Strain identifier

BacDive ID: 7436

Type strain: Yes

Species: Microbacterium marinilacus

Strain Designation: YM11-607

Strain history: CIP <- 2008, DSMZ <- Hiroaki Kasai <- Y. Matsuo, Heita, Marine Biotech. Inst., Iwate, Japan: strain YM11-607

NCBI tax ID(s): 415209 (species)

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General

@ref: 7613

BacDive-ID: 7436

DSM-Number: 18904

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

description: Microbacterium marinilacus YM11-607 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from hydra.

NCBI tax id

  • NCBI tax id: 415209
  • Matching level: species

strain history

@refhistory
7613<- Hiroaki Kasai <- Y. Matsuo, YM11-607
67770DSM 18904 <-- H. Kasai <-- Y. Matsuo YM11-607.
120805CIP <- 2008, DSMZ <- Hiroaki Kasai <- Y. Matsuo, Heita, Marine Biotech. Inst., Iwate, Japan: strain YM11-607

doi: 10.13145/bacdive7436.20240916.9.1

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 marinilacus
  • full scientific name: Microbacterium marinilacus Kageyama et al. 2007

@ref: 7613

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium marinilacus

full scientific name: Microbacterium marinilacus Kageyama et al. 2007

strain designation: YM11-607

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32148positive0.75 µm0.5 µmrod-shaped
120805positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19772Beige (1001)10-14 daysISP 2
1977210-14 daysISP 3
19772Beige10-14 daysISP 4
19772Pale yellow10-14 daysISP 5
19772Pale yellow10-14 daysISP 6
19772Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19772noISP 2
19772noISP 3
19772noISP 4
19772noISP 5
19772noISP 6
19772noISP 7

pigmentation

  • @ref: 32148
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7613BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
19772ISP 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
19772ISP 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:
19772ISP 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
19772ISP 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
19772ISP 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
19772ISP 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
37849Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120805CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
7613positivegrowth28
19772positiveoptimum28
32148positivegrowth12-38
32148positiveoptimum25
37849positivegrowth20
67770positivegrowth28

culture pH

@refabilitytypepHPH range
32148positivegrowth06-11alkaliphile
32148positiveoptimum9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32148aerobe
120805obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
32148NaClpositivegrowth<8 %
32148NaClpositiveoptimum4 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3214822599arabinose+carbon source
3214828757fructose+carbon source
3214817234glucose+carbon source
3214817306maltose+carbon source
3214829864mannitol+carbon source
3214837684mannose+carbon source
32148506227N-acetylglucosamine+carbon source
3214818257ornithine+carbon source
3214826546rhamnose+carbon source
3214827082trehalose+carbon source
3214818222xylose+carbon source
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837117151xylitol-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12080517632nitrate-reduction
12080516301nitrite-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

metabolite production

  • @ref: 120805
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32148catalase+1.11.1.6
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
68382acid phosphatase+3.1.3.2
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382esterase lipase (C 8)-
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
120805oxidase+
120805catalase+1.11.1.6
120805urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19772+----++----

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19772-+---+-+-+----+++-+
120805+---+--++++---+++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7613----+-----++++-+--+---+--+-++--+++++++-++------+-+
120805+/---+/--+/----+/-+/-+/-+/--+/---+/-------+/--+/-+/----+/------------+/---+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7613hydraSano Marine LakePalauPLWAustralia and Oceania
67770Unidentified hydroid collected from the Sano Marine LakePalauPLWAustralia and Oceania
120805Environment, Hydra, marine lakePalauPLWAustralia and Oceania

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Cnidaria (Corals)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76131Risk group (German classification)
197721Risk group (German classification)
1208051Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7613
  • description: Microbacterium marinilacus gene for 16S rRNA, partial sequence
  • accession: AB286020
  • length: 1465
  • database: nuccore
  • NCBI tax ID: 415209

Genome sequences

  • @ref: 66792
  • description: Microbacterium marinilacus YM11-607
  • accession: GCA_019753765
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 415209

GC content

@refGC-contentmethod
761371.6
6777071.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno80no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes84.335yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.253yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.707yes
69480spore-formingspore-formingAbility to form endo- or exosporesno73.965no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.467yes
69480flagellatedmotile2+Ability to perform flagellated movementno76no

External links

@ref: 7613

culture collection no.: DSM 18904, CIP 109810, JCM 16546, MBIC 07778, NBRC 104188

straininfo link

  • @ref: 76884
  • straininfo: 310974

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17911310Microbacterium sediminicola sp. nov. and Microbacterium marinilacus sp. nov., isolated from marine environments.Kageyama A, Takahashi Y, Matsuo Y, Kasai H, Shizuri Y, Omura SInt J Syst Evol Microbiol10.1099/ijs.0.65038-02007Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Mycolic Acids/analysis, Nucleic Acid Hybridization, Ornithine/analysis, Peptidoglycan/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny27756912Microbacterium lacusdiani sp. nov., a phosphate-solubilizing novel actinobacterium isolated from mucilaginous sheath of Microcystis.Zhang BH, Salam N, Cheng J, Li HQ, Yang JY, Zha DM, Guo QG, Li WJJ Antibiot (Tokyo)10.1038/ja.2016.1252016Actinobacteria/*classification/*genetics/isolation & purification, Bacteriological Techniques, DNA, Bacterial/genetics, Microcystis/*physiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsEnzymology
Phylogeny29125456Microbacterium album sp. nov. and Microbacterium deserti sp. nov., two halotolerant actinobacteria isolated from desert soil.Yang ZW, Salam N, Mohany M, Chinnathambi A, Alharbi SA, Xiao M, Hozzein WN, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0024852017Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Saudi Arabia, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome
Phylogeny34762581Microbacterium stercoris sp. nov., an indole acetic acid-producing actinobacterium isolated from cow dung.Zhang L, Jiao Y, Ling L, Wang H, Song W, Zhao T, Guo L, Xiang W, Zhao J, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0050992021Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, China, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Feces/*microbiology, Indoleacetic Acids/*metabolism, *Microbacterium/classification/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7613Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18904)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18904
19772Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18904.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
32148Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2839128776041
37849Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7595
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
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
76884Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310974.1StrainInfo: A central database for resolving microbial strain identifiers
120805Curators of the CIPCollection of Institut Pasteur (CIP 109810)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109810