Strain identifier

BacDive ID: 6027

Type strain: Yes

Species: Flavobacterium halmophilum

Strain Designation: HMSMF 1.1

Strain history: CIP <- 1998, NCIMB <- Hopkins Marine station, Stanford Univ., Pacific Grove, California, USA: strain HMSMF 1.1 <- B. Elazari-Volcani

NCBI tax ID(s): 252 (species)

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General

@ref: 1996

BacDive-ID: 6027

DSM-Number: 5349

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Flavobacterium halmophilum HMSMF 1.1 is a mesophilic, motile bacterium that was isolated from dead sea.

NCBI tax id

  • NCBI tax id: 252
  • Matching level: species

strain history

@refhistory
1996<- NCIMB (NCMB<-NCIB) <- Hopkins Marine Station <- B. Elazari-Volcani
67770IAM 14439 <-- NCIMB 1971 <-- Hopkins Mar. Sta.; MF 1.1 <-- B. E. Volcani.
119796CIP <- 1998, NCIMB <- Hopkins Marine station, Stanford Univ., Pacific Grove, California, USA: strain HMSMF 1.1 <- B. Elazari-Volcani

doi: 10.13145/bacdive6027.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium halmophilum
  • full scientific name: Flavobacterium halmophilum corrig. Elazari-Volcani 1940 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Flavobacterium halmephilium
    20215Halomonas halmophila

@ref: 1996

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas halmophila

full scientific name: Halomonas halmophila (Elazari-Volcani 1940) Franzmann et al. 1989 emend. Dobson et al. 1990

strain designation: HMSMF 1.1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.249
6948099.951negative
119796yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1996MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)yeshttps://mediadive.dsmz.de/medium/514bName: MEDIUM 514 plus additional salt (DSMZ Medium 514b; with strain-specific modifications) Composition: NaCl 80.0 g/l Agar 17.5 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
39297MEDIUM 117 - for Pseudoalteromonas haloplanktis, Cytophaga lytica and Halomonas halodenitrificansyesDistilled water make up to (250.000 ml);Yeast extract (3.000 g);Peptone(5.000 g);Synthetic sea solution - M0216 (750.000 ml)
119796CIP Medium 117yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=117
119796CIP Medium 192yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=192

culture temp

@refgrowthtypetemperaturerange
1996positivegrowth25mesophilic
39297positivegrowth25mesophilic
67770positivegrowth25mesophilic
119796positivegrowth15-30
119796nogrowth5psychrophilic
119796nogrowth37mesophilic
119796nogrowth41thermophilic
119796nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no98.808

halophily

@refsaltgrowthtested relationconcentration
119796NaClpositivegrowth8-10 %
119796NaClnogrowth0 %
119796NaClnogrowth2 %
119796NaClnogrowth4 %
119796NaClnogrowth6 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837117992sucrose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837116899D-mannitol+builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose+builds acid from
6837165327D-xylose-builds acid from
1197964853esculin-hydrolysis
119796606565hippurate-hydrolysis
11979617632nitrate-reduction
11979616301nitrite-reduction

metabolite production

  • @ref: 119796
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11979615688acetoin-
11979617234glucose-

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
119796oxidase-
119796beta-galactosidase-3.2.1.23
119796alcohol dehydrogenase-1.1.1.1
119796gelatinase-
119796amylase-
119796caseinase-3.4.21.50
119796catalase+1.11.1.6
119796tween esterase-
119796gamma-glutamyltransferase+2.3.2.2
119796lecithinase-
119796lipase-
119796lysine decarboxylase-4.1.1.18
119796ornithine decarboxylase-4.1.1.17
119796phenylalanine ammonia-lyase+4.3.1.24
119796protease-
119796tryptophan deaminase-
119796urease-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
119796-+++-+---------+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119796+/-+/-+/-+/-+/--+/-+/-+/-+/-+-+/-+/-+/-+/-+/-++/-+/-+/-+/-+/-+/-+/-+/-+/-+-+/-++/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119796---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
1996dead sea
67770Dead Sea
119796Environment, Dead seaIsraelISRAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Marine
#Condition#Saline

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
19961Risk group (German classification)
1197961Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halomonas halmophila partial 16S rRNA gene, strain ATCC 19717AJ3068891530ena252
20218Flavobacterium halmophilum 16S ribosomal RNAM591531540ena252
20218Halomonas halmophila gene for 16S rRNA, partial sequence, strain: NBRC 15537AB6808911463ena252

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas halmophila strain NBRC 15537252.3wgspatric252
67770Halomonas halmophila NBRC 15537GCA_006540005contigncbi252

GC content

  • @ref: 67770
  • GC-content: 63
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.879no
gram-positiveno98.787no
anaerobicno98.691no
aerobicyes93.645no
halophileyes93.104no
spore-formingno95.696no
glucose-utilyes93.255no
flagellatedno54.925no
thermophileno96.707yes
glucose-fermentno68.208no

External links

@ref: 1996

culture collection no.: DSM 5349, ATCC 19717, IAM 14439, NCMB 1971, JCM 21222, ACAM 71, CIP 105455, IFO 15537, LMG 4023, NBRC 15537, NCIB 8718, NCIMB 1971, NCIMB 8718

straininfo link

  • @ref: 75513
  • straininfo: 13675

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1996Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5349)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5349
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39297Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17476
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
75513Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13675.1StrainInfo: A central database for resolving microbial strain identifiers
119796Curators of the CIPCollection of Institut Pasteur (CIP 105455)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105455