Strain identifier

BacDive ID: 7269

Type strain: Yes

Species: Agromyces aurantiacus

Strain history: CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 21741 <- DSMZ <- CCTCC <- CCRC

NCBI tax ID(s): 165814 (species)

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General

@ref: 5401

BacDive-ID: 7269

DSM-Number: 14598

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

description: Agromyces aurantiacus DSM 14598 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from primeval forest soil.

NCBI tax id

  • NCBI tax id: 165814
  • Matching level: species

strain history

@refhistory
5401<- C.-L. Jiang, YIM <- CCTCC <- W.-J. Li
67770AS 4.1717 <-- C.-L. Jiang YIM 21741.
116560CIP <- 2003, W.J. Li, Yunnan Univ., Kunming, China: strain YIM 21741 <- DSMZ <- CCTCC <- CCRC

doi: 10.13145/bacdive7269.20230509.8.1

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 aurantiacus
  • full scientific name: Agromyces aurantiacus Li et al. 2003

@ref: 5401

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces aurantiacus

full scientific name: Agromyces aurantiacus Li et al. 2003

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116560positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18388Saffron yellow (1017)10-14 daysISP 2
18388Saffron yellow (1017)10-14 daysISP 3
18388Saffron yellow (1017)10-14 daysISP 4
18388Saffron yellow (1017)10-14 daysISP 5
18388Saffron yellow (1017)10-14 daysISP 6
18388Saffron yellow (1017)10-14 daysISP 7
116560

multicellular morphology

@refforms multicellular complexmedium name
18388noISP 2
18388noISP 3
18388noISP 4
18388noISP 5
18388noISP 6
18388noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5401ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636)yeshttps://mediadive.dsmz.de/medium/636Name: ISP MEDIUM 2 WITH 5% NaCl (DSMZ Medium 636; with strain-specific modifications) Composition: NaCl 50.0 g/l Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
18388ISP 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
18388ISP 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:
18388ISP 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
18388ISP 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
18388ISP 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
18388ISP 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
38247MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116560CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18388positiveoptimum28mesophilic
5401positivegrowth28mesophilic
38247positivegrowth30mesophilic
67770positivegrowth28mesophilic
116560positivegrowth25-41
116560nogrowth10psychrophilic
116560nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116560
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.964

halophily

@refsaltgrowthtested relationconcentration
116560NaClpositivegrowth0-4 %
116560NaClnogrowth6 %
116560NaClnogrowth8 %
116560NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1838817234glucose+
1838822599arabinose+
1838817992sucrose+
1838818222xylose+/-
1838817268myo-inositol+/-
1838829864mannitol+
1838828757fructose+
1838826546rhamnose+
1838816634raffinose+
1838862968cellulose+
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837127082trehalose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
11656016947citrate-carbon source
1165604853esculin+hydrolysis
116560606565hippurate-hydrolysis
11656017632nitrate-reduction
11656016301nitrite-reduction
11656017632nitrate-respiration
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

antibiotic resistance

  • @ref: 116560
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116560
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11656015688acetoin-
11656017234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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
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
116560oxidase-
116560beta-galactosidase+3.2.1.23
116560alcohol dehydrogenase-1.1.1.1
116560gelatinase-
116560amylase+
116560DNase+
116560caseinase-3.4.21.50
116560catalase+1.11.1.6
116560tween esterase+
116560gamma-glutamyltransferase-2.3.2.2
116560lecithinase-
116560lipase-
116560lysine decarboxylase-4.1.1.18
116560ornithine decarboxylase-4.1.1.17
116560phenylalanine ammonia-lyase-4.3.1.24
116560protease-
116560tryptophan deaminase-
116560urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18388--+--++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18388-+--++++-++-+-++---
116560-+--+----++-+-+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116560+/---+/--------+/-------------+/---+/--+/-+/--+/-+/-+/-+/-+/---+/---------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116560++--+-+++++----+--+-+----+-----+-+-+-------------+---+------+--------------+---++-------+-+-----+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5401primeval forest soilYunnan Province, XishuangbannaChinaCHNAsia
67770Soil from a primeval forestXishuangbanna, Yunnan ProvinceChinaCHNAsia
116560Environment, Soil, primeval forestYunnanChinaCHNAsia1998

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
54011Risk group (German classification)
183881
1165601Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5401
  • description: Agromyces aurantiacus 16S ribosomal RNA gene, partial sequence
  • accession: AF389342
  • length: 1464
  • database: ena
  • NCBI tax ID: 165814

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces aurantiacus DSM 14598GCA_016907355contigncbi165814
66792Agromyces aurantiacus strain DSM 14598165814.3wgspatric165814
66792Agromyces aurantiacus DSM 145982893554490draftimg165814

GC content

@refGC-contentmethod
540172.8
6777072.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.864no
gram-positiveyes92.359no
anaerobicno99.516no
aerobicyes93.863no
halophileno93.595no
spore-formingno92.099no
thermophileno99.146yes
glucose-utilyes83.925yes
flagellatedno97.251no
glucose-fermentno90.58yes

External links

@ref: 5401

culture collection no.: DSM 14598, AS 4.1717, CCTCC 001012, YIM 21741, JCM 12113, BCRC 16310, CCTCC AA 001012, CGMCC 4.1717, CIP 107976, IAM 15154, KCTC 9967, CCRC 16310

straininfo link

  • @ref: 76720
  • straininfo: 100489

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656188Agromyces aurantiacus sp. nov., isolated from a Chinese primeval forest.Li WJ, Zhang LP, Xu P, Cui XL, Xu LH, Zhang Z, Schumann P, Stackebrandt E, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.02350-02003Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyGenetics
Phylogeny20435752Agromyces tropicus sp. nov., isolated from soil.Thawai C, Tanasupawat S, Suwanborirux K, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.021774-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, ThailandGenetics
Phylogeny20639226Agromyces soli sp. nov., isolated from farm soil.Lee M, Ten LN, Woo SG, Park JInt J Syst Evol Microbiol10.1099/ijs.0.021568-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Amino Acids/analysis, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitle
5401Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14598)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14598
18388Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14598.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
38247Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5546
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
76720Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100489.1StrainInfo: A central database for resolving microbial strain identifiers
116560Curators of the CIPCollection of Institut Pasteur (CIP 107976)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107976