Strain identifier

BacDive ID: 7303

Type strain: Yes

Species: Terrimesophilobacter mesophilus

Strain Designation: MSL-15

Strain history: <- CJ Kim, KRIBB

NCBI tax ID(s): 433647 (species)

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General

@ref: 7986

BacDive-ID: 7303

DSM-Number: 19267

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

description: Terrimesophilobacter mesophilus MSL-15 is an aerobe, Gram-positive, motile bacterium that was isolated from soil, farming field.

NCBI tax id

  • NCBI tax id: 433647
  • Matching level: species

strain history

@refhistory
7986<- C.-J. Kim <- Y. J. Ju; MSL15
67770DSM 19267 <-- C.-J. Kim <-- Y. J. Ju MSL-15.
67771<- CJ Kim, KRIBB

doi: 10.13145/bacdive7303.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Terrimesophilobacter
  • species: Terrimesophilobacter mesophilus
  • full scientific name: Terrimesophilobacter mesophilus (Dastager et al. 2008) Hahn et al. 2021

  • synonyms

    • @ref: 20215
    • synonym: Cryobacterium mesophilum

@ref: 7986

domain: Bacteria

phylum: Actinomycetota

class: Actinomycetes

order: Micrococcales

family: Microbacteriaceae

genus: Terrimesophilobacter

species: Terrimesophilobacter mesophilus

full scientific name: Terrimesophilobacter mesophilus

strain designation: MSL-15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32536positive1.2 µm0.45 µmrod-shapedyes
67771positive
69480positive91.421
69480no90.5

colony morphology

@refcolony colorincubation periodmedium used
18333Rapeseed yellow (1021)10-14 daysISP 2
18333Rapeseed yellow (1021)10-14 daysISP 3
18333Rapeseed yellow (1021)10-14 daysISP 4
18333Rapeseed yellow (1021)10-14 daysISP 5
18333Rapeseed yellow (1021)10-14 daysISP 6
18333Rapeseed yellow (1021)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18333noISP 2
18333noISP 3
18333noISP 4
18333noISP 5
18333noISP 6
18333noISP 7

pigmentation

  • @ref: 32536
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7986TRYPTICASE 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
18333ISP 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
18333ISP 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:
18333ISP 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
18333ISP 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
18333ISP 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
18333ISP 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

@refgrowthtypetemperature
7986positivegrowth28
18333positiveoptimum28
32536positivegrowth20-28
32536positiveoptimum28
67770positivegrowth28
67771positivegrowth30

culture pH

@refabilitytypepHPH range
32536positivegrowth06-11alkaliphile
32536positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32536aerobe
67771aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

  • @ref: 32536
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3253628260galactose+carbon source
3253617234glucose+carbon source
3253617716lactose+carbon source
3253629864mannitol+carbon source
3253637684mannose+carbon source
3253628053melibiose+carbon source
3253616634raffinose+carbon source
3253626546rhamnose+carbon source
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
32536catalase+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
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
18333-+++--+--++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18333++++++-+-+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7986soil, farming fieldBigeum IslandRepublic of KoreaKORAsia
67770Soil on Bigeum IslandRepublic of KoreaKORAsia
67771From farming fieldBikeum islandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
79861Risk group (German classification)
183331German classification

Sequence information

16S sequences

  • @ref: 7986
  • description: Cryobacterium mesophilum strain MSL-15 16S ribosomal RNA gene, partial sequence
  • accession: EF466127
  • length: 1484
  • database: nuccore
  • NCBI tax ID: 433647

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Terrimesophilobacter mesophilus DSM 19267GCA_014200375contigncbi433647
66792Cryobacterium mesophilum strain CGMCC 1.10440433647.12wgspatric433647
66792Cryobacterium mesophilum strain CGMCC1.10440433647.3wgspatric433647
66792Cryobacterium mesophilum strain DSM 19267433647.16wgspatric433647
66792Cryobacterium mesophilum CGMCC 1.104402867779128draftimg433647
66792Cryobacterium mesophilum CGMCC1.104402866042470draftimg433647
66792Cryobacterium mesophilum DSM 192672844824163draftimg433647
67770Terrimesophilobacter mesophilus CGMCC1.10440GCA_002929725contigncbi433647
67770Terrimesophilobacter mesophilus CGMCC 1.10440GCA_004402605contigncbi433647

GC content

@refGC-contentmethod
798670
6777070high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.421yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.349yes
69480spore-formingspore-formingAbility to form endo- or exosporesno80.968no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes77.315no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.429yes
69480flagellatedmotile2+Ability to perform flagellated movementno90.5no

External links

@ref: 7986

culture collection no.: DSM 19267, JCM 16539, KCTC 19270, MSL 15, CGMCC 1.10440

straininfo link

  • @ref: 76753
  • straininfo: 408303

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18450721Cryobacterium mesophilum sp. nov., a novel mesophilic bacterium.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65650-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny23203625Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air.Weon HY, Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Suzuki KI, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.046599-02012Actinomycetales/*classification/genetics/isolation & purification, *Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny24535740Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae.Kim SJ, Ahn JH, Weon HY, Hamada M, Suzuki K, Kwon SWJ Microbiol10.1007/s12275-014-3278-y2014Actinomycetales/classification/*genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7986Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19267)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19267
18333Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19267.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
32536Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2875428776041
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)
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
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
76753Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408303.1StrainInfo: A central database for resolving microbial strain identifiers