Strain identifier
BacDive ID: 8021
Type strain:
Species: Micromonospora cremea
Strain Designation: CR 30
Strain history: CECT 7891 <-- M. E. Trujillo, Univ. Salamanca, Spain; CR30.
NCBI tax ID(s): 709881 (species)
General
@ref: 17740
BacDive-ID: 8021
DSM-Number: 45599
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Micromonospora cremea CR 30 is an aerobe, spore-forming, mesophilic bacterium that was isolated from rhizosphere of Pisum sativum.
NCBI tax id
- NCBI tax id: 709881
- Matching level: species
strain history
@ref | history |
---|---|
17740 | <- M. E. Trujillo, Universidad de Salamanca, Spain; CR 30 <- L. Carro |
67770 | CECT 7891 <-- M. E. Trujillo, Univ. Salamanca, Spain; CR30. |
doi: 10.13145/bacdive8021.20230509.8.1
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 cremea
- full scientific name: Micromonospora cremea Carro et al. 2012
@ref: 17740
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Micromonospora
species: Micromonospora cremea
full scientific name: Micromonospora cremea Carro et al. 2012
strain designation: CR 30
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell width | motility | confidence |
---|---|---|---|---|
30559 | positive | 0.4 µm | no | |
69480 | no | 92.914 | ||
69480 | positive | 100 |
colony morphology
@ref | colony color | medium used |
---|---|---|
69410 | Dahlia yellow (1033) | ISP 4 |
69410 | Dahlia yellow (1033) | suter with tyrosine |
69410 | Beige (1001) | ISP 7 |
69410 | Ivory/ RAL 1007 daffodil yellow (1014) | ISP 5 |
69410 | Ochre yellow (1024) | suter without tyrosine |
69410 | Pastel yellow (1034) | ISP 3 |
69410 | Sun yellow (1037) | ISP 6 |
69410 | Yellow orange (2000) | ISP 2 |
multicellular morphology
@ref | forms multicellular complex | complex name | medium name |
---|---|---|---|
69410 | no | Aerial mycelium | ISP 2 |
69410 | no | Aerial mycelium | ISP 3 |
69410 | no | Aerial mycelium | ISP 4 |
69410 | no | Aerial mycelium | ISP 5 |
69410 | no | Aerial mycelium | ISP 6 |
69410 | no | Aerial mycelium | ISP 7 |
69410 | no | Aerial mycelium | suter with tyrosine |
69410 | no | Aerial mycelium | suter without tyrosine |
pigmentation
@ref | production | color | name |
---|---|---|---|
30559 | yes | ||
69410 | yes | Ral 8001 ochre brown | soluble pigment |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
69410 | DSM_45599_image3.jpeg | Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
69410 | DSM_45599_image4.jpeg | Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
17740 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
17740 | 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 |
17740 | 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 |
17740 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17740 | positive | growth | 28 | mesophilic |
30559 | positive | growth | 10-37 | |
67770 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 30559
- ability: positive
- type: growth
- pH: 07-08
Physiology and metabolism
oxygen tolerance
- @ref: 30559
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30559 | yes | |
69481 | yes | 100 |
69480 | yes | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30559 | NaCl | positive | growth | 1 % |
69410 | NaCl | positive | growth | 0 % |
observation
- @ref: 67770
- observation: quinones: MK-10(H4), MK-9(H4), MK-9(H6), MK-10(H6)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30559 | 22599 | arabinose | + | carbon source |
30559 | 29016 | arginine | + | carbon source |
30559 | 28757 | fructose | + | carbon source |
30559 | 17234 | glucose | + | carbon source |
30559 | 17306 | maltose | + | carbon source |
30559 | 37684 | mannose | + | carbon source |
30559 | 16634 | raffinose | + | carbon source |
30559 | 17814 | salicin | + | carbon source |
30559 | 17822 | serine | + | carbon source |
30559 | 17992 | sucrose | + | carbon source |
30559 | 17632 | nitrate | + | reduction |
69410 | 22599 | arabinose | + | growth |
69410 | 62968 | cellulose | - | growth |
69410 | 28757 | fructose | - | growth |
69410 | 17234 | glucose | + | growth |
69410 | 17268 | inositol | + | growth |
69410 | 37684 | mannose | - | growth |
69410 | 16634 | raffinose | - | growth |
69410 | 26546 | rhamnose | + | growth |
69410 | 17992 | sucrose | - | growth |
69410 | 18222 | xylose | - | growth |
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 |
---|---|---|---|
30559 | acid phosphatase | + | 3.1.3.2 |
30559 | alkaline phosphatase | + | 3.1.3.1 |
30559 | catalase | + | 1.11.1.6 |
30559 | gelatinase | + | |
30559 | cytochrome oxidase | + | 1.9.3.1 |
30559 | pyrazinamidase | + | 3.5.1.B15 |
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-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 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69410 | - | - | - | + | - | +/- | + | + | - | - | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69410 | + | + | + | - | + | + | + | - | +/- | + | + | - | +/- | - | + | +/- | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|---|
17740 | rhizosphere of Pisum sativum | Pisum sativum | Zamora province, Canizal (41° 49' 00'' N 6° 13' 00'' W) | Spain | ESP | Europe | 41.8167 | -6.2167 |
67770 | Rhizosphere of a Pisum sativum plant | Pisum sativum | Zamora | Spain | ESP | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Rhizosphere |
Safety information
risk assessment
- @ref: 17740
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17740
- description: Micromonospora cremea partial 16S rRNA gene, type strain CR30T
- accession: FN658654
- length: 1452
- database: ena
- NCBI tax ID: 709881
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Micromonospora cremea strain DSM 45599 | 709881.3 | wgs | patric | 709881 |
66792 | Micromonospora cremea DSM 45599 | 2630968262 | draft | img | 709881 |
67770 | Micromonospora cremea DSM 45599 | GCA_900143515 | contig | ncbi | 709881 |
GC content
@ref | GC-content | method |
---|---|---|
17740 | 72.4 | thermal denaturation, midpoint method (Tm) |
30559 | 72.4 | |
67770 | 71.47 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 92.786 | no |
anaerobic | no | 99.324 | yes |
halophile | no | 95.579 | yes |
spore-forming | yes | 90.967 | yes |
glucose-util | yes | 88.234 | yes |
thermophile | no | 99.01 | no |
flagellated | no | 98.27 | yes |
aerobic | yes | 95.495 | yes |
glucose-ferment | no | 92.92 | yes |
motile | no | 92.523 | yes |
External links
@ref: 17740
culture collection no.: DSM 45599, CECT 7891, JCM 31700
straininfo link
- @ref: 77451
- straininfo: 382400
literature
- topic: Phylogeny
- Pubmed-ID: 22286910
- title: Micromonospora cremea sp. nov. and Micromonospora zamorensis sp. nov., isolated from the rhizosphere of Pisum sativum.
- authors: Carro L, Pukall R, Sproer C, Kroppenstedt RM, Trujillo ME
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.038695-0
- year: 2012
- mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peas/*microbiology, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spain, Vitamin K 2/analysis
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
17740 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45599) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45599 | |||
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 | |||
30559 | 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 | 26890 | 28776041 | |
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 | |||||
69410 | Wink, J. | https://cdn.dsmz.de/wink/DSM%2045599.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
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 | |||
77451 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID382400.1 | StrainInfo: A central database for resolving microbial strain identifiers |