Strain identifier
version 8.1 (current version)
General
@ref: 43123
BacDive-ID: 140491
keywords: 16S sequence, Bacteria, aerobe, thermophilic, Gram-positive
description: Nocardia shinanonensis TBRC 5149 is an aerobe, thermophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from aqueous humor of a patient with endophthalmitis.
NCBI tax id
- NCBI tax id: 1769161
- Matching level: species
doi: 10.13145/bacdive140491.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Nocardiaceae
- genus: Nocardia
- species: Nocardia shinanonensis
- full scientific name: Nocardia shinanonensis Matsumoto et al. 2016
@ref: 43123
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Mycobacteriales
family: Nocardiaceae
genus: Nocardia
species: Nocardia shinanonensis
type strain: yes
Morphology
cell morphology
- @ref: 43123
- gram stain: positive
- motility: no
multicellular morphology
- @ref: 43123
- forms multicellular complex: yes
- complex name: aerial mycelium
- complex color: white
- further description: mycelium fragments into irregular rod-shaped elements
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 43123 | positive | growth | 45 | thermophilic |
| 43123 | positive | growth | 35 | mesophilic |
| 43123 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 43123
- oxygen tolerance: aerobe
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43123 | 17234 | glucose | + | builds acid from |
| 43123 | 17268 | myo-inositol | + | builds acid from |
| 43123 | 15963 | ribitol | - | builds acid from |
| 43123 | 30849 | L-arabinose | - | builds acid from |
| 43123 | 17113 | erythritol | - | builds acid from |
| 43123 | 28260 | galactose | - | builds acid from |
| 43123 | 17306 | maltose | - | builds acid from |
| 43123 | 62345 | L-rhamnose | - | builds acid from |
| 43123 | 30911 | sorbitol | - | builds acid from |
| 43123 | 37684 | mannose | - | builds acid from |
| 43123 | 29864 | mannitol | - | builds acid from |
| 43123 | 16947 | citrate | + | carbon source |
| 43123 | 17128 | adipate | - | carbon source |
| 43123 | 24265 | gluconate | - | carbon source |
| 43123 | 16199 | urea | + | hydrolysis |
| 43123 | 16708 | adenine | - | hydrolysis |
| 43123 | casein | - | hydrolysis | |
| 43123 | 17368 | hypoxanthine | - | hydrolysis |
| 43123 | 18186 | tyrosine | - | hydrolysis |
| 43123 | 15318 | xanthine | - | hydrolysis |
Isolation, sampling and environmental information
isolation
- @ref: 43123
- sample type: aqueous humor of a patient with endophthalmitis
- geographic location: Matsumoto, Nagano
- country: Japan
- origin.country: JPN
- continent: Asia
- enrichment culture: 5 % sheep blood agar
- enrichment culture duration: 3 days
- enrichment culture temperature: 37
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body Product | #Fluids | |
| #Host Body-Site | #Organ | #Eye |
| #Infection | #Inflammation | |
| #Infection | #Patient |
taxonmaps
- @ref: 69479
- File name: preview.99_118135.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_1088;98_79721;99_118135&stattab=map
- Last taxonomy: Nocardia
- 16S sequence: LC103184
- Sequence Identity:
- Total samples: 208
- soil counts: 30
- aquatic counts: 66
- animal counts: 108
- plant counts: 4
Sequence information
16S sequences
- @ref: 43123
- description: Nocardia shinanonensis gene for 16S ribosomal RNA, partial sequence, strain: IFM 11456
- accession: LC103184
- length: 1474
- database: nuccore
- NCBI tax ID: 1769161
GC content
- @ref: 43123
- GC-content: 69.5
- method: high performance liquid chromatography (HPLC)
External links
@ref: 43123
culture collection no.: TBRC 5149, NBRC 109590, IFM 11456
literature
- topic: Phylogeny
- Pubmed-ID: 27255509
- title: Nocardia shinanonensis sp. nov., isolated from a patient with endophthalmitis.
- authors: Matsumoto T, Negishi T, Hamada M, Komaki H, Gonoi T, Yaguchi T
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001197
- year: 2016
- mesh: Aqueous Humor/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Endophthalmitis/*microbiology, Fatty Acids/chemistry, Humans, Mycolic Acids/chemistry, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Pathogenicity
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 | ||
| 43123 | Takehisa Matsumoto, Tatsuya Negishi, Moriyuki Hamada, Hisayuki Komaki, Tohru Gonoi, Takashi Yaguchi | Nocardia shinanonensis sp. nov., isolated from a patient with endophthalmitis | 10.1099/ijsem.0.001197 | IJSEM 66: 3324-3328 2016 | 27255509 |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |