Strain identifier

BacDive ID: 7271

Type strain: Yes

Species: Agromyces albus

Strain history: CIP <- 2004, VKM Ac-1800

NCBI tax ID(s): 205332 (species)

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General

@ref: 6194

BacDive-ID: 7271

DSM-Number: 15934

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

description: Agromyces albus DSM 15934 is an obligate aerobe, psychrophilic, Gram-positive bacterium that was isolated from phyllosphere of Androsace sp..

NCBI tax id

  • NCBI tax id: 205332
  • Matching level: species

strain history

@refhistory
6194<- L. I. Evtushenko, VKM <- L. V. Dorofeeva
67770CIP 108259 <-- VKM Ac-1800 <-- L. V. Dorofeeva.
116197CIP <- 2004, VKM Ac-1800

doi: 10.13145/bacdive7271.20230509.8.1

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 albus
  • full scientific name: Agromyces albus Dorofeeva et al. 2003

@ref: 6194

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces albus

full scientific name: Agromyces albus Dorofeeva et al. 2003

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116197positiverod-shapedno

colony morphology

  • @ref: 116197

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6194TRYPTICASE 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
33907MEDIUM 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)
116197CIP Medium 11yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=11
116197CIP Medium 56yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=56

culture temp

@refgrowthtypetemperaturerange
6194positivegrowth24psychrophilic
33907positivegrowth30mesophilic
67770positivegrowth28mesophilic
116197positivegrowth10-41
116197nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116197
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.959

halophily

@refsaltgrowthtested relationconcentration
116197NaClpositivegrowth0-2 %
116197NaClnogrowth4 %
116197NaClnogrowth6 %
116197NaClnogrowth8 %
116197NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-12 (MK-11)

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
68371L-fucose-builds acid from18287
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
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
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-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116197citrate-carbon source16947
116197esculin+hydrolysis4853
116197hippurate+hydrolysis606565
116197nitrate-reduction17632
116197nitrite-reduction16301
116197nitrate-respiration17632

antibiotic resistance

  • @ref: 116197
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116197
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11619715688acetoin-
11619717234glucose-

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
116197oxidase-
116197beta-galactosidase+3.2.1.23
116197alcohol dehydrogenase-1.1.1.1
116197gelatinase+/-
116197amylase+
116197DNase+
116197caseinase+3.4.21.50
116197catalase+1.11.1.6
116197tween esterase-
116197gamma-glutamyltransferase+2.3.2.2
116197lecithinase-
116197lipase-
116197lysine decarboxylase-4.1.1.18
116197ornithine decarboxylase-4.1.1.17
116197phenylalanine ammonia-lyase-4.3.1.24
116197tryptophan deaminase-
116197urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116197-+++++++++++++++++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116197------------------------+/-------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116197+++++-+++++----++-+-++++-------+++-+-+-----------+----------+-------------------+------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
6194phyllosphere of Androsace sp.AndrosaceBelgorod region, Central Chernozem Nature ParkRussiaRUSEurope
67770Plant sample (Androsace sp.)Androsace sp.Central-Chernozem Biosphere Park, Belgorod regionRussiaRUS
116197Environment, Phyllosphere of Androsace sp.ChernozemBulgariaBGREurope1996

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1487.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_994;98_1173;99_1487&stattab=map
  • Last taxonomy: Agromyces
  • 16S sequence: AF503917
  • Sequence Identity:
  • Total samples: 6274
  • soil counts: 4556
  • aquatic counts: 436
  • animal counts: 372
  • plant counts: 910

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61941Risk group (German classification)
1161971Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6194
  • description: Agromyces albus 16S ribosomal RNA gene, partial sequence
  • accession: AF503917
  • length: 1486
  • database: ena
  • NCBI tax ID: 205332

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces albus strain DSM 15934205332.3wgspatric205332
66792Agromyces albus DSM 159342867580314draftimg205332
67770Agromyces albus DSM 15934GCA_004134825scaffoldncbi205332

GC content

@refGC-contentmethod
619469
6777069thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno89.371no
gram-positiveyes91.668no
anaerobicno99.708no
aerobicyes95.881no
halophileno93.958no
spore-formingno90.209no
glucose-utilyes86.099no
flagellatedno97.475no
thermophileno98.988no
glucose-fermentno90.328no

External links

@ref: 6194

culture collection no.: DSM 15934, UCM 623, VKM Ac-1800, JCM 13565, CIP 108259, IAM 15234, IAM 15338, NBRC 103057, UCM Ac-623

straininfo link

  • @ref: 76722
  • straininfo: 97555

literature

  • topic: Phylogeny
  • Pubmed-ID: 13130029
  • title: Agromyces albus sp. nov., isolated from a plant (Androsace sp.).
  • authors: Dorofeeva LV, Krausova VI, Evtushenko LI, Tiedje JM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02428-0
  • year: 2003
  • mesh: Actinomycetales/classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phenotype, Phylogeny, Primulaceae/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6194Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15934)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15934
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
33907Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5861
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/
68371Automatically annotated from API 50CH acid
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
76722Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97555.1StrainInfo: A central database for resolving microbial strain identifiers
116197Curators of the CIPCollection of Institut Pasteur (CIP 108259)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108259