Strain identifier
BacDive ID: 141143
Type strain:
Species: Nocardioides albidus
Strain Designation: THG-S11.7, THG-S11-7
Strain history: <- Tae-Hoo Yi, Kyung Hee univ.
NCBI tax ID(s): 1517589 (species)
General
@ref: 44062
BacDive-ID: 141143
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, coccus-shaped, colony-forming
description: Nocardioides albidus THG-S11.7 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from garden soil sample.
NCBI tax id
- NCBI tax id: 1517589
- Matching level: species
strain history
@ref | history |
---|---|
67770 | CCTCC AB 2015297 <-- T.-H. Yi; Kyung Hee Univ., South Korea; THG-S11.7. |
67771 | <- Tae-Hoo Yi, Kyung Hee univ. |
doi: 10.13145/bacdive141143.20230509.8.1
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 albidus
- full scientific name: Nocardioides albidus Singh et al. 2016
@ref: 44062
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Propionibacteriales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides albidus
strain designation: THG-S11.7, THG-S11-7
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
44062 | positive | 1.0-1.2 µm | 1.0-1.2 µm | coccus-shaped | no | |
69480 | positive | 99.999 |
colony morphology
- @ref: 44062
- colony size: 1.0-3.0 mm
- colony color: white
- colony shape: circular
- incubation period: 3 days
- medium used: Nutrient agar
pigmentation
- @ref: 44062
- production: no
- name: Flexirubin-type
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
44062 | LA | no |
44062 | Marine agar (MA) | yes |
44062 | MacConkey | no |
44062 | Nutrient agar (NA) | yes |
44062 | Reasoner's 2A agar (R2A) | yes |
44062 | Trypticase Soy Agar (TSA) | no |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
44062 | positive | growth | 20-35 | |
44062 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
44062 | positive | growth | 6.0-7.5 |
44062 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
44062 | aerobe |
67771 | aerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.917
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
44062 | NaCl | positive | growth | 0.5-3.0 %(w/v) |
44062 | NaCl | positive | optimum | 2 %(w/v) |
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
44062 | 17128 | adipate | - | assimilation |
44062 | 27689 | decanoate | - | assimilation |
44062 | 16947 | citrate | - | assimilation |
44062 | 16899 | D-mannitol | - | assimilation |
44062 | 16024 | D-mannose | - | assimilation |
44062 | 30849 | L-arabinose | - | assimilation |
44062 | 25115 | malate | - | assimilation |
44062 | 17306 | maltose | - | assimilation |
44062 | 18401 | phenylacetate | - | assimilation |
44062 | 17234 | glucose | - | builds acid from |
44062 | 85146 | carboxymethylcellulose | - | hydrolysis |
44062 | casein | - | hydrolysis | |
44062 | 17029 | chitin | - | hydrolysis |
44062 | 16991 | dna | - | hydrolysis |
44062 | 5291 | gelatin | - | hydrolysis |
44062 | 17895 | L-tyrosine | - | hydrolysis |
44062 | 28017 | starch | - | hydrolysis |
44062 | 16199 | urea | - | hydrolysis |
44062 | 17632 | nitrate | - | reduction |
44062 | 17634 | D-glucose | + | assimilation |
44062 | 24265 | gluconate | + | assimilation |
44062 | 506227 | N-acetylglucosamine | + | assimilation |
44062 | 4853 | esculin | + | fermentation |
44062 | 4853 | esculin | + | hydrolysis |
44062 | 53426 | tween 80 | + | hydrolysis |
metabolite production
- @ref: 44062
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
44062 | catalase | + | 1.11.1.6 |
44062 | cytochrome oxidase | + | 1.9.3.1 |
44062 | arginine dihydrolase | - | 3.5.3.6 |
44062 | urease | - | 3.5.1.5 |
44062 | gelatinase | - | |
44062 | alkaline phosphatase | + | 3.1.3.1 |
44062 | esterase (C 4) | + | |
44062 | esterase Lipase (C 8) | + | |
44062 | leucine arylamidase | + | 3.4.11.1 |
44062 | valine arylamidase | + | |
44062 | cystine arylamidase | + | 3.4.11.3 |
44062 | acid phosphatase | + | 3.1.3.2 |
44062 | trypsin | + | 3.4.21.4 |
44062 | alpha-glucosidase | + | 3.2.1.20 |
44062 | beta-galactosidase | + | 3.2.1.23 |
44062 | beta-glucosidase | + | 3.2.1.21 |
44062 | lipase (C 14) | - | |
44062 | alpha-chymotrypsin | - | 3.4.21.1 |
44062 | alpha-galactosidase | - | 3.2.1.22 |
44062 | beta-glucuronidase | - | 3.2.1.31 |
44062 | naphthol-AS-BI-phosphohydrolase | - | |
44062 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
44062 | alpha-mannosidase | - | 3.2.1.24 |
44062 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage 44062 C17:0 anteiso 6.7 44062 C10:0 1 44062 C16:0 10 44062 10-methyl C17:0 1.2 44062 C17:1ω6c 4.1 44062 C17:1ω8c 1.1 44062 C18:1ω9c 3 44062 C14:0 iso 4.8 44062 C15:0 iso 16.6 44062 C16:0 iso 44.4 44062 C17:0 iso 2.4 44062 C18:0 iso 2.9 - type of FA analysis: whole cell analysis
- incubation medium: NA
- incubation temperature: 28
- incubation time: 2
- library/peak naming table: TSBA6.1
- system: MIS MIDI
- method/protocol: Sasser, 1990
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|
44062 | garden soil sample | Michuhol library garden, Incheon | Republic of Korea | KOR | Asia | NA agar | 7 days | 28 |
67770 | Garden soil | Incheon | Republic of Korea | KOR | Asia | |||
67771 | From garden soil in Incheon | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Garden |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_15441.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_452;97_518;98_2479;99_15441&stattab=map
- Last taxonomy: Nocardioides albidus
- 16S sequence: KM073954
- Sequence Identity:
- Total samples: 36
- soil counts: 17
- aquatic counts: 5
- animal counts: 4
- plant counts: 10
Sequence information
16S sequences
- @ref: 44062
- description: 16S rRNA gene sequence
- accession: KM073954
- database: nuccore
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardioides albidus strain CCTCC AB 2015297 | 1517589.3 | wgs | patric | 1517589 |
66792 | Nocardioides albidus CCTCC AB 2015297 | 2902201542 | draft | img | 1517589 |
67770 | Nocardioides albidus CCTCC AB 2015297 | GCA_006335005 | scaffold | ncbi | 1517589 |
GC content
- @ref: 44062
- GC-content: 72.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 74 | no |
motile | no | 75.913 | yes |
gram-positive | yes | 90.125 | yes |
anaerobic | no | 97.716 | no |
aerobic | yes | 91.923 | yes |
halophile | no | 95.91 | no |
spore-forming | no | 77.994 | no |
glucose-util | yes | 88.32 | no |
flagellated | no | 92.958 | no |
thermophile | no | 95.617 | yes |
glucose-ferment | no | 89.846 | no |
External links
@ref: 44062
culture collection no.: KCTC 39607, CCTCC AB 2015297, JCM 31749
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26530636 | Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil. | Singh H, Du J, Trinh H, Won K, Yang JE, Yin C, Kook M, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000730 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Agriculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 31535960 | Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil. | Liu SW, Xue CM, Li FN, Sun CH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003718 | 2020 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | 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 | ||
44062 | Hina Singh, Juan Du, Huan Trinh, KyungHwa Won, Jung-Eun Yang, ChangShik Yin, MooChang Kook and Tae-Hoo Yi | Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil | 10.1099/ijsem.0.000730 | IJSEM 66: 371-378 2016 | 26530636 |
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 | ||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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/ | ||
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 |