Strain identifier

BacDive ID: 8579

Type strain: Yes

Species: Mycobacterium riyadhense

Strain Designation: NLA000201958

Strain history: CIP <- 2008, J. Van Ingen, RIVM, Bilthoven, The Netherlands: strain NLA000201958 <- King Faisal Hosp., Riyadh, Saudi Arabia

NCBI tax ID(s): 486698 (species)

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General

@ref: 15640

BacDive-ID: 8579

DSM-Number: 45176

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

description: Mycobacterium riyadhense NLA000201958 is a microaerophile, mesophilic human pathogen that was isolated from patient, maxillary sinus lavage.

NCBI tax id

  • NCBI tax id: 486698
  • Matching level: species

strain history

@refhistory
15640<- J. van Ingen, RIVM; NLA 000201958 <- S.A. Al-Hajoj
122244CIP <- 2008, J. Van Ingen, RIVM, Bilthoven, The Netherlands: strain NLA000201958 <- King Faisal Hosp., Riyadh, Saudi Arabia

doi: 10.13145/bacdive8579.20230509.8.1

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 riyadhense
  • full scientific name: Mycobacterium riyadhense van Ingen et al. 2009

@ref: 15640

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium riyadhense

full scientific name: Mycobacterium riyadhense van Ingen et al. 2009 emend. Nouioui et al. 2018

strain designation: NLA000201958

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no97.086
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19718Beige10-14 daysISP 2
1971810-14 daysISP 4
1971810-14 daysISP 5
1971810-14 daysISP 6
1971810-14 daysISP 7
616933-5 days

multicellular morphology

@refforms multicellular complexmedium name
19718noISP 2
19718noISP 4
19718noISP 5
19718noISP 6
19718noISP 7

pigmentation

  • @ref: 29078
  • production: no

multimedia

  • @ref: 15640
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45176.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15640MIDDLEBROOK 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
19718ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19718ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19718ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19718ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19718ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
15640positivegrowth37mesophilic
19718positiveoptimum37mesophilic
29078positivegrowth24-45
29078positiveoptimum36mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 61693
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.736

observation

  • @ref: 29078
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2907853426tween 80+carbon source
2907816199urea+carbon source
2907817632nitrate+reduction
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29078arylsulfatase+3.1.6.1
29078catalase+1.11.1.6
29078urease+3.5.1.5
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
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19718++-------+-+--++++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19718+++------++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
15640patient, maxillary sinus lavageRiyadh, King Faisal HospitalSaudi ArabiaSAUAsia
61693Human maxillary sinus lavage,19-yr-old womanRiyadhSaudi ArabiaSAUAsia
122244Human, Sinus lavage fluidRiyadhSaudi ArabiaSAUAsia2002

isolation source categories

Cat1Cat2
#Infection#Patient
#Host Body-Site#Oral cavity and airways

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: EU274642
  • Sequence Identity:
  • Total samples: 1520
  • soil counts: 881
  • aquatic counts: 382
  • animal counts: 203
  • plant counts: 54

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
15640yes, in single cases1Risk group (German classification)
1222441Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15640
  • description: Mycobacterium riyadhense strain NLA000201958 16S ribosomal RNA gene, partial sequence
  • accession: EU274642
  • length: 1475
  • database: ena
  • NCBI tax ID: 486698

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium riyadhense DSM 45176GCA_002101845contigncbi486698
66792Mycobacterium riyadhense strain DSM 45176486698.3wgspatric486698
66792Mycobacterium riyadhense DSM 451762865423940draftimg486698
66792Mycobacterium riyadhense DSM 45176GCA_025821735scaffoldncbi486698

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno72no
gram-positiveyes89.284no
anaerobicno98.852yes
halophileno89.748no
spore-formingno87.1no
glucose-utilyes61.858no
aerobicyes90.451no
thermophileno98.545yes
motileno96.047no
flagellatedno99.186no
glucose-fermentno90.157no

External links

@ref: 15640

culture collection no.: DSM 45176, CIP 109808, CCUG 58462

straininfo link

  • @ref: 77963
  • straininfo: 399593

literature

  • topic: Phylogeny
  • Pubmed-ID: 19406791
  • title: Mycobacterium riyadhense sp. nov., a non-tuberculous species identified as Mycobacterium tuberculosis complex by a commercial line-probe assay.
  • authors: van Ingen J, Al-Hajoj SA, Boeree M, Al-Rabiah F, Enaimi M, de Zwaan R, Tortoli E, Dekhuijzen R, van Soolingen D
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.005629-0
  • year: 2009
  • mesh: Adult, Bacterial Proteins/genetics, DNA, Bacterial/analysis/genetics, DNA, Ribosomal Spacer/genetics, *Diagnostic Errors, Genes, rRNA, Humans, Male, Maxillary Sinus/*microbiology, *Maxillary Sinusitis/diagnosis/microbiology, Molecular Probe Techniques, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification/physiology, Mycobacterium Infections/diagnosis/microbiology, Mycobacterium tuberculosis/classification/genetics/*isolation & purification, Mycolic Acids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, *Reagent Kits, Diagnostic, Saudi Arabia, Sequence Analysis, DNA, Species Specificity, Therapeutic Irrigation, Tuberculosis/diagnosis/microbiology, Young Adult
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15640Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45176)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45176
19718Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45176.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
29078Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2550828776041
61693Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58462)https://www.ccug.se/strain?id=58462
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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)
77963Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399593.1StrainInfo: A central database for resolving microbial strain identifiers
122244Curators of the CIPCollection of Institut Pasteur (CIP 109808)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109808