Strain identifier

BacDive ID: 3228

Type strain: Yes

Species: Corynebacterium sputi

Strain history: CIP <- 2011, CCUG <- 2008, A.F. Yassin, Bonn Univ. Bonn, Germany: strain IMMIB L-999

NCBI tax ID(s): 1111729 (strain), 489915 (species)

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General

@ref: 15415

BacDive-ID: 3228

DSM-Number: 45148

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped, human pathogen

description: Corynebacterium sputi DSM 45148 is a facultative anaerobe, mesophilic, Gram-positive human pathogen that was isolated from sputum of a patient with pneumonia.

NCBI tax id

NCBI tax idMatching level
489915species
1111729strain

strain history

@refhistory
15415<- A. F. Yassin, Inst. Med. Mikrobiol. Immun. Univ. Bonn; IMMIB L-999
67770CCUG 55795 <-- A. F. Yassin IMMIB L-999.
123277CIP <- 2011, CCUG <- 2008, A.F. Yassin, Bonn Univ. Bonn, Germany: strain IMMIB L-999

doi: 10.13145/bacdive3228.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Corynebacteriaceae
  • genus: Corynebacterium
  • species: Corynebacterium sputi
  • full scientific name: Corynebacterium sputi Yassin and Siering 2008

@ref: 15415

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium sputi

full scientific name: Corynebacterium sputi Yassin and Siering 2008 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31188positiverod-shapedno
69480no93.617
69480positive100
123277positiverod-shapedno

pigmentation

  • @ref: 31188
  • production: yes

multimedia

  • @ref: 15415
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45148.jpg
  • caption: Medium 535a 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15415TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)yeshttps://mediadive.dsmz.de/medium/535aName: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
34075MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123277CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
15415positivegrowth37mesophilic
31188positivegrowth37mesophilic
31188positiveoptimum37mesophilic
34075positivegrowth37mesophilic
60736positivegrowth30mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
31188positivegrowth7
31188positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31188facultative anaerobe
60736microaerophile

spore formation

@refspore formationconfidence
31188no
69481no100
69480no99.982

observation

  • @ref: 31188
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3118817234glucose+carbon source
12327717632nitrate-reduction
12327716301nitrite-reduction

metabolite production

  • @ref: 123277
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31188urease+3.5.1.5
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
123277urease-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
123277--++-------+---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
15415sputum of a patient with pneumoniaBonnGermanyDEUEurope
60736Human sputum,pneumoniaBonnGermanyDEUEurope1996-02-01
67770Sputum of a patient with pneumonia
123277Human, Sputum pneumoniaBonnGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Infection#Patient
#Host Body-Site#Oral cavity and airways#Airways
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_49353.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_22289;97_27848;98_35482;99_49353&stattab=map
  • Last taxonomy: Corynebacterium sputi subclade
  • 16S sequence: AM930556
  • Sequence Identity:
  • Total samples: 5170
  • soil counts: 670
  • aquatic counts: 643
  • animal counts: 3569
  • plant counts: 288

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
15415yes, in single cases1Risk group (German classification)
1232772Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15415
  • description: Corynebacterium sputi partial 16S rRNA gene, type strain IMMIB L-999T
  • accession: AM930556
  • length: 1495
  • database: ena
  • NCBI tax ID: 1111729

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium sputi DSM 451481111729.3wgspatric1111729
66792Corynebacterium sputi DSM 451482513237121draftimg1111729
67770Corynebacterium sputi DSM 45148GCA_000427865scaffoldncbi1111729

GC content

  • @ref: 67770
  • GC-content: 61.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.864yes
flagellatedno97.231yes
gram-positiveyes92.042no
anaerobicno98.833yes
aerobicyes66.888yes
halophileyes61.453no
spore-formingno89.344no
thermophileno98.441yes
glucose-utilyes88.254yes
glucose-fermentno65.141no

External links

@ref: 15415

culture collection no.: DSM 45148, CCUG 55795, CIP 109925, JCM 17321, IMMIB L-999

straininfo link

  • @ref: 72742
  • straininfo: 360269

literature

  • topic: Phylogeny
  • Pubmed-ID: 19060075
  • title: Corynebacterium sputi sp. nov., isolated from the sputum of a patient with pneumonia.
  • authors: Yassin AF, Siering C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.2008/000414-0
  • year: 2008
  • mesh: Corynebacterium/*classification/genetics/*physiology, Corynebacterium Infections/*microbiology, Molecular Sequence Data, Phylogeny, Pneumonia/*microbiology, RNA, Ribosomal, 16S/genetics, Species Specificity, Sputum/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15415Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45148)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45148
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
31188Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2751528776041
34075Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7724
60736Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55795)https://www.ccug.se/strain?id=55795
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
72742Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360269.1StrainInfo: A central database for resolving microbial strain identifiers
123277Curators of the CIPCollection of Institut Pasteur (CIP 109925)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109925