Strain identifier

BacDive ID: 7250

Type strain: Yes

Species: Agrococcus jenensis

Strain Designation: 2002-39/1

Strain history: CIP <- 2000, CCUG <- 1996, DSMZ <- I. Groth, Hans Knoll Inst., Jena, Germany: strain 2002-39/1

NCBI tax ID(s): 46353 (species)

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General

@ref: 3644

BacDive-ID: 7250

DSM-Number: 9580

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Agrococcus jenensis 2002-39/1 is an aerobe, mesophilic bacterium that was isolated from frozen compost soil.

NCBI tax id

  • NCBI tax id: 46353
  • Matching level: species

strain history

@refhistory
3644<- I. Groth, 2002-39/1
67770DSM 9580 <-- I. Groth 2002-39/1.
120334CIP <- 2000, CCUG <- 1996, DSMZ <- I. Groth, Hans Knoll Inst., Jena, Germany: strain 2002-39/1

doi: 10.13145/bacdive7250.20230509.8.1

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 jenensis
  • full scientific name: Agrococcus jenensis Groth et al. 1996

@ref: 3644

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agrococcus

species: Agrococcus jenensis

full scientific name: Agrococcus jenensis Groth et al. 1996

strain designation: 2002-39/1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.628
69480100positive
120334nopositivecoccus-shaped

colony morphology

@refcolony colorincubation periodmedium used
19735Dahlia yellow10-14 daysISP 2
19735Dahlia yellow10-14 daysISP 3
1973510-14 daysISP 4
1973510-14 daysISP 5
19735Dahlia yellow10-14 daysISP 6
1973510-14 daysISP 7
120334

multicellular morphology

@refforms multicellular complexmedium name
19735noISP 2
19735noISP 3
19735noISP 4
19735noISP 5
19735noISP 6
19735noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3644TRYPTICASE 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
19735ISP 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
19735ISP 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:
19735ISP 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
19735ISP 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
19735ISP 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
19735ISP 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
39549MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120334CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3644positivegrowth28mesophilic
39549positivegrowth30mesophilic
52784positivegrowth30mesophilic
67770positivegrowth28mesophilic
120334positivegrowth10-30
120334nogrowth37mesophilic
120334nogrowth41thermophilic
120334nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
52784aerobe
120334obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.998

compound production

  • @ref: 20216
  • compound: 4-Hydroxyprolylleucin

halophily

@refsaltgrowthtested relationconcentration
19735NaClpositivemaximum2.5 %
120334NaClpositivegrowth0-8 %
120334NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
120334esculin+hydrolysis4853
120334hippurate-hydrolysis606565
120334nitrate-reduction17632
120334nitrite-reduction16301
120334nitrate-respiration17632
68379nitrate+reduction17632
68379esculin+hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose+fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 120334
  • 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
12033435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12033415688acetoin-
12033417234glucose-

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-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382leucine arylamidase+3.4.11.1
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
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
120334oxidase-
120334beta-galactosidase+3.2.1.23
120334alcohol dehydrogenase-1.1.1.1
120334gelatinase+/-
120334amylase+
120334DNase+
120334caseinase+3.4.21.50
120334catalase+1.11.1.6
120334tween esterase-
120334gamma-glutamyltransferase-2.3.2.2
120334lecithinase-
120334lipase-
120334lysine decarboxylase-4.1.1.18
120334ornithine decarboxylase-4.1.1.17
120334phenylalanine ammonia-lyase-4.3.1.24
120334protease+
120334tryptophan deaminase-
120334urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19735+-++--+-+---+------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19735+++++++++++-+-++---
120334-++-+-----+---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19735+--------++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120334+/---+/-+/-+/------+/-+/--+/---+/-------+/------+/---------+/-------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3644frozen compost soilJenaGermanyDEUEurope
52784Frozen compost soilJenaGermanyDEUEurope
67770Frozen compost soilnear JenaGermanyDEUEurope
120334Environment, Frozen compost soilJenaGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Environmental#Terrestrial#Soil

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: X92492
  • 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
36441Risk group (German classification)
197351Risk group (German classification)
1203341Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agrococcus jenensis partial 16S rRNA gene, type strain DSM 9580AM4106791473ena46353
3644A.jenensis 16S ribosomal RNAX924921473ena46353

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agrococcus jenensis strain DSM 958046353.3wgspatric46353
66792Agrococcus jenensis DSM 95802781126042draftimg46353
67770Agrococcus jenensis DSM 9580GCA_003752465contigncbi46353

GC content

  • @ref: 3644
  • GC-content: 74
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveyes92.946no
anaerobicno99.499no
halophileno93.564no
spore-formingno94.317no
glucose-utilyes86.676no
aerobicyes95.011yes
flagellatedno97.19no
thermophileno99.368yes
motileno87.809no
glucose-fermentno91.806no

External links

@ref: 3644

culture collection no.: DSM 9580, ATCC 700087, IFO 16126, NBRC 100415, NBRC 16126, CCUG 35514, CIP 106528, JCM 9950, CGMCC 1.7260, IAM 15121, IMSNU 22118, NCIMB 13857, VKM Ac-1839

straininfo link

  • @ref: 76702
  • straininfo: 43764

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8573501Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall.Groth I, Schumann P, Weiss N, Martin K, Rainey FAInt J Syst Bacteriol10.1099/00207713-46-1-2341996Actinomycetales/chemistry/*classification/ultrastructure, Butyrates/*analysis, Cell Wall/chemistry, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
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/urltitlejournalpubmed
3644Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9580)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9580
19735Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM9580.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39549Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18669
52784Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35514)https://www.ccug.se/strain?id=35514
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/
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
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
76702Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43764.1StrainInfo: A central database for resolving microbial strain identifiers
120334Curators of the CIPCollection of Institut Pasteur (CIP 106528)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106528