Strain identifier

BacDive ID: 7399

Type strain: Yes

Species: Microbacterium esteraromaticum

Strain history: CIP <- 1993ATCC, Aureobacterium sp. <- C.P. Hegarty, Georgetown Univ., Flavobacterium esteraromaticum

NCBI tax ID(s): 57043 (species)

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General

@ref: 3331

BacDive-ID: 7399

DSM-Number: 8609

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

description: Microbacterium esteraromaticum DSM 8609 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from Environment, Soil.

NCBI tax id

  • NCBI tax id: 57043
  • Matching level: species

strain history

@refhistory
3331<- IFO <- ATCC <- C.P. Hegarty
67770IFO 3751 <-- ATCC 8091 <-- C. P. Hegarty.
119134CIP <- 1993ATCC, Aureobacterium sp. <- C.P. Hegarty, Georgetown Univ., Flavobacterium esteraromaticum

doi: 10.13145/bacdive7399.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium esteraromaticum
  • full scientific name: Microbacterium esteraromaticum (Omelianski 1923) Takeuchi and Hatano 1998

  • synonyms

    @refsynonym
    20215Bacterium esteraromaticum
    20215Flavobacterium esteraromaticum
    20215Aureobacterium esteraromaticum

@ref: 3331

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium esteraromaticum

full scientific name: Microbacterium esteraromaticum (Omelianski 1923) Takeuchi and Hatano 1998

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
119134positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
20208Colorless10-14 daysISP 2
20208Beige (1001)10-14 daysISP 3
20208Colorless10-14 daysISP 4
20208Beige (1001)10-14 daysISP 5
20208Colorless10-14 daysISP 6
20208Beige (1001)10-14 daysISP 7
119134

multicellular morphology

@refforms multicellular complexmedium name
20208noISP 2
20208noISP 3
20208noISP 4
20208noISP 5
20208noISP 6
20208noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3331TRYPTICASE 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
20208ISP 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
20208ISP 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:
20208ISP 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
20208ISP 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
20208ISP 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
20208ISP 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
38155MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119134CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
20208positiveoptimum28mesophilic
3331positivegrowth30mesophilic
38155positivegrowth30mesophilic
67770positivegrowth30mesophilic
119134positivegrowth15-37
119134nogrowth10psychrophilic
119134nogrowth41thermophilic
119134nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119134
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.61

halophily

@refsaltgrowthtested relationconcentration
119134NaClpositivegrowth0-4 %
119134NaClnogrowth6 %
119134NaClnogrowth8 %
119134NaClnogrowth10 %

murein

  • @ref: 3331
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-13

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
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
68371turanose-builds acid from32528
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
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
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
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
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-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119134citrate-carbon source16947
119134esculin+hydrolysis4853
119134hippurate+hydrolysis606565
119134nitrate-reduction17632
119134nitrite-reduction16301
119134sodium thiosulfate+builds gas from132112
119134nitrate-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: 119134
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119134
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11913415688acetoin-
11913417234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase+3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382alpha-galactosidase-3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382valine arylamidase+
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
119134oxidase+
119134beta-galactosidase+3.2.1.23
119134alcohol dehydrogenase-1.1.1.1
119134gelatinase-
119134amylase+
119134DNase+
119134caseinase-3.4.21.50
119134catalase+1.11.1.6
119134tween esterase+
119134gamma-glutamyltransferase-2.3.2.2
119134lecithinase-
119134lipase-
119134lysine decarboxylase-4.1.1.18
119134ornithine decarboxylase-4.1.1.17
119134phenylalanine ammonia-lyase-4.3.1.24
119134protease+
119134tryptophan deaminase-
119134urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20208------+-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20208-+++++-+-----+++-++
119134+++-++++-++-+-+++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119134-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119134+++++--+-++----+--+-+-+--------+---+-----------------------++-----------++-+--+-------+---++-++--+-

Isolation, sampling and environmental information

isolation

  • @ref: 119134
  • sample type: Environment, Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33311Risk group (German classification)
202081German classification
1191341Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Microbacterium esteraromaticum 16S rRNA gene
  • accession: Y17231
  • length: 1463
  • database: ena
  • NCBI tax ID: 57043

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium esteraromaticum DSM 8609GCA_016907315contigncbi57043
66792Microbacterium esteraromaticum strain DSM 860957043.11wgspatric57043
66792Microbacterium esteraromaticum DSM 86092893536966draftimg57043

GC content

@refGC-contentmethod
333169high performance liquid chromatography (HPLC)
6777068.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes91.288no
anaerobicno99.43no
halophileno82.912no
spore-formingno88.63no
glucose-utilyes86.133no
thermophileno98.371no
flagellatedno91.684no
aerobicyes94.505no
motileyes66.15no
glucose-fermentno92.954no

External links

@ref: 3331

culture collection no.: DSM 8609, ATCC 8091, CCM 4371, IFO 3751, NBRC 3751, NRRL B-24213, JCM 9172, BCRC 15447, BUCSAV 326, CIP 103916, IAM 15198, LMG 4020, NCFB 2277, NCIMB 8186, VKM Ac-1942, VTT E-991287, NCDO 2277

straininfo link

  • @ref: 76848
  • straininfo: 2822

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8347513Proposal of six new species in the genus Aureobacterium and transfer of Flavobacterium esteraromaticum Omelianski to the genus Aureobacterium as Aureobacterium esteraromaticum comb. nov.Yokota A, Takeuchi M, Sakane T, Weiss NInt J Syst Bacteriol10.1099/00207713-43-3-5551993Bacterial Typing Techniques, Base Composition, Carbohydrate Sequence, DNA, Bacterial/chemistry, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/cytology, Gram-Positive Asporogenous Rods/chemistry/*classification/cytology, Molecular Sequence Data, Mycolic Acids/analysis, Peptidoglycan/chemistry, Vitamin K/analysisGenetics
Phylogeny19654351Microbacterium soli sp. nov., an alpha-glucosidase-producing bacterium isolated from soil of a ginseng field.Srinivasan S, Kim MK, Sathiyaraj G, Kim YJ, Jung SK, In JG, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.012526-02009Actinomycetales/*classification/enzymology/genetics/*isolation & purification, Bacterial Proteins/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, alpha-Glucosidases/*metabolismMetabolism
Phylogeny22068506Microbacterium suwonense sp. nov., isolated from cow dung.Anandham R, Tamura T, Hamada M, Weon HY, Kim SJ, Kim YS, Suzuki K, Kwon SWJ Microbiol10.1007/s12275-011-1036-y2011Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Animals, Cattle, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Feces/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3331Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8609)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8609
20208Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8609.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
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
38155Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15766
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
76848Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2822.1StrainInfo: A central database for resolving microbial strain identifiers
119134Curators of the CIPCollection of Institut Pasteur (CIP 103916)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103916