Strain identifier

BacDive ID: 7278

Type strain: Yes

Species: Agromyces fucosus

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): 41985 (species)

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General

@ref: 3323

BacDive-ID: 7278

DSM-Number: 8597

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

description: Agromyces fucosus DSM 8597 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 41985
  • Matching level: species

strain history

@refhistory
3323<- IMET <- VKM (Agromyces fucosus subsp. fucosus)
67770VKM Ac-1345 <-- DSB MGU XII-6.
119479CIP <- 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/bacdive7278.20240916.9.1

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

@ref: 3323

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces fucosus subsp. fucosus

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

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119479positiverod-shaped
69480no92.5
69480positive91.048

colony morphology

@refcolony colorincubation periodmedium used
19729Beige10-14 daysISP 2
1972910-14 daysISP 3
19729Beige10-14 daysISP 4
19729Beige10-14 daysISP 5
19729Beige10-14 daysISP 6
19729Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19729noISP 2
19729noISP 3
19729noISP 4
19729noISP 5
19729noISP 6
19729noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3323TRYPTICASE 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
19729ISP 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
19729ISP 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:
19729ISP 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
19729ISP 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
19729ISP 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
19729ISP 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
38138MEDIUM 11 - for AgromycesyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (5.000g);Yeast extract (3.000 g);Peptone (5.000 g);Di Potassium monohydrogenophosphate (0.200 g)
119479CIP Medium 11yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=11

culture temp

@refgrowthtypetemperature
19729positiveoptimum28
3323positivegrowth30
38138positivegrowth30
52776positivegrowth30
67770positivegrowth28
119479positivegrowth30-41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
52776aerobe
119479obligate aerobe
69480aerobe90.704

spore formation

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

halophily

@refsaltgrowthtested relationconcentration
119479NaClpositivegrowth0-2 %
119479NaClnogrowth6 %

murein

  • @ref: 3323
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

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

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
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371esculin+builds acid from4853
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
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371erythritol-builds acid from17113
119479glucose+fermentation17234
119479hippurate-hydrolysis606565
119479lactose+fermentation17716
119479nitrate-reduction17632
119479nitrite-reduction16301
119479sodium thiosulfate-builds gas from132112
119479glucose+/-degradation17234
68379nitrate-reduction17632
68379esculin+hydrolysis4853
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: 119479
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119479
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
119479oxidase-
119479beta-galactosidase+3.2.1.23
119479alcohol dehydrogenase-1.1.1.1
119479amylase+
119479DNase+
119479catalase+1.11.1.6
119479lysine decarboxylase-4.1.1.18
119479ornithine decarboxylase-4.1.1.17
119479urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52776C15:0715
    52776C16:01.616
    52776C18:00.618
    52776C14:0 ISO1.813.618
    52776C15:0 ANTEISO51.314.711
    52776C15:0 ISO4.914.621
    52776C16:0 iso12.115.626
    52776C17:0 anteiso12.216.722
    52776C18:2 ω6,9c/C18:0 ANTE0.717.724
    52776Unidentified0.614.923
    52776Unidentified115.926
    52776Unidentified2.416.291
    52776Unidentified0.717.022
    52776Unidentified3.118.089
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19729--+---++++---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19729-++-+++----+--+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119479+/--+/-+/--------+/---+/---------+/-++/-+/-+/-+/-------+/-+/-------+/------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3323soilMoscow regionRussiaRUSEurope
52776Soil
67770SoilMoscow RegionRussiaRUS
119479Environment, SoilMoscowRussian FederationRUSEurope1982

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7620.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_3714;98_4708;99_7620&stattab=map
  • Last taxonomy: Agromyces
  • 16S sequence: KC139245
  • Sequence Identity:
  • Total samples: 3203
  • soil counts: 1713
  • aquatic counts: 955
  • animal counts: 368
  • plant counts: 167

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33231Risk group (German classification)
197291Risk group (German classification)
1194791Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agromyces fucosus partial 16S rRNA geneAJ7847911163nuccore41985
20218Agromyces fucosus gene for 16S ribosomal RNA, partial sequence, strain: NBRC 15781AB8423001460nuccore41985
20218Agromyces fucosus strain NBRC 15781 16S ribosomal RNA gene, partial sequenceKC1392451460nuccore41985
67770Agromyces fucosus 16S ribosomal RNA gene, partial sequenceAY1580251473nuccore41985

Genome sequences

  • @ref: 67770
  • description: Agromyces fucosus CCUG 35506
  • accession: GCA_004134865
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 41985

GC content

@refGC-contentmethod
332371.0thermal denaturation, midpoint method (Tm)
6777070.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes91.048no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.576yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.704yes
69480spore-formingspore-formingAbility to form endo- or exosporesno73.458no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98yes
69480flagellatedmotile2+Ability to perform flagellated movementno92.5no

External links

@ref: 3323

culture collection no.: DSM 8597, ATCC 51764, IMET 11529, VKM Ac-1345, CCUG 35506, JCM 9085, CIP 103633, IAM 15142, IFO 15781, LMG 16156, NBRC 15781

straininfo link

  • @ref: 76729
  • straininfo: 8169

literature

  • topic: Phylogeny
  • Pubmed-ID: 33779960
  • title: Agromyces laixinhei sp. nov. isolated from bat feces in China.
  • authors: Cheng Y, Bai Y, Huang Y, Yang J, Lu S, Jin D, Pu J, Zheng H, Li J, Huang Y, Wang S, Xu J
  • journal: J Microbiol
  • DOI: 10.1007/s12275-021-0546-5
  • year: 2021
  • mesh: Actinobacteria, 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 Sequencing
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3323Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8597)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8597
19729Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8597.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
38138Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15452
52776Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35506)https://www.ccug.se/strain?id=35506
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
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
76729Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8169.1StrainInfo: A central database for resolving microbial strain identifiers
119479Curators of the CIPCollection of Institut Pasteur (CIP 103633)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103633