Strain identifier
BacDive ID: 8422
Type strain:
Species: Mycobacterium confluentis
Strain Designation: 1389/90
Strain history: CIP <- 1998, DSMZ <- K.H. Scuröder, Forschunginstitut Borstel: strain 1389/90
NCBI tax ID(s): 28047 (species)
General
@ref: 11459
BacDive-ID: 8422
DSM-Number: 44017
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Mycobacterium confluentis 1389/90 is an aerobe, mesophilic bacterium that was isolated from human sputum.
NCBI tax id
- NCBI tax id: 28047
- Matching level: species
strain history
@ref | history |
---|---|
11459 | <- K.-H. Schröder, Forschungsinstitut Borstel, 1389/90 |
67770 | CIP 105510 <-- DSM 44017 <-- K.-H. Schröder 1389/90. |
118724 | CIP <- 1998, DSMZ <- K.H. Scuröder, Forschunginstitut Borstel: strain 1389/90 |
doi: 10.13145/bacdive8422.20230509.8.1
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 confluentis
- full scientific name: Mycobacterium confluentis Kirschner et al. 1992
synonyms
- @ref: 20215
- synonym: Mycolicibacterium confluentis
@ref: 11459
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium confluentis
full scientific name: Mycobacterium confluentis Kirschner et al. 1992 emend. Nouioui et al. 2018
strain designation: 1389/90
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 93.509 | ||
69480 | 100 | positive | ||
118724 | no | rod-shaped |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19841 | Pale yellow | 10-14 days | 5006 |
19841 | Pale yellow | 10-14 days | BUG |
19841 | Pale yellow | 10-14 days | MB7H9 |
53707 | 2 days |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11459 | 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 |
11459 | 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 |
19841 | BUG | yes | ||
19841 | 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 | |
19841 | MB7H9 | yes | Name: Middlebrook 7H9 (MB7H9) Broth Base Composition: Middelbrook 7H9 Broth Base 4.7 g/l Glycerol 2.0 g/l Casaminoacids 11.0 g/l Yeast extract 5.5 g/l Tween80 (20%) 2.5 g/l OADC-Enrichment 100 ml Agar 15.0 g/l Preparation: Dissolve in Milli-Q-H2O. Before Use add 10% OADC stock solution Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Maintenance and revitalization Organisms: 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 | |
36364 | MEDIUM 55 - for Mycobacterium | yes | ||
118724 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19841 | positive | optimum | 37 | mesophilic |
11459 | positive | growth | 37 | mesophilic |
36364 | positive | growth | 37 | mesophilic |
53707 | positive | growth | 22-37 | |
67770 | positive | growth | 37 | mesophilic |
118724 | positive | growth | 25-37 | mesophilic |
118724 | no | growth | 10 | psychrophilic |
118724 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
53707 | aerobe |
118724 | obligate aerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.922
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
118724 | 606565 | hippurate | - | hydrolysis |
118724 | 17632 | nitrate | + | reduction |
118724 | 16301 | nitrite | - | reduction |
118724 | 17632 | nitrate | - | respiration |
68379 | 17632 | nitrate | + | reduction |
68379 | 16199 | urea | + | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
metabolite production
- @ref: 118724
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | catalase | + | 1.11.1.6 |
68379 | gelatinase | - | |
68379 | urease | + | 3.5.1.5 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
118724 | oxidase | - | |
118724 | beta-galactosidase | - | 3.2.1.23 |
118724 | gelatinase | - | |
118724 | amylase | - | |
118724 | DNase | - | |
118724 | caseinase | - | 3.4.21.50 |
118724 | catalase | + | 1.11.1.6 |
118724 | tween esterase | - | |
118724 | gamma-glutamyltransferase | - | 2.3.2.2 |
118724 | lecithinase | - | |
118724 | lipase | - | |
118724 | tryptophan deaminase | - | |
118724 | urease | + | 3.5.1.5 |
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 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19841 | + | + | - | - | - | + | + | - | + | + | - | - | - | - | + | + | - | - | - | ||
53707 | + | + | - | + | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19841 | + | + | + | - | + | + | - | + | - | + | - | - | - | + | + | + | + | - | - | |
53707 | - | - | + | - | + | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
118724 | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118724 | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
11459 | human sputum | Koblenz | Germany | DEU | Europe |
53707 | Human sputum | ||||
67770 | Sputum from a healthy male | ||||
118724 | Human, Sputum |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Fluids | #Sputum |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
11459 | 1 | Risk group (German classification) |
19841 | 1 | Risk group (German classification) |
118724 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Mycobacterium confluentis strain CIP 105510 16S ribosomal RNA gene, partial sequence | AF547913 | 544 | ena | 28047 |
20218 | Mycobacterium confluentis 16S rRNA gene, type strain DSM 44017T | AJ634379 | 1504 | ena | 28047 |
67770 | M.confluentis gene for 16S rRNA | X63608 | 1335 | ena | 28047 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycolicibacterium confluentis JCM 13671 | GCA_010729895 | complete | ncbi | 28047 |
66792 | Mycobacterium confluentis strain DSM 44017 | 28047.3 | wgs | patric | 28047 |
66792 | Mycolicibacterium confluentis strain JCM 13671 | 28047.9 | complete | patric | 28047 |
66792 | Mycolicibacterium confluentis DSM 44017 | 2865351897 | draft | img | 28047 |
67770 | Mycolicibacterium confluentis DSM 44017 | GCA_002102105 | contig | ncbi | 28047 |
66792 | Mycolicibacterium confluentis DSM 44017 | GCA_025822845 | scaffold | ncbi | 28047 |
GC content
- @ref: 67770
- GC-content: 67.5
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 79 | no |
motile | no | 93.22 | no |
flagellated | no | 98.628 | no |
gram-positive | yes | 86.679 | no |
anaerobic | no | 99.142 | yes |
aerobic | yes | 91.533 | no |
halophile | no | 91.472 | no |
spore-forming | no | 87.533 | no |
glucose-util | yes | 87.883 | no |
thermophile | no | 98.835 | yes |
glucose-ferment | no | 89.379 | no |
External links
@ref: 11459
culture collection no.: DSM 44017, ATCC 49920, CIP 105510, CCUG 37513, JCM 13671, KCTC 19635
straininfo link
- @ref: 77821
- straininfo: 42754
literature
- topic: Phylogeny
- Pubmed-ID: 1374623
- title: Mycobacterium confluentis sp. nov.
- authors: Kirschner P, Teske A, Schroder KH, Kroppenstedt RM, Wolters J, Bottger EC
- journal: Int J Syst Bacteriol
- DOI: 10.1099/00207713-42-2-257
- year: 1992
- mesh: Base Sequence, Chromatography, Thin Layer, DNA, Bacterial, Molecular Sequence Data, Mycobacterium/*classification/genetics, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
11459 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44017) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44017 | |||
19841 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44017.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 | |
36364 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17538 | ||||
53707 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 37513) | https://www.ccug.se/strain?id=37513 | |||
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) | |||
77821 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42754.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118724 | Curators of the CIP | Collection of Institut Pasteur (CIP 105510) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105510 |