Strain identifier

BacDive ID: 7274

Type strain: Yes

Species: Agromyces lapidis

Strain Designation: CD55

Strain history: CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: strain CD55 <- I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0324

NCBI tax ID(s): 279574 (species)

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

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

NCBI tax id

  • NCBI tax id: 279574
  • Matching level: species

strain history

@refhistory
6423<- I. Groth; HKI 0324 <- Ch. Weigel; CD55
67770I. Groth CD55 (=HKI 0324) <-- Ch. Weigel.
120559CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: strain CD55 <- I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0324

doi: 10.13145/bacdive7274.20230509.8.1

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 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

@refgram staincell widthcell shapemotilityconfidence
31369positive0.5 µmrod-shapedno
69480positive100
120559positiverod-shapedno

colony morphology

  • @ref: 120559

pigmentation

  • @ref: 31369
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6423R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6423TRYPTICASE 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
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)
120559CIP Medium 56yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=56
120559CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6423positivegrowth28mesophilic
31369positivegrowth10-37
31369positiveoptimum28mesophilic
37633positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31369positivegrowth5-9.5alkaliphile
31369positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31369aerobe
120559obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
31369NaClpositivegrowth<4 %
31369NaClpositiveoptimum2 %

murein

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

observation

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

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
12055917632nitrate+reduction
12055916301nitrite-reduction
12055917632nitrate-respiration

enzymes

@refvalueactivityec
31369catalase+1.11.1.6
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
120559oxidase+
120559alcohol dehydrogenase-1.1.1.1
120559catalase+1.11.1.6
120559lysine decarboxylase-4.1.1.18
120559ornithine decarboxylase-4.1.1.17
120559urease-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
120559--++-+++--++++-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6423carved stone wallRome, Domitilla catacombsItalyITAEurope
67770Stone wall of a tombDomitilla Catacombs, RomeItalyITAEurope
120559Carved stone wallRomeItalyITAEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64231Risk group (German classification)
1205591Risk group (French 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 strain JCM 14321279574.3wgspatric279574
67770Agromyces lapidis JCM 14321GCA_009749405contigncbi279574

GC content

@refGC-contentmethod
642370.4
6777070.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.131no
gram-positiveyes90.631no
anaerobicno99.688yes
halophileno91.238no
spore-formingno88.664no
glucose-utilyes86.159no
flagellatedno97.489yes
aerobicyes95.762yes
thermophileno99.413no
glucose-fermentno91.607no

External links

@ref: 6423

culture collection no.: DSM 16390, NCIMB 14013, HKI 0324, JCM 14321, IAM 15275, CIP 108739

straininfo link

  • @ref: 76725
  • straininfo: 137994

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774677Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs.Jurado V, Groth I, Gonzalez JM, Laiz L, Schuetze B, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijs.0.63414-02005Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, History, Ancient, Italy, Molecular Sequence Data, *Mortuary Practice, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny35085062Agromyces agglutinans sp. nov., isolated from saline lake sediment.Yi BF, Xia TT, Niu MM, Zhao ZY, Su QY, Ming H, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0052082022Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Geologic Sediments/*microbiology, *Lakes/microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Saline Waters, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
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
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
31369Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2768228776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
76725Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137994.1StrainInfo: A central database for resolving microbial strain identifiers
120559Curators of the CIPCollection of Institut Pasteur (CIP 108739)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108739