Strain identifier
BacDive ID: 8429
Type strain:
Species: Mycobacterium simiae
Strain Designation: 14 102 0001, N29, 3015
Strain history: CIP <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 102 0001 <- ATCC <- E. Runyon: strain 3015 <- J. Weiszfeiler: strain N29
NCBI tax ID(s): 1236483 (strain), 1784 (species)
General
@ref: 11563
BacDive-ID: 8429
DSM-Number: 44165
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, human pathogen
description: Mycobacterium simiae 14 102 0001 is an obligate aerobe, mesophilic human pathogen that was isolated from Indian monkey .
NCBI tax id
NCBI tax id | Matching level |
---|---|
1784 | species |
1236483 | strain |
strain history
@ref | history |
---|---|
11563 | <- ATCC <- E. Runyon, 3015 <- J. Weiszfeiler, N 29 |
67770 | CCUG 29114 <-- M. Ridell <-- A. Lind <-- ATCC 25275 <-- E. H. Runyon 3015 <-- J. Weiszfeiler N29. |
122614 | CIP <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 102 0001 <- ATCC <- E. Runyon: strain 3015 <- J. Weiszfeiler: strain N29 |
doi: 10.13145/bacdive8429.20230509.8.1
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 simiae
- full scientific name: Mycobacterium simiae Karassova et al. 1965 (Approved Lists 1980)
@ref: 11563
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium simiae
full scientific name: Mycobacterium simiae Karassova et al. 1965 emend. Nouioui et al. 2018
strain designation: 14 102 0001, N29, 3015
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 96.185 | ||
69480 | 100 | positive | ||
122614 | no | oval-shaped |
colony morphology
@ref | incubation period | medium used | colony color |
---|---|---|---|
19845 | 10-14 days | 5006 | |
19845 | 10-14 days | MB7H10 | Daffodil yellow |
19845 | 10-14 days | MB7H11 | Daffodil yellow |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11563 | MYCOBACTERIUM MEDIUM (DSMZ Medium 219) | yes | https://mediadive.dsmz.de/medium/219 | Name: MYCOBACTERIUM MEDIUM (DSMZ Medium 219) Composition: Agar 20.0 g/l Na2HPO4 x 12 H2O 2.5 g/l Yeast extract 2.0 g/l Proteose peptone no. 3 2.0 g/l Casein peptone 2.0 g/l Sodium citrate 1.5 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.6 g/l Tween 0.5 g/l Glycerol Distilled water |
11563 | 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 |
19845 | 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 | |
19845 | 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 | |
19845 | 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 | |
36246 | MEDIUM 55 - for Mycobacterium | yes | ||
122614 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19845 | positive | optimum | 37 | mesophilic |
11563 | positive | growth | 37 | mesophilic |
36246 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
122614 | positive | growth | 30-37 | mesophilic |
122614 | no | growth | 10 | psychrophilic |
122614 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 122614
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 94 |
69480 | no | 99.966 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
122614 | 4853 | esculin | - | hydrolysis |
122614 | 606565 | hippurate | + | hydrolysis |
122614 | 17632 | nitrate | + | reduction |
122614 | 16301 | nitrite | - | reduction |
122614 | 17632 | nitrate | - | respiration |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | - | 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: 122614
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 122614
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | gelatinase | - | |
68379 | urease | - | 3.5.1.5 |
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 |
122614 | oxidase | - | |
122614 | beta-galactosidase | - | 3.2.1.23 |
122614 | alcohol dehydrogenase | - | 1.1.1.1 |
122614 | gelatinase | - | |
122614 | catalase | + | 1.11.1.6 |
122614 | tween esterase | - | |
122614 | lysine decarboxylase | - | 4.1.1.18 |
122614 | ornithine decarboxylase | - | 4.1.1.17 |
122614 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
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 | 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 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19845 | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19845 | - | + | + | + | + | + | - | - | - | + | + | - | - | - | - | - | - | - | - | |
122614 | - | + | + | - | + | - | + | - | - | + | + | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species |
---|---|---|
11563 | Indian monkey (Macaca mulatta) | Macaca mulatta |
67770 | Indian monkey (Macaca mulatta) | Macaca mulatta |
122614 | Indian monkey |
isolation source categories
- Cat1: #Host
- Cat2: #Mammals
- Cat3: #Primates
Safety information
risk assessment
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
11563 | yes | yes | 2 | Risk group (German classification) |
19845 | 2 | Risk group (German classification) | ||
122614 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Mycobacterium simiae DNA, 16S-23S ribosomal RNA intergenic spacer, strain: ATCC 25275 | AB547405 | 281 | ena | 1784 |
20218 | Mycobacterium simiae gene for 16S ribosomal RNA, partial cds, strain: ATCC 25275 | AB547406 | 1471 | ena | 1784 |
20218 | Mycobacterium simiae partial 16S rRNA gene, strain ATCC 25275 | AJ439538 | 644 | ena | 1784 |
20218 | M.simiae 16S ribosomal RNA gene | M59269 | 145 | ena | 1784 |
20218 | Mycobacterium simiae 16S rRNA gene | X52931 | 1484 | ena | 1784 |
20218 | Mycobacterium simiae strain CIP 104531 16S ribosomal RNA gene, partial sequence | AF547966 | 542 | ena | 1784 |
20218 | Mycobacterium simiae DNA for 16S rRNA, internal transcribed spacer, 23S rRNA | AB026694 | 440 | ena | 1784 |
11563 | Mycobacterium simiae strain ATCC 25275 16S ribosomal RNA gene, partial sequence | GQ153280 | 1483 | ena | 1784 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycobacterium simiae JCM 12377 | GCA_010727605 | complete | ncbi | 1784 |
66792 | Mycobacterium simiae ATCC 25275 = DSM 44165 | 1236483.3 | wgs | patric | 1236483 |
66792 | Mycobacterium simiae strain JCM 12377 | 1784.27 | complete | patric | 1784 |
66792 | Mycobacterium simiae ATCC 25275 | 2600254956 | draft | img | 1236483 |
67770 | Mycobacterium simiae ATCC 25275 = DSM 44165 | GCA_000455305 | scaffold | ncbi | 1236483 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 65.15 | genome sequence analysis |
67770 | 66.2 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 94 | no |
motile | no | 93.203 | no |
flagellated | no | 98.613 | no |
gram-positive | yes | 89.396 | no |
anaerobic | no | 99.051 | no |
aerobic | yes | 92.861 | no |
halophile | no | 95.512 | no |
spore-forming | no | 87.84 | no |
glucose-util | yes | 71.401 | no |
thermophile | no | 97.767 | yes |
glucose-ferment | no | 92.988 | yes |
External links
@ref: 11563
culture collection no.: DSM 44165, ATCC 25275, TMC 1226, JCM 12377, CCUG 29114, CCUG 42427, CIP 104531
straininfo link
- @ref: 77828
- straininfo: 38461
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9611792 | Analysis of lipids reveals differences between 'Mycobacterium habana' and Mycobacterium simiae. | Mederos LM, Valdivia JA, Sempere MA, Valero-Guillen PL | Microbiology (Reading) | 10.1099/00221287-144-5-1181 | 1998 | Bacterial Typing Techniques, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Fatty Acids/*analysis, Glycolipids/*analysis, Mycolic Acids/analysis, Nontuberculous Mycobacteria/*chemistry/*classification, Species Specificity | |
Phylogeny | 18397261 | New variants of polar glycopeptidolipids detected in Mycobacterium simiae, including 'habana' strains, as evidenced by electrospray ionization-ion trap-mass spectrometry. | Mederos L, Valdivia JA, Valero-Guillen PL | J Appl Microbiol | 10.1111/j.1365-2672.2008.03796.x | 2008 | Bacteriological Techniques, Glycolipids/*analysis, Nontuberculous Mycobacteria/*chemistry, Species Specificity, Spectrometry, Mass, Electrospray Ionization, Tuberculosis/*microbiology | |
Phylogeny | 20639227 | Mycobacterium sherrisii sp. nov., a slow-growing non-chromogenic species. | van Ingen J, Tortoli E, Selvarangan R, Coyle MB, Crump JA, Morrissey AB, Dekhuijzen PNR, Boeree MJ, van Soolingen D | Int J Syst Evol Microbiol | 10.1099/ijs.0.024752-0 | 2010 | Africa, Bacterial Proteins/genetics, Bacterial Typing Techniques, Cell Wall/chemistry, Chaperonin 60/genetics, Chromatography, High Pressure Liquid, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Enzyme Stability, Enzymes/metabolism, Hot Temperature, Humans, Molecular Sequence Data, Mycobacterium/*classification/genetics/growth & development/*isolation & purification, Mycolic Acids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Time Factors | Enzymology |
Pathogenicity | 20688816 | Structural studies of cord factors from Mycobacterium simiae related to the capacity for tumour necrosis factor alpha (alpha-TNF) induction. | Mederos LM, Montoro EH, Bernabeu A, Linares C, Valero-Guillen PL | Microbiology (Reading) | 10.1099/mic.0.042077-0 | 2010 | Animals, Cell Line, Cord Factors/*chemistry/genetics/*immunology, Humans, Mice, Molecular Structure, Mycobacterium/chemistry/genetics/*immunology, Tuberculosis/*immunology/microbiology, Tumor Necrosis Factor-alpha/*immunology | |
Genetics | 23991261 | Non-contiguous genome sequence of Mycobacterium simiae strain DSM 44165(T.). | Sassi M, Robert C, Raoult D, Drancourt M | Stand Genomic Sci | 10.4056/sigs.3707349 | 2013 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11563 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44165) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44165 | |||
19845 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44165.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 | |
36246 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16450 | ||||
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/ | ||||
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 | |||
77828 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38461.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122614 | Curators of the CIP | Collection of Institut Pasteur (CIP 104531) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104531 |