Strain identifier

BacDive ID: 7252

Type strain: Yes

Species: Agrococcus citreus

Strain Designation: D-1/1a

Strain history: CIP <- 1999, H.J. Busse, Vienna Univ., Vienna, Austria: strain D-1/1a

NCBI tax ID(s): 84643 (species)

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General

@ref: 4726

BacDive-ID: 7252

DSM-Number: 12453

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

description: Agrococcus citreus D-1/1a is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from medieval wall painting.

NCBI tax id

  • NCBI tax id: 84643
  • Matching level: species

strain history

@refhistory
4726<- H.-J. Busse <- M. Wieser; D-1/1a
67770CIP 106287 <-- H.-J. Busse D-1/1a.
118300CIP <- 1999, H.J. Busse, Vienna Univ., Vienna, Austria: strain D-1/1a

doi: 10.13145/bacdive7252.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agrococcus
  • species: Agrococcus citreus
  • full scientific name: Agrococcus citreus Wieser et al. 1999

@ref: 4726

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agrococcus

species: Agrococcus citreus

full scientific name: Agrococcus citreus Wieser et al. 1999

strain designation: D-1/1a

type strain: yes

Morphology

cell morphology

  • @ref: 118300
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18500Rapeseed yellow (1021)10-14 days5006
18500Broom yellow (1032)10-14 daysISP 2
18500Rapeseed yellow (1021)10-14 daysISP 3
18500Rapeseed yellow (1021)10-14 daysISP 4
18500Rapeseed yellow (1021)10-14 daysISP 5
118300

multicellular morphology

@refmedium nameforms multicellular complex
185005006
18500ISP 2no
18500ISP 3no
18500ISP 4no
18500ISP 5no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4726TRYPTICASE 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
185005006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
18500ISP 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
18500ISP 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:
18500ISP 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
18500ISP 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
40294MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118300CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
118300CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18500positiveoptimum28mesophilic
4726positivegrowth28mesophilic
40294positivegrowth30mesophilic
67770positivegrowth28mesophilic
118300positivegrowth10-37
118300nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118300
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
18500NaClpositivemaximum2.5 %
118300NaClpositivegrowth0-6 %
118300NaClnogrowth8 %
118300NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1850062968cellulose+
1850016634raffinose-
1850026546rhamnose+
1850028757fructose+
1850029864mannitol+
1850017268myo-inositol-
1850018222xylose-
1850017992sucrose+
1850022599arabinose+
1850017234glucose+
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1183004853esculin+hydrolysis
118300606565hippurate+hydrolysis
11830017632nitrate-reduction
11830016301nitrite-reduction
11830017632nitrate-respiration
6837917632nitrate-reduction
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 118300
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11830035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11830015688acetoin-
11830017234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
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
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
68379gelatinase+
68379urease+3.5.1.5
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
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
118300oxidase-
118300beta-galactosidase+3.2.1.23
118300alcohol dehydrogenase-1.1.1.1
118300gelatinase-
118300amylase-
118300DNase+
118300caseinase-3.4.21.50
118300catalase+1.11.1.6
118300tween esterase-
118300gamma-glutamyltransferase+2.3.2.2
118300lecithinase-
118300lipase-
118300lysine decarboxylase-4.1.1.18
118300ornithine decarboxylase-4.1.1.17
118300phenylalanine ammonia-lyase-4.3.1.24
118300protease-
118300tryptophan deaminase-
118300urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18500--+---+-+/-++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18500--+-++-------+++---
118300-++-+---------+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18500-++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118300+--+++----+++-+--+------++++/---++------++------+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118300---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4726medieval wall paintingAustria, Steiermark, chapel of castle HerbersteinAustriaAUTEurope
67770Medieval wall painting of the chapel of the castle HerbersteinStyriaAustriaAUTEurope
118300Medieval wall paintingStyriaAustriaAUTEurope1995

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Painting
#Engineered#Built environment

taxonmaps

  • @ref: 69479
  • File name: preview.99_19669.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_301;97_333;98_374;99_19669&stattab=map
  • Last taxonomy: Agrococcus
  • 16S sequence: AB279547
  • Sequence Identity:
  • Total samples: 3892
  • soil counts: 776
  • aquatic counts: 789
  • animal counts: 2180
  • plant counts: 147

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47261Risk group (German classification)
185001German classification
1183001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4726Agrococcus citreus DSM 12453, 16S rRNA gene, partialAJ0128261212ena84643
67770Agrococcus citreus gene for 16S rRNA, partial sequence, strain: IAM 15145AB2795471422ena84643

GC content

  • @ref: 4726
  • GC-content: 74
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 4726

culture collection no.: DSM 12453, JCM 12398, ATCC 700859, CCM 4975, CGMCC 1.7258, CIP 106287, IAM 15145, NCIMB 13599

straininfo link

  • @ref: 76704
  • straininfo: 49291

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10425775Agrococcus citreus sp. nov., isolated from a medieval wall painting of the chapel of Castle Herberstein (Austria).Wieser M, Schumann P, Martin K, Altenburger P, Burghardt J, Lubitz W, Busse HJInt J Syst Bacteriol10.1099/00207713-49-3-11651999Actinomycetales/chemistry/*classification/*isolation & purification/physiology, Austria, Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Humans, Molecular Sequence Data, *Paintings, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny12148630Agrococcus baldri sp. nov., isolated from the air in the 'Virgilkapelle' in Vienna.Zlamala C, Schumann P, Kampfer P, Rossello-Mora R, Lubitz W, Busse HJInt J Syst Evol Microbiol10.1099/00207713-52-4-12112002Actinomycetales/chemistry/*classification/isolation & purification/physiology, *Air Microbiology, Austria, Bacterial Typing Techniques, DNA, Ribosomal/analysis, Fatty Acids/analysis, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Paintings, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny16902012Agrococcus lahaulensis sp. nov., isolated from a cold desert of the Indian Himalayas.Mayilraj S, Suresh K, Schumann P, Kroppenstedt RM, Saini HSInt J Syst Evol Microbiol10.1099/ijs.0.64247-02006Actinomycetales/*classification/isolation & purification/physiology, Cold Temperature, DNA, Bacterial/genetics, Desert Climate, India, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitle
4726Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12453)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12453
18500Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12453.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
40294Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18401
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
76704Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49291.1StrainInfo: A central database for resolving microbial strain identifiers
118300Curators of the CIPCollection of Institut Pasteur (CIP 106287)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106287