Strain identifier

BacDive ID: 5535

Type strain: Yes

Species: Flavobacterium limicola

Strain Designation: ST-82

Strain history: CIP <- 2003, JCM <- H. Tamaki: strain ST-82

NCBI tax ID(s): 180441 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 5707

BacDive-ID: 5535

DSM-Number: 15094

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

description: Flavobacterium limicola ST-82 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from river sediment.

NCBI tax id

  • NCBI tax id: 180441
  • Matching level: species

strain history

@refhistory
5707<- H. Tamaki; ST-82
67770H. Tamaki ST-82.
120600CIP <- 2003, JCM <- H. Tamaki: strain ST-82

doi: 10.13145/bacdive5535.20230509.8.1

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 limicola
  • full scientific name: Flavobacterium limicola Tamaki et al. 2003

@ref: 5707

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium limicola

full scientific name: Flavobacterium limicola Tamaki et al. 2003

strain designation: ST-82

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.998
120600negativerod-shapedno

colony morphology

@refincubation period
617732-3 days
120600

pigmentation

  • @ref: 120600
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5707TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
5707NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
42254MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120600CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5707positivegrowth15psychrophilic
42254positivegrowth15psychrophilic
61773positivegrowth20psychrophilic
67770positivegrowth15psychrophilic
120600positivegrowth5-15psychrophilic
120600nogrowth25mesophilic
120600nogrowth30mesophilic
120600nogrowth37mesophilic
120600nogrowth41thermophilic
120600nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
61773aerobe
120600obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
120600NaClpositivegrowth0 %
120600NaClnogrowth2 %
120600NaClnogrowth4 %
120600NaClnogrowth6 %
120600NaClnogrowth8 %
120600NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12060016947citrate-carbon source
1206004853esculin+hydrolysis
120600606565hippurate+hydrolysis
12060017632nitrate-builds gas from
12060017632nitrate-reduction
12060016301nitrite-builds gas from
12060016301nitrite-reduction
12060015792malonate-assimilation
12060017234glucose+degradation

antibiotic resistance

  • @ref: 120600
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120600
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12060015688acetoin-
12060017234glucose+

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
120600oxidase-
120600beta-galactosidase-3.2.1.23
120600alcohol dehydrogenase-1.1.1.1
120600gelatinase-
120600amylase-
120600DNase-
120600caseinase-3.4.21.50
120600catalase+1.11.1.6
120600tween esterase-
120600gamma-glutamyltransferase+2.3.2.2
120600lecithinase-
120600lipase-
120600lysine decarboxylase-4.1.1.18
120600ornithine decarboxylase-4.1.1.17
120600phenylalanine ammonia-lyase-4.3.1.24
120600protease-
120600tryptophan deaminase-
120600urease-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
120600-+---++-+-++---+-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120600++-----+-++-------+------------------------------------+----------------------------------++-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5707river sedimentIbaraki Pref., Shin riverJapanJPNAsia
61773Fresh water sedimentJapanJPNAsia
67770Freshwater river sedimentsIbaraki Pref.JapanJPNAsia
120600Environment, Frest water sedimentsJapanJPNAsia1997

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57071Risk group (German classification)
1206001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flavobacterium limicola strain DSM 15094 16S ribosomal RNA gene, partial sequenceJX6570411256ena180441
5707Flavobacterium limicola gene for 16S ribosomal RNA, strain:ST-82AB0752301475ena180441

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium limicola DSM 15094GCA_003634755contigncbi180441
66792Flavobacterium limicola strain DSM 15094180441.4wgspatric180441
66792Flavobacterium limicola DSM 150942698536747draftimg180441

GC content

@refGC-content
570735
6777034

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.948no
gram-positiveno98.802no
anaerobicno99.5no
aerobicyes93.677yes
halophileno94.218no
spore-formingno94.998no
glucose-utilyes86.12no
flagellatedno94.012no
thermophileno99.651yes
glucose-fermentno94.085no

External links

@ref: 5707

culture collection no.: DSM 15094, JCM 11473, CCUG 58906, LMG 21930, CIP 107957, KCTC 12494, NBRC 103156

straininfo link

  • @ref: 75018
  • straininfo: 99541

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19622646Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet.Ali Z, Cousin S, Fruhling A, Brambilla E, Schumann P, Yang Y, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.008771-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Flavobacterium/chemistry/classification/genetics/*isolation & purification, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny19625423Flavobacterium tiangeerense sp. nov., a cold-living bacterium isolated from a glacier.Xin YH, Liang ZH, Zhang DC, Liu HC, Zhang JL, Yu Y, Xu MS, Zhou PJ, Zhou YGInt J Syst Evol Microbiol10.1099/ijs.0.007906-02009China, Cold Temperature, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Flavobacterium/classification/genetics/*isolation & purification/metabolism, Ice Cover/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny19651737Flavobacterium fluvii sp. nov., isolated from stream sediment.Lee SH, Kim JM, Lee JR, Park W, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.010850-02009Base Composition, Base Sequence, DNA, Bacterial/chemistry, Flavobacterium/chemistry/*classification/physiology, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Homology, Nucleic Acid, *Water MicrobiologyGenetics
Phylogeny30994432Flavobacterium laiguense sp. nov., a psychrophilic bacterium isolated from Laigu glacier on the Tibetan Plateau.Yang LL, Liu Q, Liu HC, Zhou YG, Xin YHInt J Syst Evol Microbiol10.1099/ijsem.0.0034002019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Ice Cover/*microbiology, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5707Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15094)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15094
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
42254Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5525
61773Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58906)https://www.ccug.se/strain?id=58906
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/
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
75018Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99541.1StrainInfo: A central database for resolving microbial strain identifiers
120600Curators of the CIPCollection of Institut Pasteur (CIP 107957)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107957