Strain identifier
BacDive ID: 8433
Type strain:
Species: Mycobacterium obuense
Strain Designation: 4388, 47001
Strain history: CIP <- 2000, JCM <- M. Tsukamura: strain 47001
NCBI tax ID(s): 1807 (species)
General
@ref: 11474
BacDive-ID: 8433
DSM-Number: 44075
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, human pathogen
description: Mycobacterium obuense 4388 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from sputum in a case of pulmonary disease.
NCBI tax id
- NCBI tax id: 1807
- Matching level: species
strain history
@ref | history |
---|---|
11474 | <- S. Rüsch-Gerdes <- ATCC <- M. Tsukamura, 4388 <- N. Kita |
67771 | <- CCUG <- JCM, RIKEN, Saitama, Japan 02 Apr 1997 <- 1987, M Tsukamura 47001 |
67770 | M. Tsukamura 47001. |
121377 | CIP <- 2000, JCM <- M. Tsukamura: strain 47001 |
doi: 10.13145/bacdive8433.20230509.8.1
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 obuense
- full scientific name: Mycobacterium obuense (ex Tsukamura and Mizuno 1971) Tsukamura and Mizuno 1981
synonyms
- @ref: 20215
- synonym: Mycolicibacterium obuense
@ref: 11474
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium obuense
full scientific name: Mycobacterium obuense (ex Tsukamura and Mizuno 1971) Tsukamura and Mizuno 1981 emend. Nouioui et al. 2018
strain designation: 4388, 47001
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility |
---|---|---|---|
67771 | positive | ||
121377 | rod-shaped | no |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19842 | Pure orange | 10-14 days | 5006 |
19842 | Pure orange | 10-14 days | MB7H10 |
19842 | Pure orange | 10-14 days | MB7H11 |
53796 | 3 days |
multimedia
- @ref: 11474
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44075.jpg
- caption: Medium 645 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11474 | LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354) | yes | https://mediadive.dsmz.de/medium/354 | Name: LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354) Composition: Potato flour 18.6104 g/l L-Asparagin 2.23325 g/l KH2PO4 1.55087 g/l Mg-citrate 0.372208 g/l Malachite green 0.248139 g/l MgSO4 0.148883 g/l Glycerol Fresh egg mixture Distilled water |
11474 | 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 |
19842 | MB7H10 | yes | Name: Middlebrook 7H10 (MB7H10) Broth Base Composition: amount in percent Middlebrook 7H10 Agar 1.9% Glycerol 0.5% OADC-Enrichment in ml (NL5633) 10ml Comments: Add broth base and glycerol to ddh2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria | |
19842 | MB7H11 | yes | Name: Middlebrook 7H11 (MB7H11) Broth Base Composition: Middlebrook 7H11 Agar 2% Glycerol 0.5% OADC-Enrichment 10ml Comments: Add broth base and glycerol to ddH2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-Stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria | |
19842 | 5006 | yes | Medium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes | |
36381 | MEDIUM 55 - for Mycobacterium | yes | ||
121377 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19842 | positive | optimum | 37 | mesophilic |
11474 | positive | growth | 37 | mesophilic |
36381 | positive | growth | 30 | mesophilic |
53796 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
67771 | positive | growth | 37 | mesophilic |
121377 | positive | growth | 22-37 | |
121377 | no | growth | 10 | psychrophilic |
121377 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
53796 | aerobe |
67771 | aerobe |
121377 | obligate aerobe |
observation
@ref | observation |
---|---|
67770 | quinones: MK-9(H2) |
67771 | quinones: MK-9(H2) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
121377 | 606565 | hippurate | - | hydrolysis |
121377 | 17632 | nitrate | - | reduction |
121377 | 16301 | nitrite | - | reduction |
121377 | 17632 | nitrate | - | respiration |
68379 | 17632 | nitrate | - | reduction |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
metabolite production
- @ref: 121377
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | catalase | + | 1.11.1.6 |
68379 | gelatinase | - | |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
121377 | oxidase | - | |
121377 | beta-galactosidase | - | 3.2.1.23 |
121377 | gelatinase | - | |
121377 | amylase | - | |
121377 | DNase | - | |
121377 | caseinase | - | 3.4.21.50 |
121377 | catalase | + | 1.11.1.6 |
121377 | tween esterase | - | |
121377 | gamma-glutamyltransferase | + | 2.3.2.2 |
121377 | lecithinase | - | |
121377 | lipase | - | |
121377 | protease | - | |
121377 | urease | + | 3.5.1.5 |
68382 | esterase lipase (C 8) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG | Control | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19842 | - | + | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | ||
53796 | - | - | - | + | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | + |
11474 | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - |
API zym
@ref | 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 | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19842 | - | + | + | + | + | + | + | - | - | + | + | - | + | - | + | + | - | - | - | |
53796 | + | - | + | - | + | + | + | - | - | + | + | - | - | - | + | - | - | - | - | - |
11474 | - | - | + | - | + | +/- | +/- | - | - | + | - | - | - | - | + | - | - | - | - | - |
121377 | - | + | + | - | + | + | + | - | - | + | + | - | - | - | + | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121377 | - | + | - | - | - | - | - | + | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
11474 | sputum in a case of pulmonary disease |
53796 | Soil |
67770 | Soil |
67771 | From sputum in a case of pulmonary disease |
121377 | Environment, Soil |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Inflammation | |
#Host Body Product | #Fluids | #Sputum |
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
11474 | yes, in single cases | 1 | Risk group (German classification) |
19842 | 1 | Risk group (German classification) | |
121377 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Mycobacterium obuense strain CIP 106803 16S ribosomal RNA gene, partial sequence | AF547954 | 540 | ena | 1807 |
11474 | M.obuense 16S ribosomal RNA, part | X55597 | 1458 | ena | 1807 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycobacterium obuense strain DSM 44075 | 1807.14 | wgs | patric | 1807 |
66792 | Mycolicibacterium obuense DSM 44075 | 2636415843 | draft | img | 1807 |
67770 | Mycolicibacterium obuense DSM 44075 | GCA_001044245 | contig | ncbi | 1807 |
GC content
- @ref: 67770
- GC-content: 68
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 92.793 | no |
gram-positive | yes | 90.003 | no |
anaerobic | no | 99.237 | yes |
aerobic | yes | 89.148 | no |
halophile | no | 92.576 | no |
spore-forming | no | 85.899 | no |
glucose-util | yes | 88.037 | no |
flagellated | no | 97.871 | no |
thermophile | no | 99.121 | yes |
glucose-ferment | no | 91.35 | yes |
External links
@ref: 11474
culture collection no.: CCUG 37669, CIP 106803, KCTC 19097, DSM 44075, ATCC 27023, JCM 6372, NCTC 10778, HAMBI 2272
straininfo link
- @ref: 77832
- straininfo: 45780
literature
- topic: Genetics
- Pubmed-ID: 26079817
- title: Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.
- authors: Das S, Pettersson BM, Behra PR, Ramesh M, Dasgupta S, Bhattacharya A, Kirsebom LA
- journal: Genome Biol Evol
- DOI: 10.1093/gbe/evv111
- year: 2015
- mesh: Biodegradation, Environmental, Copper/metabolism, Gene Transfer, Horizontal, Genes, Bacterial, *Genome, Bacterial, Genomics, Molecular Sequence Data, Mycobacterium/classification/*genetics/metabolism, Oxygenases/genetics, Phylogeny, RNA, Untranslated/genetics, Sequence Alignment, Sequence Analysis, DNA
- topic2: Phylogeny
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11474 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44075) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44075 | |||
19842 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44075.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
36381 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18973 | ||||
53796 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 37669) | https://www.ccug.se/strain?id=37669 | |||
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/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
77832 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45780.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121377 | Curators of the CIP | Collection of Institut Pasteur (CIP 106803) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106803 |