Strain identifier

BacDive ID: 7266

Type strain: Yes

Species: Agromyces luteolus

Strain Designation: 8

Strain history: CIP <- 2001, IFO

NCBI tax ID(s): 88373 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 5398

BacDive-ID: 7266

DSM-Number: 14595

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

description: Agromyces luteolus 8 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, rhizospere of Sonneratia alba.

NCBI tax id

  • NCBI tax id: 88373
  • Matching level: species

strain history

@refhistory
5398<- IFO <- K. Hatano; 8
336262001, IFO
67770IFO 16235 <-- M. Takeuchi 8.
120694CIP <- 2001, IFO

doi: 10.13145/bacdive7266.20230509.8.1

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

@ref: 5398

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces luteolus

full scientific name: Agromyces luteolus Takeuchi and Hatano 2001

strain designation: 8

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120694positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18518Broom yellow (1032)10-14 daysISP 2
18518Broom yellow (1032)10-14 daysISP 3
18518Beige (1001)10-14 daysISP 4
18518Beige (1001)10-14 daysISP 5
18518Broom yellow (1032)10-14 daysISP 6
18518Beige (1001)10-14 daysISP 7
120694

multicellular morphology

@refforms multicellular complexmedium name
18518noISP 2
18518noISP 3
18518noISP 4
18518noISP 5
18518noISP 6
18518noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5398PP-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
18518ISP 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
18518ISP 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:
18518ISP 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
18518ISP 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
18518ISP 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
18518ISP 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
33626MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120694CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18518positiveoptimum28mesophilic
5398positivegrowth28mesophilic
33626positivegrowth30mesophilic
67770positivegrowth28mesophilic
120694positivegrowth30-37mesophilic
120694nogrowth10psychrophilic
120694nogrowth25mesophilic
120694nogrowth41thermophilic
120694nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120694
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no97
69480no99.98

halophily

@refsaltgrowthtested relationconcentration
120694NaClpositivegrowth0-4 %
120694NaClnogrowth6 %
120694NaClnogrowth8 %
120694NaClnogrowth10 %

murein

  • @ref: 5398
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
120694citrate-carbon source16947
120694esculin+hydrolysis4853
120694hippurate+hydrolysis606565
120694nitrate-reduction17632
120694nitrite-reduction16301
120694nitrate-respiration17632
68379nitrate-reduction17632
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 120694
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120694
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12069415688acetoin-
12069417234glucose-

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
68382beta-glucuronidase-3.2.1.31
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
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
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
120694oxidase-
120694beta-galactosidase+3.2.1.23
120694alcohol dehydrogenase-1.1.1.1
120694gelatinase-
120694amylase+
120694caseinase-3.4.21.50
120694catalase+1.11.1.6
120694tween esterase+
120694gamma-glutamyltransferase+2.3.2.2
120694lecithinase-
120694lipase-
120694lysine decarboxylase-4.1.1.18
120694ornithine decarboxylase-4.1.1.17
120694phenylalanine ammonia-lyase-4.3.1.24
120694tryptophan deaminase-
120694urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18518-----++-+/-----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18518-++-+++-----+--+---
120694-+--+---------++----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120694+/---+/--+/----+/-+/-+/-+/--+--+/-------+--+/--+/-+/---+/-+/-+/-+/---+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120694+-----------------+-------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
5398soil, rhizospere of Sonneratia albaSonneratia albaJapan, Priomote Island, OkinawaJapanJPNAsia
67770Surface of roots of Sonneratia alba, mangrove in the estuary of the Shiira RiverSonneratia albaIriomote IslandJapanJPNAsia
120694Plant, Surface of roots of Sonneratia albaIriomote IslandJapanJPNAsia1997

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53981Risk group (German classification)
185181Risk group (German classification)
1206941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5398
  • description: Agromyces sp. IFO16235 gene for 16S rRNA
  • accession: AB023356
  • length: 1493
  • database: ena
  • NCBI tax ID: 88373

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces luteolus strain JCM 1143188373.3wgspatric88373
67770Agromyces luteolus JCM 11431GCA_009729855contigncbi88373

GC content

@refGC-contentmethod
539871.1
6777071.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileno88.924no
flagellatedno97.328no
gram-positiveyes91.347no
anaerobicno99.616no
halophileno78.902no
spore-formingno90.152no
thermophileno99.083yes
glucose-utilyes89.213no
aerobicyes95.116no
glucose-fermentno92.331no

External links

@ref: 5398

culture collection no.: DSM 14595, IFO 16235, NBRC 16235, VKM Ac-2085, JCM 11431, CIP 107131, IAM 15144, KCTC 13907, NCIMB 13882

straininfo link

  • @ref: 76717
  • straininfo: 49556

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
5398Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14595)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14595
18518Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14595.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
33626Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4533
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/
68371Automatically annotated from API 50CH acid
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
76717Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49556.1StrainInfo: A central database for resolving microbial strain identifiers
120694Curators of the CIPCollection of Institut Pasteur (CIP 107131)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107131