Strain identifier
BacDive ID: 8509
Type strain:
Species: Mycobacterium saskatchewanense
Strain history: CIP <- 2003, C.Y. Turenne, Nat. Microbiol. Lab., Winnipeg, Canada: strain NRCM 00-250 <- K. Williams
NCBI tax ID(s): 220927 (species)
General
@ref: 11929
BacDive-ID: 8509
DSM-Number: 44616
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, rod-shaped
description: Mycobacterium saskatchewanense DSM 44616 is an obligate aerobe, mesophilic, rod-shaped bacterium that was isolated from sputum.
NCBI tax id
- NCBI tax id: 220927
- Matching level: species
strain history
@ref | history |
---|---|
11929 | <- C. Turenne; NRCM 00-250 <- D. Cheke |
67770 | KCTC 9978 <-- C. Y. Turenne 00-250. |
122492 | CIP <- 2003, C.Y. Turenne, Nat. Microbiol. Lab., Winnipeg, Canada: strain NRCM 00-250 <- K. Williams |
doi: 10.13145/bacdive8509.20230509.8.1
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 saskatchewanense
- full scientific name: Mycobacterium saskatchewanense Turenne et al. 2004
@ref: 11929
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium saskatchewanense
full scientific name: Mycobacterium saskatchewanense Turenne et al. 2004 emend. Nouioui et al. 2018
type strain: yes
Morphology
cell morphology
@ref | cell shape | motility | confidence | gram stain |
---|---|---|---|---|
29954 | rod-shaped | |||
69480 | no | 91.665 | ||
69480 | 100 | positive | ||
122492 | rod-shaped | no |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19870 | Beige | 10-14 days | 5006 |
19870 | Beige | 10-14 days | MB7H10 |
19870 | Pale yellow | 10-14 days | MB7H11 |
pigmentation
- @ref: 29954
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11929 | 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 |
19870 | 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 | |
19870 | 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 | |
19870 | 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 | |
37410 | MEDIUM 55 - for Mycobacterium | yes | ||
122492 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 | |
122492 | CIP Medium 267 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=267 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19870 | positive | optimum | 37 | mesophilic |
11929 | positive | growth | 37 | mesophilic |
29954 | positive | growth | 25-37 | mesophilic |
29954 | positive | optimum | 31 | mesophilic |
37410 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
122492 | positive | growth | 30-37 | mesophilic |
122492 | no | growth | 10 | psychrophilic |
122492 | no | growth | 22 | psychrophilic |
122492 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 122492
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 91 |
69480 | no | 99.844 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29954 | 53426 | tween 80 | + | carbon source |
122492 | 606565 | hippurate | - | hydrolysis |
122492 | 17632 | nitrate | - | reduction |
122492 | 16301 | nitrite | - | reduction |
122492 | 17632 | nitrate | - | respiration |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | - | hydrolysis |
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: 122492
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
29954 | catalase | + | 1.11.1.6 |
68379 | gelatinase | + | |
68379 | beta-glucosidase | - | 3.2.1.21 |
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 | alkaline phosphatase | - | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
122492 | oxidase | - | |
122492 | beta-galactosidase | - | 3.2.1.23 |
122492 | gelatinase | - | |
122492 | catalase | + | 1.11.1.6 |
122492 | gamma-glutamyltransferase | + | 2.3.2.2 |
122492 | 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 | cystine arylamidase | - | 3.4.11.3 |
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 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19870 | + | + | + | - | - | - | - | - | - | +/- | + | + | + | - | + | + | + | + | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19870 | - | + | + | - | + | + | - | + | - | + | + | - | - | - | + | - | + | - | - | |
122492 | - | + | + | - | + | - | - | - | - | + | + | - | - | - | + | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
11929 | sputum | Saskatchewan | Canada | CAN | North America | |
67770 | Sputum of a patient with bronchiectasis | Saskatchewan | Canada | CAN | North America | |
122492 | Human, Sputum | Saskatchewan | Canada | CAN | North America | 2000 |
isolation source categories
- Cat1: #Host Body Product
- Cat2: #Fluids
- Cat3: #Sputum
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
11929 | 2 | Risk group (German classification) |
19870 | 2 | Risk group (German classification) |
122492 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Mycobacterium saskatchewanense strain CIP 108114 16S ribosomal RNA gene, partial sequence | AY943213 | 481 | ena | 220927 |
29954 | Mycobacterium saskatchewanense strain NRCM 00-250 16S ribosomal RNA gene, partial sequence; and 16S-23S intergenic spacer, complete sequence | AY208856 | 1824 | nuccore | 220927 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycobacterium saskatchewanense JCM 13016 | GCA_010729105 | complete | ncbi | 220927 |
66792 | Mycobacterium saskatchewanense strain DSM 44616 | 220927.3 | wgs | patric | 220927 |
66792 | Mycobacterium saskatchewanense strain JCM 13016 | 220927.8 | complete | patric | 220927 |
66792 | Mycobacterium saskatchewanense DSM 44616 | 2865429847 | draft | img | 220927 |
67770 | Mycobacterium saskatchewanense DSM 44616 | GCA_002101875 | contig | ncbi | 220927 |
66792 | Mycobacterium saskatchewanense DSM 44616 | GCA_025821405 | scaffold | ncbi | 220927 |
GC content
- @ref: 67770
- GC-content: 68.3
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 91 | no |
motile | no | 92.491 | no |
flagellated | no | 98.46 | no |
gram-positive | yes | 89.608 | no |
anaerobic | no | 99.257 | no |
aerobic | yes | 91.933 | no |
halophile | no | 93.933 | no |
spore-forming | no | 83.881 | no |
thermophile | no | 98.4 | yes |
glucose-util | yes | 70.348 | no |
glucose-ferment | no | 91.149 | no |
External links
@ref: 11929
culture collection no.: DSM 44616, ATCC BAA 544, CIP 108114, NRCM 00-250, JCM 13016, KCTC 9978
straininfo link
- @ref: 77899
- straininfo: 127875
literature
- topic: Phylogeny
- Pubmed-ID: 15143004
- title: Mycobacterium saskatchewanense sp. nov., a novel slowly growing scotochromogenic species from human clinical isolates related to Mycobacterium interjectum and Accuprobe-positive for Mycobacterium avium complex.
- authors: Turenne CY, Thibert L, Williams K, Burdz TV, Cook VJ, Wolfe JN, Cockcroft DW, Kabani A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02739-0
- year: 2004
- mesh: Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Sequence, Chaperonin 60, Chaperonins/genetics, DNA, Bacterial/genetics, DNA, Intergenic/genetics, Drug Resistance, Bacterial, Genes, Bacterial, Humans, Molecular Sequence Data, Mycobacterium avium Complex/*classification/*isolation & purification, Mycolic Acids/analysis, Nontuberculous Mycobacteria/*classification/genetics/*isolation & purification/metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid
- topic2: Pathogenicity
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
11929 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44616) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44616 | ||||
19870 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44616.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 | ||
29954 | 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 | 28776041 | 26323 | ||
37410 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5701 | |||||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68379 | Automatically annotated from API Coryne | ||||||
68382 | Automatically annotated from API zym | ||||||
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) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
77899 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID127875.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
122492 | Curators of the CIP | Collection of Institut Pasteur (CIP 108114) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108114 |