and Photobacterium andalusiense sp. nov., two new bacteria isolated from diseased farmed fish in Southern Spain.

Syst Appl Microbiol 2018 Sep 24;41(5):444-451. Epub 2018 May 24.

Universidad de Málaga, Departamento de Microbiología, Facultad de Ciencias, 29071 Málaga, Spain. Electronic address:

Three strains, H01100409B, H01100413B, and H27100402H, 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 (H27100402H and H01100409B) 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 H27100402H and H01100409B 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 H27100402H and H01100409B strains confirmed their differentiation from the related taxa. The results demonstrated that strain H01100413B was classified as P. aquimaris and the strains H27100402H and H01100409B represented a new species each in the genus Photobacterium, for which we propose the names Photobacterium malacitanum sp. nov., type strain H27100402H (=CECT 9190=LMG 29992), and Photobacterium andalusiense sp. nov., type strain H01100409B (=CECT 9192=LMG 29994).
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http://dx.doi.org/10.1016/j.syapm.2018.04.005DOI Listing
September 2018

Comparative Genomics of Including the Description of sp. nov., and sp. nov.

Front Microbiol 2017 12;8:2645. Epub 2018 Jan 12.

Departamento de Microbiología and Colección Española de Cultivos Tipo, Universitat de València, Valencia, Spain.

A taxogenomic study was conducted to describe two new species and to analyze the internal consistency of the genus along with and . Strains CECT 5113, CECT 5114, CECT 5118, 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 5113 and CECT 5114 were C ω7c/ω6c and C 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, . Based on these data, strains CECT 5113 and CECT 5114 are recognized as a new species, for which the name is proposed, with strain CECT 5113 (=LMG 29900) as type strain. Strains CECT 5118 and CECT 5120 were found to constitute another new species, with major cellular fatty acids C ω/ω and C ω 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 , with values of 99.6% 16S rRNA gene sequence similarity, 79.1% ANIb and 23.2% digital DDH compared to the type strain, CECT 5383. The name is proposed for this second new species, with strain CECT 5118 (=LMG 29904) as type strain. To better determine the phylogenetic relationship of the two new species, we submitted 12 genomes representing species of , and , 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 was divided in three clades, sensu stricto ( sp. nov., and ), plus the three spp (, and sp. SK013) and finally, plus sp. nov. remained apart from the two genera. Phenotypic inferences from explored genomes are presented.
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http://dx.doi.org/10.3389/fmicb.2017.02645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770400PMC
January 2018

Photobacterium toruni sp. nov., a bacterium isolated from diseased farmed fish.

Int J Syst Evol Microbiol 2017 Nov 21;67(11):4518-4525. Epub 2017 Sep 21.

Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain.

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 H01100410B, 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 H01100410B (=CECT 9189=LMG 29991).
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http://dx.doi.org/10.1099/ijsem.0.002325DOI Listing
November 2017

Vibrio palustris sp. nov. and Vibrio spartinae sp. nov., two novel members of the Gazogenes clade, isolated from salt-marsh plants (Arthrocnemum macrostachyum and Spartina maritima).

Int J Syst Evol Microbiol 2017 Sep 31;67(9):3506-3512. Epub 2017 Aug 31.

Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain.

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).
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http://dx.doi.org/10.1099/ijsem.0.002155DOI Listing
September 2017

International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Halobacteria and Subcommittee on the taxonomy of Halomonadaceae. Minutes of the joint open meeting, 11 July 2017, Valencia, Spain.

Int J Syst Evol Microbiol 2017 Oct 31;67(10):4279-4283. Epub 2017 Aug 31.

Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla 41012, Spain.

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http://dx.doi.org/10.1099/ijsem.0.002296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5845653PMC
October 2017

Revisiting the genus Photobacterium: taxonomy, ecology and pathogenesis.

Int Microbiol 2017 Mar;20(1):1-10

Universidad de Málaga, Andalucía Tech, Departamento de Microbiología, Campus de Teatinos, Málaga, Spain.

The genus Photobacterium, one of the eight genera included in the family Vibrionaceae, contains 27 species with valid names and it has received attention because of the bioluminescence and pathogenesis mechanisms that some of its species exhibit. However, the taxonomy and phylogeny of this genus are not completely elucidated; for example, P. logei and P. fischeri are now considered members of the genus Aliivibrio, and previously were included in the genus Vibrio. In addition, P. damselae subsp. piscicida was formed as a new combination for former Vibrio damsela and Pasteurella piscicida. Moreover, P. damselae subsp. damselae is an earlier heterotypic synonym of P. histaminum. To avoid these incovenences draft and complete genomic sequences of members of Photobacterium are increasingly becoming available and their use is now routine for many research laboratories to address diverse goals: species delineation with overall genomic indexes, phylogenetic analyses, comparative genomics, and phenotypic inference. The habitats and isolation source of the Photobacterium species include seawater, sea sediments, saline lake waters, and a variety of marine organisms with which the photobacteria establish different relationships, from symbiosis to pathogenic interactions. Several species of this genus contain bioluminescent strains in symbiosis with marine fish and cephalopods; in addition, other species enhance its growth at pressures above 1 atmosphere, by means of several high-pressure adaptation mechanisms and for this, they may be considered as piezophilic (former barophilic) bacteria. Until now, only P. jeanii, P. rosenbergii, P. sanctipauli, and the two subspecies of P. damselae have been reported as responsible agents of several pathologies on animal hosts, such as corals, sponges, fish and homeothermic animals. In this review we have revised and updated the taxonomy, ecology and pathogenicity of several members of this genus. [Int Microbiol 20(1): 1-10 (2017)].
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http://dx.doi.org/10.2436/20.1501.01.280DOI Listing
March 2017

Whole genome sequences reveal Vibrio hemicentroti Kim et al. 2013 as a later heterotypic synonym of Vibrio splendidus (Beijerinck 1900) Baumann et al. 1981.

Int J Syst Evol Microbiol 2017 Jun 30;67(6):1669-1671. Epub 2017 Jun 30.

Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain.

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.
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http://dx.doi.org/10.1099/ijsem.0.001842DOI Listing
June 2017

Marinomonas blandensis sp. nov., a novel marine gammaproteobacterium.

Int J Syst Evol Microbiol 2016 Dec 9;66(12):5544-5549. Epub 2016 Oct 9.

Departamento de Microbiología y Ecología, Universitat de València, 46100 Burjassot (València), Spain.

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).
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http://dx.doi.org/10.1099/ijsem.0.001554DOI Listing
December 2016

An MLSA approach for the taxonomic update of the Splendidus clade, a lineage containing several fish and shellfish pathogenic Vibrio spp.

Syst Appl Microbiol 2016 Sep 6;39(6):361-9. Epub 2016 May 6.

Departamento de Microbiología y Ecología, and Colección Española de Cultivos Tipo, CECT, Universitat de València, Spain. Electronic address:

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.
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http://dx.doi.org/10.1016/j.syapm.2016.03.010DOI Listing
September 2016

Grimontia celer sp. nov., from sea water.

Int J Syst Evol Microbiol 2016 Aug 28;66(8):2906-2909. Epub 2016 Apr 28.

Departamento de Microbiología y Ecología & Colección Española de Cultivos Tipo, Universitat de València, Spain.

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.
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http://dx.doi.org/10.1099/ijsem.0.001119DOI Listing
August 2016

Draft genome sequence of Thalassobius mediterraneus CECT 5383(T), a poly-beta-hydroxybutyrate producer.

Genom Data 2016 Mar 15;7:237-9. Epub 2016 Jan 15.

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain.

Thalassobius mediterraneus is the type species of the genus Thalassobius and a member of the Roseobacter clade, an abundant representative of marine bacteria. T. mediterraneus XSM19(T) (= CECT 5383(T)) was isolated from the Western Mediterranean coast near Valencia (Spain) in 1989. We present here the draft genome sequence and annotation of this strain (ENA/DDBJ/NCBI accession number CYSF00000000), which is comprised of 3,431,658 bp distributed in 19 contigs and encodes 10 rRNA genes, 51 tRNA genes and 3276 protein coding genes. Relevant findings are commented, including the complete set of genes required for poly-beta-hydroxybutyrate (PHB) synthesis and genes related to degradation of aromatic compounds.
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http://dx.doi.org/10.1016/j.gdata.2016.01.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778676PMC
March 2016

Draft genome of Leisingera aquaemixtae CECT 8399(T), a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South Korea.

Genom Data 2016 Mar 15;7:233-6. Epub 2016 Jan 15.

Departamento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain.

We report the draft genome sequence and annotation of Leisingera aquaemixtae CECT 8399(T) (DDBJ/EMBL/GenBank accession number CYSR00000000) which comprises 4,614,060 bp, 4313 protein coding genes, 54 tRNA coding genes and 7 rRNA coding genes. General findings of the annotated genome, such as pigment indigoidine operon, phenylacetate oxidation genes or predictable number of replicons, are commented in comparison to other Leisingera species. Average Nucleotide Identity between available genomes of type strains of species of Leisingera and Phaeobacter genera has been calculated to evaluate its current classification.
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http://dx.doi.org/10.1016/j.gdata.2016.01.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778666PMC
March 2016

Draft genomic sequence of Nereida ignava CECT 5292(T), a marine bacterium of the family Rhodobacteraceae.

Stand Genomic Sci 2016 29;11:21. Epub 2016 Feb 29.

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Burjassot, 46100 Valencia Spain.

Nereida ignava strain 2SM4(T) (= CECT 5292(T) = DSM 16309(T) = CIP 108404(T) = CCUG 49433(T)) is a marine bacterium belonging to the Roseobacter group of the family Rhodobacteraceae within the class Alphaproteobacteria. The strain was isolated from sea water surrounding cultivated oysters 2-3 miles off the Mediterranean coast near Valencia (Spain) and was phylogenetically related to uncultured clones of gall symbiont bacteria of some species of Prionitis alga. Here we describe the genome sequence and annotation of this organism, the type strain of the single species of this genus. The genome comprised 2,888,349 bp, 2,872 protein-coding genes and 52 RNA genes. The annotation revealed the capacity to produce bacteriocins, vitamins and auxins. Besides, it contained sulfur cycling related genes.
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http://dx.doi.org/10.1186/s40793-016-0141-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770636PMC
March 2016

Draft genome sequence of Shimia marina CECT 7688(T).

Mar Genomics 2016 Aug 3;28:83-86. Epub 2016 Feb 3.

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain. Electronic address:

Shimia marina is a member of the family Rhodobacteraceae described in 2006. Strain CL-TA03(T) (=CECT 7688(T)) was isolated from a biofilm formed on an acrylic slide submerged in surface water in a coastal fish farm in Tongyeong, Korea. Here we report the draft genome sequence and annotation of S. marina CECT 7688(T) which is composed by 4,001,860bp arranged in 45 scaffolds with a G+C content of 57.4%, 3878 protein coding genes, 40 tRNA genes, 4 rRNA genes and 1 repeat region. An overview of annotated genes revealed diverse genes encoding for exopolysaccharide and capsular biosynthesis enzymes, secondary metabolite biosynthesis enzymes, multiple antibiotic and metal resistance and the ability for degrading aromatic compounds.
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http://dx.doi.org/10.1016/j.margen.2016.01.006DOI Listing
August 2016

Draft genomes of Nautella italica strains CECT 7645(T) and CECT 7321: Two roseobacters with potential pathogenic and biotechnological traits.

Mar Genomics 2016 Apr 13;26:73-80. Epub 2016 Jan 13.

Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain. Electronic address:

Nautella italica is a member of the family Rhodobacteraceae described in 2009. Strain LMG 24365(T) (=CECT 7645(T), =DSM 26436(T), =CCUG 55857(T)) was isolated from a marine electroactive biofilm growing in a stainless steel cathode exposed to natural water in Genoa, Italy. Strain AD 41 (=CECT 7321) was isolated from water surrounding cultivated gilthead seabream larvae in Cádiz, Spain. The genomes of strains CECT 7645(T) and CECT 7321 were sequenced, assembled, annotated and compared. Here we describe the most relevant findings: biofilm formation, quorum sensing, resistance to multiple drugs, heavy metals and oxidative stress, cytotoxins, and poly-β-hydroxybutyrate (PHB) production genes. These genomes were also compared to current available genomes in NCBI Genome Database from members of the genus Nautella, Nautella sp. R11 and Nautella sp. ECSMB14104. The comparison showed a higher similarity between strains CECT 7645(T) and R11 compared to strain CECT 7321 and strain ECSMB14104. The genome similarity indexes allowed confirming and assigning strains CECT 7321, R11 and ECSMB14104 to the species N. italica.
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http://dx.doi.org/10.1016/j.margen.2016.01.001DOI Listing
April 2016

Multilocus Sequence Analysis of the redefined clade Scophthalmi in the genus Vibrio.

Syst Appl Microbiol 2015 May 25;38(3):169-75. Epub 2015 Mar 25.

Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain. Electronic address:

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.
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http://dx.doi.org/10.1016/j.syapm.2015.03.005DOI Listing
May 2015