Strain identifier

BacDive ID: 7301

Type strain: Yes

Species: Cryobacterium psychrophilum

Strain Designation: 27-O-b

Strain history: CIP <- 1997, JCM <- IAM <- K. Inoue and K. Komagata: strain 27-O-b

NCBI tax ID(s): 41988 (species)

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General

@ref: 1762

BacDive-ID: 7301

DSM-Number: 4854

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

description: Cryobacterium psychrophilum 27-O-b is an obligate aerobe, psychrophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 41988
  • Matching level: species

strain history

@refhistory
1762<- JCM <- IAM <- K. Inoue and K.Komagata, 27-0-b
67770IAM 12024 <-- K. Inoue and K. Komagata 27-O-b.
122024CIP <- 1997, JCM <- IAM <- K. Inoue and K. Komagata: strain 27-O-b

doi: 10.13145/bacdive7301.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Cryobacterium
  • species: Cryobacterium psychrophilum
  • full scientific name: Cryobacterium psychrophilum (ex Inoue and Komagata 1976) Suzuki et al. 1997

  • synonyms

    • @ref: 20215
    • synonym: Curtobacterium psychrophilum

@ref: 1762

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Cryobacterium

species: Cryobacterium psychrophilum

full scientific name: Cryobacterium psychrophilum (ex Inoue and Komagata 1976) Suzuki et al. 1997

strain designation: 27-O-b

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
122024positiverod-shapedno

colony morphology

  • @ref: 122024

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1762RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
39232MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122024CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
1762positivegrowth10-12psychrophilic
39232positivegrowth10psychrophilic
67770positivegrowth10psychrophilic
122024positivegrowth5-15psychrophilic
122024nogrowth18psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122024
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.95

halophily

@refsaltgrowthtested relationconcentration
122024NaClpositivegrowth2-6 %
122024NaClnogrowth0 %
122024NaClnogrowth8 %
122024NaClnogrowth10 %

murein

  • @ref: 1762
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-10

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
122024esculin-hydrolysis4853
122024nitrate-reduction17632
122024nitrite-reduction16301
122024nitrate-respiration17632

metabolite production

  • @ref: 122024
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12202415688acetoin-
12202417234glucose-

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
122024oxidase-
122024beta-galactosidase+3.2.1.23
122024alcohol dehydrogenase-1.1.1.1
122024gelatinase-
122024amylase-
122024DNase+
122024caseinase-3.4.21.50
122024catalase+1.11.1.6
122024tween esterase-
122024gamma-glutamyltransferase-2.3.2.2
122024lecithinase-
122024lipase-
122024lysine decarboxylase-4.1.1.18
122024ornithine decarboxylase-4.1.1.17
122024phenylalanine ammonia-lyase-4.3.1.24
122024protease-
122024tryptophan deaminase-
122024urease-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
122024--++-+----++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122024+--------++++-----------------+---------------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
1762soilSyowa stationAustralia and Oceania
67770Soil in Showa StationAntarcticaAntarcticaATA
122024Environment, SoilAntarcticaAntarcticaATA

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17621Risk group (German classification)
1220241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Cryobacterium psychrophilum 16S rRNA gene, strain DSM 4854AJ5440631527ena41988
20218Cryobacterium psychrophilum partial 16S rRNA gene, type strain DSM 4854AM4106761501ena41988
1762Cryobacterium psychrophilum gene for 16S ribosomal RNAD450581501ena41988

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cryobacterium psychrophilum strain CGMCC 1.429241988.4wgspatric41988
66792Cryobacterium psychrophilum strain DSM 485441988.3wgspatric41988
66792Cryobacterium psychrophilum DSM 48542781126036draftimg41988
67770Cryobacterium psychrophilum DSM 4854GCA_004365915contigncbi41988
67770Cryobacterium psychrophilum CGMCC 1.4292GCA_004403975contigncbi41988

GC content

@refGC-contentmethod
176265high performance liquid chromatography (HPLC)
6777066.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes96.262no
anaerobicno99.591no
halophileno66.188no
spore-formingno91.521no
glucose-utilyes88.422no
aerobicyes93.643no
thermophileno98.68yes
motileno80.405no
flagellatedno97.767no
glucose-fermentno88.324no

External links

@ref: 1762

culture collection no.: DSM 4854, ATCC 43563, IAM 12024, IFO 15735, JCM 1463, NBRC 15735, NCIMB 2068, CCM 3311, CGMCC 1.1912, CGMCC 1.4292, CIP 105227, KCTC 3487, LMG 23845, VKM Ac-2100

straininfo link

  • @ref: 76751
  • straininfo: 41917

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9103638Cryobacterium psychrophilum gen. nov., sp. nov., nom. rev., comb. nov., an obligately psychrophilic actinomycete to accommodate "Curtobacterium psychrophilum" Inoue and Komagata 1976.Suzuki K, Sasaki J, Uramoto M, Nakase T, Komagata KInt J Syst Bacteriol10.1099/00207713-47-2-4741997Actinomycetales/*classification/genetics/metabolism, Aminobutyrates/metabolism, Antarctic Regions, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Terminology as Topic, Vitamin K/metabolismMetabolism
Phylogeny17392221Cryobacterium psychrotolerans sp. nov., a novel psychrotolerant bacterium isolated from the China No. 1 glacier.Zhang DC, Wang HX, Cui HL, Yang Y, Liu HC, Dong XZ, Zhou PJInt J Syst Evol Microbiol10.1099/ijs.0.64750-02007Actinomycetales/*classification/genetics/isolation & purification/physiology, China, *Cold Temperature, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Ice Cover/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny18450721Cryobacterium mesophilum sp. nov., a novel mesophilic bacterium.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65650-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19661491Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil.Reddy GSN, Pradhan S, Manorama R, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.011775-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, *Cold Temperature, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Ice Cover/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny23203625Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air.Weon HY, Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Suzuki KI, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.046599-02012Actinomycetales/*classification/genetics/isolation & purification, *Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny23315411Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice.Liu Q, Liu H, Zhang J, Zhou Y, Xin YInt J Syst Evol Microbiol10.1099/ijs.0.046896-02013Actinomycetales/*classification/genetics/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny24535740Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae.Kim SJ, Ahn JH, Weon HY, Hamada M, Suzuki K, Kwon SWJ Microbiol10.1007/s12275-014-3278-y2014Actinomycetales/classification/*genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1762Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4854)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4854
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
39232Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17224
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
76751Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41917.1StrainInfo: A central database for resolving microbial strain identifiers
122024Curators of the CIPCollection of Institut Pasteur (CIP 105227)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105227