Strain identifier

BacDive ID: 8464

Type strain: Yes

Species: Mycobacterium agri

Strain Designation: 90012

Strain history: M. Tsukamura 90012.

NCBI tax ID(s): 36811 (species)

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General

@ref: 11836

BacDive-ID: 8464

DSM-Number: 44515

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive

description: Mycobacterium agri 90012 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 36811
  • Matching level: species

strain history

@refhistory
11836<- JCM <- M. Tsukamura; 90012
67771<- JCM <- M Tsukamura 90012
67770M. Tsukamura 90012.

doi: 10.13145/bacdive8464.20230509.8.1

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 agri
  • full scientific name: Mycobacterium agri (ex Tsukamura 1972) Tsukamura 1981

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium agri

@ref: 11836

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium agri

full scientific name: Mycobacterium agri (ex Tsukamura 1972) Tsukamura 1981

strain designation: 90012

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
67771positive
69480no91.37
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19867Pale orange10-14 days5006
19867Rape yellow10-14 daysBUG
19867Pale orange10-14 daysMB7H9

multimedia

  • @ref: 11836
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44515.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11836MIDDLEBROOK 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
19867BUGyes
198675006yesMedium: 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
19867MB7H9yesName: 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

culture temp

@refgrowthtypetemperaturerange
19867positiveoptimum37mesophilic
11836positivegrowth37mesophilic
53800positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
53800microaerophile
67771aerobe

spore formation

@refspore formationconfidence
69481no93
69480no98.77

observation

@refobservation
67770quinones: MK-9(H2)
67771quinones: MK-9(H_2_)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

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
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
19867-+/-++-+-++---++---+/--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19867+++-+----++-+--++-+

Isolation, sampling and environmental information

isolation

@refsample type
11836soil
53800Soil
67770Soil
67771From soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118361Risk group (German classification)
198671Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium agri 16S ribosomal RNA gene, partial sequenceAY438067541ena36811
11836Mycobacterium agri 16S rRNA gene, strain DSM 44515TAJ4290451456ena36811

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycolicibacterium agri JCM 6377GCA_010722915contigncbi36811
66792Mycobacterium agri strain CCUG3767336811.3wgspatric36811
66792Mycolicibacterium agri strain JCM 637736811.10wgspatric36811
66792Mycolicibacterium agri CCUG 376732865750426draftimg36811
67770Mycolicibacterium agri CCUG37673GCA_002553505contigncbi36811

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
gram-positiveyes87.972no
anaerobicno98.97yes
halophileno91.539no
spore-formingno75.951no
glucose-utilyes86.142no
aerobicyes86.863no
motileno92.056no
flagellatedno97.59no
thermophileno99.189yes
glucose-fermentno89.822yes

External links

@ref: 11836

culture collection no.: CCUG 37673 B, KCTC 9502, DSM 44515, ATCC 27406, CCUG 37673, CIP 105391, JCM 6377, CCUG 37673 A

straininfo link

  • @ref: 77859
  • straininfo: 310252

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11836Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44515)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44515
19867Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44515.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
53800Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37673 B)https://www.ccug.se/strain?id=37673
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77859Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310252.1StrainInfo: A central database for resolving microbial strain identifiers