Strain identifier

BacDive ID: 7261

Type strain: Yes

Species: Agromyces cerinus

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): 33878 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 3321

BacDive-ID: 7261

DSM-Number: 8595

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

description: Agromyces cerinus DSM 8595 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 33878
  • Matching level: species

strain history

@refhistory
3321<- IMET <- VKM
67770VKM Ac-1340 <-- DSB MGU XI-15.
118213CIP <- 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/bacdive7261.20230509.8.1

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

@ref: 3321

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces cerinus subsp. cerinus

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

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shape
69480positive100
118213positiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20204Colorless10-14 daysISP 2
20204Colorless10-14 daysISP 3
20204Beige (1001)10-14 daysISP 4
20204Beige (1001)10-14 daysISP 5
20204Beige (1001)10-14 daysISP 6
20204Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20204noISP 2
20204noISP 3
20204noISP 4
20204noISP 5
20204noISP 6
20204noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3321TRYPTICASE 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
20204ISP 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
20204ISP 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:
20204ISP 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
20204ISP 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
20204ISP 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
20204ISP 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
38137MEDIUM 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)
118213CIP Medium 11yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=11

culture temp

@refgrowthtypetemperaturerange
20204positiveoptimum28mesophilic
3321positivegrowth30mesophilic
38137positivegrowth30mesophilic
67770positivegrowth28mesophilic
118213positivegrowth30mesophilic
118213nogrowth5psychrophilic
118213nogrowth10psychrophilic
118213nogrowth37mesophilic
118213nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118213
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
118213NaClpositivegrowth0-2 %
118213NaClnogrowth4 %
118213NaClnogrowth6 %

murein

  • @ref: 3321
  • 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
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371esculin+builds acid from4853
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
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
68371L-arabinose-builds acid from30849
68371erythritol-builds acid from17113
118213glucose+fermentation17234
118213hippurate-hydrolysis606565
118213lactose+fermentation17716
118213nitrate-reduction17632
118213nitrite-reduction16301
118213sodium thiosulfate-builds gas from132112
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: 118213
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118213
  • 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
118213oxidase-
118213beta-galactosidase+3.2.1.23
118213amylase+
118213DNase+
118213catalase+1.11.1.6
118213urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20204--+---+-++---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20204-++-+++----+--+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118213+/--+/-------+/-+/-+/-+/--+/--------+/-+/-++/-+/-+/---+/------+/-------+/------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3321soilMoscow regionRussiaRUSEurope
67770SoilMoscow RegionRussiaRUS
118213Environment, SoilMoscowRussian FederationRUSEurope1982

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33211Risk group (German classification)
202041German classification
1182131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agromyces cerinus subsp. cerinus partial 16S rRNA gene, type strain DSM 8595AM4106801483ena232089
3321Agromyces cerinus subsp. cerinus 16S ribosomal RNA, partial sequenceNR_1150291483nuccore232089
67770Agromyces cerinus gene for 16S ribosomal RNA, strain: JCM9083D450601486ena232089
67770A.cerinus (DSM 8595) 16S rRNA geneX774481483ena232089

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces cerinus subsp. cerinus strain DSM 8595232089.3wgspatric232089
66792Agromyces cerinus cerinus DSM 85952698536811draftimg232089
67770Agromyces cerinus subsp. cerinus DSM 8595GCA_900142065contigncbi232089

GC content

@refGC-contentmethod
332172.0thermal denaturation, midpoint method (Tm)
6777072thermal denaturation, midpoint method (Tm)
6777070genome sequence analysis
6777070.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno87.478no
gram-positiveyes92.115no
anaerobicno99.592no
aerobicyes94.015no
halophileno90.029no
spore-formingno86.381no
glucose-utilyes85.71no
flagellatedno97.591no
thermophileno99.449yes
glucose-fermentno92.202yes

External links

@ref: 3321

culture collection no.: DSM 8595, ATCC 51762, IMET 11525, VKM Ac-1340, JCM 9083, CIP 103632, IAM 15140, IFO 15780, LMG 16155, NBRC 15780

straininfo link

  • @ref: 76712
  • straininfo: 92506

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics7672119Poly(arabitol phosphate) teichoic acid in the cell wall of Agromyces cerinus subsp. cerinus VKM Ac-1340T.Shashkov AS, Streshinskaya GM, Gnilozub VA, Evtushenko LI, Naumova IBFEBS Lett10.1016/0014-5793(95)00896-h1995Actinomycetales/*chemistry, Carbohydrate Sequence, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Repetitive Sequences, Nucleic Acid, Teichoic Acids/analysis/*chemistry
Phylogeny19666805Agromyces atrinae sp. nov., isolated from fermented seafood.Park EJ, Kim MS, Jung MJ, Roh SW, Chang HW, Shin KS, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.012294-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fermentation, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
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/urltitlejournalpubmed
3321Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8595)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8595
20204Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8595.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
38137Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15451
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
76712Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92506.1StrainInfo: A central database for resolving microbial strain identifiers
118213Curators of the CIPCollection of Institut Pasteur (CIP 103632)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103632