Strain identifier

BacDive ID: 7283

Type strain: Yes

Species: Agromyces flavus

Strain history: <- YQ Zhang, IMB, CAMS & Peking Union Medical College, China

NCBI tax ID(s): 589382 (species)

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General

@ref: 16113

BacDive-ID: 7283

DSM-Number: 22059

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

description: Agromyces flavus DSM 22059 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 589382
  • Matching level: species

strain history

@refhistory
16113<- Y.-Q. Zhang; CPCC 202695 <- Y.-Q. Zhang et al.
67770CCM 7623 <-- Y.-Q. Zhang CPCC 202695.
67771<- YQ Zhang, IMB, CAMS & Peking Union Medical College, China

doi: 10.13145/bacdive7283.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces flavus
  • full scientific name: Agromyces flavus Chen et al. 2011

@ref: 16113

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces flavus

full scientific name: Agromyces flavus Chen et al. 2011

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
67771positive
69480positive100

colony morphology

@refcolony colormedium used
69223Ivory (1014)suter without tyrosine
69223Lemon yellow (1012)ISP 2
69223Lemon yellow (1012)ISP 6
69223Light ivory (1015)ISP 3
69223Zinc yellow (1018)ISP 4
69223Zinc yellow (1018)ISP 5
69223Zinc yellow (1018)ISP 7
69223Zinc yellow (1018)suter with tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69223noAerial myceliumISP 2
69223noAerial myceliumISP 3
69223noAerial myceliumISP 4
69223noAerial myceliumISP 5
69223noAerial myceliumISP 6
69223noAerial myceliumISP 7
69223noAerial myceliumsuter with tyrosine
69223noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69223noMelanin
69223nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69223DSM_22059_image3.jpegPlates (92, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69223DSM_22059_image4.jpegPlates (92, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 16113
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16113positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.987

halophily

  • @ref: 69223
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6922322599arabinose+growth
6922362968cellulose+/-growth
6922328757fructose+growth
6922317234glucose+growth
6922317268inositol+/-growth
6922337684mannose+growth
6922316634raffinose+/-growth
6922326546rhamnose+growth
6922317992sucrose+growth
6922318222xylose+growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69223------+--++/---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69223-+/-+-++++/--+/--+--++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16113soil sampleQinghai Province, Tibet plateauChinaCHNAsia
67771From soilQinghai ProvinceChinaCHNAsia
67770Soil from the Qinghai-Tibet plateauChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 16113
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16113
  • description: Agromyces flavus strain CPCC 202695 16S ribosomal RNA gene, partial sequence
  • accession: FJ529717
  • length: 1466
  • database: ena
  • NCBI tax ID: 589382

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces flavus CCM 7623GCA_014635805scaffoldncbi589382
66792Agromyces flavus CPCC 202695GCA_900104685chromosomencbi589382
66792Agromyces flavus strain CCM 7623589382.12wgspatric589382
66792Agromyces flavus strain CPCC 202695589382.3completepatric589382
66792Agromyces flavus strain CPCC 202695589382.7wgspatric589382
66792Agromyces flavus CPCC 2026952681812891draftimg589382
66792Agromyces flavus DSM 220592634166342draftimg589382
66792Agromyces flavus CPCC 2026952880787586draftimg589382
67770Agromyces flavus CPCC 202695GCA_004366335contigncbi589382

GC content

  • @ref: 16113
  • GC-content: 70.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
gram-positiveyes93.815yes
anaerobicno99.696yes
halophileno88.936no
spore-formingno92.054no
glucose-utilyes85.706no
thermophileno98.815yes
flagellatedno98.08no
aerobicyes95.982yes
motileno88.991no
glucose-fermentno89.299yes

External links

@ref: 16113

culture collection no.: DSM 22059, CCM 7623, KCTC 19578, CPCC 202695, JCM 30488, NBRC 109064

straininfo link

  • @ref: 76734
  • straininfo: 398772

literature

  • topic: Phylogeny
  • Pubmed-ID: 20802064
  • title: Agromyces flavus sp. nov., an actinomycete isolated from soil.
  • authors: Chen J, Chen HM, Zhang YQ, Wei YZ, Li QP, Liu HY, Su J, Zhang YQ, Yu LY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.023242-0
  • year: 2010
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
16113Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22059)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22059
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
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)
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
69223Wink, J.https://cdn.dsmz.de/wink/DSM%2022059.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
76734Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398772.1StrainInfo: A central database for resolving microbial strain identifiers