Strain identifier

BacDive ID: 7381

Type strain: Yes

Species: Microbacterium gubbeenense

Strain history: CIP <- 2003, NCIMB <- 2001, T.M. Cogan, (DPRC) National Dairy Products Research Centre, Fermoy, County Cork, Ireland: strain DPC 5286

NCBI tax ID(s): 1122237 (strain), 159896 (species)

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General

@ref: 6201

BacDive-ID: 7381

DSM-Number: 15944

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

description: Microbacterium gubbeenense DSM 15944 is an obligate aerobe, mesophilic bacterium that was isolated from surface of a smear-ripened cheese.

NCBI tax id

NCBI tax idMatching level
1122237strain
159896species

strain history

@refhistory
6201<- D. Janssens, LMG <- T. M. Cogan; DPC 5286 <- N. M. Brennan
67770NCIMB 30129 <-- T. M. Cogan DPC 5286.
119750CIP <- 2003, NCIMB <- 2001, T.M. Cogan, (DPRC) National Dairy Products Research Centre, Fermoy, County Cork, Ireland: strain DPC 5286

doi: 10.13145/bacdive7381.20230509.8.1

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 gubbeenense
  • full scientific name: Microbacterium gubbeenense Brennan et al. 2001

@ref: 6201

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium gubbeenense

full scientific name: Microbacterium gubbeenense Brennan et al. 2001 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.23
69480100positive
119750nopositiverod-shaped

colony morphology

  • @ref: 119750

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6201R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6201TRYPTICASE 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
33091MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119750CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6201positivegrowth28mesophilic
33091positivegrowth30mesophilic
67770positivegrowth30mesophilic
119750positivegrowth15-30
119750nogrowth10psychrophilic
119750nogrowth37mesophilic
119750nogrowth41thermophilic
119750nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119750
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

  • @ref: 119750
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 6201
  • murein short key: B01
  • type: B1alpha {Gly} [L-Lys] D-Glu(Hyg)-Gly-L-Lys

observation

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

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
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
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
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
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose+builds acid from15824
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119750citrate-carbon source16947
119750esculin+hydrolysis4853
119750hippurate-hydrolysis606565
119750nitrate-reduction17632
119750nitrite-reduction16301
119750nitrate-respiration17632

antibiotic resistance

  • @ref: 119750
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119750
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11975015688acetoin-
11975017234glucose-

enzymes

@refvalueactivityec
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
119750oxidase-
119750beta-galactosidase+3.2.1.23
119750alcohol dehydrogenase-1.1.1.1
119750gelatinase-
119750amylase-
119750DNase-
119750caseinase-3.4.21.50
119750catalase+1.11.1.6
119750tween esterase-
119750gamma-glutamyltransferase-2.3.2.2
119750lecithinase-
119750lipase-
119750lysine decarboxylase-4.1.1.18
119750ornithine decarboxylase-4.1.1.17
119750phenylalanine ammonia-lyase-4.3.1.24
119750protease-
119750tryptophan deaminase-
119750urease-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
119750-++--+----++-+-+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119750--+/-+/-+/-+/-----+/-++/-----+/-------++/-+/-+/-+/---+/---------+/---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119750+++++--+-+++---++-++++-++-+------+-+---++---------+--+-----++--------------+----------+--++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6201surface of a smear-ripened cheeseCorkIrelandIRLEurope
67770Surface of a smear-ripened cheeseIrelandIRLEurope
119750Food, CheeseIrelandIRLEurope1998

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_2483.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1340;97_1590;98_1934;99_2483&stattab=map
  • Last taxonomy: Microbacterium gubbeenense
  • 16S sequence: AF263563
  • Sequence Identity:
  • Total samples: 2588
  • soil counts: 639
  • aquatic counts: 712
  • animal counts: 1131
  • plant counts: 106

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62011Risk group (German classification)
1197501Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6201
  • description: Microbacterium gubbeenense strain LMG S-19263 16S ribosomal RNA gene, partial sequence
  • accession: AF263563
  • length: 1317
  • database: ena
  • NCBI tax ID: 159896

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium gubbeenense DSM 159441122237.3wgspatric1122237
66792Microbacterium gubbeenense DSM 159442524614763draftimg1122237
67770Microbacterium gubbeenense DSM 15944GCA_000422745scaffoldncbi1122237

GC content

@refGC-contentmethod
620169-75
6777069-75high performance liquid chromatography (HPLC)
6777068.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.211no
flagellatedno96.036no
gram-positiveyes94.008no
anaerobicno99.617no
aerobicyes87.528no
halophileno65.564no
spore-formingno91.732no
thermophileno99.276no
glucose-utilyes85.523no
glucose-fermentno82.207no

External links

@ref: 6201

culture collection no.: DSM 15944, LMG 19263, NCIMB 30129, DPC 5286, JCM 12075, CCM 7309, CIP 107184, IAM 15193, LMG S-19263, NBRC 103073, NRRL B-24242

straininfo link

  • @ref: 76830
  • straininfo: 63600

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11760936Microbacterium gubbeenense sp. nov., from the surface of a smear-ripened cheese.Brennan NM, Brown R, Goodfellow M, Ward AC, Beresford TP, Vancanneyt M, Cogan TM, Fox PFInt J Syst Evol Microbiol10.1099/00207713-51-6-19692001Actinomycetales/chemistry/*classification/genetics/isolation & purification, Base Composition, Cell Wall/chemistry, Cheese/*microbiology, DNA, Ribosomal/genetics, Food Microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNABiotechnology
Metabolism17921266Growth characteristics of Brevibacterium, Corynebacterium, Microbacterium, and Staphylococcus spp. isolated from surface-ripened cheese.Mounier J, Rea MC, O'Connor PM, Fitzgerald GF, Cogan TMAppl Environ Microbiol10.1128/AEM.01260-072007Actinomycetales/*growth & development/isolation & purification/metabolism, Amino Acids/metabolism, Biotin/metabolism, Brevibacterium/*growth & development/isolation & purification/metabolism, Carbohydrate Metabolism, Cheese/*microbiology, Corynebacterium/*growth & development/isolation & purification/metabolism, Food Microbiology, L-Lactate Dehydrogenase/metabolism, Lactic Acid/metabolism, Lactose/metabolism, Staphylococcus/*growth & development/isolation & purification/metabolismEnzymology
Phylogeny22039005Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site.Anand S, Bala K, Saxena A, Schumann P, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.034439-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, India, *Industrial Waste, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny26220793Microbacterium nanhaiense sp. nov., an actinobacterium isolated from sea sediment.Yan L, Wang J, Chen Z, Guan Y, Li JInt J Syst Evol Microbiol10.1099/ijsem.0.0004802015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Ornithine/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics
Phylogeny27902249Microbacterium sorbitolivorans sp. nov., a novel member of Microbacteriaceae isolated from fermentation bed in pigpen.Meng YC, Liu HC, Yang LL, Kang YQ, Zhou YG, Cai MInt J Syst Evol Microbiol10.1099/ijsem.0.0015562016Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Fermentation, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Swine, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
6201Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15944)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15944
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
33091Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4591
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/
68371Automatically annotated from API 50CH acid
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
76830Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID63600.1StrainInfo: A central database for resolving microbial strain identifiers
119750Curators of the CIPCollection of Institut Pasteur (CIP 107184)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107184