Strain identifier
BacDive ID: 133130
Type strain:
Species: Nocardioides intraradicalis
Strain history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM DR1091.
NCBI tax ID(s): 1817596 (species)
General
@ref: 24891
BacDive-ID: 133130
keywords: 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped, colony-forming
description: Nocardioides intraradicalis YIM DR1091 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu.
NCBI tax id
- NCBI tax id: 1817596
- Matching level: species
strain history
- @ref: 67770
- history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM DR1091.
doi: 10.13145/bacdive133130.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Nocardioidaceae
- genus: Nocardioides
- species: Nocardioides intraradicalis
- full scientific name: Nocardioides intraradicalis Huang et al. 2016
@ref: 24891
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Propionibacteriales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides intraradicalis
type strain: yes
Morphology
cell morphology
- @ref: 24891
- gram stain: positive
- cell length: 0.5-2.0 µm
- cell width: 0.4-0.6 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 24891
- colony color: white
- colony shape: circular
- incubation period: 6 days
- medium used: R2A agar (Reasoner's 2A agar)
Culture and growth conditions
culture medium
- @ref: 24891
- name: Reasoner's 2A agar (R2A)
- growth: yes
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
24891 | positive | growth | 15.0-30.0 | |
24891 | positive | optimum | 28.0-30.0 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
24891 | positive | growth | 4.0-11.0 | alkaliphile |
24891 | positive | optimum | 6.0-7.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 24891
- oxygen tolerance: aerobe
spore formation
- @ref: 24891
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
24891 | NaCl | positive | growth | <1.0 %(w/v) |
24891 | NaCl | positive | growth | 0.0-1.0 %(w/v) |
murein
- @ref: 24891
- murein short key: A41.01
- type: A3gamma LL-Dpm-Gly
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
24891 | 62968 | cellulose | - | hydrolysis |
24891 | 5291 | gelatin | - | hydrolysis |
24891 | 28017 | starch | - | hydrolysis |
24891 | 53424 | tween 20 | - | hydrolysis |
24891 | 53423 | tween 40 | - | hydrolysis |
24891 | 53425 | tween 60 | - | hydrolysis |
24891 | 53426 | tween 80 | - | hydrolysis |
24891 | 73918 | 3-O-methyl-D-glucose | + | carbon source |
24891 | 17836 | 4-aminobenzoate | + | nitrogen source |
24891 | 16449 | alanine | + | nitrogen source |
24891 | 17968 | butyrate | + | carbon source |
24891 | 78697 | D-fructose 6-phosphate | + | carbon source |
24891 | 28847 | D-fucose | + | carbon source |
24891 | 12936 | D-galactose | + | carbon source |
24891 | 14314 | D-glucose 6-phosphate | + | carbon source |
24891 | 16899 | D-mannitol | + | carbon source |
24891 | 17924 | D-sorbitol | + | carbon source |
24891 | 28066 | gentiobiose | + | carbon source |
24891 | 73804 | glycyl L-aspartic acid | + | nitrogen source |
24891 | 16828 | L-tryptophan | + | nitrogen source |
24891 | 17632 | nitrate | + | reduction |
24891 | 17814 | salicin | + | carbon source |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | is resistant |
---|---|---|---|---|---|
24891 | 2637 | amikacin | yes | yes | |
24891 | 3515 | cefuroxime | yes | yes | |
24891 | 17698 | chloramphenicol | yes | yes | |
24891 | 48923 | erythromycin | yes | yes | |
24891 | 17833 | gentamicin | yes | yes | |
24891 | 7809 | oxacillin | yes | yes | |
24891 | 17334 | penicillin | yes | yes | |
24891 | 8309 | polymyxin b | yes | yes | |
24891 | 27902 | tetracycline | yes | yes | |
24891 | 28001 | vancomycin | yes | yes | |
24891 | 100241 | ciprofloxacin | yes | yes | |
24891 | 100246 | norfloxacin | yes | yes | |
24891 | 28368 | novobiocin | yes | yes | |
24891 | 9332 | sulfamethoxazole | yes | yes | |
24891 | 8232 | piperacillin | yes | yes | |
24891 | 86455 | optochin | yes | yes |
metabolite production
- @ref: 24891
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
24891 | acid phosphatase | + | 3.1.3.2 |
24891 | alkaline phosphatase | + | 3.1.3.1 |
24891 | alpha-chymotrypsin | - | 3.4.21.1 |
24891 | alpha-fucosidase | - | 3.2.1.51 |
24891 | alpha-galactosidase | - | 3.2.1.22 |
24891 | alpha-glucosidase | + | 3.2.1.20 |
24891 | alpha-mannosidase | - | 3.2.1.24 |
24891 | beta-galactosidase | + | 3.2.1.23 |
24891 | beta-glucosidase | + | 3.2.1.21 |
24891 | beta-glucuronidase | - | 3.2.1.31 |
24891 | catalase | + | 1.11.1.6 |
24891 | cystine arylamidase | - | 3.4.11.3 |
24891 | cytochrome oxidase | + | 1.9.3.1 |
24891 | esterase (C 4) | + | |
24891 | esterase lipase (C 8) | + | |
24891 | leucine arylamidase | + | 3.4.11.1 |
24891 | lipase (C 14) | - | |
24891 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
24891 | naphthol-AS-BI-phosphohydrolase | + | |
24891 | trypsin | + | 3.4.21.4 |
24891 | urease | - | 3.5.1.5 |
24891 | valine arylamidase | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature | host species |
---|---|---|---|---|---|---|---|---|---|---|
24891 | roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu | Gejiu, Yunnan | Republic of China | CHN | Asia | YECD (yeast extract-casein hydrolysate) | containing (g l-1): yeast, 0.3; casein, 0.3; glucose, 0.3; bone meal, 0.3; agar 1.3; pH 6.5;supplemented with nalidixic acid (25 mg l-1) and nystatin (50 mg l-1) | 30 days | 28 | |
67770 | Roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu from Gejiu | Yunnan | China | CHN | Asia | Psammosilene tunicoides |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Shrub (Scrub) |
#Host Body-Site | #Plant | #Root (Rhizome) |
Sequence information
16S sequences
- @ref: 24891
- description: Nocardioides intraradicalis strain YIM DR1091 16S ribosomal RNA gene, partial sequence
- accession: KU940252
- length: 1520
- database: nuccore
- NCBI tax ID: 1817596
GC content
- @ref: 24891
- GC-content: 74.6
- method: high performance liquid chromatography (HPLC)
External links
@ref: 24891
culture collection no.: YIM DR1091, JCM 30632, CGMCC 4.7251
literature
- topic: Phylogeny
- Pubmed-ID: 27381405
- title: Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu.
- authors: Huang MJ, Huang HQ, Salam N, Xiao M, Duan YQ, Kim CJ, Li QQ, Chen W, Li WJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001274
- year: 2016
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Caryophyllaceae/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | 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 | ||
24891 | M.-J. H. Huang, Hai-Quan,Salam, Nimaichand,Xiao, Min,Duan, Yan-Qing,Kim, Chang-Jin,Li, Qing-Qing,Chen, Wei,Li, Wen-Jun | Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu | 10.1099/ijsem.0.001274 | IJSEM 66: 3841-3847 2016 | 27381405 |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ |