Strain identifier

BacDive ID: 8422

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
11459<- K.-H. Schröder, Forschungsinstitut Borstel, 1389/90
67770CIP 105510 <-- DSM 44017 <-- K.-H. Schröder 1389/90.
118724CIP <- 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

@refmotilityconfidencegram staincell shape
69480no93.509
69480100positive
118724norod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19841Pale yellow10-14 days5006
19841Pale yellow10-14 daysBUG
19841Pale yellow10-14 daysMB7H9
537072 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11459MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
11459LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)yeshttps://mediadive.dsmz.de/medium/354Name: 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
19841BUGyes
198415006yesMedium: 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
19841MB7H9yesName: 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
36364MEDIUM 55 - for Mycobacteriumyes
118724CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
19841positiveoptimum37mesophilic
11459positivegrowth37mesophilic
36364positivegrowth37mesophilic
53707positivegrowth22-37
67770positivegrowth37mesophilic
118724positivegrowth25-37mesophilic
118724nogrowth10psychrophilic
118724nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
53707aerobe
118724obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.922

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
118724606565hippurate-hydrolysis
11872417632nitrate+reduction
11872416301nitrite-reduction
11872417632nitrate-respiration
6837917632nitrate+reduction
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 118724
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68379catalase+1.11.1.6
68379gelatinase-
68379urease+3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
118724oxidase-
118724beta-galactosidase-3.2.1.23
118724gelatinase-
118724amylase-
118724DNase-
118724caseinase-3.4.21.50
118724catalase+1.11.1.6
118724tween esterase-
118724gamma-glutamyltransferase-2.3.2.2
118724lecithinase-
118724lipase-
118724tryptophan deaminase-
118724urease+3.5.1.5
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
19841++---++-++----++---
53707++-+--+--+----------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19841+++-++-+-+---++++--
53707--+-+----+----------
118724+++-+----++---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118724++--+---------------+------------+--------------------------+-----------+--+--------------------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11459human sputumKoblenzGermanyDEUEurope
53707Human sputum
67770Sputum from a healthy male
118724Human, Sputum

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114591Risk group (German classification)
198411Risk group (German classification)
1187241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium confluentis strain CIP 105510 16S ribosomal RNA gene, partial sequenceAF547913544ena28047
20218Mycobacterium confluentis 16S rRNA gene, type strain DSM 44017TAJ6343791504ena28047
67770M.confluentis gene for 16S rRNAX636081335ena28047

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium confluentis JCM 13671GCA_010729895completencbi28047
66792Mycobacterium confluentis strain DSM 4401728047.3wgspatric28047
66792Mycolicibacterium confluentis strain JCM 1367128047.9completepatric28047
66792Mycolicibacterium confluentis DSM 440172865351897draftimg28047
67770Mycolicibacterium confluentis DSM 44017GCA_002102105contigncbi28047
66792Mycolicibacterium confluentis DSM 44017GCA_025822845scaffoldncbi28047

GC content

  • @ref: 67770
  • GC-content: 67.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno79no
motileno93.22no
flagellatedno98.628no
gram-positiveyes86.679no
anaerobicno99.142yes
aerobicyes91.533no
halophileno91.472no
spore-formingno87.533no
glucose-utilyes87.883no
thermophileno98.835yes
glucose-fermentno89.379no

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

@idauthorscataloguedoi/urltitlejournalpubmed
11459Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44017)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44017
19841Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44017.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
36364Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17538
53707Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37513)https://www.ccug.se/strain?id=37513
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
77821Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42754.1StrainInfo: A central database for resolving microbial strain identifiers
118724Curators of the CIPCollection of Institut Pasteur (CIP 105510)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105510