Strain identifier

BacDive ID: 7435

Type strain: Yes

Species: Microbacterium sediminicola

Strain Designation: YM10-847

Strain history: CIP <- 2008, DSMZ <- H. Kasai <- Y. Matsuo, Heita, Marine Biotech. Inst., Iwate, Japan: strain YM10-847

NCBI tax ID(s): 415210 (species)

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General

@ref: 7614

BacDive-ID: 7435

DSM-Number: 18905

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

description: Microbacterium sediminicola YM10-847 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sediment.

NCBI tax id

  • NCBI tax id: 415210
  • Matching level: species

strain history

@refhistory
7614<- Hiroaki Kasai <- Y. Matsuo, YM10-847
67770DSM 18905 <-- H. Kasai <-- Y. Matsuo YM10-847.
122534CIP <- 2008, DSMZ <- H. Kasai <- Y. Matsuo, Heita, Marine Biotech. Inst., Iwate, Japan: strain YM10-847

doi: 10.13145/bacdive7435.20230509.8.1

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

@ref: 7614

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium sediminicola

full scientific name: Microbacterium sediminicola Kageyama et al. 2007

strain designation: YM10-847

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32148positive1.15 µm0.55 µmrod-shaped
122534positiverod-shapedno

colony morphology

@refincubation periodmedium used
1841410-14 daysISP 2
1841410-14 daysISP 3
1841410-14 daysISP 4
1841410-14 daysISP 5
1841410-14 daysISP 6
1841410-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18414noISP 2
18414noISP 3
18414noISP 4
18414noISP 5
18414noISP 6
18414noISP 7

pigmentation

  • @ref: 32148
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7614TRYPTICASE 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
18414ISP 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
18414ISP 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:
18414ISP 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
18414ISP 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
18414ISP 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
18414ISP 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
37848MEDIUM 338 - for Sanguibacter keddieiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (3.000 g);Trypto casein soy agar (30.000 g)
122534CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperaturerange
7614positivegrowth28mesophilic
32148positivegrowth19-38
32148positiveoptimum28.5mesophilic
37848positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32148positivegrowth06-11alkaliphile
32148positiveoptimum9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32148aerobe
122534obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
32148NaClpositivegrowth<7 %
32148NaClpositiveoptimum3.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3214822599arabinose+carbon source
3214828260galactose+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 5-ketogluconate-builds acid from
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
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12253417632nitrate-reduction
12253416301nitrite-reduction

metabolite production

  • @ref: 122534
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32148catalase+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
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382alkaline phosphatase-3.1.3.1
122534oxidase+
122534catalase+1.11.1.6
122534urease-3.5.1.5

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18414-----------++-+++--
122534-++-++-+-++++-+++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7614----+-----++------+-----++++----------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7614sedimentSamambula River, FijiFijiFJIAustralia and Oceania
67770Sediment from the mouth of the Samambula RiverFijiFJIAustralia and Oceania
122534Environment, River sediment, marine lakeSamambula riverFijiFJIAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76141Risk group (German classification)
184141German classification
1225341Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7614
  • description: Microbacterium sediminicola gene for 16S rRNA, partial sequence
  • accession: AB286021
  • length: 1472
  • database: ena
  • NCBI tax ID: 415210

GC content

@refGC-contentmethod
761467.8
6777067.8high performance liquid chromatography (HPLC)

External links

@ref: 7614

culture collection no.: DSM 18905, CIP 109809, JCM 15577, MBIC 08264, MBIC 07778, DSM 18904

literature

  • topic: Phylogeny
  • Pubmed-ID: 17911310
  • title: Microbacterium sediminicola sp. nov. and Microbacterium marinilacus sp. nov., isolated from marine environments.
  • authors: Kageyama A, Takahashi Y, Matsuo Y, Kasai H, Shizuri Y, Omura S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65038-0
  • year: 2007
  • mesh: Actinomycetales/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/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7614Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18905)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18905
18414Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18905.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
37848Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7594
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
122534Curators of the CIPCollection of Institut Pasteur (CIP 109809)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109809