Strain identifier

BacDive ID: 7423

Type strain: Yes

Species: Microbacterium halotolerans

Strain history: CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70130

NCBI tax ID(s): 246613 (species)

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General

@ref: 6125

BacDive-ID: 7423

DSM-Number: 15855

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

description: Microbacterium halotolerans DSM 15855 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from hypersaline soil.

NCBI tax id

  • NCBI tax id: 246613
  • Matching level: species

strain history

@refhistory
6125<- W.-J. Li
381752003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70130
67770KCTC 19017 <-- W.-J. Li YIM 70130.
67771<- WJ Li
119827CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 70130

doi: 10.13145/bacdive7423.20230509.8.1

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 halotolerans
  • full scientific name: Microbacterium halotolerans Li et al. 2005

@ref: 6125

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium halotolerans

full scientific name: Microbacterium halotolerans Li et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31298positive1.5 µm1.5 µmrod-shapedno
67771positive
69480no91.584
69480positive100
119827positiverod-shaped

colony morphology

  • @ref: 119827

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6125MODIFIED ISP5 MEDIUM (DSMZ Medium 993b)yeshttps://mediadive.dsmz.de/medium/993bName: MODIFIED ISP5 MEDIUM (DSMZ Medium 993b) Composition: KCl 100.0 g/l Agar 20.0 g/l Glycerol 10.0 g/l Yeast extract 5.0 g/l L-Asparagine 1.0 g/l K2HPO4 1.0 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
38175Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
6125TRYPTICASE 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
119827CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
119827CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6125positivegrowth28mesophilic
31298positivegrowth29mesophilic
31298positiveoptimum28-30
38175positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
119827positivegrowth10-37
119827nogrowth41thermophilic
119827nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31298positivegrowth05-13alkaliphile
31298positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31298aerobe
67771aerobe
119827obligate aerobe

spore formation

@refspore formationconfidence
31298no
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
31298NaClpositivegrowth0-15 %
31298NaClpositiveoptimum5 %
119827NaClpositivegrowth0-10 %

observation

@refobservation
67770quinones: MK-10, MK-11
67771quinones: MK-10, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3129822599arabinose+carbon source
3129817057cellobiose+carbon source
3129828757fructose+carbon source
3129828260galactose+carbon source
3129817234glucose+carbon source
3129817716lactose+carbon source
3129817306maltose+carbon source
3129829864mannitol+carbon source
3129837684mannose+carbon source
3129833942ribose+carbon source
3129817992sucrose+carbon source
3129818222xylose+carbon source
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
6837117306maltose-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
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11982716947citrate-carbon source
1198274853esculin+hydrolysis
119827606565hippurate-hydrolysis
11982717632nitrate-reduction
11982716301nitrite-reduction
11982717632nitrate-respiration

antibiotic resistance

  • @ref: 119827
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119827
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11982715688acetoin-
11982717234glucose-

enzymes

@refvalueactivityec
31298catalase+1.11.1.6
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
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
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
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
119827oxidase-
119827beta-galactosidase+3.2.1.23
119827alcohol dehydrogenase-1.1.1.1
119827gelatinase+/-
119827amylase-
119827DNase-
119827caseinase-3.4.21.50
119827catalase+1.11.1.6
119827tween esterase-
119827gamma-glutamyltransferase-2.3.2.2
119827lecithinase-
119827lipase-
119827lysine decarboxylase-4.1.1.18
119827ornithine decarboxylase-4.1.1.17
119827phenylalanine ammonia-lyase-4.3.1.24
119827tryptophan deaminase-
119827urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119827-+++------------+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119827----+/--------------------+-----------------------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119827------------------+--------------------------------------+----+------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
6125hypersaline soilChinaCHNAsia
67770Saline soilChinaCHNAsiaQinghai Province
67771Hypersaline soilChinaCHNAsiaQinghai Province
119827Environment, Hypersaline soilChinaCHNAsiaQinghai2002

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61251Risk group (German classification)
1198271Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6125
  • description: Microbacterium halotolerans strain YIM 70130 16S ribosomal RNA gene, partial sequence
  • accession: AY376165
  • length: 1488
  • database: ena
  • NCBI tax ID: 246613

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium halotolerans strain YIM 70130246613.3wgspatric246613
66792Microbacterium halotolerans YIM 701302861987423draftimg246613
67770Microbacterium halotolerans YIM 70130GCA_003569805scaffoldncbi246613

GC content

@refGC-contentmethod
612566.5
6777166.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.463no
gram-positiveyes94.765no
anaerobicno99.496no
aerobicyes92.798yes
halophileno58.373no
spore-formingno90.409yes
glucose-utilyes86.379no
flagellatedno96.78yes
thermophileno99.399yes
glucose-fermentno86.096no

External links

@ref: 6125

culture collection no.: DSM 15855, CIP 108071, KCTC 19017, YIM 70130, JCM 13013, NRRL B-24569

straininfo link

  • @ref: 76872
  • straininfo: 134256

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653854Microbacterium halotolerans sp. nov., isolated from a saline soil in the west of China.Li WJ, Chen HH, Kim CJ, Park DJ, Tang SK, Lee JC, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63239-02005Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil MicrobiologyGenetics
Phylogeny20023059Microbacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil.Lal D, Gupta SK, Schumann P, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.017699-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Hexachlorocyclohexane/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Soil Pollutants/*metabolismMetabolism
Phylogeny25678677Microbacterium populi sp. nov., isolated from Populusxeuramericana bark.Li Y, Wang T, Fang W, Xue H, Piao CG, Guo MW, Zhu THInt J Syst Evol Microbiol10.1099/ijs.0.0001172015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, Plant Bark/*microbiology, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics
Phylogeny27260265Microbacterium gilvum sp. nov., isolated from civet faeces.Chen X, Li QY, Li GD, Xu FJ, Jiang Y, Han L, Jiang CL, Huang XSAntonie Van Leeuwenhoek10.1007/s10482-016-0718-12016Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Animals, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Feces/*microbiology, Malaysia, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/metabolism, Viverridae/*microbiologyMetabolism
Phylogeny30362936Microbacterium halophytorum sp. nov., a novel endophytic actinobacterium isolated from halophytes.Li YR, Zhu ZN, Li YQ, Xiao M, Han MX, Wadaan MAM, Hozzein WN, An DD, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0030922018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6125Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15855)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15855
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
31298Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2761728776041
38175Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5653
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
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
76872Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134256.1StrainInfo: A central database for resolving microbial strain identifiers
119827Curators of the CIPCollection of Institut Pasteur (CIP 108071)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108071