Strain identifier

BacDive ID: 7601

Type strain: Yes

Species: Glutamicibacter bergerei

Strain Designation: Ca106

Strain history: CIP <- 2003, F. Irlinger, INRA, Thiverval Grignon, France: strain Ca106 <- UMR GMPA, INRA <- Adria Normandie

NCBI tax ID(s): 256702 (species)

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General

@ref: 6405

BacDive-ID: 7601

DSM-Number: 16367

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

description: Glutamicibacter bergerei Ca106 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from camembert cheese.

NCBI tax id

  • NCBI tax id: 256702
  • Matching level: species

strain history

@refhistory
6405<- C. Bizet, CIP <- F. Irlinger, INRA
67770CIP 108036 <-- F. Irlinger Ca106.
116790CIP <- 2003, F. Irlinger, INRA, Thiverval Grignon, France: strain Ca106 <- UMR GMPA, INRA <- Adria Normandie

doi: 10.13145/bacdive7601.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Glutamicibacter
  • species: Glutamicibacter bergerei
  • full scientific name: Glutamicibacter bergerei (Irlinger et al. 2005) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter bergerei

@ref: 6405

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Glutamicibacter

species: Glutamicibacter bergerei

full scientific name: Glutamicibacter bergerei (Irlinger et al. 2005) Busse 2016

strain designation: Ca106

type strain: yes

Morphology

cell morphology

  • @ref: 116790
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18609Rapeseed yellow (1021)10-14 daysISP 2
18609Rapeseed yellow (1021)10-14 daysISP 3
18609Rapeseed yellow (1021)10-14 daysISP 4
18609Rapeseed yellow (1021)10-14 daysISP 5
18609Rapeseed yellow (1021)10-14 daysISP 6
18609Rapeseed yellow (1021)10-14 daysISP 7
116790

multicellular morphology

@refforms multicellular complexmedium name
18609noISP 2
18609noISP 3
18609noISP 4
18609noISP 5
18609noISP 6
18609noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6405TRYPTICASE 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
18609ISP 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
18609ISP 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:
18609ISP 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
18609ISP 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
18609ISP 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
18609ISP 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
41910MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116790CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18609positiveoptimum28mesophilic
6405positivegrowth28mesophilic
41910positivegrowth30mesophilic
59516positivegrowth20-30
67770positivegrowth28mesophilic
116790positivegrowth10-30
116790nogrowth37mesophilic
116790nogrowth41thermophilic
116790nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59516aerobe
116790obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116790NaClpositivegrowth4 %
116790NaClnogrowth0 %
116790NaClnogrowth2 %
116790NaClnogrowth6 %
116790NaClnogrowth8 %
116790NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11679016947citrate-carbon source
1167904853esculin-hydrolysis
116790606565hippurate+hydrolysis
11679017632nitrate-reduction
11679016301nitrite-reduction
11679017632nitrate-respiration
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose-fermentation

antibiotic resistance

  • @ref: 116790
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116790
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11679015688acetoin-
11679017234glucose+

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
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
68379pyrazinamidase+3.5.1.B15
116790oxidase-
116790beta-galactosidase+3.2.1.23
116790alcohol dehydrogenase-1.1.1.1
116790gelatinase+/-
116790amylase-
116790DNase-
116790caseinase-3.4.21.50
116790catalase+1.11.1.6
116790tween esterase-
116790gamma-glutamyltransferase+2.3.2.2
116790lecithinase-
116790lipase-
116790lysine decarboxylase-4.1.1.18
116790ornithine decarboxylase-4.1.1.17
116790phenylalanine ammonia-lyase-4.3.1.24
116790protease+
116790tryptophan deaminase-
116790urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18609++--++--++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18609-++-++------+-+--+-
116790+++-+-+---+------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116790+++-+--+-++++------+++----+----+------------------++-+------++++++++----+--+------------+++++++-++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6405camembert cheeseFranceFRAEurope
59516Cheese,CamembertFranceFRAEurope
67770Surface of Camembert cheese
116790Food, Cheese, CamembertFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Dairy product
#Host#Fungi

taxonmaps

  • @ref: 69479
  • File name: preview.99_16201.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1446;97_1726;98_2111;99_16201&stattab=map
  • Last taxonomy: Glutamicibacter
  • 16S sequence: AJ609630
  • Sequence Identity:
  • Total samples: 1486
  • soil counts: 175
  • aquatic counts: 119
  • animal counts: 1072
  • plant counts: 120

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64051Risk group (German classification)
186091Hazard group
1167901Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6405
  • description: Arthrobacter bergeri partial 16S rRNA gene, strain CIP 108036
  • accession: AJ609630
  • length: 1468
  • database: ena
  • NCBI tax ID: 256702

External links

@ref: 6405

culture collection no.: DSM 16367, CIP 108036, CCUG 52342, JCM 13567, IAM 15319, NCIMB 14259

straininfo link

  • @ref: 77045
  • straininfo: 128535

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653918Arthrobacter bergerei sp. nov. and Arthrobacter arilaitensis sp. nov., novel coryneform species isolated from the surfaces of cheeses.Irlinger F, Bimet F, Delettre J, Lefevre M, Grimont PADInt J Syst Evol Microbiol10.1099/ijs.0.63125-02005Arthrobacter/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Cheese/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny25858247Arthrobacter endophyticus sp. nov., an endophytic actinobacterium isolated from root of Salsola affinis C. A. Mey.Wang HF, Li L, Zhang YG, Hozzein WN, Zhou XK, Liu WH, Duan YQ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.0002352015Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Salsola/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
6405Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16367)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16367
18609Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16367.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
41910Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5614
59516Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52342)https://www.ccug.se/strain?id=52342
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
77045Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128535.1StrainInfo: A central database for resolving microbial strain identifiers
116790Curators of the CIPCollection of Institut Pasteur (CIP 108036)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108036