Strain identifier

BacDive ID: 16985

Type strain: Yes

Species: Actinomadura mexicana

Strain Designation: A290

Strain history: CIP <- 2004, DSMZ <- M. Goodfellow, UK: strain A290, Actinomadura sp.

NCBI tax ID(s): 134959 (species)

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General

@ref: 11811

BacDive-ID: 16985

DSM-Number: 44485

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive

description: Actinomadura mexicana A290 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 134959
  • Matching level: species

strain history

@refhistory
11811<- M. Goodfellow; A290 (Actinomadura sp.)
67770DSM 44485 <-- M. Goodfellow A290.
120927CIP <- 2004, DSMZ <- M. Goodfellow, UK: strain A290, Actinomadura sp.

doi: 10.13145/bacdive16985.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinomadura
  • species: Actinomadura mexicana
  • full scientific name: Actinomadura mexicana Quintana et al. 2004

@ref: 11811

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinomadura

species: Actinomadura mexicana

full scientific name: Actinomadura mexicana Quintana et al. 2004 emend. Nouioui et al. 2018

strain designation: A290

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120927positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11811TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
11811N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium554.pdf
33240MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120927CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
33240positivegrowth30mesophilic
67770positivegrowth28mesophilic
11811positivegrowth28mesophilic
120927positivegrowth30-41
120927nogrowth5psychrophilic
120927nogrowth15psychrophilic
120927nogrowth22psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120927
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
120927NaClpositivegrowth0-2 %
120927NaClnogrowth4 %
120927NaClnogrowth6 %
120927NaClnogrowth8 %
120927NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12092717632nitrate-reduction
12092716301nitrite-reduction
12092717632nitrate-respiration

metabolite production

  • @ref: 120927
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12092715688acetoin-
12092717234glucose-

enzymes

@refvalueactivityec
120927oxidase-
120927beta-galactosidase+3.2.1.23
120927alcohol dehydrogenase-1.1.1.1
120927gelatinase-
120927catalase+1.11.1.6
120927gamma-glutamyltransferase-2.3.2.2
120927lysine decarboxylase-4.1.1.18
120927ornithine decarboxylase-4.1.1.17
120927phenylalanine ammonia-lyase-4.3.1.24
120927tryptophan deaminase-
120927urease-3.5.1.5
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120927-+++-+++--++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11811garden soilMexico CityMexicoMEXNorth America
67770Garden soilMexico CityMexicoMEXNorth America
120927Environment, Garden soilMexicoMEXNorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118111Risk group (German classification)
1209271Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura mexicana gene for 16S ribosomal RNA, partial sequence, strain: A290AB821481646ena134959
20218Actinomadura mexicana 16S ribosomal RNA gene, partial sequenceAF2771951421ena134959

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomadura mexicana strain DSM 44485134959.3wgspatric134959
66792Actinomadura mexicana DSM 444852724679706draftimg134959
67770Actinomadura mexicana DSM 44485GCA_900188105contigncbi134959

GC content

  • @ref: 67770
  • GC-content: 72.3
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.081no
gram-positiveyes91.236no
anaerobicno98.245no
halophileno91.789no
spore-formingyes93.41no
thermophileno96.429yes
glucose-utilyes89.26no
aerobicyes89.441no
flagellatedno98.075no
glucose-fermentno89.28no

External links

@ref: 11811

culture collection no.: DSM 44485, NRRL B-24203, JCM 13236, CIP 108420

straininfo link

  • @ref: 85988
  • straininfo: 131405

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14666978Actinomadura mexicana sp. nov. and Actinomadura meyerii sp. nov., two novel soil sporoactinomycetes.Quintana ET, Trujillo ME, Goodfellow MSyst Appl Microbiol10.1078/0723202037708658002003Actinomycetales/*classification/cytology/*isolation & purification/physiology, Carbohydrates/analysis/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Lipids/analysis/chemistry, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Vitamin K 2/analysis/chemistryEnzymology
Phylogeny32701429Description of the bacterial RNA polymerase inhibitor GE23077-producer Actinomadura sp. NRRL B-65521(T) as Actinomadura lepetitiana sp. nov.Dalmastri C, Gastaldo L, Berini F, Marinelli F, Marcone GLInt J Syst Evol Microbiol10.1099/ijsem.0.0043482020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11811Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44485)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44485
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
33240Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6041
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/
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
85988Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131405.1StrainInfo: A central database for resolving microbial strain identifiers
120927Curators of the CIPCollection of Institut Pasteur (CIP 108420)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108420