Strain identifier

BacDive ID: 8474

Type strain: Yes

Species: Mycobacterium bohemicum

Strain Designation: 2938-X86

Strain history: CIP <- 1998, U. Reischl and L. Naumann, Regensburg Univ., Regensburg, Germany

NCBI tax ID(s): 1236609 (strain), 56425 (species)

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General

@ref: 11643

BacDive-ID: 8474

DSM-Number: 44277

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, human pathogen

description: Mycobacterium bohemicum 2938-X86 is an obligate aerobe, mesophilic, Gram-positive human pathogen that was isolated from sputum.

NCBI tax id

NCBI tax idMatching level
56425species
1236609strain

strain history

@refhistory
11643<- L. Naumann, Univ. Regensburg, 2938-X86 <- Usti nad Laben, Masaryk Hospital
362521998, U. Reischl and L. Naumann, Inst. für Med., Regensburg, Germany
67770CIP 105811 <-- U. Reischl and L. Naumann 2938-X86 <-- Masaryk Hosp., Ústí nad Labem, Czech Republic.
116831CIP <- 1998, U. Reischl and L. Naumann, Regensburg Univ., Regensburg, Germany

doi: 10.13145/bacdive8474.20230509.8.1

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 bohemicum
  • full scientific name: Mycobacterium bohemicum Reischl et al. 1998

@ref: 11643

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium bohemicum

full scientific name: Mycobacterium bohemicum Reischl et al. 1998 emend. Nouioui et al. 2018

strain designation: 2938-X86

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116831rod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20039Beige (1001)10-14 days5006
20039Beige (1001)10-14 daysBHI
20039Beige (1001)10-14 daysBUG
20039Corn yellow (1006)10-14 daysMB7H9

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11643MIDDLEBROOK 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
20039BUGyes
20039BHIyes
200395006yesMedium: 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
20039MB7H9yesName: 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
36252MEDIUM 55 - for Mycobacteriumyes
116831CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
20039positiveoptimum37mesophilic
11643positivegrowth37mesophilic
36252positivegrowth37mesophilic
54992positivegrowth37mesophilic
67770positivegrowth37mesophilic
116831positivegrowth22-41
116831nogrowth10psychrophilic
116831nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116831
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.984

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
116831606565hippurate-hydrolysis
11683117632nitrate-reduction
11683116301nitrite-reduction
11683117632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11683135581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
116831oxidase-
116831beta-galactosidase-3.2.1.23
116831gelatinase-
116831catalase+1.11.1.6
116831gamma-glutamyltransferase+2.3.2.2
116831urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20039-+---------------+/--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20039-++----------------
11643-+/-+-+---------------
116831-++-+----++---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11643--------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
11643sputumOstravaCzech RepublicCZEEurope
54992Human sputum,53-yr-old patient with Down's syndr.Czech RepublicCZEEurope1991
67770Sputum
116831Human, SputumGermanyDEUEurope1991

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_75.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_75&stattab=map
  • Last taxonomy: Mycobacterium
  • 16S sequence: U84502
  • Sequence Identity:
  • Total samples: 1520
  • soil counts: 881
  • aquatic counts: 382
  • animal counts: 203
  • plant counts: 54

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11643yes, in single casesyes, in single cases1Risk group (German classification)
200391German classification
1168311Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium bohemicum strain CIP 105811 16S ribosomal RNA gene, partial sequenceAF547901554ena56425
20218Mycobacterium bohemicum 16S ribosomal RNA gene, partial sequenceU845021516ena56425

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium bohemicum DSM 442771236609.3wgspatric1236609
66792Mycobacterium bohemicum strain DSM 4427756425.4wgspatric56425
66792Mycobacterium bohemicum DSM 442772630968850draftimg1236609
67770Mycobacterium bohemicum DSM 44277GCA_001053185scaffoldncbi1236609
67770Mycobacterium bohemicum DSM 44277GCA_002102025contigncbi56425
66792Mycobacterium bohemicum DSM 44277GCA_025821915scaffoldncbi56425

GC content

@refGC-contentmethod
6777063.5high performance liquid chromatography (HPLC)
6777068.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno83no
motileno94.996no
gram-positiveyes89.369no
anaerobicno99.001no
aerobicyes89.94no
halophileno93.396no
spore-formingno85.513no
glucose-utilyes61.67yes
flagellatedno98.697no
glucose-fermentno93.114yes
thermophileno97.016yes

External links

@ref: 11643

culture collection no.: CCUG 39919, CIP 105811, DSM 44277, JCM 12402, ATCC BAA 2097

straininfo link

  • @ref: 77869
  • straininfo: 50546

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9828436Mycobacterium bohemicum sp. nov., a new slow-growing scotochromogenic mycobacterium.Reischl U, Emler S, Horak Z, Kaustova J, Kroppenstedt RM, Lehn N, Naumann LInt J Syst Bacteriol10.1099/00207713-48-4-13491998Base Composition, Base Sequence, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Down Syndrome/*complications, Fatty Acids/analysis, Genes, rRNA, Humans, Middle Aged, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sputum/microbiology, Terminology as Topic, Tuberculosis/complications/*microbiologyPathogenicity
Genetics26251499Draft Genome Sequence of Mycobacterium bohemicum Strain DSM 44277T.Asmar S, Phelippeau M, Robert C, Croce O, Drancourt MGenome Announc10.1128/genomeA.00878-152015

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11643Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44277)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44277
20039Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44277.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
36252Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17872
54992Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39919)https://www.ccug.se/strain?id=39919
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
77869Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50546.1StrainInfo: A central database for resolving microbial strain identifiers
116831Curators of the CIPCollection of Institut Pasteur (CIP 105811)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105811