Strain identifier
BacDive ID: 132433
Type strain:
Species: Pseudoclavibacter endophyticus
Strain history: <- Wenjun Li
NCBI tax ID(s): 1778590 (species)
General
@ref: 24222
BacDive-ID: 132433
DSM-Number: 29943
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped, colony-forming
description: Pseudoclavibacter endophyticus DSM 29943 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized healthy roots of Glycyrrhiza uralensis F..
NCBI tax id
- NCBI tax id: 1778590
- Matching level: species
strain history
@ref | history |
---|---|
24222 | <- W.-J. Li, YIM; EGI60007 <- L. Li |
67770 | W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; EGI 60007. |
67771 | <- Wenjun Li |
doi: 10.13145/bacdive132433.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Pseudoclavibacter
- species: Pseudoclavibacter endophyticus
- full scientific name: Pseudoclavibacter endophyticus Li et al. 2016
@ref: 24222
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Pseudoclavibacter
species: Pseudoclavibacter endophyticus
full scientific name: Pseudoclavibacter endophyticus Li et al. 2016
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43744 | positive | 1.1-2.3 µm | 0.4-0.6 µm | rod-shaped | no | |
69480 | positive | 100 | ||||
69480 | no | 96.031 |
colony morphology
- @ref: 43744
- colony color: White, opaque
- colony shape: circular
- incubation period: 7 days
- medium used: R2A agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43744 | GYEA | yes | ||
43744 | LB (Luria-Bertani) MEDIUM | yes | ||
43744 | Reasoner's 2A agar (R2A) | yes | ||
43744 | Trypticase Soy Agar (TSA) | yes | ||
24222 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43744 | positive | growth | 10-60 | |
43744 | positive | optimum | 25-35 | mesophilic |
24222 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43744 | positive | growth | 7-9 | alkaliphile |
43744 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43744 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43744 | NaCl | positive | growth | 0-11 %(w/v) |
43744 | NaCl | positive | optimum | 4 %(w/v) |
observation
- @ref: 67770
- observation: quinones: MK-9
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43744 | 22599 | arabinose | - | builds acid from |
43744 | 15824 | D-fructose | - | builds acid from |
43744 | 16024 | D-mannose | - | builds acid from |
43744 | 65327 | D-xylose | - | builds acid from |
43744 | 17234 | glucose | - | builds acid from |
43744 | 17754 | glycerol | - | builds acid from |
43744 | 17268 | myo-inositol | - | builds acid from |
43744 | 29864 | mannitol | - | builds acid from |
43744 | 28053 | melibiose | - | builds acid from |
43744 | 506227 | N-acetylglucosamine | - | builds acid from |
43744 | 26546 | rhamnose | - | builds acid from |
43744 | 30911 | sorbitol | - | builds acid from |
43744 | 17992 | sucrose | - | builds acid from |
43744 | 5291 | gelatin | - | hydrolysis |
43744 | 15588 | D-malate | - | respiration |
43744 | 16651 | (S)-lactate | - | respiration |
43744 | 15589 | L-malate | - | respiration |
43744 | 16763 | 2-oxobutanoate | - | respiration |
43744 | 30916 | 2-oxoglutarate | - | respiration |
43744 | 64552 | 2-hydroxybutyrate | - | respiration |
43744 | 16947 | citrate | - | respiration |
43744 | 78697 | D-fructose 6-phosphate | - | respiration |
43744 | 8391 | D-gluconate | - | respiration |
43744 | 14314 | D-glucose 6-phosphate | - | respiration |
43744 | 17754 | glycerol | - | respiration |
43744 | 51850 | methyl pyruvate | - | respiration |
43744 | 17268 | myo-inositol | - | respiration |
43744 | 506227 | N-acetylglucosamine | - | respiration |
43744 | 17309 | pectin | - | respiration |
43744 | 17272 | propionate | - | respiration |
43744 | 4853 | esculin | + | fermentation |
43744 | 18101 | 4-hydroxyphenylacetic acid | + | respiration |
43744 | 30089 | acetate | + | respiration |
43744 | 13705 | acetoacetate | + | respiration |
43744 | 8295 | beta-hydroxybutyrate | + | respiration |
43744 | 15824 | D-fructose | + | respiration |
43744 | 16899 | D-mannitol | + | respiration |
43744 | 15740 | formate | + | respiration |
43744 | 29991 | L-aspartate | + | respiration |
43744 | 29985 | L-glutamate | + | respiration |
antibiotic resistance
@ref | metabolite | is antibiotic | is sensitive | ChEBI |
---|---|---|---|---|
43744 | 1 % sodium lactate | yes | yes | |
43744 | troleandomycin | yes | yes | 45735 |
43744 | lincomycin | yes | yes | 6472 |
43744 | tetrazolium violet | yes | yes | 75193 |
43744 | nalidixic acid | yes | yes | 100147 |
43744 | potassium tellurite | yes | yes | 75248 |
43744 | aztreonam | yes | yes | 161680 |
43744 | sodium butyrate | yes | yes | 64103 |
43744 | sodium bromate | yes | yes | 75229 |
metabolite production
- @ref: 43744
- Chebi-ID: 35581
- metabolite: indole
- production: yes
enzymes
@ref | value | activity | ec |
---|---|---|---|
43744 | catalase | + | 1.11.1.6 |
43744 | esterase (C 4) | + | |
43744 | esterase Lipase (C 8) | + | |
43744 | leucine arylamidase | + | 3.4.11.1 |
43744 | valine arylamidase | + | |
43744 | cystine arylamidase | + | 3.4.11.3 |
43744 | naphthol-AS-BI-phosphohydrolase | + | |
43744 | chymotrypsin | + | 3.4.4.5 |
43744 | beta-glucosidase | + | 3.2.1.21 |
43744 | cytochrome oxidase | - | 1.9.3.1 |
43744 | lipase (C 14) | - | |
43744 | alkaline phosphatase | - | 3.1.3.1 |
43744 | acid phosphatase | - | 3.1.3.2 |
43744 | trypsin | - | 3.4.21.4 |
43744 | alpha-galactosidase | - | 3.2.1.22 |
43744 | beta-galactosidase | - | 3.2.1.23 |
43744 | beta-glucuronidase | - | 3.2.1.31 |
43744 | alpha-glucosidase | - | 3.2.1.20 |
43744 | beta-D-fucosidase | - | 3.2.1.38 |
43744 | alpha-mannosidase | - | 3.2.1.24 |
43744 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43744 | urease | - | 3.5.1.5 |
43744 | gelatinase | - |
fatty acid profile
fatty acids
@ref fatty acid percentage 43744 C10:0 3OH 1.1 43744 C12:0 10.9 43744 C12:0 3OH 2.8 43744 C14:0 0.8 43744 C16:0 11.6 43744 C16:1ω5c 0.5 43744 C16:1ω7c / C16:1ω6c 8.2 43744 C17:0 0.8 43744 C17:0cyclo 13 43744 C17:1ω8c 0.9 43744 C18:0 0.6 43744 C18:1ω7c / C18:1ω6c 18.3 43744 C18:1ω9c 0.4 43744 C19:0ω8c-cyclo 9.3 43744 C11:0 iso 3OH 0.3 - type of FA analysis: whole cell analysis
- incubation medium: TSA
- agar/liquid: agar
- incubation temperature: 30
- incubation_oxygen: aerobic
- software version: Sherlock 6.1
- library/peak naming table: TSBA6
- system: MIS MIDI
- instrument: Agilent 7890A
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|---|
24222 | surface-sterilized healthy roots of Glycyrrhiza uralensis F. | Glycyrrhiza uralensis | Xinjiang Province, Yili County (43.39° N 83.84° E) | China | CHN | Asia | 43.39 | 83.84 |
43744 | Healthy root of Glycyrrhiza uralensis F. collected from Yili County | Yili County, Xinjiang Province | China | CHN | Asia | |||
67770 | Healthy roots of Glycyrrhiza uralensis F. from Yili County | Glycyrrhiza uralensis | Xinjiang Province, north-west China | China | CHN | Asia | ||
67771 | From Liquorice | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host Body-Site | #Plant | #Sterilized plant part |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root (Rhizome) |
Safety information
risk assessment
- @ref: 24222
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24222
- description: Pseudoclavibacter endophyticus strain EGI 60007 16S ribosomal RNA gene, partial sequence
- accession: KP721484
- length: 1490
- database: ena
- NCBI tax ID: 1778590
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudoclavibacter endophyticus CGMCC 1.15081 | GCA_014640595 | contig | ncbi | 1778590 |
66792 | Pseudoclavibacter endophyticus strain CGMCC 1.15081 | 1778590.4 | wgs | patric | 1778590 |
67770 | Pseudoclavibacter endophyticus EGI 60007 | GCA_008831085 | contig | ncbi | 1778590 |
GC content
- @ref: 24222
- GC-content: 63.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.006 | yes |
gram-positive | yes | 92.107 | no |
anaerobic | no | 99.521 | yes |
aerobic | yes | 95.146 | no |
halophile | no | 70.546 | no |
spore-forming | no | 92.695 | no |
thermophile | no | 99.392 | yes |
glucose-util | yes | 83.863 | no |
flagellated | no | 97.657 | yes |
glucose-ferment | no | 92.195 | no |
External links
@ref: 24222
culture collection no.: DSM 29943, CGMCC 1.15081, KCTC 39112, EGI 60007, JCM 30633
straininfo link
- @ref: 90772
- straininfo: 407283
literature
- topic: Phylogeny
- Pubmed-ID: 26739161
- title: Pseudoclavibacter endophyticus sp. nov., isolated from roots of Glycyrrhiza uralensis.
- authors: Li YQ, Li L, Fu YS, Cui ZQ, Duan YQ, Salam N, Guo JW, Chen W, Li WJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000876
- year: 2016
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 | |||
24222 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29943 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29943) | |||
43744 | Yan-Qiong Li, Li Li, Yu-Song Fu, Zhao-Qiong Cui, Yan-Qing Duan, Nimaichand Salam, Jian-Wei Guo, Wei Chen, Wen-Jun Li | Pseudoclavibacter endophyticus sp. nov., isolated from roots of Glycyrrhiza uralensis | 10.1099/ijsem.0.000876 | IJSEM 66: 1287-1292 2016 | 26739161 | |
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 | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
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 | |||
90772 | 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-ID407283.1 |