Strain identifier
BacDive ID: 7408
Type strain:
Species: Microbacterium thalassium
Strain Designation: No. 10
Strain history: NBRC 16060 <-- IFO 16060 <-- M. Takeuchi No. 10.
NCBI tax ID(s): 362649 (species)
General
@ref: 4756
BacDive-ID: 7408
DSM-Number: 12511
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Microbacterium thalassium No. 10 is a mesophilic, Gram-positive bacterium that was isolated from rhizosphere of mangrove trees.
NCBI tax id
- NCBI tax id: 362649
- Matching level: species
strain history
@ref | history |
---|---|
4756 | <- IFO <- K. Hatano, No. 10 |
67770 | NBRC 16060 <-- IFO 16060 <-- M. Takeuchi No. 10. |
doi: 10.13145/bacdive7408.20230509.8.1
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 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
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
18501 | Zinc yellow (1018) | 10-14 days | ISP 2 |
18501 | Zinc yellow (1018) | 10-14 days | ISP 3 |
18501 | Beige (1001) | 10-14 days | ISP 4 |
18501 | Beige (1001) | 10-14 days | ISP 5 |
18501 | Zinc yellow (1018) | 10-14 days | ISP 6 |
18501 | Beige (1001) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18501 | no | ISP 2 |
18501 | no | ISP 3 |
18501 | no | ISP 4 |
18501 | no | ISP 5 |
18501 | no | ISP 6 |
18501 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4756 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: 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 |
18501 | ISP 2 | yes | Name: 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 | |
18501 | ISP 3 | yes | Name: 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: | |
18501 | ISP 4 | yes | Name: 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 | |
18501 | ISP 5 | yes | Name: 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 | |
18501 | ISP 6 | yes | Name: 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 | |
18501 | ISP 7 | yes | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
18501 | positive | optimum | 28 | mesophilic |
4756 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.963 |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | + | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68379 | gelatinase | + | |
68379 | urease | + | 3.5.1.5 |
68379 | beta-glucosidase | - | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | - | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | - | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18501 | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18501 | - | + | + | - | + | - | - | - | - | + | - | - | + | - | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
4756 | rhizosphere of mangrove trees | Japan | JPN | Asia | |
67770 | Mangrove rhizosphere | Japan | JPN | Asia | Okinawa Pref. |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Microbacterium thalassium partial 16S rRNA gene, type strain DSM 12511 | AM181507 | 1513 | ena | 362649 |
4756 | Microbacterium thalassium gene for 16S rRNA, partial sequence | AB004713 | 1533 | ena | 362649 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium thalassium DSM 12511 | GCA_014208045 | contig | ncbi | 362649 |
66792 | Microbacterium thalassium strain DSM 12511 | 362649.3 | wgs | patric | 362649 |
66792 | Microbacterium thalassium DSM 12511 | 2870628048 | draft | img | 362649 |
GC content
- @ref: 4756
- GC-content: 69.7
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 91.776 | no |
anaerobic | no | 99.486 | no |
halophile | no | 80.381 | no |
spore-forming | no | 96.44 | no |
glucose-util | yes | 87.941 | no |
aerobic | yes | 91.451 | no |
motile | no | 91.302 | no |
flagellated | no | 97.663 | no |
thermophile | no | 99.007 | yes |
glucose-ferment | no | 91.168 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9734054 | Proposal 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 K | Int J Syst Bacteriol | 10.1099/00207713-48-3-973 | 1998 | Actinomycetales/chemistry/*classification/genetics, DNA, Bacterial/analysis, Flavobacterium/*classification, Nucleic Acid Hybridization | |
Phylogeny | 27506590 | Microbacterium 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 S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001407 | 2016 | Actinomycetales/*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/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4756 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12511) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12511 | |||
18501 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM12511.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
76857 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49312.1 | StrainInfo: A central database for resolving microbial strain identifiers |