Strain identifier

BacDive ID: 140369

Type strain: Yes

Species: Mycobacterium eburneum

Strain Designation: X82

Strain history: <- L. Naumann, Univ. Regensburg, Germany; X82 <- Zentralkrankenhaus Gauting, Germany

NCBI tax ID(s): 2035343 (species)

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General

@ref: 42976

BacDive-ID: 140369

DSM-Number: 44358

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

description: Mycobacterium eburneum X82 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from sputum.

NCBI tax id

  • NCBI tax id: 2035343
  • Matching level: species

strain history

  • @ref: 42976
  • history: <- L. Naumann, Univ. Regensburg, Germany; X82 <- Zentralkrankenhaus Gauting, Germany

doi: 10.13145/bacdive140369.20230509.8.1

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 eburneum
  • full scientific name: Mycobacterium eburneum Nouioui et al. 2017

@ref: 42976

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium eburneum

full scientific name: Mycobacterium eburneum Nouioui et al. 2017

strain designation: X82

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
43890positiveno
69480no94.024
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
43890ivory coloured colonies7 daysMiddelbrock 7H10
43890ivory coloured colonies7 daysPeptone-meat extract-glycerol agar

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
43890Glucose-yeast-malt extract agaryes
43890Lowstein-Jensen agaryes
43890Middelbrock 7H10 agaryessupplemented with oleic acid, albumin, dextrose, catalase
43890Peptone-meat extract-glycerolyes
42976MIDDLEBROOK MEDIUM (DSMZ Medium 645)yesName: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled waterhttps://mediadive.dsmz.de/medium/645
42976LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)yesName: 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 waterhttps://mediadive.dsmz.de/medium/354

culture temp

@refgrowthtypetemperaturerange
43890positivegrowth28-37mesophilic
43890positiveoptimum37mesophilic
42976positivegrowth37mesophilic

culture pH

@refabilitytypepH
43890positivegrowth7.0-8.0
43890positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43890
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43890no
69480no99.671

observation

  • @ref: 43890
  • observation: quinone MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4389015588D-malate-carbon source
4389015589L-malate-carbon source
4389013705acetoacetate-carbon source
4389016947citrate-carbon source
4389016523D-serine-carbon source
4389017924D-sorbitol-carbon source
4389023652dextrin-carbon source
4389016537galactarate-carbon source
4389032323glucuronamide-carbon source
4389016634raffinose-carbon source
4389017632nitrate-reduction
43890167632-oxobutanoate+carbon source
4389017057cellobiose+carbon source
4389015824D-fructose+carbon source
4389028847D-fucose+carbon source
4389012936D-galactose+carbon source
438908391D-gluconate+carbon source
4389014314D-glucose 6-phosphate+carbon source
4389015748D-glucuronate+carbon source
4389033801D-saccharate+carbon source
4389016977L-alanine+carbon source
4389018287L-fucose+carbon source
4389029985L-glutamate+carbon source
4389017306maltose+carbon source
43890320055methyl beta-D-glucopyranoside+carbon source
4389017268myo-inositol+carbon source
43890506227N-acetylglucosamine+carbon source
4389017164stachyose+carbon source
4389017992sucrose+carbon source
4389032528turanose+carbon source
4389053426tween 80+degradation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
4389062965sodium formateyesyes
4389071321fusidateyesyes
4389032735guanidinium chlorideyesyes
438906472lincomycinyesyes
4389048607lithium chlorideyesyes
43890100147nalidixic acidyesyes
4389075273niaproofyesyes
4389075198tetrazolium blueyesyes
4389045735troleandomycinyesyes
4389028001vancomycinyesyes
438902676amoxicillinyesyes
43890474053cefazolinyesyes
4389029007ceftriaxoneyesyes
43890157175enoxacinyesyes
4389017833gentamicinyesyes
43890116278lomefloxacinyesyes
4389050694minocyclineyesyes
438907507neomycinyesyes
438908309polymyxin byesyes
438909215spectinomycinyesyes
438909337sulfathiazoleyesyes
4389073908vibriostatyesyes
438909332sulfamethoxazoleyesyes
4389075248potassium telluriteyesyes
4389075229sodium bromateyesyes
4389026710sodium chlorideyesyes
438902637amikacinyesyes
438903542cephalothinyesyes
4389027644chlortetracyclinyesyes
438903393carbenicillinyesyes
4389085260spiramycinyesyes
4389027902tetracyclineyesyes
4389028864tobramycinyesyes

enzymes

@refvalueactivityec
43890acid phosphatase+3.1.3.2
43890alkaline phosphatase+3.1.3.1
43890beta-glucosidase+3.2.1.21
43890catalase+1.11.1.6
43890esterase Lipase (C 8)+
43890esterase (C 4)+
43890lipase (C 14)+
43890leucine arylamidase+3.4.11.1
43890naphthol-AS-BI-phosphohydrolase+
43890urease+3.5.1.5
43890valine arylamidase+
43890arylsulfatase+3.1.6.1
43890alpha-chymotrypsin-3.4.21.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
42976sputumBavariaSwitzerlandCHEEurope
43890sputum specimen collected in Switzerland in 1998SwitzerlandCHEEurope1998

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Sputum
#Infection#Patient#Specimen

Safety information

risk assessment

  • @ref: 42976
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42976
  • description: Mycobacterium eburneum 16S ribosomal RNA gene, partial sequence
  • accession: KX879093
  • length: 1394
  • database: ena
  • NCBI tax ID: 2035343

Genome sequences

  • @ref: 66792
  • description: Mycobacterium eburneum strain DSM 44358
  • accession: 2035343.3
  • assembly level: wgs
  • database: patric
  • NCBI tax ID: 2035343

GC content

  • @ref: 42976
  • GC-content: 68.7
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno68no
motileno95.923yes
gram-positiveyes90.403no
anaerobicno99.409yes
aerobicyes90.274no
halophileno91.118no
spore-formingno82.392yes
glucose-utilyes70.128no
flagellatedno98.562yes
thermophileno98.181yes
glucose-fermentno88.618no

External links

@ref: 42976

culture collection no.: DSM 44358, CECT 8775

straininfo link

  • @ref: 96667
  • straininfo: 404303

literature

  • topic: Phylogeny
  • Pubmed-ID: 28869002
  • title: Mycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum.
  • authors: Nouioui I, Carro L, Teramoto K, Igual JM, Jando M, Del Carmen Montero-Calasanz M, Sutcliffe I, Sangal V, Goodfellow M, Klenk HP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002033
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Humans, Mycobacterium/*classification/genetics/isolation & purification, Mycobacterium Infections/microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sputum/*microbiology, Switzerland
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42976Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-44358Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44358)
43890Imen Nouioui, Lorena Carro, Kanae Teramoto, José M. Igual, Marlen Jando, Maria del Carmen Montero-Calasanz, Iain Sutcliffe, Vartul Sangal, Michael Goodfellow, Hans-Peter KlenkMycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum10.1099/ijsem.0.002033IJSEM 67: 3174-3181 201728869002
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
96667Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404303.1