Strain identifier

BacDive ID: 130342

Type strain: Yes

Species: Geodermatophilus aquaeductus

Strain history: CECT 8822 <-- M. Gtari; Univ. Tunis El Manar, Tunisia; BMG 801 <-- K. Hezbri.

NCBI tax ID(s): 1564161 (species)

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General

@ref: 21600

BacDive-ID: 130342

DSM-Number: 46834

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

description: Geodermatophilus aquaeductus DSM 46834 is a mesophilic, Gram-positive bacterium that was isolated from surface of an altered calcarinite stone.

NCBI tax id

  • NCBI tax id: 1564161
  • Matching level: species

strain history

@refhistory
21600<- M. Gtari,Tunesia; BMG 801 <- K. Hezbri, Tunesia
67770CECT 8822 <-- M. Gtari; Univ. Tunis El Manar, Tunisia; BMG 801 <-- K. Hezbri.

doi: 10.13145/bacdive130342.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Geodermatophilales
  • family: Geodermatophilaceae
  • genus: Geodermatophilus
  • species: Geodermatophilus aquaeductus
  • full scientific name: Geodermatophilus aquaeductus Hezbri et al. 2015

@ref: 21600

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Geodermatophilus

species: Geodermatophilus aquaeductus

full scientific name: Geodermatophilus aquaeductus Hezbri et al. 2015 emend. Montero-Calasanz et al. 2017

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colormedium used
69476Grey olive (6006)ISP 5
69476Grey olive (6006)ISP 7
69476Jet black (9005)ISP 2
69476Traffic black (9017)ISP 3
69476Traffic black (9017)ISP 4
69476Traffic black (9017)ISP 6
69476Yellow olive (6014)suter with tyrosine
69476Yellow olive (6014)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69476noAerial myceliumISP 2
69476noAerial myceliumISP 3
69476noAerial myceliumISP 4
69476noAerial myceliumISP 5
69476noAerial myceliumISP 6
69476noAerial myceliumISP 7
69476noAerial myceliumsuter with tyrosine
69476noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69476noMelanin
69476nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
21600https://www.dsmz.de/microorganisms/photos/DSM_46834.jpgMedium 65 28°C© Leibniz-Institut DSMZ
66793EM_DSM_46834_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_46834_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_46834_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_46834_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_46834_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21600GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
21600GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21600positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

halophily

  • @ref: 69476
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6947622599arabinose+growth
6947662968cellulose+/-growth
6947628757fructose+growth
6947617234glucose+growth
6947617268inositol+/-growth
6947637684mannose+/-growth
6947616634raffinose+growth
6947626546rhamnose+/-growth
6947617992sucrose+growth
6947618222xylose+growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69476---+------+/---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69476+++/--++/----+/-+---+/-+/----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
21600surface of an altered calcarinite stoneZaghouan, ruins of the Aqueduct of Hadrian (10° 9' 0'' E, 36° 24' 0'' N)TunisiaTUNAfrica36.410.15
67770Surface of an altered calcarinite stone in the ruins of a Roman aqueductZaghouanTunisiaTUNAfrica

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_42219.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_2459;98_3041;99_42219&stattab=map
  • Last taxonomy: Geodermatophilus
  • 16S sequence: LN626272
  • Sequence Identity:
  • Total samples: 6810
  • soil counts: 4562
  • aquatic counts: 408
  • animal counts: 721
  • plant counts: 1119

Safety information

risk assessment

  • @ref: 21600
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21600
  • description: Geodermatophilus aquaeductus BMG 801 partial 16S rRNA gene, type strain BMG 801T
  • accession: LN626272
  • length: 1340
  • database: ena
  • NCBI tax ID: 1564161

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geodermatophilus aquaeductus DSM 46834GCA_900182545scaffoldncbi1564161
66792Geodermatophilus aquaeductus strain DSM 468341564161.3wgspatric1564161
66792Geodermatophilus aquaeductus DSM 468342724679686draftimg1564161

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes71no
motileyes76.95no
flagellatedno92.141no
gram-positiveyes92.605no
anaerobicno99.273no
aerobicyes93.768no
halophileno92.108no
spore-formingno69.724no
thermophileno99.113yes
glucose-utilyes89.131yes
glucose-fermentno89.967yes

External links

@ref: 21600

culture collection no.: DSM 46834, CECT 8822, BMG 801, JCM 31697

straininfo link

  • @ref: 88874
  • straininfo: 404836

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26025303Geodermatophilus aquaeductus sp. nov., isolated from the ruins of Hadrian's aqueduct.Hezbri K, Ghodhbane-Gtari F, Del Carmen Montero-Calasanz M, Sghaier H, Rohde M, Sproer C, Schumann P, Klenk HP, Gtari MAntonie Van Leeuwenhoek10.1007/s10482-015-0461-z2015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, *Environmental Microbiology, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Tunisia, Vitamin K 2/analysisGenetics
Phylogeny28289918Geodermatophilus daqingensis sp. nov., isolated from petroleum-contaminated soil.Wang Y, Zhang L, Zhang X, Huang J, Zhao Y, Zhao Y, Liu J, Huang C, Wang J, Hu Y, Ren G, Xu XAntonie Van Leeuwenhoek10.1007/s10482-017-0853-32017Actinobacteria/*isolation & purification/metabolism, Bacterial Typing Techniques, China, DNA, Bacterial, Fatty Acids, *Petroleum, Phospholipids, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Soil, *Soil MicrobiologyTranscriptome
Phylogeny28809149Cumulibacter manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine.Huang J, Li J, Cao M, Liao S, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0020042017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Manganese, *Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21600Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-46834Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46834)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66793Mukherjee et al.GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life10.1038/nbt.3886 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69476Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%2046834.pdf
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
88874Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404836.1