Strain identifier

BacDive ID: 7256

Type strain: Yes

Species: Agrococcus casei

Strain Designation: R-17892t 2, R-17892t2

Strain history: CIP <- 2007, DSMZ <- M. Vancanneyt, BCCM/LMG, Ghent, Belgium: strain R-17892t2

NCBI tax ID(s): 1255656 (strain), 343512 (species)

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General

@ref: 7355

BacDive-ID: 7256

DSM-Number: 18061

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

description: Agrococcus casei R-17892t 2 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Gubbeen cheese.

NCBI tax id

NCBI tax idMatching level
343512species
1255656strain

strain history

@refhistory
7355<- M. Vancanneyt <- T. Cogan
67770LMG 22410 <-- R. Gelsomino R-17892t2 <-- M. Goodfellow <-- T. M. Cogan <-- N. Brennan.
117196CIP <- 2007, DSMZ <- M. Vancanneyt, BCCM/LMG, Ghent, Belgium: strain R-17892t2

doi: 10.13145/bacdive7256.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agrococcus
  • species: Agrococcus casei
  • full scientific name: Agrococcus casei Bora et al. 2007

@ref: 7355

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agrococcus

species: Agrococcus casei

full scientific name: Agrococcus casei Bora et al. 2007

strain designation: R-17892t 2, R-17892t2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31785positive0.9 µm0.35 µmrod-shapedno
117196positivecoccus-shapedno
69480positive92.594
69480no93.5

colony morphology

@refcolony colorincubation periodmedium used
18410Beige (1001)10-14 daysISP 2
18410Beige (1001)10-14 daysISP 3
18410Beige (1001)10-14 daysISP 4
18410Beige (1001)10-14 daysISP 5
18410Beige (1001)10-14 daysISP 6
18410Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18410noISP 2
18410noISP 3
18410noISP 4
18410noISP 5
18410noISP 6
18410noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7355TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18410ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18410ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18410ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18410ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18410ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18410ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37794MEDIUM 338 - for Sanguibacter keddieiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (3.000 g);Trypto casein soy agar (30.000 g)
117196CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperature
7355positivegrowth28
18410positiveoptimum28
31785positivegrowth20-30
31785positiveoptimum25
37794positivegrowth30
67770positivegrowth28

culture pH

@refabilitytypepHPH range
31785positivegrowth6.0-10.0alkaliphile
31785positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31785aerobe
117196obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

observation

@refobservation
31785aggregates in clumps
67770quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3178517234glucose+carbon source
3178537684mannose+carbon source
3178553426tween 80+carbon source
11719617632nitrate-reduction
11719616301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 117196
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31785catalase+1.11.1.6
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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
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
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
117196oxidase-
117196catalase+1.11.1.6
117196urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18410-+/-+---+--++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18410-++-+---------+----
117196-++-+-----+---------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7355Gubbeen cheeseIrelandIRLEurope
67770Gubbeen cheese
117196Food, Sear-ripened cheeses, surfacesUnited KingdomGBREurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_118409.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_7191;97_8627;98_10582;99_118409&stattab=map
  • Last taxonomy: Agrococcus casei subclade
  • 16S sequence: DQ168427
  • Sequence Identity:
  • Total samples: 478
  • soil counts: 147
  • aquatic counts: 88
  • animal counts: 74
  • plant counts: 169

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
73551Risk group (German classification)
184101German classification
1171961Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7355
  • description: Agrococcus casei strain LMG 22410 16S ribosomal RNA gene, partial sequence
  • accession: DQ168427
  • length: 1466
  • database: nuccore
  • NCBI tax ID: 343512

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agrococcus casei LMG 22410 strain LMG 224101255656.3wgspatric1255656
66792Agrococcus casei LMG 224102835022881draftimg1255656
67770Agrococcus casei LMG 22410GCA_900163565contigncbi1255656

GC content

@refGC-contentmethod
3178565
6777065high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes92.594yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.071yes
69480spore-formingspore-formingAbility to form endo- or exosporesno81.613no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.19yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno93.5no

External links

@ref: 7355

culture collection no.: DSM 18061, CIP 109629, LMG 22410, JCM 14916

straininfo link

  • @ref: 76708
  • straininfo: 93713

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220448Agrococcus casei sp. nov., isolated from the surfaces of smear-ripened cheeses.Bora N, Vancanneyt M, Gelsomino R, Swings J, Brennan N, Cogan TM, Larpin S, Desmasures N, Lechner FE, Kroppenstedt RM, Ward AC, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.64270-02007Actinomycetales/*classification/genetics/isolation & purification/physiology, Cheese/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNAGenetics
Metabolism36109598In silico prediction of the enzymes involved in the degradation of the herbicide molinate by Gulosibacter molinativorax ON4T.Lopes AR, Bunin E, Viana AT, Froufe H, Munoz-Merida A, Pinho D, Figueiredo J, Barroso C, Vaz-Moreira I, Bellanger X, Egas C, Nunes OCSci Rep10.1038/s41598-022-18732-52022Actinobacteria, *Actinomycetales/genetics, Azepines, *Herbicides/metabolism, Hydrolases/genetics/metabolism, ThiocarbamatesEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7355Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18061)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18061
18410Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18061.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
31785Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2805728776041
37794Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7394
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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
76708Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93713.1StrainInfo: A central database for resolving microbial strain identifiers
117196Curators of the CIPCollection of Institut Pasteur (CIP 109629)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109629