Strain identifier

BacDive ID: 158311

Type strain: Yes

Species: Mycobacterium kyogaense

Strain history: <- I. Nouioui, Univ. Newcastle, Newcastle upon Tyne, UK; NCTC 11659 <- J.L. Paul and Immodulon Therapeutics Ltd, The school of Pathology, The Middlesex Hospital Medical School; NCTC 11659

NCBI tax ID(s): 2212479 (species)

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General

@ref: 64977

BacDive-ID: 158311

DSM-Number: 107316

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped

description: Mycobacterium kyogaense CECT 9646 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from mud.

NCBI tax id

  • NCBI tax id: 2212479
  • Matching level: species

strain history

  • @ref: 64977
  • history: <- I. Nouioui, Univ. Newcastle, Newcastle upon Tyne, UK; NCTC 11659 <- J.L. Paul and Immodulon Therapeutics Ltd, The school of Pathology, The Middlesex Hospital Medical School; NCTC 11659

doi: 10.13145/bacdive158311.20240916.9.1

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 kyogaense
  • full scientific name: Mycobacterium kyogaense Nouioui et al. 2018

@ref: 64977

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium kyogaense

full scientific name: Mycobacterium kyogaense Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapeconfidence
66749positiverod-shaped
69480positive91.784

colony morphology

@refcolony colorincubation periodmedium used
66749yellow-orange5 daysLöwenstein-Jensen medium
66749yellow-orange5 daysTryptic Soy Agar
66749yellow-orange5 daysMB7H10 agar
66749yellow-orange5 daysPMG agar
66749yellow-orange5 daysglucose-yeast extract-malt extract agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64977MIDDLEBROOK 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
64977PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250)yeshttps://mediadive.dsmz.de/medium/250Name: PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250) Composition: Agar 20.0 g/l Proteose peptone no. 3 5.0 g/l Meat extract 3.0 g/l Glycerol Distilled water
66749glucose-yeast extract-malt extract agaryes
66749Löwenstein-Jensen mediumyes
66749MB7H10 agaryes
66749PMG agaryes
66749tryptic soy agar (TSA)yes

culture temp

@refgrowthtypetemperature
64977positivegrowth37
66749nogrowth4
66749nogrowth15
66749positiveoptimum37
66749nogrowth42
66749nogrowth45
66749positivegrowth20-28

culture pH

@refabilitytypepH
66749nogrowth5
66749positivegrowth6
66749positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 66749
  • oxygen tolerance: aerobe

halophily

  • @ref: 66749
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 8 %(w/v)

observation

  • @ref: 66749
  • observation: acid-alcohol fast, rapidly growing species

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
667495291gelatin-assimilation
6674913705acetoacetate-assimilation
6674915748D-glucuronate-assimilation
6674915895D-galactonic acid lactone-assimilation
6674915971L-histidine-assimilation
6674916467L-arginine-assimilation
6674916523D-serine-assimilation
6674916537galactarate-assimilation
6674916634raffinose-assimilation
6674916651(S)-lactate-assimilation
6674917057cellobiose-assimilation
6674917306maltose-assimilation
6674917596inosine-assimilation
6674917716lactose-assimilation
6674917814salicin-assimilation
6674917924D-sorbitol-assimilation
6674918024D-galacturonic acid-assimilation
66749181014-hydroxyphenylacetic acid-assimilation
6674918183L-pyroglutamic acid-assimilation
6674918287L-fucose-assimilation
6674926490quinate-assimilation
6674928053melibiose-assimilation
6674928066gentiobiose-assimilation
6674928800N-acetylgalactosamine-assimilation
6674929991L-aspartate-assimilation
6674930612D-glucarate-assimilation
6674932323glucuronamide-assimilation
6674932528turanose-assimilation
6674935418n-acetylneuraminate-assimilation
6674953258citric acid-assimilation
6674962345L-rhamnose-assimilation
66749739183-O-methyl-D-glucose-assimilation
66749320055methyl beta-D-glucopyranoside-assimilation
667498391D-gluconate+assimilation
6674912936D-galactose+assimilation
6674914314D-glucose 6-phosphate+assimilation
6674915824D-fructose+assimilation
6674916024D-mannose+assimilation
6674916411acetic acid+assimilation
66749167632-oxobutanoate+assimilation
6674916865gamma-aminobutyric acid+assimilation
6674916899D-mannitol+assimilation
6674916977L-alanine+assimilation
6674917115L-serine+assimilation
6674917268myo-inositol+assimilation
6674917272propionate+assimilation
6674917754glycerol+assimilation
6674917925alpha-D-glucose+assimilation
6674917992sucrose+assimilation
6674918333D-arabitol+assimilation
6674923652dextrin+assimilation
6674927082trehalose+assimilation
6674929985L-glutamate+assimilation
6674930796(R)-malic acid+assimilation
6674930797(S)-malic acid+assimilation
66749370543-hydroxybutyrate+assimilation
6674951850methyl pyruvate+assimilation
6674953423tween 40+assimilation
6674953426tween 80+assimilation
6674959640N-acetylglucosamine+assimilation
6674963153N-acetyl-D-mannosamine+assimilation
66749645522-hydroxybutyrate+assimilation
6674970744glycine-proline+assimilation
6674973706bromosuccinate+assimilation
6674975248potassium tellurite+assimilation
66749168102-oxoglutarate+assimilation
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
66749alpha-chymotrypsin-3.4.21.1
66749alpha-fucosidase-3.2.1.51
66749alpha-mannosidase-3.2.1.24
66749beta-galactosidase-3.2.1.23
66749beta-glucosidase-3.2.1.21
66749N-acetyl-beta-glucosaminidase-3.2.1.52
66749acid phosphatase+3.1.3.2
66749alkaline phosphatase+3.1.3.1
66749alpha-galactosidase+3.2.1.22
66749alpha-glucosidase+3.2.1.20
66749arylsulfatase+3.1.6.1
66749beta-glucuronidase+3.2.1.31
66749catalase+1.11.1.6
66749cystine arylamidase+3.4.11.3
66749esterase (C 4)+
66749esterase Lipase (C 8)+
66749leucine arylamidase+3.4.11.1
66749lipase (C 14)+
66749naphthol-AS-BI-phosphohydrolase+
66749trypsin+3.4.21.4
66749urease+3.5.1.5
66749valine arylamidase+
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
68379pyrazinamidase+3.5.1.B15
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
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66749C18:1 w9c15
    66749C16:1 w9c2.1
    66749C16:032.3
    66749C10 Me- 18:04.6
    66749C16:1w6c6.6
    66749C14:08.2
    66749C17:1 w7c/18 alcohol9.3
    6674920:0 ALC9.5
    66749C18:09.9
  • type of FA analysis: whole cell analysis
  • incubation medium: PMG broth
  • agar/liquid: liquid
  • incubation temperature: 37
  • incubation time: 7
  • software version: Sherlock 4.5
  • library/peak naming table: myco6
  • system: MIS MIDI
  • cutoff value:

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYG
64977-++/-+--+-------------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
64977-++/-+-+/-----+/-----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
64977mudLake KyogaUgandaUGAAfrica1.716632.7
66749Kyoga LakeUgandaUGAAfrica

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Mud (Sludge)

Sequence information

16S sequences

  • @ref: 66749
  • description: Mycobacterium kyogaense strain NCTC 11659 16S ribosomal RNA gene, partial sequence
  • accession: MH401762
  • length: 1529
  • database: nuccore
  • NCBI tax ID: 2212479

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium kyogaense NCTC 11659GCA_003254575contigncbi2212479
66792Mycobacterium sp. NCTC 116592212479.3wgspatric2212479
66792Mycolicibacterium kyogaense NCTC 116592869209271draftimg2212479

GC content

  • @ref: 66749
  • GC-content: 67.9
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno89no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.784no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.483yes
69480spore-formingspore-formingAbility to form endo- or exosporesno65.491no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.27yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97yes
69480flagellatedmotile2+Ability to perform flagellated movementno86.871no

External links

@ref: 64977

culture collection no.: CECT 9646, DSM 107316, NCTC 11659

straininfo link

  • @ref: 111125
  • straininfo: 403136

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny30300123Description of a novel species of fast growing mycobacterium: Mycobacterium kyogaense sp. nov., a scotochromogenic strain received as Mycobacterium vaccae.Nouioui I, Brunet LR, Simpson D, Klenk HP, Goodfellow MInt J Syst Evol Microbiol10.1099/ijsem.0.0030392018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Genes, Bacterial, Mycobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Pathogenicity34884743Rapidly Growing Mycobacterium Species: The Long and Winding Road from Tuberculosis Vaccines to Potent Stress-Resilience Agents.Amoroso M, Langgartner D, Lowry CA, Reber SOInt J Mol Sci10.3390/ijms2223129382021Animals, Humans, *Immunomodulating Agents, Inflammation/etiology/*prevention & control, *Mycobacteriaceae, Stress, Psychological/*complicationsStress
Phylogeny36282561Mycolicibacterium aurantiacum sp. nov. and Mycolicibacterium xanthum sp. nov., two novel actinobacteria isolated from mangrove sediments.Pan X, Li Z, Huang S, Huang Y, Wang Q, Tao Z, Hu WInt J Syst Evol Microbiol10.1099/ijsem.0.0055952022*Actinobacteria, Bacterial Typing Techniques, Base Composition, Copper, DNA, Bacterial/genetics, Fatty Acids/chemistry, Kerosene, Nucleic Acid Hybridization, Nucleotides, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Geologic SedimentsTranscriptome

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
64977Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107316Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107316)
66749Imen Nouioui, Laura Rosa Brunet, David Simpson, Hans-Peter Klenk, Michael GoodfellowDescription of a novel species of fast growing mycobacterium: Mycobacterium kyogaense sp. nov., a scotochromogenic strain received as Mycobacterium vaccae10.1099/ijsem.0.003039IJSEM 68: 3726-3734 201830300123
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
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111125Reimer, 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-ID403136.1