Strain identifier

BacDive ID: 3053

Type strain: Yes

Species: Cryptobacterium curtum

Strain Designation: 12-3

Strain history: <- J. Tang, ATCC <- Niigata Univ. <- E. Hoshino

NCBI tax ID(s): 469378 (strain), 84163 (species)

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General

@ref: 6011

BacDive-ID: 3053

DSM-Number: 15641

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped, colony-forming

description: Cryptobacterium curtum 12-3 is an anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from peridontal pocket of an adult with peridontal disease.

NCBI tax id

NCBI tax idMatching level
469378strain
84163species

strain history

  • @ref: 6011
  • history: <- J. Tang, ATCC <- Niigata Univ. <- E. Hoshino

doi: 10.13145/bacdive3053.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Eggerthellales
  • family: Eggerthellaceae
  • genus: Cryptobacterium
  • species: Cryptobacterium curtum
  • full scientific name: Cryptobacterium curtum Nakazawa et al. 1999

@ref: 6011

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Eggerthellaceae

genus: Cryptobacterium

species: Cryptobacterium curtum

full scientific name: Cryptobacterium curtum Nakazawa et al. 1999

strain designation: 12-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23098positive0.8-1.0 µm0.4 µmrod-shapedno
69480no90.144
69480positive99.639

colony morphology

@reftype of hemolysiscolony sizecolony colorcolony shapemedium usedincubation period
23098gamma<1.0 mmtranslucentcircularBrain Heart Infusion-blood agar plates
607243 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_15641_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6011CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
23098Brain Heart Infusion-blood agar platesyes

culture temp

@refgrowthtypetemperaturerange
6011positivegrowth37mesophilic
60724positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6011anaerobe
23098obligate anaerobe
60724anaerobe
69480anaerobe99.441

spore formation

@refspore formationconfidence
23098no
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2309815963ribitol-assimilation
2309827613amygdalin-assimilation
2309822599arabinose-assimilation
2309817057cellobiose-assimilation
2309817113erythritol-assimilation
230984853esculin-assimilation
2309828757fructose-assimilation
2309828260galactose-assimilation
2309817234glucose-assimilation
2309828087glycogen-assimilation
2309817268myo-inositol-assimilation
2309817716lactose-assimilation
2309817306maltose-assimilation
2309829864mannitol-assimilation
2309837684mannose-assimilation
230986731melezitose-assimilation
2309828053melibiose-assimilation
2309826546rhamnose-assimilation
2309833942ribose-assimilation
2309817814salicin-assimilation
2309830911sorbitol-assimilation
2309828017starch-assimilation
2309817992sucrose-assimilation
2309827082trehalose-assimilation
2309818222xylose-assimilation
230984853esculin-hydrolysis
2309828017starch-hydrolysis
2309817632nitrate-reduction

metabolite production

  • @ref: 23098
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
23098catalase-1.11.1.6
23098urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment cultureenrichment culture duration
6011peridontal pocket of an adult with peridontal diseaseJapanJPNAsia
23098human periodontal pocket sample (oral cavities)brain-heart infusion (BHI)-blood agar plates7-10 days
60724Human periodontal pocket,adult,periodontal disease

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Infection#Inflammation
#Host Body-Site#Oral cavity and airways#Periodontal pocket

Safety information

risk assessment

  • @ref: 6011
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6011
  • description: Cryptobacterium curtum gene for 16S rRNA, partial sequence
  • accession: AB019260
  • length: 1429
  • database: ena
  • NCBI tax ID: 469378

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cryptobacterium curtum DSM 15641GCA_000023845completencbi469378
66792Cryptobacterium curtum DSM 15641469378.5completepatric469378
66792Cryptobacterium curtum 12-3, DSM 15641644736346completeimg469378

GC content

@refGC-contentmethod
601150-51
2309851.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.066yes
flagellatedno98.269no
gram-positiveyes90.995yes
anaerobicyes98.732yes
aerobicno97.717yes
halophileno82.468no
spore-formingno96.163yes
thermophileno92.883no
glucose-utilyes57.278yes
glucose-fermentno53.826no

External links

@ref: 6011

culture collection no.: DSM 15641, ATCC 700683, CCUG 55773

straininfo link

  • @ref: 72573
  • straininfo: 44077

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10425779Cryptobacterium curtum gen. nov., sp. nov., a new genus of gram-positive anaerobic rod isolated from human oral cavities.Nakazawa F, Poco SE, Ikeda T, Sato M, Kalfas S, Sundqvist G, Hoshino EInt J Syst Bacteriol10.1099/00207713-49-3-11931999Adult, Bacteria, Anaerobic/chemistry/classification/*isolation & purification/ultrastructure, Bacterial Proteins/chemistry, Base Composition, Blotting, Western, DNA, Bacterial/chemistry/genetics/isolation & purification, DNA, Ribosomal/chemistry/genetics/isolation & purification, Electrophoresis, Polyacrylamide Gel, Genes, rRNA, Gram-Positive Asporogenous Rods/chemistry/*classification/*isolation & purification/ultrastructure, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Periodontal Diseases/*microbiology, Periodontal Pocket/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Metabolism17064396Degradation of arginine by Slackia exigua ATCC 700122 and Cryptobacterium curtum ATCC 700683.Uematsu H, Sato N, Djais A, Hoshino EOral Microbiol Immunol10.1111/j.1399-302X.2006.00307.x2006Ammonia/metabolism, Arginine/*metabolism, Chromatography, High Pressure Liquid, Citrulline/metabolism, Dental Pulp Necrosis/microbiology, Eubacterium/*enzymology/*growth & development, Humans, Hydrolases/*metabolism, Ornithine/metabolism, Periodontal Pocket/microbiologyPathogenicity
Genetics21304644Complete genome sequence of Cryptobacterium curtum type strain (12-3).Mavrommatis K, Pukall R, Rohde C, Chen F, Sims D, Brettin T, Kuske C, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Ovchinnikova G, Pati A, Ivanova N, Chen A, Palaniappan K, Chain P, D'haeseleer P, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Rohde M, Klenk HP, Kyrpides NCStand Genomic Sci10.4056/sigs.122602009

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6011Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15641)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15641
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
23098Futoshi Nakazawa,Sergio E. Poco,Tetsuro Ikeda,Michiko Sato,Sotos Kalfas,Göran Sundqvist,Etsuro Hoshino10.1099/00207713-49-3-1193Cryptobacterium curtum gen. nov., sp. nov., a new genus of Gram-positive anaerobic rod isolated from human oral cavitiesIJSEM 49: 1193-1200 199910425779
60724Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55773)https://www.ccug.se/strain?id=55773
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
72573Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44077.1StrainInfo: A central database for resolving microbial strain identifiers