Strain identifier
BacDive ID: 5826
Type strain:
Species: Modestobacter roseus
Strain Designation: 5NBRC 108673
Strain history: <- S Qin, Xuzhou Normal Univ., China
NCBI tax ID(s): 1181884 (species)
General
@ref: 18182
BacDive-ID: 5826
DSM-Number: 45764
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped
description: Modestobacter roseus 5NBRC 108673 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from surface-sterilized roots of the coastal halophyte Salicornia europaea L., healthy plant tissue.
NCBI tax id
- NCBI tax id: 1181884
- Matching level: species
strain history
@ref | history |
---|---|
18182 | <- S. Qin, Jiangsu Normal University, China; KLBMP 1279 |
67771 | <- S Qin, Xuzhou Normal Univ., China |
doi: 10.13145/bacdive5826.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Geodermatophilales
- family: Geodermatophilaceae
- genus: Modestobacter
- species: Modestobacter roseus
- full scientific name: Modestobacter roseus Qin et al. 2013
@ref: 18182
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Geodermatophilaceae
genus: Modestobacter
species: Modestobacter roseus
full scientific name: Modestobacter roseus Qin et al. 2013
strain designation: 5NBRC 108673
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
30790 | positive | rod-shaped | yes | |
67771 | positive | |||
69480 | positive | 100 |
colony morphology
@ref | colony color | medium used |
---|---|---|
69428 | Colorless | ISP 4 |
69428 | Oyster white (1013) | ISP 7 |
69428 | Oyster white (1013) | suter with tyrosine |
69428 | Oyster white (1013) | suter without tyrosine |
69428 | Pastel yellow (1034) | ISP 2 |
69428 | Pastel yellow (1034) | ISP 3 |
69428 | Yellow orange (2000) | ISP 6 |
multicellular morphology
@ref | forms multicellular complex | complex name | medium name |
---|---|---|---|
69428 | no | Aerial mycelium | ISP 2 |
69428 | no | Aerial mycelium | ISP 3 |
69428 | no | Aerial mycelium | ISP 4 |
69428 | no | Aerial mycelium | ISP 6 |
69428 | no | Aerial mycelium | ISP 7 |
69428 | no | Aerial mycelium | suter with tyrosine |
69428 | no | Aerial mycelium | suter without tyrosine |
pigmentation
@ref | production | name |
---|---|---|
30790 | yes | |
69428 | no | Melanin |
69428 | no | soluble pigment |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
18182 | https://www.dsmz.de/microorganisms/photos/DSM_45764.jpg | Medium 830 28°C | © Leibniz-Institut DSMZ |
69428 | DSM_45764_image3.jpeg | Plates (830, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
69428 | DSM_45764_image4.jpeg | Plates (830, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
18182 | 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 |
18182 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
18182 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water |
18182 | 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 |
---|---|---|---|---|
18182 | positive | growth | 28 | mesophilic |
30790 | positive | growth | 10-37 | |
30790 | positive | optimum | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30790 | positive | growth | 06-11 | alkaliphile |
30790 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
30790 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
30790 | no | |
69481 | no | 95 |
69480 | no | 93.568 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30790 | NaCl | positive | growth | 0-10 % |
69428 | NaCl | positive | growth | 0-5 % |
observation
- @ref: 67771
- observation: quinones: MK-9(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
69428 | 22599 | arabinose | + | growth |
30790 | 22599 | arabinose | + | carbon source |
30790 | 24265 | gluconate | + | carbon source |
30790 | 17234 | glucose | + | carbon source |
30790 | 25115 | malate | + | carbon source |
30790 | 17306 | maltose | + | carbon source |
30790 | 29864 | mannitol | + | carbon source |
30790 | 37684 | mannose | + | carbon source |
30790 | 506227 | N-acetylglucosamine | + | carbon source |
30790 | 4853 | esculin | + | hydrolysis |
69428 | 62968 | cellulose | + | growth |
69428 | 28757 | fructose | + | growth |
69428 | 17234 | glucose | + | growth |
69428 | 17268 | inositol | +/- | growth |
69428 | 37684 | mannose | + | growth |
69428 | 16634 | raffinose | +/- | growth |
69428 | 26546 | rhamnose | + | growth |
69428 | 17992 | sucrose | + | growth |
69428 | 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 |
---|---|---|---|
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 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | leucine arylamidase | + | 3.4.11.1 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69428 | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69428 | - | + | + | +/- | + | +/- | +/- | - | + | +/- | +/- | - | - | - | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|---|
18182 | surface-sterilized roots of the coastal halophyte Salicornia europaea L., healthy plant tissue | Salicornia europaea | Jiangsu Province, Nantong coast (121° 0' 38.96'' E 32° 34' 24.91'' N) | China | CHN | Asia | 32.5736 | 121.011 |
67771 | Fromfrom surface-sterilized roots of a coastal halophyte | Salicornia europaea Linn., collected from Jiangsu | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root (Rhizome) |
#Host Body-Site | #Plant | #Sterilized plant part |
taxonmaps
- @ref: 69479
- File name: preview.99_1976.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_1096;97_1284;98_1546;99_1976&stattab=map
- Last taxonomy: Modestobacter
- 16S sequence: JQ819258
- Sequence Identity:
- Total samples: 31692
- soil counts: 18491
- aquatic counts: 2890
- animal counts: 5702
- plant counts: 4609
Safety information
risk assessment
- @ref: 18182
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18182
- description: Modestobacter roseus strain KLBMP 1279 16S ribosomal RNA gene, partial sequence
- accession: JQ819258
- length: 1451
- database: ena
- NCBI tax ID: 1181884
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Modestobacter roseus DSM 45764 | GCA_007994135 | contig | ncbi | 1181884 |
66792 | Modestobacter roseus strain DSM 45764 | 1181884.3 | wgs | patric | 1181884 |
66792 | Modestobacter roseus DSM 45764 | 2585427561 | draft | img | 1181884 |
GC content
@ref | GC-content | method |
---|---|---|
18182 | 71.7 | high performance liquid chromatography (HPLC) |
30790 | 71.7 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 95 | no |
motile | yes | 78.715 | yes |
gram-positive | yes | 91.381 | yes |
anaerobic | no | 98.768 | yes |
aerobic | yes | 87.738 | yes |
halophile | no | 89.028 | no |
spore-forming | no | 81.386 | yes |
flagellated | no | 93.572 | no |
thermophile | no | 99.123 | yes |
glucose-util | yes | 87.909 | yes |
glucose-ferment | no | 89.47 | yes |
External links
@ref: 18182
culture collection no.: DSM 45764, KCTC 19887, NBRC 108673, KLBMP 1279
straininfo link
- @ref: 75308
- straininfo: 405268
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23148095 | Modestobacter roseus sp. nov., an endophytic actinomycete isolated from the coastal halophyte Salicornia europaea Linn., and emended description of the genus Modestobacter. | Qin S, Bian GK, Zhang YJ, Xing K, Cao CL, Liu CH, Dai CC, Li WJ, Jiang JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.044412-0 | 2012 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Phylogeny | 27537546 | Modestobacter lacusdianchii sp. nov., a Phosphate-Solubilizing Actinobacterium with Ability to Promote Microcystis Growth. | Zhang BH, Salam N, Cheng J, Li HQ, Yang JY, Zha DM, Zhang YQ, Ai MJ, Hozzein WN, Li WJ | PLoS One | 10.1371/journal.pone.0161069 | 2016 | Actinobacteria/genetics/*metabolism, Culture Media, DNA, Bacterial/genetics, Microcystis/genetics/*growth & development, Phosphates/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 28809149 | Cumulibacter manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine. | Huang J, Li J, Cao M, Liao S, Wang G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002004 | 2017 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Manganese, *Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
18182 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45764) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45764 | ||||
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 | ||||
30790 | 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 | 27121 | 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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
68379 | Automatically annotated from API Coryne | ||||||
68382 | Automatically annotated from API zym | ||||||
69428 | Wink, J. | https://cdn.dsmz.de/wink/DSM%2045764.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | ||||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | ||||
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 | ||||
75308 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405268.1 | StrainInfo: A central database for resolving microbial strain identifiers |