Strain identifier

BacDive ID: 7365

Type strain: Yes

Species: Microbacterium saperdae

Strain Designation: 48-1-4, 3126

Strain history: CIP <- 1995, JCM <- K. Suzuki: strain CNF 058 <- AJ: strain 3126 <- CCEB <- O. Lysenko: strain 48-1-4

NCBI tax ID(s): 69368 (species)

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General

@ref: 8600

BacDive-ID: 7365

DSM-Number: 20169

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

description: Microbacterium saperdae 48-1-4 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from elm borer .

NCBI tax id

  • NCBI tax id: 69368
  • Matching level: species

strain history

@refhistory
8600<- ATCC <- CCEB <- O. Lysenko, 48-1-4
67770K. Suzuki CNF 058 <-- AJ 3126 <-- CCEB 366 <-- O. Lysenko 48-1-4.
122485CIP <- 1995, JCM <- K. Suzuki: strain CNF 058 <- AJ: strain 3126 <- CCEB <- O. Lysenko: strain 48-1-4

doi: 10.13145/bacdive7365.20230509.8.1

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 saperdae
  • full scientific name: Microbacterium saperdae (Lysenko 1959) Takeuchi and Hatano 1998

  • synonyms

    @refsynonym
    20215Curtobacterium saperdae
    20215Aureobacterium saperdae
    20215Brevibacterium saperdae

@ref: 8600

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium saperdae

full scientific name: Microbacterium saperdae (Lysenko 1959) Takeuchi and Hatano 1998

strain designation: 48-1-4, 3126

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
122485positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
18635Sand yellow (1002)10-14 daysISP 2
18635Zinc yellow (1018)10-14 daysISP 3
18635Colorless10-14 daysISP 4
18635Colorless10-14 daysISP 6
122485

multicellular morphology

@refforms multicellular complexmedium name
18635noISP 2
18635noISP 3
18635noISP 4
18635noISP 6

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18635ISP 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
18635ISP 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:
18635ISP 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
18635ISP 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
38667MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8600CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
122485CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18635positiveoptimum28mesophilic
8600positivegrowth30mesophilic
38667positivegrowth30mesophilic
51373positivegrowth26mesophilic
67770positivegrowth30mesophilic
122485positivegrowth15-30
122485nogrowth10psychrophilic
122485nogrowth37mesophilic
122485nogrowth41thermophilic
122485nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
51373aerobe
122485obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.874

halophily

@refsaltgrowthtested relationconcentration
18635NaClpositivegrowth0 %
122485NaClpositivegrowth0-4 %
122485NaClnogrowth6 %
122485NaClnogrowth8 %
122485NaClnogrowth10 %

murein

  • @ref: 8600
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-12 (MK-11)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1863562968cellulose+
1863516634raffinose-
1863526546rhamnose-
1863528757fructose-
1863529864mannitol-
1863517268myo-inositol-
1863518222xylose-
1863517992sucrose-
1863522599arabinose-
1863517234glucose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12248516947citrate-carbon source
1224854853esculin+hydrolysis
122485606565hippurate+hydrolysis
12248517632nitrate-reduction
12248516301nitrite-reduction
122485132112sodium thiosulfate-builds gas from
12248517632nitrate-respiration
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: 122485
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12248535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12248515688acetoin-
12248517234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
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
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
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
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
122485oxidase-
122485beta-galactosidase+3.2.1.23
122485alcohol dehydrogenase-1.1.1.1
122485gelatinase-
122485amylase+
122485DNase+
122485caseinase-3.4.21.50
122485catalase+1.11.1.6
122485gamma-glutamyltransferase-2.3.2.2
122485lecithinase-
122485lipase-
122485lysine decarboxylase-4.1.1.18
122485ornithine decarboxylase-4.1.1.17
122485phenylalanine ammonia-lyase-4.3.1.24
122485protease-
122485tryptophan deaminase-
122485urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18635+/-++-+++--++++-++++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18635+++-+++--++++-++++-
122485+++-+----++++-+++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18635+--------+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122485+++++--+-++----+--++++++-+-----+-+-+---+--+--------------+++--------------------------+----------+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountrycontinent
8600elm borer (Saperda carcharias)Saperda carcharias
67770Saperda carcharias Linnaeus (Coleoptera)Saperda carchariasMikulovCzechoslovakiaEurope
122485Elm borer, Saperda carcharias

isolation source categories

  • Cat1: #Host
  • Cat2: #Arthropoda
  • Cat3: #Insecta

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
86001Risk group (German classification)
186351Risk group (German classification)
1224851Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium saperdae 16S rRNA geneY172361473ena69368
20218Microbacterium saperdae gene for 16S rRNA, partial sequenceAB0047191407ena69368

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium saperdae JCM 1352GCA_014646775contigncbi69368
66792Microbacterium saperdae strain DSM 2016969368.3wgspatric69368
66792Microbacterium saperdae strain JCM 135269368.4wgspatric69368
66792Microbacterium saperdae DSM 201692816332114draftimg69368
67770Microbacterium saperdae DSM 20169GCA_006716345contigncbi69368

GC content

@refGC-contentmethod
860068.5
6777069.1thermal denaturation, midpoint method (Tm)
6777068.5thermal denaturation, midpoint method (Tm)
6777072.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveyes90.659no
anaerobicno99.273yes
halophileno92.443no
spore-formingno89.096no
glucose-utilyes77.796yes
flagellatedno91.754no
thermophileno99.729no
aerobicyes93.349yes
glucose-fermentno87.43yes
motileyes58.84no

External links

@ref: 8600

culture collection no.: DSM 20169, ATCC 19272, CCEB 366, CCUG 33092, JCM 1352, BCRC 12119, CCM 4972, CGMCC 1.1906, CIP 104420, HAMBI 1890, IAM 12547, IFO 15038, IMET 11076, KCTC 3469, LMG 16343, NBRC 15038, NCDO 2265, NCIMB 702265, NRRL B-14833, VKM Ac-1022, VKM Ac-1414, CNF 058

straininfo link

  • @ref: 76814
  • straininfo: 8205

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774639Microbacterium oleivorans sp. nov. and Microbacterium hydrocarbonoxydans sp. nov., novel crude-oil-degrading Gram-positive bacteria.Schippers A, Bosecker K, Sproer C, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.63305-02005Actinomycetales/*classification/genetics/metabolism/ultrastructure, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Gram-Positive Bacteria/classification/metabolism, Molecular Sequence Data, Petroleum/*metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityMetabolism
Phylogeny33263510Microbacterium algeriense sp. nov., a novel actinobacterium isolated from Algerian oil production waters.Lenchi N, Anzil A, Servais P, Kebbouche-Gana S, Gana ML, Lliros MInt J Syst Evol Microbiol10.1099/ijsem.0.0044342020Algeria, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Microbacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry, WaterTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8600Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20169)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20169
18635Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20169.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
38667Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16327
51373Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33092)https://www.ccug.se/strain?id=33092
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
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
76814Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8205.1StrainInfo: A central database for resolving microbial strain identifiers
122485Curators of the CIPCollection of Institut Pasteur (CIP 104420)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104420