Strain identifier

BacDive ID: 7267

Type strain: Yes

Species: Agromyces bracchium

Strain Designation: 65

Strain history: CIP <- 2005, JCM <- M. Takeuchi, IFO

NCBI tax ID(s): 88376 (species)

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General

@ref: 5399

BacDive-ID: 7267

DSM-Number: 14596

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

description: Agromyces bracchium 65 is a mesophilic, Gram-positive bacterium that was isolated from soil, rhizosphere of Bruguera gymnorrhiza.

NCBI tax id

  • NCBI tax id: 88376
  • Matching level: species

strain history

@refhistory
5399<- K. Hatano; no. 65
67770IFO 16238 <-- M. Takeuchi 65.
116987CIP <- 2005, JCM <- M. Takeuchi, IFO

doi: 10.13145/bacdive7267.20230509.8.1

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 bracchium
  • full scientific name: Agromyces bracchium Takeuchi and Hatano 2001

@ref: 5399

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces bracchium

full scientific name: Agromyces bracchium Takeuchi and Hatano 2001

strain designation: 65

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116987positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18386Beige (1001)10-14 daysISP 2
18386Beige (1001)10-14 daysISP 3
18386Beige (1001)10-14 daysISP 4
18386Beige (1001)10-14 daysISP 5
18386Beige (1001)10-14 daysISP 6
18386Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18386noISP 2
18386noISP 3
18386noISP 4
18386noISP 5
18386noISP 6
18386noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5399PP-MEDIUM (DSMZ Medium 513)yeshttps://mediadive.dsmz.de/medium/513Name: PP-MEDIUM (DSMZ Medium 513) Composition: Agar 15.0 g/l Polypeptone 10.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Distilled water
18386ISP 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
18386ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18386ISP 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
18386ISP 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
18386ISP 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
18386ISP 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
39704MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
116987CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
18386positiveoptimum28mesophilic
5399positivegrowth28mesophilic
39704positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no96
69480no99.994

murein

  • @ref: 5399
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-13, NK-11

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
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+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18386+--++++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18386+++-+++--++-++++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
5399soil, rhizosphere of Bruguera gymnorrhizaBruguiera gymnorhizaJapan, Okinawa, Iriomote IslandJapanJPNAsia
67770Soil of the rhizosphere of Bruguera gymnorrhiza, mangrove in the estuary of the Shiira RiverBruguera gymnorrhizaIriomote IslandJapanJPNAsia
116987Environment, Soil, rhizosphere of Bruguera gymmorrhizaShiira river, Iriomote IslandJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53991Risk group (German classification)
183861German classification
1169871Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5399
  • description: Agromyces sp. IFO16238 gene for 16S rRNA
  • accession: AB023359
  • length: 1511
  • database: ena
  • NCBI tax ID: 88376

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces bracchium strain JCM 1143388376.3wgspatric88376
67770Agromyces bracchium JCM 11433GCA_009709675contigncbi88376

GC content

@refGC-contentmethod
539970
6777070high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileno91.063no
flagellatedno97.828no
gram-positiveyes91.81no
anaerobicno99.659no
halophileno84.785no
spore-formingno93.328no
thermophileno98.809no
glucose-utilyes89.898no
aerobicyes96.525no
glucose-fermentno90.915yes

External links

@ref: 5399

culture collection no.: DSM 14596, IFO 16238, NBRC 16238, VKM Ac-2088, JCM 11433, CIP 108985, IAM 15146, KCTC 13909, NCIMB 13881

straininfo link

  • @ref: 76718
  • straininfo: 49557

literature

  • topic: Phylogeny
  • Pubmed-ID: 11491355
  • title: Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere.
  • authors: Takeuchi M, Hatano K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-4-1529
  • year: 2001
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Ecosystem, Japan, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Soil Microbiology, Species Specificity, Trees
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
5399Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14596)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14596
18386Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14596.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
39704Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6675
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/
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
76718Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49557.1StrainInfo: A central database for resolving microbial strain identifiers
116987Curators of the CIPCollection of Institut Pasteur (CIP 108985)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108985