Strain identifier

BacDive ID: 7263

Type strain: Yes

Species: Agromyces fucosus subsp. hippuratus

Strain history: CIP <- 1993, L.I. Evtushenko, Inst. Biochem. Physiol. Microorganisms, Moscow State Univ., Moscow, Russia <- T.B. Dobrovolskaga, Moscow State Univ., Pushchine, Moscow, Russia

NCBI tax ID(s): 286438 (species)

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General

@ref: 3324

BacDive-ID: 7263

DSM-Number: 8598

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

description: Agromyces fucosus subsp. hippuratus DSM 8598 is an obligate aerobe, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 286438
  • Matching level: species

strain history

@refhistory
3324<- IMET <- VKM
67770VKM Ac-1352 <-- DSB MGU 15-6.
119906CIP <- 1993, L.I. Evtushenko, Inst. Biochem. Physiol. Microorganisms, Moscow State Univ., Moscow, Russia <- T.B. Dobrovolskaga, Moscow State Univ., Pushchine, Moscow, Russia

doi: 10.13145/bacdive7263.20240916.9.1

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 fucosus subsp. hippuratus
  • full scientific name: Agromyces fucosus subsp. hippuratus Zgurskaya et al. 1992

  • synonyms

    • @ref: 20215
    • synonym: Agromyces hippuratus

@ref: 3324

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces fucosus subsp. hippuratus

full scientific name: Agromyces fucosus subsp. hippuratus Zgurskaya et al. 1992

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119906positiverod-shapedno
69480no93.5
69480positive91.076

colony morphology

@refcolony colorincubation periodmedium used
20205Ivory (1014)10-14 daysISP 2
20205Ivory (1014)10-14 daysISP 3
20205Ivory (1014)10-14 daysISP 4
20205Ivory (1014)10-14 daysISP 5
20205Ivory (1014)10-14 daysISP 6
20205Ivory (1014)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20205noISP 2
20205noISP 3
20205noISP 4
20205noISP 5
20205noISP 6
20205noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3324TRYPTICASE 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
20205ISP 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
20205ISP 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:
20205ISP 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
20205ISP 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
20205ISP 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
20205ISP 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
119906CIP Medium 11yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=11

culture temp

@refgrowthtypetemperature
20205positiveoptimum28
3324positivegrowth30
67770positivegrowth28
119906positivegrowth25-30
119906nogrowth37
119906nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 119906
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
119906NaClpositivegrowth0-2 %
119906NaClnogrowth4 %
119906NaClnogrowth6 %

murein

  • @ref: 3324
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2020517234glucose-
2020522599arabinose-
2020517992sucrose-
2020518222xylose-
2020517268myo-inositol+
2020529864mannitol-
2020528757fructose+
2020526546rhamnose-
2020516634raffinose-
2020562968cellulose+
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
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-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
6837117266L-sorbose-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
1199064853esculin+hydrolysis
119906606565hippurate+hydrolysis
11990617632nitrate+reduction
11990616301nitrite-reduction
119906132112sodium thiosulfate-builds gas from
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

antibiotic resistance

  • @ref: 119906
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119906
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 119906
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382beta-glucuronidase-3.2.1.31
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382lipase (C 14)-
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
119906oxidase-
119906alcohol dehydrogenase-1.1.1.1
119906amylase-
119906caseinase-3.4.21.50
119906catalase+1.11.1.6
119906lysine decarboxylase-4.1.1.18
119906ornithine decarboxylase-4.1.1.17
119906urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
20205-+--+++++--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20205-++-++++-+-++-+++++
119906--------------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119906+/--+/-+/--+/----+/-+/-+/-+/--+/--------+/-+/-+/-+/-+/-+/---+/------+/-------+/------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3324soilMoscow regionRussiaRUSEurope
67770SoilMoscow RegionRussiaRUS
119906Environment, SoilMoscowRussian FederationRUSEurope1982

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33241Risk group (German classification)
202051German classification
1199061Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agromyces hippuratus gene for 16S ribosomal RNA, strain: JCM 9086D450611466nuccore286438
67770Agromyces hippuratus gene for 16S ribosomal RNA, partial sequence, strain: JCM 9086LC0620881450nuccore286438

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces hippuratus strain DSM 8598286438.3wgspatric286438
66792Agromyces hippuratus DSM 85982852717997draftimg286438
67770Agromyces hippuratus DSM 8598GCA_013410355contigncbi286438

GC content

@refGC-contentmethod
332472.0thermal denaturation, midpoint method (Tm)
6777072thermal denaturation, midpoint method (Tm)
6777070.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.076no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.631yes
69480spore-formingspore-formingAbility to form endo- or exosporesno75.771no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.528yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno93.5no

External links

@ref: 3324

culture collection no.: DSM 8598, ATCC 51765, IMET 11533, VKM Ac-1352, JCM 9086, CIP 103635, IAM 15143, IFO 15782, LMG 16158, NBRC 15782, JCM 9087

straininfo link

  • @ref: 76714
  • straininfo: 8170

literature

  • topic: Phylogeny
  • Pubmed-ID: 15388709
  • title: Reclassification of Agromyces fucosus subsp. hippuratus as Agromyces hippuratus sp. nov., comb. nov. and emended description of Agromyces fucosus.
  • authors: Ortiz-Martinez A, Gonzalez JM, Evtushenko LI, Jurado V, Laiz L, Groth I, Saiz-Jimenez C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02856-0
  • year: 2004
  • mesh: Actinomycetales/*classification/genetics, Cell Wall/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Teichoic Acids/chemistry
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3324Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8598)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8598
20205Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8598.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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
76714Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8170.1StrainInfo: A central database for resolving microbial strain identifiers
119906Curators of the CIPCollection of Institut Pasteur (CIP 103635)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103635