Strain identifier
BacDive ID: 132636
Type strain:
Species: Dyadobacter endophyticus
Strain Designation: 65
Strain history: <- J.-l. Gao, Beijing Academy of Agriculture and Forestry Science; 65 <-
NCBI tax ID(s): 1749036 (species)
General
@ref: 24425
BacDive-ID: 132636
DSM-Number: 100786
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Dyadobacter endophyticus 65 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root tissue of maize.
NCBI tax id
- NCBI tax id: 1749036
- Matching level: species
strain history
- @ref: 24425
- history: <- J.-l. Gao, Beijing Academy of Agriculture and Forestry Science; 65 <-
doi: 10.13145/bacdive132636.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Spirosomataceae
- genus: Dyadobacter
- species: Dyadobacter endophyticus
- full scientific name: Dyadobacter endophyticus Gao et al. 2016
@ref: 24425
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Spirosomaceae
genus: Dyadobacter
species: Dyadobacter endophyticus
full scientific name: Dyadobacter endophyticus Gao et al. 2016
strain designation: 65
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
24908 | negative | 0.6-1.5 µm | 0.4-0.6 µm | rod-shaped | ||
69480 | no | 93.253 | ||||
69480 | negative | 99.997 |
colony morphology
- @ref: 24908
- colony size: 1.0-1.5 mm
- colony color: yellowish
- colony shape: circular
- incubation period: 4 days
- medium used: LB agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
24908 | LB (Luria-Bertani) MEDIUM | yes | ||
24425 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
24908 | positive | growth | 20-45 | |
24908 | positive | optimum | 30 | mesophilic |
24425 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
24908 | positive | growth | 6.0-8.0 |
24908 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 24908
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.994 |
halophily
- @ref: 24908
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
24908 | 27613 | amygdalin | + | builds acid from |
24908 | 18305 | arbutin | + | builds acid from |
24908 | 17057 | cellobiose | + | builds acid from |
24908 | 15824 | D-fructose | + | builds acid from |
24908 | 17634 | D-glucose | + | builds acid from |
24908 | 17716 | lactose | + | builds acid from |
24908 | 16024 | D-mannose | + | builds acid from |
24908 | 65327 | D-xylose | + | builds acid from |
24908 | 4853 | esculin | + | builds acid from |
24908 | 28066 | gentiobiose | + | builds acid from |
24908 | 15443 | inulin | + | builds acid from |
24908 | 17306 | maltose | + | builds acid from |
24908 | 6731 | melezitose | + | builds acid from |
24908 | 28053 | melibiose | + | builds acid from |
24908 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
24908 | 506227 | N-acetylglucosamine | + | builds acid from |
24908 | 16634 | raffinose | + | builds acid from |
24908 | 17814 | salicin | + | builds acid from |
24908 | 17992 | sucrose | + | builds acid from |
24908 | 27082 | trehalose | + | builds acid from |
24908 | 32528 | turanose | + | builds acid from |
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
24908 | acid phosphatase | + | 3.1.3.2 |
24908 | alkaline phosphatase | + | 3.1.3.1 |
24908 | alpha-chymotrypsin | - | 3.4.21.1 |
24908 | alpha-fucosidase | - | 3.2.1.51 |
24908 | alpha-galactosidase | + | 3.2.1.22 |
24908 | alpha-glucosidase | + | 3.2.1.20 |
24908 | alpha-mannosidase | + | 3.2.1.24 |
24908 | beta-galactosidase | + | 3.2.1.23 |
24908 | beta-glucosidase | + | 3.2.1.21 |
24908 | beta-glucuronidase | - | 3.2.1.31 |
24908 | catalase | + | 1.11.1.6 |
24908 | cystine arylamidase | + | 3.4.11.3 |
24908 | cytochrome oxidase | + | 1.9.3.1 |
24908 | esterase (C 4) | + | |
24908 | esterase lipase (C 8) | + | |
24908 | leucine arylamidase | + | 3.4.11.1 |
24908 | lipase (C 14) | - | |
24908 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
24908 | naphthol-AS-BI-phosphohydrolase | + | |
24908 | trypsin | + | 3.4.21.4 |
24908 | valine arylamidase | + | |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
24425 | - | - | - | - | - | + | - | + | + | + | + | - | + | + | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 24425
- sample type: surface-sterilized root tissue of maize
- geographic location: Beijing, Fangshan District
- country: China
- origin.country: CHN
- continent: 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 |
Safety information
risk assessment
- @ref: 24425
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24425
- description: Dyadobacter endophyticus strain 65 16S ribosomal RNA gene, partial sequence
- accession: KT003984
- length: 1374
- database: ena
- NCBI tax ID: 1749036
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Dyadobacter endophyticus CGMCC 1.15288 | GCA_014641595 | scaffold | ncbi | 1749036 |
66792 | Dyadobacter endophyticus strain CGMCC 1.15288 | 1749036.3 | wgs | patric | 1749036 |
GC content
@ref | GC-content | method |
---|---|---|
24908 | 46.6 | Thermal denaturation, fluorometry |
24425 | 46.6 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 96.964 | no |
gram-positive | no | 98.017 | yes |
anaerobic | no | 99.485 | yes |
aerobic | yes | 88.709 | yes |
halophile | no | 95.808 | yes |
spore-forming | no | 91.942 | no |
thermophile | no | 99.575 | yes |
glucose-util | yes | 87.394 | no |
motile | no | 92.31 | no |
glucose-ferment | no | 87.937 | yes |
External links
@ref: 24425
culture collection no.: DSM 100786, CGMCC 1.15288
straininfo link
- @ref: 90950
- straininfo: 402180
literature
- topic: Phylogeny
- Pubmed-ID: 27412002
- title: Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root.
- authors: Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yuan M, Yang MM, Sun JG
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001304
- year: 2016
- mesh: Bacterial Typing Techniques, Base Composition, Beijing, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
24425 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100786 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100786) | |||
24908 | J.-l. S. Gao, Pengbo,Wang, Xu-ming,Qiu, Tian-lei,Lv, Fan-yang,Yuan, Mei,Yang, Ming-ming,Sun, Jian-guang | Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root | 10.1099/ijsem.0.001304 | IJSEM 66: 4022-4026 2016 | 27412002 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
68369 | Automatically annotated from API 20NE | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
90950 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID402180.1 |