Strain identifier

BacDive ID: 14040

Type strain: Yes

Species: Flavimobilis marinus

Strain Designation: 1-19

Strain history: CIP <- 2005, JCM <- 2004, Y. Huang, Chinese Academy Sciences, Beijing, China: strain 1-19

NCBI tax ID(s): 285351 (species)

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General

@ref: 7875

BacDive-ID: 14040

DSM-Number: 19083

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, coccus-shaped

description: Flavimobilis marinus 1-19 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from coastal sediment.

NCBI tax id

  • NCBI tax id: 285351
  • Matching level: species

strain history

@refhistory
7875<- JCM <- Y. Huang, strain 1-19
67770Y. Huang 1-19.
120814CIP <- 2005, JCM <- 2004, Y. Huang, Chinese Academy Sciences, Beijing, China: strain 1-19

doi: 10.13145/bacdive14040.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Jonesiaceae
  • genus: Flavimobilis
  • species: Flavimobilis marinus
  • full scientific name: Flavimobilis marinus (Huang et al. 2005) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Sanguibacter marinus

@ref: 7875

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Jonesiaceae

genus: Flavimobilis

species: Flavimobilis marinus

full scientific name: Flavimobilis marinus (Huang et al. 2005) Nouioui et al. 2018

strain designation: 1-19

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31400positivecoccus-shapedyes
69480positive100
120814positiverod-shapedyes

pigmentation

  • @ref: 31400
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7875TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
38376MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
120814CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
7875positivegrowth28mesophilic
31400positivegrowth15-37
31400positiveoptimum27.5mesophilic
38376positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31400positivegrowth5.5-9.0alkaliphile
31400positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31400aerobe
120814facultative anaerobe

spore formation

@refspore formationconfidence
31400no
69481no100
69480no99.987

halophily

@refsaltgrowthtested relationconcentration
31400NaClpositivegrowth0-7 %
31400NaClpositiveoptimum3.5 %

observation

@refobservation
31400aggregates in clumps
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3140022599arabinose+carbon source
3140017057cellobiose+carbon source
3140028757fructose+carbon source
3140028260galactose+carbon source
3140017234glucose+carbon source
3140028087glycogen+carbon source
3140017716lactose+carbon source
3140017306maltose+carbon source
3140037684mannose+carbon source
3140017814salicin+carbon source
3140017992sucrose+carbon source
3140027082trehalose+carbon source
3140018222xylose+carbon source
314004853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12081417632nitrate+reduction
12081416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3140035581indoleyes
12081435581indoleno

metabolite tests

  • @ref: 31400
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31400catalase+1.11.1.6
31400gelatinase+
120814oxidase-
120814alcohol dehydrogenase-1.1.1.1
120814catalase+1.11.1.6
120814lysine decarboxylase-4.1.1.18
120814ornithine decarboxylase-4.1.1.17
120814urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120814--++-+++-++--+-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120814+--+++---++++----++-++++++++--+++/---++-++------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7875coastal sedimentFujian ProvinceChinaCHNAsia
67770Coastal sedimentFujian ProvinceChinaCHNAsia
120814Environment, Coastal sedimentFujianChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_31247.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_8118;97_18657;98_23236;99_31247&stattab=map
  • Last taxonomy: Flavimobilis marinus subclade
  • 16S sequence: AJ783958
  • Sequence Identity:
  • Total samples: 1029
  • soil counts: 188
  • aquatic counts: 146
  • animal counts: 546
  • plant counts: 149

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78751Risk group (German classification)
1208141Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7875
  • description: Sanguibacter marinus partial 16S rRNA gene, type strain 1-19T
  • accession: AJ783958
  • length: 1486
  • database: ena
  • NCBI tax ID: 285351

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavimobilis marinus CGMCC 1.3457GCA_014653315scaffoldncbi285351
66792Flavimobilis marinus strain CGMCC 1.3457285351.5wgspatric285351
66792Sanguibacter marinus strain DSM 19083285351.4wgspatric285351
66792Sanguibacter marinus DSM 190832622736429draftimg285351
67770Flavimobilis marinus DSM 19083GCA_900113055scaffoldncbi285351

GC content

@refGC-contentmethod
787573.6
3140073.4
6777073.4thermal denaturation, midpoint method (Tm)
6777072genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno91.959no
gram-positiveyes90.937yes
anaerobicno98.774no
aerobicyes72.346no
halophileno87.652no
spore-formingno90.586yes
thermophileno97.073no
glucose-utilyes85.568yes
motileyes82.682yes
glucose-fermentno64.767no

External links

@ref: 7875

culture collection no.: DSM 19083, CGMCC 1.3457, CIP 109015, JCM 12547

straininfo link

  • @ref: 83209
  • straininfo: 265631

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166662Sanguibacter marinus sp. nov., isolated from coastal sediment.Huang Y, Dai X, He L, Wang YN, Wang BJ, Liu Z, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.63471-02005Actinomycetales/*classification/genetics/isolation & purification/metabolism, Bacterial Typing Techniques, China, DNA, Bacterial/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny18319451Sanguibacter soli sp. nov., isolated from soil of a ginseng field.Kim MK, Pulla RK, Kim SY, Yi TH, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.65399-02008Actinomycetales/classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7875Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19083)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19083
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
31400Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2770928776041
38376Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6710
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
83209Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265631.1StrainInfo: A central database for resolving microbial strain identifiers
120814Curators of the CIPCollection of Institut Pasteur (CIP 109015)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109015