Strain identifier

BacDive ID: 7274

Type strain: Yes

Species: Agromyces lapidis

Strain Designation: CD55

Culture col. no.: DSM 16390, NCIMB 14013, HKI 0324

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6423

BacDive-ID: 7274

DSM-Number: 16390

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

description: Agromyces lapidis CD55 is an aerobe, mesophilic, gram-positive bacterium that was isolated from carved stone wall.

strain history: <- I. Groth; HKI 0324 <- Ch. Weigel; CD55

doi: 10.13145/bacdive7274.20201210.5

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinobacteria
  • domain: Bacteria
  • phylum: Actinobacteria
  • class: Actinobacteria
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces lapidis
  • full scientific name: Agromyces lapidis Jurado et al. 2005

@ref: 6423

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces lapidis

full scientific name: Agromyces lapidis Jurado et al. 2005

strain designation: CD55

type strain: yes

Morphology

cell morphology

  • @ref: 31369
  • gram stain: positive
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 31369
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6423R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
6423TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
37633MEDIUM 56 - for Micromonospora purpureayesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (10.000g);Yeast extract (5.000 g);Starch maize (20.000 g);Calcium carbonate (1.000 g);Casamino acids (5.000 g)

culture temp

@refgrowthtypetemperaturerange
6423positivegrowth28mesophilic
31369positivegrowth10-37
31369positiveoptimum28mesophilic
37633positivegrowth30mesophilic

culture pH

@refabilitytypepH
31369positivegrowth5-9.5
31369positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

  • @ref: 31369
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
31369NaClpositivegrowth<4 %
31369NaClpositiveoptimum2 %

murein

  • @ref: 6423
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3136922599arabinose+carbon source
3136917057cellobiose+carbon source
3136933984fucose+carbon source
3136928260galactose+carbon source
3136917234glucose+carbon source
3136917754glycerol+carbon source
31369506227N-acetylglucosamine+carbon source
3136916634raffinose+carbon source
3136917814salicin+carbon source
3136917992sucrose+carbon source
3136917632nitrate+reduction

enzymes

  • @ref: 31369
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 6423
  • sample type: carved stone wall
  • geographic location: Rome, Domitilla catacombs
  • country: Italy
  • origin.country: ITA
  • continent: Europe

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial

Safety information

risk assessment

  • @ref: 6423
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6423
  • description: Agromyces lapidis 16S ribosomal RNA gene, partial sequence
  • accession: AY618217
  • length: 1470
  • database: ena
  • NCBI tax ID: 279574

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces lapidis JCM 14321GCA_009749405contigncbi279574
66792Agromyces lapidis strain JCM 14321279574.3wgspatric279574

GC content

  • @ref: 6423
  • GC-content: 70.4

External links

@ref: 6423

culture collection no.: DSM 16390, NCIMB 14013, HKI 0324

straininfo link

@refpassport
20218http://www.straininfo.net/strains/386371
20218http://www.straininfo.net/strains/386373

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6423Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16390)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16390
20215D.Gleim, M.Kracht, N.Weiss et. al.http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.htmlProkaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
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
2768210.1099/ijs.0.63414-0
31369Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information27682
37633Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6401
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)