Strain identifier

BacDive ID: 3777

Type strain: Yes

Species: Dyadobacter crusticola

Strain Designation: CP 183-8, CP183-8

Strain history: CIP <- 2005, F. Garcia-Pichel, Arizona State Univ., Tempe, Arizona, USA: strain CP183-8

NCBI tax ID(s): 1121483 (strain), 292407 (species)

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General

@ref: 6485

BacDive-ID: 3777

DSM-Number: 16708

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

description: Dyadobacter crusticola CP 183-8 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from biological soil crusts.

NCBI tax id

NCBI tax idMatching level
292407species
1121483strain

strain history

@refhistory
6485<- F. Garcia-Pichel, Arizona; CP 183-8 <- G. S. N. Reddy
67771<- DSM <- F. Garcia-Pichel, Arizona; CP 183-8 <- G. S. N. Reddy
118793CIP <- 2005, F. Garcia-Pichel, Arizona State Univ., Tempe, Arizona, USA: strain CP183-8

doi: 10.13145/bacdive3777.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Dyadobacter
  • species: Dyadobacter crusticola
  • full scientific name: Dyadobacter crusticola Reddy and Garcia-Pichel 2005

@ref: 6485

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter crusticola

full scientific name: Dyadobacter crusticola Reddy and Garcia-Pichel 2005 emend. Hahnke et al. 2016

strain designation: CP 183-8, CP183-8

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31418negativerod-shapedno
27725negativerod-shapedno
67771negative
69480no92.075
69480negative99.995
118793negativerod-shapedno

colony morphology

@refcolony colorcolony shapemedium used
27725yellowcircular10x BG11-PGY medium
118793

pigmentation

@refproductioncolorname
31418yes
27725yesorangeFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6485R2A 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
40086MEDIUM 372 - for AquabacteriumyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.050 g);Agar (15.000 g);Glucose (0.500 g);Yeast extract (0.500 g);Pyruvic acid (0.300g);Tween 80 (1.000 ml);Casamino acids (0.500 g);Proteose Peptone N°3 (0.500 g);Di Potassium mon
2772510x BG11-PGY mediumyes
118793CIP Medium 372yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=372

culture temp

@refgrowthtypetemperaturerange
6485positivegrowth30mesophilic
31418positivegrowth5.0-30
31418positiveoptimum25mesophilic
40086positivegrowth30mesophilic
27725positiveoptimum25mesophilic
27725nogrowth37mesophilic
27725positivegrowth5-30
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31418positivegrowth6.0-8.0
31418positiveoptimum7
27725positivegrowth6-8
27725positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31418aerobe
27725aerobe
67771aerobe
118793obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
31418NaClpositivegrowth0.0-1.0 %
31418NaClpositiveoptimum0.05 %
27725NaClpositivegrowth1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3141822599arabinose+carbon source
3141817057cellobiose+carbon source
3141828757fructose+carbon source
3141828260galactose+carbon source
3141817234glucose+carbon source
3141824996lactate+carbon source
3141817716lactose+carbon source
3141817306maltose+carbon source
3141829864mannitol+carbon source
3141828053melibiose+carbon source
3141816634raffinose+carbon source
3141833942ribose+carbon source
3141830911sorbitol+carbon source
3141817992sucrose+carbon source
3141827082trehalose+carbon source
3141818222xylose+carbon source
2772515963ribitol-carbon source
27725casein-hydrolysis
2772562968cellulose-hydrolysis
2772516947citrate-carbon source
2772517057cellobiose+carbon source
2772515824D-fructose-fermentation
2772515824D-fructose+builds acid from
2772512936D-galactose-builds acid from
2772512936D-galactose+fermentation
2772517634D-glucose-builds acid from
2772517634D-glucose-fermentation
2772517634D-glucose+carbon source
2772517306maltose-builds acid from
2772517306maltose+fermentation
2772516899D-mannitol-builds acid from
2772516899D-mannitol+carbon source
2772516024D-mannose-fermentation
2772528053melibiose+carbon source
2772516634raffinose+carbon source
2772516988D-ribose+carbon source
2772517924D-sorbitol-builds acid from
2772517924D-sorbitol-fermentation
2772517924D-sorbitol+carbon source
2772516551D-trehalose+carbon source
2772565327D-xylose-builds acid from
2772565327D-xylose+fermentation
2772565327D-xylose+carbon source
2772516813galactitol+carbon source
277254853esculin+/-hydrolysis
2772517234glucose-fermentation
2772517234glucose+carbon source
2772515443inulin+carbon source
2772530849L-arabinose-builds acid from
2772530849L-arabinose+fermentation
2772524996lactate+carbon source
2772517716lactose-builds acid from
2772517716lactose-fermentation
2772517716lactose+carbon source
27725391504-oxopentanoate+carbon source
2772517268myo-inositol+carbon source
2772517632nitrate-reduction
2772528017starch-hydrolysis
2772517992sucrose-builds acid from
2772517992sucrose-fermentation
2772517992sucrose+carbon source
2772527897tryptophan-energy source
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
6837117151xylitol-builds acid from
6837115443inulin-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
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11879317632nitrate-reduction
11879316301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
277258309polymyxin byesyes300 Unit (disc)
277253393carbenicillinyesyes100 µg (disc)
2772550845doxycyclineyesyes30 µg (disc)
2772528368novobiocinyesyes30 µg (disc)
2772528077rifampicinyesyes30 µg (disc)
2772527902tetracyclineyesyes30 µg (disc)
277259337sulfathiazoleyesyes300 µg (disc)
27725102484sulfisoxazoleyesyes300 µg (disc)
2772571415nitrofurantoinyesyes150 µg (disc)
277254877ethambutolyesyes50 µg (disc)
27725161680aztreonamyesyes30 µg (disc)
2772529007ceftriaxoneyesyes30 µg (disc)
277253542cephalothinyesyes30 µg (disc)
2772517698chloramphenicolyesyes30 µg (disc)
2772528001vancomycinyesyes30 µg (disc)
277252955azithromycinyesyes15 µg (disc)
2772528669bacitracinyesyes10 Unit (disc)
2772537943colistinyesyes10 µg (disc)
2772517833gentamicinyesyes10 µg (disc)
2772517334penicillinyesyes10 Unit (disc)
2772517076streptomycinyesyes10 µg (disc)
27725100241ciprofloxacinyesyes5 µg (disc)
2772545924trimethoprimyesyes5 µg (disc)
2772548923erythromycinyesyes2 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
2772515688acetoinno
2772535581indoleno
2772516136hydrogen sulfideno
11879335581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole testcitrate test
2772517234glucose-
2772515688acetoin-
2772535581indole-
2772516947citrate-

enzymes

@refvalueactivityec
31418catalase+1.11.1.6
31418cytochrome oxidase+1.9.3.1
27725catalase+1.11.1.6
27725cytochrome oxidase+1.9.3.1
27725lipase+
27725phosphatase+
277256-phospho-beta-galactosidase+3.2.1.85
27725urease-3.5.1.5
27725gelatinase-
27725DNase-
27725arginine decarboxylase-4.1.1.19
27725lysine decarboxylase-4.1.1.18
27725ornithine decarboxylase-4.1.1.17
27725phenylalanine deaminase-4.3.1.5
27725arginine dihydrolase-3.5.3.6
27725tryptophan deaminase-4.1.99.1
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
118793oxidase+
118793alcohol dehydrogenase-1.1.1.1
118793catalase+1.11.1.6
118793lysine decarboxylase-4.1.1.18
118793ornithine decarboxylase-4.1.1.17
118793urease-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
118793-+++-++-+-++++-++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118793--+/-+/--+/---+/-+/-+/-+/-+/-------+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/--+/-+/-+/-+/--+/-+/-+/--------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
6485biological soil crustsColorada PlateauUSAUSANorth America
27725Biological soil crustColorado PlateauUSAUSANorth America38-1092003-05
67771From biological soil crustsColorado PlateauUSAUSANorth America
118793Environment, Biological soil crustsColorado canyonUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_26599.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_496;96_3325;97_4079;98_5216;99_26599&stattab=map
  • Last taxonomy: Dyadobacter crusticola subclade
  • 16S sequence: AJ821885
  • Sequence Identity:
  • Total samples: 42
  • soil counts: 15
  • aquatic counts: 2
  • animal counts: 20
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64851Risk group (German classification)
1187931Risk group (French classification)

Sequence information

16S sequences

  • @ref: 27725
  • description: 16S rRNA gene sequence
  • accession: AJ821885
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter crusticola DSM 16708GCA_000701505scaffoldncbi1121483
66792Dyadobacter crusticola DSM 167081121483.3wgspatric1121483
66792Dyadobacter crusticola DSM 167082561511040draftimg1121483

GC content

@refGC-contentmethod
3141848
648546.7sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.401no
flagellatedno97.131no
gram-positiveno97.647no
anaerobicno99.469no
halophileno94.437yes
spore-formingno94.7no
thermophileno99.059yes
glucose-utilyes90.068yes
aerobicyes89.414yes
glucose-fermentno89.278yes

External links

@ref: 6485

culture collection no.: DSM 16708, ATCC BAA 1036, KCTC 23639, CIP 109009, VTT E-072669

straininfo link

  • @ref: 73289
  • straininfo: 138980

literature

  • topic: Phylogeny
  • Pubmed-ID: 15879270
  • title: Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000.
  • authors: Reddy GSN, Garcia-Pichel F
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63498-0
  • year: 2005
  • mesh: Aerobiosis, Colorado, Cytophagaceae/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, Bacterial, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Movement, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlepubmedID_cross_reference
6485Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16708)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16708
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
2772510.1099/ijs.0.63498-015879270
31418Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127725
40086Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6703
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)
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.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
73289Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138980.1StrainInfo: A central database for resolving microbial strain identifiers
118793Curators of the CIPCollection of Institut Pasteur (CIP 109009)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109009