Strain identifier

BacDive ID: 5544

Type strain: Yes

Species: Flavobacterium micromati

Strain Designation: R-9192

Strain history: CIP <- 2003, S. Van Trappen, Gent, Belgium: strain R-9192 <- J. Mergaert

NCBI tax ID(s): 229205 (species)

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General

@ref: 7111

BacDive-ID: 5544

DSM-Number: 17659

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

description: Flavobacterium micromati R-9192 is a psychrophilic, Gram-negative, rod-shaped bacterium that was isolated from microbial mats.

NCBI tax id

  • NCBI tax id: 229205
  • Matching level: species

strain history

@refhistory
7111<- S. Van Trappen, LMG; R-9192 <- J. Mergaert
120948CIP <- 2003, S. Van Trappen, Gent, Belgium: strain R-9192 <- J. Mergaert

doi: 10.13145/bacdive5544.20230509.8.1

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 micromati
  • full scientific name: Flavobacterium micromati Van Trappen et al. 2004

@ref: 7111

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium micromati

full scientific name: Flavobacterium micromati Van Trappen et al. 2004

strain designation: R-9192

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapeconfidencemotility
30030negative04-06 µmrod-shaped
69480negative99.988
120948negativerod-shapedno

pigmentation

  • @ref: 30030
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7111R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
33902MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120948CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
120948CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7111positivegrowth15psychrophilic
30030positivegrowth05-25
30030positiveoptimum15psychrophilic
33902positivegrowth15psychrophilic
120948positivegrowth5-15psychrophilic
120948nogrowth25mesophilic
120948nogrowth30mesophilic
120948nogrowth37mesophilic
120948nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
30030NaClpositivegrowth0-5 %
30030NaClpositiveoptimum2.5 %
120948NaClpositivegrowth0-2 %
120948NaClnogrowth4 %
120948NaClnogrowth6 %
120948NaClnogrowth8 %
120948NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3003017234glucose+carbon source
3003017306maltose+carbon source
3003037684mannose+carbon source
300304853esculin+hydrolysis
3003017632nitrate+reduction
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
6837115443inulin-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
12094816947citrate-carbon source
1209484853esculin+hydrolysis
120948606565hippurate-hydrolysis
12094817632nitrate-reduction
12094816301nitrite-reduction
12094815792malonate-assimilation

antibiotic resistance

  • @ref: 120948
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120948
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12094815688acetoin-
12094817234glucose-

enzymes

@refvalueactivityec
30030catalase+1.11.1.6
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
120948oxidase+
120948beta-galactosidase+3.2.1.23
120948alcohol dehydrogenase-1.1.1.1
120948gelatinase-
120948catalase+1.11.1.6
120948gamma-glutamyltransferase+2.3.2.2
120948lysine decarboxylase-4.1.1.18
120948ornithine decarboxylase-4.1.1.17
120948phenylalanine ammonia-lyase-4.3.1.24
120948tryptophan deaminase-
120948urease-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
120948-+++-+++--++---+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120948-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120948+--++--+-++-------+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
7111microbial matsLake Grace in the Vestfold Hills and Lake Fryxell in the McMurdo Dry ValleysAustralia and Oceania
120948Microbial materialVestfold lakeAntarcticaAntarcticaATA1999

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Microbial community
  • Cat3: #Microbial mat

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71111Risk group (German classification)
1209481Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7111
  • description: Flavobacterium micromati 16S rRNA gene, strain LMG 21919
  • accession: AJ557888
  • length: 1480
  • database: ena
  • NCBI tax ID: 229205

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium micromati DSM 17659GCA_900129585scaffoldncbi229205
66792Flavobacterium micromati strain DSM 17659229205.4wgspatric229205
66792Flavobacterium micromati DSM 176592695420959draftimg229205

GC content

  • @ref: 30030
  • GC-content: 33.8-34.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.764no
flagellatedno94.625no
gram-positiveno97.854yes
anaerobicno99.037no
aerobicyes91.201no
halophileno88.008no
spore-formingno92.808no
thermophileno99.702no
glucose-utilyes87.627no
glucose-fermentno93.038no

External links

@ref: 7111

culture collection no.: DSM 17659, CIP 108161, LMG 21919, KCTC 2284

straininfo link

  • @ref: 75027
  • straininfo: 22964

literature

  • topic: Phylogeny
  • Pubmed-ID: 14742463
  • title: Flavobacterium degerlachei sp. nov., Flavobacterium frigoris sp. nov. and Flavobacterium micromati sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes.
  • authors: Van Trappen S, Vandecandelaere I, Mergaert J, Swings J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02857-0
  • year: 2004
  • mesh: Antarctic Regions, Classification, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacterium/*classification/genetics/growth & development/isolation & purification, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7111Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17659)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17659
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
30030Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2639428776041
33902Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5753
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
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
75027Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID22964.1StrainInfo: A central database for resolving microbial strain identifiers
120948Curators of the CIPCollection of Institut Pasteur (CIP 108161)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108161