Strain identifier

BacDive ID: 7260

Type strain: Yes

Species: Agromyces ramosus

Strain Designation: PSU 38L

Strain history: KCC A-0108 <-- L. E. Casida PSU 38L.

NCBI tax ID(s): 33879 (species)

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General

@ref: 10715

BacDive-ID: 7260

DSM-Number: 43045

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

description: Agromyces ramosus PSU 38L is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 33879
  • Matching level: species

strain history

@refhistory
10715<- KCC <- L.E. Casida Jr., PSU 38L
67770KCC A-0108 <-- L. E. Casida PSU 38L.

doi: 10.13145/bacdive7260.20230509.8.1

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 ramosus
  • full scientific name: Agromyces ramosus Gledhill and Casida 1969 (Approved Lists 1980)

@ref: 10715

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces ramosus

full scientific name: Agromyces ramosus Gledhill and Casida 1969

strain designation: PSU 38L

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
19933Colorless10-14 daysISP 4
19933Colorless10-14 daysISP 5
19933Colorless10-14 daysISP 6
19933Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19933noISP 2
19933noISP 3
19933noISP 4
19933noISP 5
19933noISP 6
19933noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19933ISP 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
19933ISP 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
19933ISP 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
19933ISP 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
10715R2A MEDIUM (DSMZ Medium 830)yesName: 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 waterhttps://mediadive.dsmz.de/medium/830

culture temp

@refgrowthtypetemperaturerange
19933positiveoptimum28mesophilic
10715positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
10715microaerophile
10715aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.989

halophily

  • @ref: 19933
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1993362968cellulose+
1993316634raffinose-
1993326546rhamnose+
1993328757fructose-
1993329864mannitol-
1993317268myo-inositol+
1993318222xylose+
1993317992sucrose-
1993322599arabinose-
1993317234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19933------+-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19933-++-+++-------+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19933-----------

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
107151Risk group (German classification)
199331German classification

Sequence information

16S sequences

  • @ref: 10715
  • description: A.ramosum (DSM 43045) 16S rRNA gene
  • accession: X77447
  • length: 1482
  • database: ena
  • NCBI tax ID: 33879

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces ramosus strain DSM 4304533879.4wgspatric33879
66792Agromyces ramosus DSM 430452799112209draftimg33879
67770Agromyces ramosus DSM 43045GCA_004216665scaffoldncbi33879

GC content

@refGC-contentmethod
6777071.4Buoyant density centrifugation (BD)
6777068.9high performance liquid chromatography (HPLC)
6777076.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes92.147no
anaerobicno99.703yes
halophileno92.013yes
spore-formingno92.883no
glucose-utilyes87.33yes
motileno90.388no
flagellatedno97.735no
thermophileno98.9no
aerobicyes95.244no
glucose-fermentno91.464yes

External links

@ref: 10715

culture collection no.: DSM 43045, ATCC 25173, KCC A-0108, JCM 3108, BCRC 12879, CIP 103037, IAM 15120, IFO 13895, IFO 13899, IMET 11027, KCTC 9232, LMG 16680, MTCC 267, NBRC 13895, NBRC 13899, NCIMB 10801, VKM Ac-1198

straininfo link

  • @ref: 76711
  • straininfo: 8891

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14745160Rare bacterium of new genus isolated with prolonged enrichment culture.Hashizume A, Fudou R, Jojima Y, Nakai R, Hiraishi A, Tabuchi A, Sen K, Shibai HBiosci Biotechnol Biochem10.1271/bbb.68.282004Afipia/genetics, Bacteriological Techniques/*methods, Bradyrhizobium/genetics/growth & development/isolation & purification, Cell Division, Culture Media, DNA, Ribosomal/genetics, Electrochemistry/methods, Electrodes, Methylobacterium/genetics/growth & development/isolation & purification, Molecular Sequence Data, Oxygen, Phylogeny, Proteobacteria/*genetics/growth & development/*isolation & purification, RNA, Ribosomal, 16S, Sequence Homology, Nucleic AcidEnzymology
Phylogeny26883212Agromyces insulae sp. nov., an actinobacterium isolated from a soil sample.Huang JR, Ming H, Li S, Meng XL, Zhang JX, Khieu TN, Tang Z, Li WJ, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0009782016Actinomycetales/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vietnam, Vitamin K 2/chemistryTranscriptome
Phylogeny31355738Agromyces tardus sp. nov., an actinobacterium isolated from the rhizosphere soil of wheat (Triticum aestivum L.).Sun T, Cao P, Sun K, Li C, Jiang M, Jia W, Wang X, Zhao J, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0036212019Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Triticum/*microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10715Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43045)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43045
19933Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43045.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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
76711Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8891.1StrainInfo: A central database for resolving microbial strain identifiers