Strain identifier

BacDive ID: 131684

Type strain: Yes

Species: Corynebacterium crudilactis

Strain Designation: JZ16

Strain history: <- A. Lipski, Universität Bonn; JZ16 <- J. Zimmermann, Universität Bonn

NCBI tax ID(s): 1652495 (species)

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General

@ref: 23480

BacDive-ID: 131684

DSM-Number: 100882

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

description: Corynebacterium crudilactis JZ16 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from raw cow's milk.

NCBI tax id

  • NCBI tax id: 1652495
  • Matching level: species

strain history

  • @ref: 23480
  • history: <- A. Lipski, Universität Bonn; JZ16 <- J. Zimmermann, Universität Bonn

doi: 10.13145/bacdive131684.20230509.8.1

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 crudilactis
  • full scientific name: Corynebacterium crudilactis Zimmermann et al. 2016

@ref: 23480

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium crudilactis

full scientific name: Corynebacterium crudilactis Zimmermann et al. 2016

strain designation: JZ16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25085positive0.9-1.8 µm0.6-1.3 µmrod-shapedno
69480positive100
69480no91.398

colony morphology

@refcolony sizecolony colormedium usedincubation period
250853 mmbeigeTSA (Trypticase soy agar)
635541 day

multimedia

  • @ref: 23480
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_100882.jpg
  • caption: Medium 693 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
25085brain-heart infusion agaryessupplemented with 0.25 g l-1 potassium tellurite and 1.0 % Tween 80
25085TSA (Trypticase soy agar)yes
23480TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)yesName: 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 waterhttps://mediadive.dsmz.de/medium/535a

culture temp

@refgrowthtypetemperaturerange
63554positivegrowth30mesophilic
23480positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25085anaerobe
63554aerobe

spore formation

@refspore formationconfidence
25085no
69481no100
69480no99.918

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2508565327D-xylose-builds acid from
250855291gelatin-hydrolysis
2508528087glycogen-builds acid from
2508517716lactose-builds acid from
2508517306maltose-builds acid from
2508517306maltose-fermentation
2508517992sucrose-builds acid from
2508517992sucrose-fermentation
2508517634D-glucose+builds acid from
2508516899D-mannitol+builds acid from
2508516988D-ribose+builds acid from
2508529864mannitol+fermentation
2508517632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.group ID
250857809oxacillinyesyes1 µg
2508528971ampicillinyesyes10 µg
250856104kanamycinyesyes30 µg
2508517076streptomycinyesyes10 µg
2508545924trimethoprimyesyes1.25 µg25
25085102130sulfamerazineyesyes23.75 µg25

enzymes

@refvalueactivityec
25085acid phosphatase-3.1.3.2
25085alkaline phosphatase-3.1.3.1
25085alpha-glucosidase-3.2.1.20
25085beta-galactosidase-3.2.1.23
25085beta-glucosidase+3.2.1.21
25085beta-glucuronidase+3.2.1.31
25085catalase+1.11.1.6
25085cytochrome oxidase-1.9.3.1
25085esterase (C 4)+
25085esterase Lipase (C 8)+
25085N-acetyl-beta-glucosaminidase-3.2.1.52
25085pyrazinamidase+3.5.1.B15
25085pyrrolidonyl arylamidase-3.4.19.3
25085trypsin-3.4.21.4
25085urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture temperaturesampling date
23480raw cow's milkSchlausenbachGermanyDEUEurope
25085raw cow ’s milk from the bulk tank of a dairy farmbrain-heart infusion agar (Oxoid)supplemented with 0.25 g l-1 potassium tellurite and 1.0 % Tween 8030
63554Raw milk from cowRheinland-Pfalz,SchlausenbachGermanyDEUEurope2014-11-01

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Container (Reservoir)
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Fluids#Milk

taxonmaps

  • @ref: 69479
  • File name: preview.99_3298.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_223;97_375;98_431;99_3298&stattab=map
  • Last taxonomy: Corynebacterium crudilactis
  • 16S sequence: KR534194
  • Sequence Identity:
  • Total samples: 13749
  • soil counts: 2143
  • aquatic counts: 1445
  • animal counts: 9718
  • plant counts: 443

Safety information

risk assessment

  • @ref: 23480
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23480
  • description: Corynebacterium crudilactis strain JZ16 16S ribosomal RNA gene, partial sequence
  • accession: KR534194
  • length: 1443
  • database: ena
  • NCBI tax ID: 1652495

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium crudilactis JZ16GCA_001643015completencbi1652495
66792Corynebacterium crudilactis strain JZ161652495.6plasmidpatric1652495
66792Corynebacterium crudilactis strain JZ161652495.5plasmidpatric1652495
66792Corynebacterium crudilactis JZ162718217777completeimg1652495

GC content

@refGC-contentmethod
2508551.59genome sequence analysis
2348051.59sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.261yes
gram-positiveyes87.894no
anaerobicno99.285no
aerobicyes74.544no
halophileyes66.306no
spore-formingno92.387yes
glucose-utilyes86.639no
motileno94.588yes
glucose-fermentyes70.187no
thermophileno97.117yes

External links

@ref: 23480

culture collection no.: DSM 100882, CCUG 69192, LMG 29813

straininfo link

  • @ref: 90080
  • straininfo: 397611

literature

  • topic: Phylogeny
  • Pubmed-ID: 27666312
  • title: Corynebacterium crudilactis sp. nov., isolated from raw cow's milk.
  • authors: Zimmermann J, Ruckert C, Kalinowski J, Lipski A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001509
  • year: 2016
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Cattle, Corynebacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Germany, Milk/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
23480Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100882Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100882)
25085J. R. Zimmermann, C.,Kalinowski, J.,Lipski, A.Corynebacterium crudilactis sp. nov., isolated from raw cow's milk10.1099/ijsem.0.001509IJSEM 66: 5288-5293 201627666312
63554Curators of the CCUGhttps://www.ccug.se/strain?id=69192Culture Collection University of Gothenburg (CCUG) (CCUG 69192)
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
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
90080Reimer, 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-ID397611.1