Strain identifier

BacDive ID: 7398

Type strain: Yes

Species: Microbacterium trichothecenolyticum

Strain Designation: 114-2

Strain history: CIP <- 1993, IFO <- 1990, JCM <- K. Nakayama: strain 114-2

NCBI tax ID(s): 69370 (species)

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General

@ref: 3330

BacDive-ID: 7398

DSM-Number: 8608

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

description: Microbacterium trichothecenolyticum 114-2 is an obligate aerobe, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 69370
  • Matching level: species

strain history

@refhistory
3330<- IFO <- JCM <- K. Nakayama, 114-2
67770K. Nakayama 114-2.
123583CIP <- 1993, IFO <- 1990, JCM <- K. Nakayama: strain 114-2

doi: 10.13145/bacdive7398.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium trichothecenolyticum
  • full scientific name: Microbacterium trichothecenolyticum (Yokota et al. 1993) Takeuchi and Hatano 1998

  • synonyms

    • @ref: 20215
    • synonym: Aureobacterium trichothecenolyticum

@ref: 3330

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium trichothecenolyticum

full scientific name: Microbacterium trichothecenolyticum (Yokota et al. 1993) Takeuchi and Hatano 1998 emend. Nouioui et al. 2018

strain designation: 114-2

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123583positiverod-shapedno
69480no93.5
69480positive92.624

colony morphology

@refcolony colorincubation periodmedium used
20207Beige (1001)10-14 daysISP 2
20207Beige (1001)10-14 daysISP 3
20207Beige (1001)10-14 daysISP 4
20207Beige (1001)10-14 daysISP 5
20207Lemon yellow (1012)10-14 daysISP 6
20207Beige (1001)10-14 daysISP 7
123583

multicellular morphology

@refforms multicellular complexmedium name
20207noISP 2
20207noISP 3
20207noISP 4
20207noISP 5
20207noISP 6
20207noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3330TRYPTICASE 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
20207ISP 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
20207ISP 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:
20207ISP 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
20207ISP 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
20207ISP 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
20207ISP 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
39859MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123583CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
20207positiveoptimum28
3330positivegrowth30
39859positivegrowth30
67770positivegrowth30
123583positivegrowth15-37
123583nogrowth10
123583nogrowth41
123583nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 123583
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 94

halophily

@refsaltgrowthtested relationconcentration
123583NaClpositivegrowth0-4 %
123583NaClnogrowth6 %
123583NaClnogrowth8 %
123583NaClnogrowth10 %

murein

  • @ref: 3330
  • 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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12358316947citrate+carbon source
1235834853esculin+hydrolysis
123583606565hippurate+hydrolysis
12358317632nitrate+reduction
12358316301nitrite-reduction
12358335020tributyrin-hydrolysis
123583132112sodium thiosulfate+builds gas from
12358317632nitrate-respiration
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

antibiotic resistance

  • @ref: 123583
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123583
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12358315688acetoin-
12358317234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
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
68379pyrazinamidase-3.5.1.B15
123583oxidase-
123583beta-galactosidase+3.2.1.23
123583alcohol dehydrogenase-1.1.1.1
123583gelatinase+/-
123583amylase+
123583DNase+
123583caseinase+3.4.21.50
123583catalase+1.11.1.6
123583gamma-glutamyltransferase-2.3.2.2
123583lecithinase-
123583lipase-
123583lysine decarboxylase-4.1.1.18
123583ornithine decarboxylase-4.1.1.17
123583phenylalanine ammonia-lyase-4.3.1.24
123583protease-
123583tryptophan deaminase-
123583urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20207--------+++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20207-+++++-+---++-++-+-
123583-++-++---++++-+++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123583++-++-+++++----++++-+++--+-----+++-+-------------+-------+-++--++----------+--+++---------------++-

Isolation, sampling and environmental information

isolation

@refsample type
3330soil
67770Soil
123583Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_7457.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_246;98_275;99_7457&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: Y17240
  • Sequence Identity:
  • Total samples: 337
  • soil counts: 125
  • aquatic counts: 21
  • animal counts: 83
  • plant counts: 108

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33301Risk group (German classification)
202071German classification
1235831Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium trichotecenolyticum 16S rRNA geneY172401461nuccore69370
20218Microbacterium trichotecenolyticum gene for 16S rRNA, partial sequenceAB0047221463nuccore69370

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium trichothecenolyticum strain DSM 860869370.6wgspatric69370
66792Microbacterium trichothecenolyticum DSM 86082698536670draftimg69370
67770Microbacterium trichothecenolyticum DSM 8608GCA_000956465contigncbi69370

GC content

@refGC-contentmethod
333069high performance liquid chromatography (HPLC)
6777070.2genome sequence analysis
6777070.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno94no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes92.624no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.566no
69480spore-formingspore-formingAbility to form endo- or exosporesno79.254no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.676no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.875yes
69480flagellatedmotile2+Ability to perform flagellated movementno93.5no

External links

@ref: 3330

culture collection no.: DSM 8608, ATCC 51475, CCM 4373, CIP 103817, IFO 15077, JCM 1358, NBRC 15077, NRRL B-24212, IAM 15206, LMG 16696, VKM Ac-1948

straininfo link

  • @ref: 76847
  • straininfo: 8211

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
Phylogeny24729394Microbacterium kyungheense sp. nov. and Microbacterium jejuense sp. nov., isolated from salty soil.Kook M, Son HM, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.054973-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Ornithine/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Vitamin K 2/chemistryGenetics
Phylogeny27506590Microbacterium aureliae sp. nov., a novel actinobacterium isolated from Aurelia aurita, the moon jellyfish.Kaur G, Mual P, Kumar N, Verma A, Kumar A, Krishnamurthi S, Mayilraj SInt J Syst Evol Microbiol10.1099/ijsem.0.0014072016Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Scyphozoa/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome
Phylogeny28875898Microbacterium hibisci sp. nov., isolated from rhizosphere of mugunghwa (Hibiscus syriacus L.).Yan ZF, Lin P, Won KH, Yang JE, Li CT, Kook M, Wang QJ, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0021672017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Vitamin K 2/chemistryTranscriptome
Phylogeny33860851Microbacterium helvum sp. nov., a novel actinobacterium isolated from cow dung.Li X, Zhang L, Huang F, Zhao J, Wang H, Jiao Y, Qian L, Wang X, Xiang WArch Microbiol10.1007/s00203-021-02311-92021Amino Acids/analysis, Animals, Base Composition, Cattle, DNA, Bacterial/chemistry, Fatty Acids/chemistry, Feces/microbiology, Female, Lipids/analysis, Microbacterium/chemistry/classification/genetics/*isolation & purification, Phylogeny, Sugars/analysisEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3330Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8608)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8608
20207Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8608.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
39859Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15657
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/
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
76847Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8211.1StrainInfo: A central database for resolving microbial strain identifiers
123583Curators of the CIPCollection of Institut Pasteur (CIP 103817)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103817