Strain identifier
BacDive ID: 8576
Type strain:
Species: Mycobacterium rufum
Strain Designation: JS14
Strain history: CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain JS14, "Mycobacterium fluranthenivorans"
NCBI tax ID(s): 1305629 (strain), 318424 (species)
General
@ref: 16675
BacDive-ID: 8576
DSM-Number: 45406
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Mycobacterium rufum JS14 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
318424 | species |
1305629 | strain |
strain history
@ref | history |
---|---|
37496 | 2006, Q. X. Li, Honolulu, Hawaii, USA: strain JS14, "Mycobacterium fluranthenivorans" |
16675 | <- CIP <- Q. X. Li,Honolulu,Hawai,USA ; JS14 |
67770 | CIP 109273 <-- Q. X. Li JS14. |
122303 | CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain JS14, "Mycobacterium fluranthenivorans" |
doi: 10.13145/bacdive8576.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Mycobacteriaceae
- genus: Mycobacterium
- species: Mycobacterium rufum
- full scientific name: Mycobacterium rufum Hennessee et al. 2009
synonyms
- @ref: 20215
- synonym: Mycolicibacterium rufum
@ref: 16675
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium rufum
full scientific name: Mycobacterium rufum Hennessee et al. 2009 emend. Nouioui et al. 2018
strain designation: JS14
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
32638 | positive | rod-shaped | no | |
69480 | positive | 99.999 | ||
122303 | no |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16675 | MIDDLEBROOK MEDIUM (DSMZ Medium 645) | yes | https://mediadive.dsmz.de/medium/645 | Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water |
37496 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122303 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16675 | positive | growth | 28 | mesophilic |
32638 | positive | growth | 28 | mesophilic |
32638 | positive | optimum | 28 | mesophilic |
37496 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32638 | aerobe |
122303 | obligate aerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.997
observation
- @ref: 32638
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32638 | 28757 | fructose | + | carbon source |
32638 | 17234 | glucose | + | carbon source |
32638 | 29864 | mannitol | + | carbon source |
32638 | 30911 | sorbitol | + | carbon source |
32638 | 27082 | trehalose | + | carbon source |
32638 | 17151 | xylitol | + | carbon source |
32638 | 18222 | xylose | + | carbon source |
32638 | 4853 | esculin | + | hydrolysis |
32638 | 17632 | nitrate | + | reduction |
122303 | 17632 | nitrate | + | reduction |
122303 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 122303
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
32638 | catalase | + | 1.11.1.6 |
32638 | urease | + | 3.5.1.5 |
122303 | oxidase | - | |
122303 | catalase | + | 1.11.1.6 |
122303 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122303 | - | + | + | + | + | + | + | + | + | - | + | + | - | - | - | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
16675 | soil | Hawai, Hilo | USA | USA | North America | |
67770 | Polycyclic aromatic hydrocarbon-contaminated soil of a former oil-gasification company site in Hilo | HI | USA | USA | North America | |
122303 | Environment, Soil | Hilo, Hawaii | United States of America | USA | North America | 2003 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_6383.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_219;98_419;99_6383&stattab=map
- Last taxonomy: Mycolicibacterium
- 16S sequence: AY943385
- Sequence Identity:
- Total samples: 4905
- soil counts: 1619
- aquatic counts: 1667
- animal counts: 1470
- plant counts: 149
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
16675 | 1 | Risk group (German classification) |
122303 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 16675
- description: Mycobacterium rufum strain JS14 16S ribosomal RNA gene, partial sequence
- accession: AY943385
- length: 1329
- database: ena
- NCBI tax ID: 318424
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycolicibacterium rufum JCM 16372 | GCA_001313925 | contig | ncbi | 1305629 |
66792 | Mycobacterium rufum JS14 | 318424.3 | wgs | patric | 318424 |
66792 | Mycolicibacterium rufum JCM 16372 | 1305629.4 | wgs | patric | 1305629 |
66792 | Mycolicibacterium rufum JCM 16372 | 2734481965 | draft | img | 1305629 |
67770 | Mycolicibacterium rufum JS14 | GCA_000762985 | contig | ncbi | 318424 |
66792 | Mycolicibacterium rufum JCM 16372 | GCA_022374875 | complete | ncbi | 318424 |
66792 | Mycolicibacterium rufum DSM 45406 | GCA_025821255 | scaffold | ncbi | 318424 |
GC content
- @ref: 67770
- GC-content: 69.2
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 80 | no |
flagellated | no | 98.378 | yes |
flagellated | no | 98.378 | yes |
flagellated | no | 98.378 | yes |
gram-positive | yes | 90.96 | yes |
gram-positive | yes | 90.96 | yes |
gram-positive | yes | 90.96 | yes |
anaerobic | no | 99.488 | yes |
anaerobic | no | 99.488 | yes |
anaerobic | no | 99.488 | yes |
aerobic | yes | 92.436 | no |
aerobic | yes | 92.436 | no |
aerobic | yes | 92.436 | no |
halophile | no | 93.669 | no |
halophile | no | 93.669 | no |
halophile | no | 93.669 | no |
spore-forming | no | 86.048 | no |
spore-forming | no | 86.048 | no |
spore-forming | no | 86.048 | no |
motile | no | 91.886 | no |
motile | no | 91.886 | no |
motile | no | 91.886 | no |
glucose-ferment | no | 90.923 | no |
glucose-ferment | no | 90.923 | no |
glucose-ferment | no | 90.923 | no |
thermophile | no | 99.326 | yes |
thermophile | no | 99.326 | yes |
thermophile | no | 99.326 | yes |
glucose-util | yes | 88.332 | yes |
glucose-util | yes | 88.332 | yes |
glucose-util | yes | 88.332 | yes |
External links
@ref: 16675
culture collection no.: DSM 45406, ATCC BAA 1377, CIP 109273, JCM 16372
straininfo link
- @ref: 77960
- straininfo: 300731
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19196782 | Polycyclic aromatic hydrocarbon-degrading species isolated from Hawaiian soils: Mycobacterium crocinum sp. nov., Mycobacterium pallens sp. nov., Mycobacterium rutilum sp. nov., Mycobacterium rufum sp. nov. and Mycobacterium aromaticivorans sp. nov. | Hennessee CT, Seo JS, Alvarez AM, Li QX | Int J Syst Evol Microbiol | 10.1099/ijs.0.65827-0 | 2009 | Genes, Bacterial/genetics, Hawaii, Molecular Sequence Data, Mycobacterium/chemistry/*classification/genetics/metabolism, Phenotype, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity | Genetics |
Genetics | 27486485 | Draft genome sequence of Mycobacterium rufum JS14(T), a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated soil in Hawaii. | Kwak Y, Li QX, Shin JH | Stand Genomic Sci | 10.1186/s40793-016-0167-5 | 2016 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16675 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45406) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45406 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
32638 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28849 | 28776041 | |
37496 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6996 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
77960 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID300731.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122303 | Curators of the CIP | Collection of Institut Pasteur (CIP 109273) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109273 |