Strain identifier

BacDive ID: 7262

Type strain: Yes

Species: Agromyces cerinus subsp. nitratus

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): 231391 (subspecies)

« 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: 3322

BacDive-ID: 7262

DSM-Number: 8596

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped

description: Agromyces cerinus subsp. nitratus DSM 8596 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 231391
  • Matching level: subspecies

strain history

@refhistory
3322<- IMET <- VKM
67770VKM Ac-1351 <-- DSB MGU 14-3.
118214CIP <- 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/bacdive7262.20230509.8.1

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

@ref: 3322

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces cerinus subsp. nitratus

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

type strain: yes

Morphology

cell morphology

  • @ref: 118214
  • gram stain: positive
  • cell shape: rod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3322TRYPTICASE 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
38139MEDIUM 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)
118214CIP Medium 11yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=11

culture temp

@refgrowthtypetemperaturerange
3322positivegrowth30mesophilic
38139positivegrowth30mesophilic
67770positivegrowth28mesophilic
118214positivegrowth30mesophilic
118214nogrowth37mesophilic
118214nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118214
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
118214NaClpositivegrowth0-4 %
118214NaClnogrowth6 %

murein

  • @ref: 3322
  • 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
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
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
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118214glucose+fermentation17234
118214hippurate-hydrolysis606565
118214lactose+fermentation17716
118214nitrate+reduction17632
118214nitrite-reduction16301
118214sodium thiosulfate-builds gas from132112
118214glucose+/-degradation17234

antibiotic resistance

  • @ref: 118214
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

enzymes

@refvalueactivityec
118214oxidase-
118214beta-galactosidase+3.2.1.23
118214alcohol dehydrogenase-1.1.1.1
118214DNase+
118214catalase+1.11.1.6
118214lysine decarboxylase-4.1.1.18
118214ornithine decarboxylase-4.1.1.17

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118214---------+/-+/-+/-+/--+/--------+/-++++/-+--+/----+/-+/-+/-------+/------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
3322soilMoscow regionRussiaRUSEurope
67770SoilMoscow RegionRussiaRUS
118214Environment, SoilMoscowRussian FederationRUSEurope1982

isolation source categories

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

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: AM410681
  • 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
33221Risk group (German classification)
1182141Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agromyces cerinus subsp. nitratus strain IMET 11532 16S ribosomal RNA gene, partial sequenceAY2776191465ena231391
20218Agromyces cerinus subsp. nitratus partial 16S rRNA gene, type strain DSM 8596AM4106811465ena231391

Genome sequences

  • @ref: 66792
  • description: Agromyces cerinus DSM 8596
  • accession: 2893688764
  • assembly level: draft
  • database: img
  • NCBI tax ID: 33878

GC content

@refGC-contentmethod
332272.0thermal denaturation, midpoint method (Tm)
6777070thermal denaturation, midpoint method (Tm)
6777070.9high performance liquid chromatography (HPLC)

External links

@ref: 3322

culture collection no.: DSM 8596, ATCC 51763, IMET 11532, VKM Ac-1351, JCM 9084, CIP 103634, IAM 15141, IFO 15783, LMG 16157, NBRC 15783

straininfo link

  • @ref: 76713
  • straininfo: 8168

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3322Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8596)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8596
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
38139Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15453
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
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
76713Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8168.1StrainInfo: A central database for resolving microbial strain identifiers
118214Curators of the CIPCollection of Institut Pasteur (CIP 103634)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103634