Strain identifier
BacDive ID: 8470
Type strain:
Species: Mycobacterium hiberniae
Strain Designation: Hi 11, 14 403 0001
Strain history: CIP <- 2002, DSMZ <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 403 0001 <- ATCC <- J. Kadza, Borstel, Germany: strain Hi 11
NCBI tax ID(s): 29314 (species)
General
@ref: 11616
BacDive-ID: 8470
DSM-Number: 44241
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Mycobacterium hiberniae Hi 11 is a mesophilic bacterium that was isolated from moss .
NCBI tax id
- NCBI tax id: 29314
- Matching level: species
strain history
@ref | history |
---|---|
11616 | <- A.F. Yassin <- ATCC <- J. Kazda, IR 103 [Hi 11] |
67770 | CIP 104537 <-- DSM 44241 <-- A. F. Yassin <-- ATCC 49874 <-- J. Kazda Hi 11. |
119888 | CIP <- 2002, DSMZ <- 1995, V. Vincent, Inst. Pasteur, Paris, France: strain 14 403 0001 <- ATCC <- J. Kadza, Borstel, Germany: strain Hi 11 |
doi: 10.13145/bacdive8470.20230509.8.1
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 hiberniae
- full scientific name: Mycobacterium hiberniae Kazda et al. 1993
synonyms
- @ref: 20215
- synonym: Mycolicibacter hiberniae
@ref: 11616
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium hiberniae
full scientific name: Mycobacterium hiberniae Kazda et al. 1993 emend. Nouioui et al. 2018
strain designation: Hi 11, 14 403 0001
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 93.311 | ||
69480 | 100 | positive | ||
119888 | no | rod-shaped |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19855 | Ivory | 10-14 days | 5006 |
19855 | Ivory | 10-14 days | MB7H10 |
19855 | Ivory | 10-14 days | MB7H11 |
multimedia
- @ref: 11616
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44241.jpg
- caption: Medium 645 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11616 | 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 |
19855 | 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 | |
19855 | 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 | |
19855 | 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 | |
36391 | MEDIUM 55 - for Mycobacterium | yes | ||
119888 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19855 | positive | optimum | 37 | mesophilic |
11616 | positive | growth | 37 | mesophilic |
36391 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
119888 | positive | growth | 22-37 | |
119888 | no | growth | 10 | psychrophilic |
119888 | no | growth | 45 | thermophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.959 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
119888 | 17632 | nitrate | + | reduction |
119888 | 16301 | nitrite | - | reduction |
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: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole 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 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
119888 | oxidase | - | |
119888 | catalase | + | 1.11.1.6 |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
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 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19855 | + | + | + | + | - | + | - | - | - | + | - | + | + | + | + | + | + | + | + |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase | Control | Acid phosphatase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19855 | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | ||
119888 | + | + | + | - | + | - | - | - | - | + | - | + | - | - | + | - | - | - | - | + |
11616 | - | +/- | + | - | - | - | - | - | - | +/- | - | - | - | +/- | - | - | - | - | - | + |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
11616 | +/- | - | - | - | - | +/- | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119888 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent |
---|---|---|---|---|---|
11616 | moss (Ctenidium molluscum) | Ctenidium molluscum | Ireland | IRL | Europe |
54691 | Moss (Ctenidium molluscum) | Ireland | IRL | Europe | |
67770 | Moss (Ctenidium molluscum) | Ctenidium molluscum | |||
119888 | Environment, Soil | Ireland | IRL | Europe |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Moss
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
11616 | 1 | Risk group (German classification) |
19855 | 1 | Risk group (German classification) |
119888 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Mycobacterium hiberniae strain ATCC 49874 16S ribosomal RNA gene, partial sequence | JN571173 | 479 | ena | 29314 |
20218 | M.hiberniae 16S rRNA | X67096 | 1419 | ena | 29314 |
20218 | Mycobacterium hiberniae 16S ribosomal RNA gene, partial sequence | AY438069 | 556 | ena | 29314 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycolicibacter hiberniae JCM 13571 | GCA_010729485 | complete | ncbi | 29314 |
66792 | Mycobacterium hiberniae strain ATCC 49874 | 29314.3 | wgs | patric | 29314 |
66792 | Mycolicibacter hiberniae strain JCM 13571 | 29314.9 | complete | patric | 29314 |
66792 | Mycolicibacter hiberniae ATCC 49874 | 2865376297 | draft | img | 29314 |
67770 | Mycolicibacter hiberniae ATCC 49874 | GCA_002101655 | contig | ncbi | 29314 |
66792 | Mycolicibacter hiberniae DSM 44241 | GCA_025821605 | scaffold | ncbi | 29314 |
GC content
- @ref: 67770
- GC-content: 68.5
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | no | 94.752 | no |
flagellated | no | 98.752 | no |
gram-positive | yes | 93.052 | no |
anaerobic | no | 99.514 | no |
aerobic | yes | 93.649 | no |
halophile | no | 91.319 | no |
spore-forming | no | 89.189 | no |
glucose-util | yes | 56.327 | no |
thermophile | no | 98.468 | no |
glucose-ferment | no | 91.554 | yes |
External links
@ref: 11616
culture collection no.: CCUG 39184, JCM 13571, DSM 44241, ATCC 49874, CIP 104537, KCTC 19638
straininfo link
- @ref: 77865
- straininfo: 42729
literature
- topic: Phylogeny
- Pubmed-ID: 7684243
- title: Mycobacterium hiberniae sp. nov.
- authors: Kazda J, Cooney R, Monaghan M, Quinn PJ, Stackebrandt E, Dorsch M, Daffe M, Muller K, Cook BR, Tarnok ZS
- journal: Int J Syst Bacteriol
- DOI: 10.1099/00207713-43-2-352
- year: 1993
- mesh: Bacterial Typing Techniques, Biological Evolution, Classification, Cluster Analysis, DNA, Bacterial/genetics, Ireland, Molecular Sequence Data, Mycobacterium/*classification/growth & development/isolation & purification, Mycolic Acids/analysis, Nucleic Acid Hybridization, Phylogeny, Plants/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11616 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44241) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44241 | |||
19855 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44241.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 | |
36391 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16457 | ||||
54691 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 39184) | https://www.ccug.se/strain?id=39184 | |||
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/ | ||||
68369 | Automatically annotated from API 20NE | |||||
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 | |||
77865 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42729.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119888 | Curators of the CIP | Collection of Institut Pasteur (CIP 104537) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104537 |