Strain identifier

BacDive ID: 7427

Type strain: Yes

Species: Microbacterium paludicola

Strain Designation: US15

Strain history: <- KK Kim, KAIST

NCBI tax ID(s): 300019 (species)

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General

@ref: 6640

BacDive-ID: 7427

DSM-Number: 16915

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

description: Microbacterium paludicola US15 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 300019
  • Matching level: species

strain history

@refhistory
6640<- K. K. Kim <- H. Y. Park; US15
67770DSM 16915 <-- K. K. Kim <-- H. Y. Park US15.
67771<- KK Kim, KAIST

doi: 10.13145/bacdive7427.20230509.8.1

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 paludicola
  • full scientific name: Microbacterium paludicola Park et al. 2006

@ref: 6640

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium paludicola

full scientific name: Microbacterium paludicola Park et al. 2006

strain designation: US15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31638positive1-2.5 µm0.8-1 µmrod-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
19744Daffodil yellow (1007)10-14 daysISP 3
19744Daffodil yellow (1007)10-14 daysISP 4
1974410-14 daysISP 5
19744Daffodil yellow (1007)10-14 daysISP 6
1974410-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19744noISP 3
19744noISP 4
19744noISP 5
19744noISP 6
19744noISP 7

pigmentation

  • @ref: 31638
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6640TRYPTICASE 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
19744ISP 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:
19744ISP 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
19744ISP 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
19744ISP 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
19744ISP 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

culture temp

@refgrowthtypetemperaturerange
6640positivegrowth28mesophilic
19744positiveoptimum28mesophilic
31638positivegrowth15-37
31638positiveoptimum25-30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31638positivegrowth06-09alkaliphile
31638positiveoptimum06-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31638aerobe
67771aerobe

spore formation

  • @ref: 31638
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31638NaClpositivegrowth1-6.5 %
31638NaClpositiveoptimum1-6.5 %

observation

@refobservation
31638aggregates in chains
67770quinones: MK-12, MK-11
67771quinones: MK-12, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31638168082-dehydro-D-gluconate+carbon source
31638581435-dehydro-D-gluconate+carbon source
3163817128adipate+carbon source
3163822599arabinose+carbon source
3163824265gluconate+carbon source
3163817234glucose+carbon source
3163828087glycogen+carbon source
3163824996lactate+carbon source
3163817306maltose+carbon source
3163829864mannitol+carbon source
3163837684mannose+carbon source
3163817272propionate+carbon source
3163826546rhamnose+carbon source
3163817814salicin+carbon source
3163817992sucrose+carbon source
3163831011valerate+carbon source
316384853esculin+hydrolysis
6837917632nitrate-reduction
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

enzymes

@refvalueactivityec
31638catalase+1.11.1.6
31638cytochrome oxidase+1.9.3.1
31638urease+3.5.1.5
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19744-+-+--+-++---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19744+++-++---++---++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6640soilUlsanRepublic of KoreaKORAsia
67770Swamp forest soilUlsanRepublic of KoreaKORAsia
67771From soilUlsanRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_85653.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_417;97_2954;98_3694;99_85653&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: AJ853909
  • Sequence Identity:
  • Total samples: 7
  • soil counts: 1
  • aquatic counts: 4
  • animal counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66401Risk group (German classification)
197441Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6640
  • description: Microbacterium paludicola partial 16S rRNA gene, type strain US15T
  • accession: AJ853909
  • length: 1452
  • database: ena
  • NCBI tax ID: 300019

GC content

@refGC-contentmethod
664066.5
6777066.5high performance liquid chromatography (HPLC)

External links

@ref: 6640

culture collection no.: DSM 16915, KCTC 19080, JCM 14308, NCIMB 14545, CIP 109197

straininfo link

  • @ref: 76876
  • straininfo: 232310

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16514023Microbacterium paludicola sp. nov., a novel xylanolytic bacterium isolated from swamp forest.Park HY, Kim KK, Jin L, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63945-02006Actinomycetales/*classification/genetics/isolation & purification/physiology, DNA, Ribosomal/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees, Xylans/*metabolismTranscriptome
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
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_referencepubmedjournal
6640Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16915)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16915
19744Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16915.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
31638Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2792128776041
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
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
76876Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232310.1StrainInfo: A central database for resolving microbial strain identifiers