Strain identifier

BacDive ID: 8510

Type strain: Yes

Species: Mycobacterium branderi

Strain Designation: 52157

Strain history: CIP <- 1995, M.L. Katila, Kuopio Univ. Hosp., Kuopio, Finland: strain 52157 <- E. Brander

NCBI tax ID(s): 43348 (species)

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

@ref: 11936

BacDive-ID: 8510

DSM-Number: 44624

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic

description: Mycobacterium branderi 52157 is a microaerophile, mesophilic bacterium that was isolated from human sputum.

NCBI tax id

  • NCBI tax id: 43348
  • Matching level: species

strain history

@refhistory
11936<- CIP; CIP 104592 <- M.-L. Katila, Kuopio Univ. Hosp.; 52157 <- E. Brander;
67770CIP 104592 <-- M. L. Katila 52157 <-- E. Brander.
116989CIP <- 1995, M.L. Katila, Kuopio Univ. Hosp., Kuopio, Finland: strain 52157 <- E. Brander

doi: 10.13145/bacdive8510.20230509.8.1

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 branderi
  • full scientific name: Mycobacterium branderi Koukila-Kähkölä et al. 1995

@ref: 11936

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium branderi

full scientific name: Mycobacterium branderi Koukila-Kähkölä et al. 1995 emend. Nouioui et al. 2018

strain designation: 52157

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.851
69480100positive
116989rod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20081Beige (1001)10-14 days5006
2008110-14 daysBHI
2008110-14 daysBUG
20081Ivory (1014)10-14 daysMB7H9
600654-5 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11936MIDDLEBROOK 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
20081BUGyes
20081BHIyes
200815006yesMedium: 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
20081MB7H9yesName: 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
36329MEDIUM 55 - for Mycobacteriumyes
116989CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
20081positiveoptimum37mesophilic
11936positivegrowth37mesophilic
36329positivegrowth37mesophilic
67770positivegrowth37mesophilic
116989positivegrowth30-45
116989nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60065
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.543

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1169894853esculin-hydrolysis
116989606565hippurate-hydrolysis
11698917632nitrate-reduction
11698916301nitrite-reduction

metabolite production

  • @ref: 116989
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11698915688acetoin-
11698917234glucose+

enzymes

@refvalueactivityec
116989oxidase-
116989alcohol dehydrogenase-1.1.1.1
116989catalase+1.11.1.6
116989lysine decarboxylase-4.1.1.18
116989ornithine decarboxylase-4.1.1.17
116989tryptophan deaminase-
116989urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116989-+++++-+--++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling dateisolation date
11936human sputumHeinolaFinlandFINEurope61.205626.0381
60065Human sputumFinlandFINEurope1982
67770Human sputum, HeinolaFinlandFINEurope
116989Human, SputumFinlandFINEurope1982

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119362Risk group (German classification)
200812German classification
1169891Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium branderi 16S ribosomal RNA gene, partial sequenceAF4805741469ena43348
20218Mycobacterium branderi strain CIP 104592 16S ribosomal RNA gene, partial sequenceAF547906557ena43348
67770Mycobacterium sp.16S rRNA geneX822341417ena1785

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium branderi JCM 12687GCA_010728725completencbi43348
66792Mycobacterium branderi strain DSM 4462443348.3wgspatric43348
66792Mycobacterium branderi strain JCM 1268743348.9wgspatric43348
66792Mycobacterium branderi DSM 446242865532394draftimg43348
67770Mycobacterium branderi DSM 44624GCA_002086575contigncbi43348
66792Mycobacterium branderi DSM 44624GCA_025822465contigncbi43348

GC content

  • @ref: 67770
  • GC-content: 66.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno67no
motileno94.684no
flagellatedno98.907no
gram-positiveyes84.655no
anaerobicno98.661yes
aerobicyes79.514yes
halophileno93.89no
spore-formingno86.728no
thermophileno96.201yes
glucose-utilyes62.615no
glucose-fermentno90.865no

External links

@ref: 11936

culture collection no.: DSM 44624, ATCC 51789, CIP 104592, CCUG 53896, JCM 12687, KCTC 19634

straininfo link

  • @ref: 77900
  • straininfo: 43178

literature

  • topic: Phylogeny
  • Pubmed-ID: 8590682
  • title: Mycobacterium branderi sp. nov., a new potential human pathogen.
  • authors: Koukila-Kahkola P, Springer B, Bottger EC, Paulin L, Jantzen E, Katila ML
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-45-3-549
  • year: 1995
  • mesh: Antibiotics, Antitubercular/pharmacology, Arylsulfatases/metabolism, Bacterial Proteins/metabolism, Base Sequence, Drug Resistance, Microbial, Humans, Hydrolases/metabolism, Molecular Sequence Data, Mycobacterium/chemistry/*classification/genetics/metabolism, Mycolic Acids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Temperature, Tuberculosis, Pulmonary/*microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11936Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44624)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44624
20081Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44624.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
36329Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16517
60065Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53896)https://www.ccug.se/strain?id=53896
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/
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)
77900Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43178.1StrainInfo: A central database for resolving microbial strain identifiers
116989Curators of the CIPCollection of Institut Pasteur (CIP 104592)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104592