Strain identifier

BacDive ID: 7408

Type strain: Yes

Species: Microbacterium thalassium

Strain Designation: No. 10

Strain history: NBRC 16060 <-- IFO 16060 <-- M. Takeuchi No. 10.

NCBI tax ID(s): 362649 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 4756

BacDive-ID: 7408

DSM-Number: 12511

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Microbacterium thalassium No. 10 is a mesophilic bacterium that was isolated from rhizosphere of mangrove trees.

NCBI tax id

  • NCBI tax id: 362649
  • Matching level: species

strain history

@refhistory
4756<- IFO <- K. Hatano, No. 10
67770NBRC 16060 <-- IFO 16060 <-- M. Takeuchi No. 10.

doi: 10.13145/bacdive7408.20250331.9.3

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 thalassium
  • full scientific name: Microbacterium thalassium Takeuchi and Hatano 1998

@ref: 4756

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium thalassium

full scientific name: Microbacterium thalassium Takeuchi and Hatano 1998

strain designation: No. 10

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
125439positive95.4
12543893no

colony morphology

@refcolony colorincubation periodmedium used
18501Zinc yellow (1018)10-14 daysISP 2
18501Zinc yellow (1018)10-14 daysISP 3
18501Beige (1001)10-14 daysISP 4
18501Beige (1001)10-14 daysISP 5
18501Zinc yellow (1018)10-14 daysISP 6
18501Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18501noISP 2
18501noISP 3
18501noISP 4
18501noISP 5
18501noISP 6
18501noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4756TRYPTICASE 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
18501ISP 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
18501ISP 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:
18501ISP 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
18501ISP 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
18501ISP 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
18501ISP 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
18501positiveoptimum28
4756positivegrowth28
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 98

murein

  • @ref: 4756
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917632nitrate-reduction
683794853esculin-hydrolysis

enzymes

@refvalueactivityec
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68379beta-glucosidase-3.2.1.21
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68379gelatinase+
68379urease+3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18501---------++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18501-++-+----+--+--+---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
4756rhizosphere of mangrove treesJapanJPNAsia
67770Mangrove rhizosphereJapanJPNAsiaOkinawa Pref.

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Mangrove
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 4756
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium thalassium partial 16S rRNA gene, type strain DSM 12511AM1815071513nuccore362649
4756Microbacterium thalassium gene for 16S rRNA, partial sequenceAB0047131533nuccore362649

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium thalassium DSM 12511GCA_014208045contigncbi362649
66792Microbacterium thalassium strain DSM 12511362649.3wgspatric362649
66792Microbacterium thalassium DSM 125112870628048draftimg362649

GC content

  • @ref: 4756
  • GC-content: 69.7

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes87.909no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.92no
125438spore-formingspore-formingAbility to form endo- or exosporesno80.697no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.949no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.795no
125438motile2+flagellatedAbility to perform flagellated movementno93no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno85.7
125439BacteriaNetmotilityAbility to perform movementno50
125439BacteriaNetgram_stainReaction to gram-stainingpositive95.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98

External links

@ref: 4756

culture collection no.: DSM 12511, IFO 16060, NBRC 16060, NRRL B-24222, JCM 12079, CIP 105728, IAM 15194, LMG 22183, NCIMB 13604, VKM Ac-2084

straininfo link

  • @ref: 76857
  • straininfo: 49312

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734054Proposal of six new species in the genus Microbacterium and transfer of Flavobacterium marinotypicum ZoBell and Upham to the genus Microbacterium as Microbacterium maritypicum comb. nov.Takeuchi M, Hatano KInt J Syst Bacteriol10.1099/00207713-48-3-9731998Actinomycetales/chemistry/*classification/genetics, DNA, Bacterial/analysis, Flavobacterium/*classification, Nucleic Acid Hybridization
Phylogeny27506590Microbacterium aureliae sp. nov., a novel actinobacterium isolated from Aurelia aurita, the moon jellyfish.Kaur G, Mual P, Kumar N, Verma A, Kumar A, Krishnamurthi S, Mayilraj SInt J Syst Evol Microbiol10.1099/ijsem.0.0014072016Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Scyphozoa/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4756Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12511)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12511
18501Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12511.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
76857Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49312.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1