Strain identifier

BacDive ID: 7444

Type strain: Yes

Species: Microbacterium profundi

Strain Designation: Shh49

Strain history: CIP <- 2008, JCM <- 2007, X.W. Xu, Zhejiang Univ., Hangzhou, China: strain Shh49

NCBI tax ID(s): 450380 (species)

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General

@ref: 16220

BacDive-ID: 7444

DSM-Number: 22239

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

description: Microbacterium profundi Shh49 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from deep-sea sediment sample collected from a polymetallic nodule region.

NCBI tax id

  • NCBI tax id: 450380
  • Matching level: species

strain history

@refhistory
16220<- JCM/RIKEN <- X.-W. Xu; Shh49
67770X.-W. Xu Shh49.
121956CIP <- 2008, JCM <- 2007, X.W. Xu, Zhejiang Univ., Hangzhou, China: strain Shh49

doi: 10.13145/bacdive7444.20230509.8.1

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 profundi
  • full scientific name: Microbacterium profundi Wu et al. 2008

@ref: 16220

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium profundi

full scientific name: Microbacterium profundi Wu et al. 2008

strain designation: Shh49

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidencemotility
31189positive01-02 µm0.4-0.6 µmrod-shaped
69480positive100
121956positiverod-shapedno

pigmentation

  • @ref: 31189
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16220R2A 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
16220BACTO 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
37695Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121956CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
16220positivegrowth28mesophilic
31189positivegrowth04-35
31189positiveoptimum28mesophilic
37695positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31189positivegrowth6-9.5alkaliphile
31189positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31189aerobe
121956obligate aerobe

spore formation

@refspore formationconfidence
31189no
69481no100
69480no99.982

halophily

@refsaltgrowthtested relationconcentration
31189NaClpositivegrowth0-7.5 %
31189NaClpositiveoptimum0-1 %

observation

@refobservation
31189aggregates in chains
67770quinones: MK-12, MK-13

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3118930089acetate+carbon source
3118922599arabinose+carbon source
3118929016arginine+carbon source
3118935391aspartate+carbon source
3118917057cellobiose+carbon source
3118928757fructose+carbon source
3118928260galactose+carbon source
3118917234glucose+carbon source
3118917754glycerol+carbon source
3118924996lactate+carbon source
3118917716lactose+carbon source
3118925115malate+carbon source
3118917306maltose+carbon source
3118929864mannitol+carbon source
3118937684mannose+carbon source
3118917272propionate+carbon source
3118915361pyruvate+carbon source
3118916634raffinose+carbon source
3118926546rhamnose+carbon source
3118933942ribose+carbon source
3118917814salicin+carbon source
3118917822serine+carbon source
3118930031succinate+carbon source
3118917992sucrose+carbon source
3118927082trehalose+carbon source
3118918222xylose+carbon source
311894853esculin+hydrolysis
12195617632nitrate-reduction
12195616301nitrite-reduction

metabolite production

  • @ref: 121956
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31189catalase+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
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
121956oxidase-
121956catalase+1.11.1.6
121956urease-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
121956--+--+----+--+-+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitudecountry
16220deep-sea sediment sample collected from a polymetallic nodule regionEast Pacific Ocean (station ES0301; 8° 22' 38'' N 145° 23' 56'' W) at a depth of 5280 m8.3772-145.399
67770Deep-sea sediment from a polymetallic nodule region in the East Pacific Ocean
121956Environment, Deep sea sediment, polymetallic noduleEastPacific Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Geologic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
162201Risk group (German classification)
1219561Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16220
  • description: Microbacterium profundi strain Shh49 16S ribosomal RNA gene, partial sequence
  • accession: EF623999
  • length: 1488
  • database: ena
  • NCBI tax ID: 450380

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium profundi Shh49450380.4wgspatric450380
66792Microbacterium profundi Shh492617271234draftimg450380
67770Microbacterium profundi Shh49GCA_000763375contigncbi450380

GC content

@refGC-contentmethod
1622066.8thermal denaturation, midpoint method (Tm)
3118966.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes93.588yes
anaerobicno99.379no
halophileno89.965yes
spore-formingno90.521yes
glucose-utilyes87.801yes
aerobicyes94.422no
flagellatedno98.22no
motileno90.448no
thermophileno99.556yes
glucose-fermentno89.388no

External links

@ref: 16220

culture collection no.: DSM 22239, CGMCC 1.6777, CIP 109927, JCM 14840

straininfo link

  • @ref: 76892
  • straininfo: 360277

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19060085Microbacterium profundi sp. nov., isolated from deep-sea sediment of polymetallic nodule environments.Wu YH, Wu M, Wang CS, Wang XG, Yang JY, Oren A, Xu XWInt J Syst Evol Microbiol10.1099/ijs.0.2008/000455-02008Actinomycetales/*classification/genetics/*physiology/ultrastructure, *Environment, Geologic Sediments/*microbiology, *Metals, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny22199224Microbacterium murale sp. nov., isolated from an indoor wall.Kampfer P, Schafer J, Lodders N, Martin KInt J Syst Evol Microbiol10.1099/ijs.0.037705-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Environmental Microbiology, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny25678679Microbacterium shaanxiense sp. nov., isolated from the nodule surface of soybean.Peng S, Dongying L, Bingxin Y, Mingjun L, Gehong WInt J Syst Evol Microbiol10.1099/ijs.0.0001162015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Soybeans/*microbiology, Vitamin K 2/chemistryGenetics
Genetics26067975Draft Genome Sequence of Microbacterium profundi Shh49T, an Actinobacterium Isolated from Deep-Sea Sediment of a Polymetallic Nodule Environment.Wu YH, Zhou P, Cheng H, Wang CS, Wu M, Xu XWGenome Announc10.1128/genomeA.00642-152015Phylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16220Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22239)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22239
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
31189Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2751628776041
37695Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7726
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/
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
76892Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360277.1StrainInfo: A central database for resolving microbial strain identifiers
121956Curators of the CIPCollection of Institut Pasteur (CIP 109927)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109927