Strain identifier

BacDive ID: 131161

Type strain: Yes

Species: Sediminitomix flava

Strain Designation: Mok-1-85, MOK1-85

Strain history: CIP <- 2006, NRBC <- S. Thabrez Khan, NBDC:strain MOK1-85

NCBI tax ID(s): 379075 (species)

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General

@ref: 22453

BacDive-ID: 131161

DSM-Number: 28229

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

description: Sediminitomix flava Mok-1-85 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 379075
  • Matching level: species

strain history

@refhistory
22453<- CIP
67771<- Y Nakagawa, NBRC <- ST Khan, NBDC
119366CIP <- 2006, NRBC <- S. Thabrez Khan, NBDC:strain MOK1-85

doi: 10.13145/bacdive131161.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Flammeovirgaceae
  • genus: Sediminitomix
  • species: Sediminitomix flava
  • full scientific name: Sediminitomix flava Khan et al. 2007

@ref: 22453

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Flammeovirgaceae

genus: Sediminitomix

species: Sediminitomix flava

full scientific name: Sediminitomix flava Khan et al. 2007

strain designation: Mok-1-85, MOK1-85

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32037negative22.5 µm0.6 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.914
119366negativerod-shapedno

pigmentation

  • @ref: 32037
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22453BACTO 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
37001Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119366CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
22453positivegrowth25mesophilic
32037positivegrowth15-40
32037positiveoptimum37.5mesophilic
37001positivegrowth25mesophilic
67771positivegrowth25-30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.103

halophily

@refsaltgrowthtested relationconcentration
32037NaClpositivegrowth1.0-4.0 %
32037NaClpositiveoptimum2.5 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32037168082-dehydro-D-gluconate+carbon source
3203717057cellobiose+carbon source
3203728260galactose+carbon source
3203717234glucose+carbon source
3203728087glycogen+carbon source
3203753424tween 20+carbon source
3203753423tween 40+carbon source
3203753426tween 80+carbon source
3203718222xylose+carbon source
320374853esculin+hydrolysis
3203717632nitrate+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
11936617632nitrate-reduction
11936616301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3203716136hydrogen sulfideyes
11936635581indoleno

enzymes

@refvalueactivityec
32037acid phosphatase+3.1.3.2
32037alkaline phosphatase+3.1.3.1
32037catalase+1.11.1.6
32037gelatinase+
32037cytochrome oxidase+1.9.3.1
119366oxidase+
119366catalase-1.11.1.6
119366urease-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
119366-+++-++---++-+-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119366-----+---++-+--------+--+-+++--+---++-+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
22453marine sedimentOkinawa IslandJapanJPNAsia
67771From sea sedimentOkinawaJapanJPNAsia
119366Environment, Sea, sedimentJapanJPNAsia2005

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_163199.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14042;96_61282;97_79388;98_107311;99_163199&stattab=map
  • Last taxonomy: Sediminitomix flava subclade
  • 16S sequence: AB255370
  • Sequence Identity:
  • Total samples: 863
  • soil counts: 18
  • aquatic counts: 603
  • animal counts: 238
  • plant counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
224531Risk group (German classification)
1193661Risk group (French classification)

Sequence information

16S sequences

  • @ref: 22453
  • description: Sediminitomix flava gene for 16S rRNA, partial sequence
  • accession: AB255370
  • length: 1415
  • database: ena
  • NCBI tax ID: 379075

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sediminitomix flava DSM 28229GCA_003149185scaffoldncbi379075
66792Sediminitomix flava strain DSM 28229379075.3wgspatric379075
66792Sediminitomix flava DSM 282292695420929draftimg379075

GC content

@refGC-content
2245338
6777138.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno93.756yes
gram-positiveno97.901yes
anaerobicno96.878no
halophileno72.773no
spore-formingno91.341no
glucose-utilyes87.771yes
aerobicyes84.584no
thermophileno98.307yes
motileno90.877yes
glucose-fermentno81.279no

External links

@ref: 22453

culture collection no.: DSM 28229, CIP 109411, KCTC 12970, NBRC 101625

straininfo link

  • @ref: 89606
  • straininfo: 309489

literature

  • topic: Phylogeny
  • Pubmed-ID: 17684238
  • title: Sediminitomix flava gen. nov., sp. nov., of the phylum Bacteroidetes, isolated from marine sediment.
  • authors: Khan ST, Nakagawa Y, Harayama S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64854-0
  • year: 2007
  • mesh: Bacteroidetes/chemistry/*classification/genetics/*isolation & purification, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
22453Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28229Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28229)
32037Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172828728776041
37001Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7150
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89606Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID309489.1
119366Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109411Collection of Institut Pasteur (CIP 109411)