Strain identifier

BacDive ID: 7273

Type strain: Yes

Species: Agromyces salentinus

Strain Designation: 108989, 20-5

Strain history: CIP <- 2005, DSMZ <- I. Groth, Hans Knöll Inst., Jena, Germany <- C. Weigel: strain 20-5

NCBI tax ID(s): 269421 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6320

BacDive-ID: 7273

DSM-Number: 16198

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

description: Agromyces salentinus 108989 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 269421
  • Matching level: species

strain history

@refhistory
6320<- I. Groth, HKI; 20-5 <- Ch. Weigel
67770I. Groth 20-5 (=HKI 0320) <-- Ch. Weigel.
122364CIP <- 2005, DSMZ <- I. Groth, Hans Knöll Inst., Jena, Germany <- C. Weigel: strain 20-5

doi: 10.13145/bacdive7273.20230509.8.1

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 salentinus
  • full scientific name: Agromyces salentinus Jurado et al. 2005

@ref: 6320

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces salentinus

full scientific name: Agromyces salentinus Jurado et al. 2005

strain designation: 108989, 20-5

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31281positiverod-shapedno
122364positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18303Rapeseed yellow (1021)10-14 daysISP 2
18303Rapeseed yellow (1021)10-14 daysISP 3
18303Rapeseed yellow (1021)10-14 daysISP 4
18303Rapeseed yellow (1021)10-14 daysISP 5
18303Rapeseed yellow (1021)10-14 daysISP 6
18303Rapeseed yellow (1021)10-14 daysISP 7
122364

multicellular morphology

@refforms multicellular complexmedium name
18303noISP 2
18303noISP 3
18303noISP 4
18303noISP 5
18303noISP 6
18303noISP 7

pigmentation

  • @ref: 31281
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6320R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6320TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
18303ISP 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
18303ISP 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:
18303ISP 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
18303ISP 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
18303ISP 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
18303ISP 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
36774MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122364CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122364CIP Medium 291yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=291

culture temp

@refgrowthtypetemperaturerange
18303positiveoptimum28mesophilic
6320positivegrowth28mesophilic
31281positivegrowth10-37
31281positiveoptimum24psychrophilic
36774positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31281aerobe
122364obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
31281NaClpositivegrowth0-4 %
31281NaClpositiveoptimum2 %

observation

@refobservation
31281aggregates in clumps
67770quinones: MK-12, MK-11, MK-10, MK-13

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3128130089acetate+carbon source
3128122599arabinose+carbon source
3128117057cellobiose+carbon source
3128128757fructose+carbon source
3128133984fucose+carbon source
3128128260galactose+carbon source
3128117234glucose+carbon source
3128117754glycerol+carbon source
3128128087glycogen+carbon source
3128117306maltose+carbon source
3128116634raffinose+carbon source
3128126546rhamnose+carbon source
3128133942ribose+carbon source
3128117814salicin+carbon source
3128117992sucrose+carbon source
3128127082trehalose+carbon source
3128118222xylose+carbon source
312814853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837117151xylitol-builds acid from
683716731melezitose-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+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
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12236417632nitrate-reduction
12236416301nitrite-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
3128116136hydrogen sulfideyes
12236435581indoleno

enzymes

@refvalueactivityec
31281catalase+1.11.1.6
31281cytochrome oxidase+1.9.3.1
31281urease+3.5.1.5
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
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
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
122364oxidase+
122364alcohol dehydrogenase-1.1.1.1
122364catalase+1.11.1.6
122364lysine decarboxylase-4.1.1.18
122364ornithine decarboxylase-4.1.1.17
122364urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18303+++/--++-++--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18303-++-++++-++++++++++
122364-++-++++-++-+-+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122364--+/-+/--+/----+/-++/-+/-----------+++++--+-+/--+/-+/-+/--+/-+/----+/------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6320soil samplePorto BadiscoItalyITAEurope
67770Top soil sample collected a few meters from the entrance of Grotta dei CerviPorto BadiscoItalyITAEurope
122364Environment, Soil sampleGrotta dei CerviItalyITAEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6092.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_1358;98_4520;99_6092&stattab=map
  • Last taxonomy: Agromyces
  • 16S sequence: AY507129
  • Sequence Identity:
  • Total samples: 413
  • soil counts: 271
  • aquatic counts: 38
  • animal counts: 92
  • plant counts: 12

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63201Risk group (German classification)
1223641Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6320
  • description: Agromyces salentinus strain 20-5 16S ribosomal RNA gene, partial sequence
  • accession: AY507129
  • length: 1381
  • database: ena
  • NCBI tax ID: 269421

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces salentinus strain JCM 14323269421.3wgspatric269421
66792Agromyces terreus strain JCM 14323424795.3wgspatric424795
67770Agromyces salentinus JCM 14323GCA_009749395contigncbi269421

GC content

@refGC-contentmethod
632072.3
6777072.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.125yes
gram-positiveyes93.765no
anaerobicno99.725yes
halophileno89.643no
spore-formingno89.392no
glucose-utilyes87.718no
flagellatedno97.39no
aerobicyes95.977no
thermophileno99.438no
glucose-fermentno92.381no

External links

@ref: 6320

culture collection no.: DSM 16198, HKI 0320, JCM 14323, CIP 108989, IAM 15297, NCIMB 13989, NCIMB 13990

straininfo link

  • @ref: 76724
  • straininfo: 362279

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653869Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijs.0.63199-02005Actinomycetales/chemistry/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Italy, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny33779960Agromyces laixinhei sp. nov. isolated from bat feces in China.Cheng Y, Bai Y, Huang Y, Yang J, Lu S, Jin D, Pu J, Zheng H, Li J, Huang Y, Wang S, Xu JJ Microbiol10.1007/s12275-021-0546-52021Actinobacteria, Actinomycetales/*classification/genetics/*isolation & purification/physiology, Animals, Base Composition, China, Chiroptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Whole Genome SequencingTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6320Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16198)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16198
18303Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16198.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
31281Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2760128776041
36774Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6679
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
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
76724Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362279.1StrainInfo: A central database for resolving microbial strain identifiers
122364Curators of the CIPCollection of Institut Pasteur (CIP 108989)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108989