Strain identifier

BacDive ID: 6031

Type strain: Yes

Species: Halomonas halocynthiae

Strain Designation: 2.1.2

Strain history: CIP <- 2002, DSMZ <- L.A. Romanenko

NCBI tax ID(s): 1121940 (strain), 176290 (species)

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General

@ref: 5391

BacDive-ID: 6031

DSM-Number: 14573

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative

description: Halomonas halocynthiae 2.1.2 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from gill tissue of the ascidian Halocynthia aurantium.

NCBI tax id

NCBI tax idMatching level
1121940strain
176290species

strain history

@refhistory
5391<- L. A. Romanenko; 2.1.2
119800CIP <- 2002, DSMZ <- L.A. Romanenko

doi: 10.13145/bacdive6031.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas halocynthiae
  • full scientific name: Halomonas halocynthiae Romanenko et al. 2002

@ref: 5391

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas halocynthiae

full scientific name: Halomonas halocynthiae Romanenko et al. 2002

strain designation: 2.1.2

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.993
119800negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5391BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37540Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119800CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5391positivegrowth25mesophilic
37540positivegrowth25mesophilic
119800positivegrowth15-37
119800nogrowth5psychrophilic
119800nogrowth41thermophilic
119800nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119800
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

  • @ref: 119800
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119800D-fructose-degradation15824
119800D-glucose-degradation17634
119800D-mannose-degradation16024
119800lactose-degradation17716
119800maltose-degradation17306
119800sucrose-degradation17992
119800citrate-carbon source16947
119800esculin-hydrolysis4853
119800hippurate-hydrolysis606565
119800nitrate+reduction17632
119800nitrite-reduction16301
119800malonate-assimilation15792
119800nitrate-respiration17632

antibiotic resistance

  • @ref: 119800
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119800
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
119800oxidase+
119800beta-galactosidase-3.2.1.23
119800alcohol dehydrogenase-1.1.1.1
119800gelatinase-
119800amylase-
119800caseinase-3.4.21.50
119800catalase+1.11.1.6
119800tween esterase-
119800gamma-glutamyltransferase+2.3.2.2
119800lecithinase-
119800lipase-
119800lysine decarboxylase-4.1.1.18
119800ornithine decarboxylase-4.1.1.17
119800phenylalanine ammonia-lyase-4.3.1.24
119800protease-
119800tryptophan deaminase-
119800urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119800-+++-++----+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119800-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119800---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
5391gill tissue of the ascidian Halocynthia aurantiumHalocynthia aurantiumJapanJPNAsia
119800Gill tissue of the ascidian Halocynthia aurantiumJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Tunicata
#Host Body-Site#Organ#Vascular system

taxonmaps

  • @ref: 69479
  • File name: preview.99_96086.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_39312;97_50082;98_65900;99_96086&stattab=map
  • Last taxonomy: Halomonas halocynthiae subclade
  • 16S sequence: AJ417388
  • Sequence Identity:
  • Total samples: 165
  • soil counts: 8
  • aquatic counts: 132
  • animal counts: 23
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53911Risk group (German classification)
1198001Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5391
  • description: Halomonas halocynthiae 16S rRNA gene, strain KMM 1376
  • accession: AJ417388
  • length: 1514
  • database: ena
  • NCBI tax ID: 176290

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas halocynthiae DSM 14573GCA_000425725scaffoldncbi1121940
66792Halomonas halocynthiae DSM 145731121940.3wgspatric1121940
66792Halomonas halocynthiae DSM 145732526164533draftimg1121940

GC content

  • @ref: 5391
  • GC-content: 53.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno77.929no
flagellatedno92.513no
gram-positiveno98.839no
anaerobicno98.584no
aerobicyes73.012no
halophileyes94.744no
spore-formingno97.932no
thermophileno99.667yes
glucose-utilyes60.335no
glucose-fermentno82.215no

External links

@ref: 5391

culture collection no.: DSM 14573, CIP 107736, KMM 1376

straininfo link

  • @ref: 75517
  • straininfo: 88292

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361285Halomonas halocynthiae sp. nov., isolated from the marine ascidian Halocynthia aurantium.Romanenko LA, Schumann P, Rohde M, Mikhailov VV, Stackebrandt EInt J Syst Evol Microbiol10.1099/00207713-52-5-17672002Animals, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Halomonas/*classification/genetics/*isolation & purification/metabolism, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Urochordata/microbiologyGenetics
Pathogenicity31826483Structure and bioactivity of sulfated alpha-D-mannan from marine bacterium Halomonas halocynthiae KMM 1376(T).Kokoulin MS, Filshtein AP, Romanenko LA, Chikalovets IV, Chernikov OVCarbohydr Polym10.1016/j.carbpol.2019.1155562019Acetates/chemistry, Animals, Cell Line, Tumor, Cell Survival/drug effects, Cell Transformation, Neoplastic/drug effects, Epidermal Growth Factor/pharmacology, Halomonas/*metabolism, Humans, Hydrolysis, Lipopolysaccharides/chemistry, Mannans/*chemistry/pharmacology, Mice, Polysaccharides, Bacterial/chemistry/pharmacology, Sulfates/chemistryMetabolism

Reference

@idauthorscataloguedoi/urltitle
5391Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14573)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14573
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
37540Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5204
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75517Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88292.1StrainInfo: A central database for resolving microbial strain identifiers
119800Curators of the CIPCollection of Institut Pasteur (CIP 107736)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107736