Strain identifier
BacDive ID: 7985
Type strain:
Species: Micromonospora mirobrigensis
Strain history: CIP <- 2005, M.E. Trujillo, Salamanca Univ., Salamanca, Spain: WA201
NCBI tax ID(s): 262898 (species)
General
@ref: 12012
BacDive-ID: 7985
DSM-Number: 44830
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Micromonospora mirobrigensis DSM 44830 is an aerobe, spore-forming, mesophilic bacterium that was isolated from water.
NCBI tax id
- NCBI tax id: 262898
- Matching level: species
strain history
@ref | history |
---|---|
12012 | <- M. E. Trujillo, Universidad de Salamanca, Spain; WA201 |
36416 | 2005, M.E. Trujillo, Salamanca Univ., Salamanca, Spain: WA201 |
67770 | DSM 44830 <-- M. E. Trujillo WA201. |
120973 | CIP <- 2005, M.E. Trujillo, Salamanca Univ., Salamanca, Spain: WA201 |
doi: 10.13145/bacdive7985.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micromonosporales
- family: Micromonosporaceae
- genus: Micromonospora
- species: Micromonospora mirobrigensis
- full scientific name: Micromonospora mirobrigensis Trujillo et al. 2005
@ref: 12012
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Micromonospora
species: Micromonospora mirobrigensis
full scientific name: Micromonospora mirobrigensis Trujillo et al. 2005
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence | cell shape |
---|---|---|---|---|
31344 | positive | |||
69480 | no | 92.839 | ||
69480 | positive | 100 | ||
120973 | positive | no | rod-shaped |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
20129 | Deep orange (2011) | 10-14 days | ISP 2 |
20129 | Yellow orange (2000) | 10-14 days | ISP 3 |
20129 | Yellow orange (2000) | 10-14 days | ISP 6 |
20129 | Yellow orange (2000) | 10-14 days | ISP 7 |
120973 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
20129 | no | ISP 2 |
20129 | no | ISP 3 |
20129 | no | ISP 4 |
20129 | no | ISP 5 |
20129 | no | ISP 6 |
20129 | no | ISP 7 |
pigmentation
- @ref: 31344
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12012 | N-Z-AMINE-MEDIUM (DSMZ Medium 554) | yes | https://mediadive.dsmz.de/medium/554 | Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water |
20129 | 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 | |
20129 | 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: | |
20129 | 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 | |
20129 | 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 | |
36416 | MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum | yes | Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g) | |
12012 | BENNETT'S AGAR (DSMZ Medium 548) | yes | https://mediadive.dsmz.de/medium/548 | Name: BENNETT'S AGAR (DSMZ Medium 548) Composition: Agar 15.0 g/l Glucose 10.0 g/l N-Z amine 2.0 g/l Yeast extract 1.0 g/l Beef extract 1.0 g/l Distilled water |
12012 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://mediadive.dsmz.de/medium/553 | Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water |
120973 | CIP Medium 57 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20129 | positive | optimum | 28 | mesophilic |
31344 | positive | growth | 20-37 | |
31344 | positive | optimum | 28 | mesophilic |
36416 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
12012 | positive | growth | 28 | mesophilic |
120973 | positive | growth | 25-41 | |
120973 | no | growth | 10 | psychrophilic |
120973 | no | growth | 45 | thermophilic |
culture pH
- @ref: 31344
- ability: positive
- type: optimum
- pH: 7
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31344 | aerobe |
120973 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31344 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
120973 | no |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31344 | NaCl | positive | growth | <3 % |
31344 | NaCl | positive | optimum | 1.5 % |
120973 | NaCl | positive | growth | 0 % |
120973 | NaCl | no | growth | 2 % |
120973 | NaCl | no | growth | 4 % |
120973 | NaCl | no | growth | 6 % |
120973 | NaCl | no | growth | 8 % |
120973 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-10(H4), MK-10(H6), MK-9(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
20129 | 17234 | glucose | +/- | |
20129 | 22599 | arabinose | +/- | |
20129 | 17992 | sucrose | +/- | |
20129 | 18222 | xylose | +/- | |
20129 | 17268 | myo-inositol | +/- | |
20129 | 29864 | mannitol | +/- | |
20129 | 28757 | fructose | - | |
20129 | 26546 | rhamnose | +/- | |
20129 | 16634 | raffinose | +/- | |
20129 | 62968 | cellulose | +/- | |
31344 | 22599 | arabinose | + | carbon source |
31344 | 17057 | cellobiose | + | carbon source |
31344 | 28260 | galactose | + | carbon source |
31344 | 17234 | glucose | + | carbon source |
31344 | 27570 | histidine | + | carbon source |
31344 | 17306 | maltose | + | carbon source |
31344 | 37684 | mannose | + | carbon source |
31344 | 28053 | melibiose | + | carbon source |
31344 | 16634 | raffinose | + | carbon source |
31344 | 17992 | sucrose | + | carbon source |
31344 | 27082 | trehalose | + | carbon source |
31344 | 4853 | esculin | + | hydrolysis |
120973 | 16947 | citrate | - | carbon source |
120973 | 4853 | esculin | + | hydrolysis |
120973 | 606565 | hippurate | + | hydrolysis |
120973 | 17632 | nitrate | - | reduction |
120973 | 16301 | nitrite | - | reduction |
120973 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 120973
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
120973 | 15688 | acetoin | - | |
120973 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31344 | catalase | + | 1.11.1.6 |
31344 | cytochrome oxidase | + | 1.9.3.1 |
31344 | urease | + | 3.5.1.5 |
120973 | oxidase | + | |
120973 | beta-galactosidase | - | 3.2.1.23 |
120973 | alcohol dehydrogenase | - | 1.1.1.1 |
120973 | gelatinase | + | |
120973 | amylase | + | |
120973 | DNase | + | |
120973 | caseinase | + | 3.4.21.50 |
120973 | catalase | + | 1.11.1.6 |
120973 | tween esterase | - | |
120973 | gamma-glutamyltransferase | - | 2.3.2.2 |
120973 | lecithinase | - | |
120973 | lipase | - | |
120973 | lysine decarboxylase | - | 4.1.1.18 |
120973 | ornithine decarboxylase | - | 4.1.1.17 |
120973 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
120973 | tryptophan deaminase | - | |
120973 | urease | - | 3.5.1.5 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20129 | - | + | + | - | + | - | - | - | - | + | + | + | + | - | + | + | + | - | - | |
120973 | + | + | + | - | + | + | - | + | - | + | + | + | + | - | + | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
12012 | water | Salamaca, Ciudad Rodrigo | Spain | ESP | Europe | |
67770 | Water of a pond located on a former uranium mine | Ciudad Rodrigo | Spain | ESP | Europe | |
120973 | Environment, Water | Ciudad Rodrigo, Salamanca | Spain | ESP | Europe | 2003 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
12012 | 1 | Risk group (German classification) |
20129 | 1 | German classification |
120973 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 12012
- description: Micromonospora mirobrigensis 16S rRNA gene, type strain WA201
- accession: AJ626950
- length: 1511
- database: ena
- NCBI tax ID: 262898
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Micromonospora mirobrigensis strain DSM 44830 | 262898.5 | wgs | patric | 262898 |
66792 | Micromonospora mirobrigensis DSM 44830 | 2619619047 | draft | img | 262898 |
67770 | Micromonospora mirobrigensis DSM 44830 | GCA_900091555 | scaffold | ncbi | 262898 |
GC content
@ref | GC-content | method |
---|---|---|
31344 | 68.6 | |
67770 | 68.6 | thermal denaturation, midpoint method (Tm) |
67770 | 73.34 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 94.3 | no |
gram-positive | yes | 92.319 | yes |
anaerobic | no | 99.405 | yes |
aerobic | yes | 95.305 | yes |
halophile | no | 94.167 | yes |
spore-forming | yes | 92.737 | yes |
glucose-util | yes | 87.585 | yes |
flagellated | no | 97.683 | no |
thermophile | no | 98.917 | yes |
glucose-ferment | no | 93.71 | no |
External links
@ref: 12012
culture collection no.: DSM 44830, LMG 22229, NBRC 101890, NRRL B-24769, WA 201, JCM 13240, CIP 108755
straininfo link
- @ref: 77418
- straininfo: 129610
literature
- topic: Phylogeny
- Pubmed-ID: 15774678
- title: Micromonospora mirobrigensis sp. nov.
- authors: Trujillo ME, Fernandez-Molinero C, Velazquez E, Kroppenstedt RM, Schumann P, Mateos PF, Martinez-Molina E
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.63361-0
- year: 2005
- mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Micromonospora/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, *Radon, Sequence Analysis, DNA, *Water Pollutants, Radioactive
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
12012 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44830) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44830 | |||
20129 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44830.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 | |||
31344 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27658 | 28776041 | |
36416 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6419 | ||||
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/ | ||||
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 | |||
77418 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID129610.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120973 | Curators of the CIP | Collection of Institut Pasteur (CIP 108755) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108755 |