Strain identifier

BacDive ID: 17873

Type strain: Yes

Species: Amorphus coralli

Strain Designation: R5 Sph 026, RS.Sph.026

Strain history: <- D. Zeevi Ben Yosef, Ben-Gurion-Univ., Beer-Sheva, Israel; R5 Sph 026 <- E. Ben Dov

NCBI tax ID(s): 1120983 (strain), 340680 (species)

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General

@ref: 8300

BacDive-ID: 17873

DSM-Number: 19760

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

description: Amorphus coralli R5 Sph 026 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Coral mucus Fungia granulosa.

NCBI tax id

NCBI tax idMatching level
340680species
1120983strain

strain history

  • @ref: 8300
  • history: <- D. Zeevi Ben Yosef, Ben-Gurion-Univ., Beer-Sheva, Israel; R5 Sph 026 <- E. Ben Dov

doi: 10.13145/bacdive17873.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Amorphaceae
  • genus: Amorphus
  • species: Amorphus coralli
  • full scientific name: Amorphus coralli Zeevi Ben Yosef et al. 2008

@ref: 8300

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Amorphaceae

genus: Amorphus

species: Amorphus coralli

full scientific name: Amorphus coralli Zeevi Ben Yosef et al. 2008

strain designation: R5 Sph 026, RS.Sph.026

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
32416negative0.5-3 µmrod-shapedno
69480negative99.969

pigmentation

  • @ref: 32416
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_19760_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19760_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19760_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19760_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19760_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 8300
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8300positivegrowth28mesophilic
32416positivegrowth25-30mesophilic
32416positiveoptimum25-30mesophilic

culture pH

@refabilitytypepH
32416positivegrowth7.5-8
32416positiveoptimum7.5-8

Physiology and metabolism

oxygen tolerance

  • @ref: 32416
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32416no
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
32416NaClpositivegrowth03-04 %
32416NaClpositiveoptimum03-04 %

observation

  • @ref: 32416
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3241622599arabinose+carbon source
3241617234glucose+carbon source
3241627570histidine+carbon source
3241617306maltose+carbon source
3241629864mannitol+carbon source
3241637684mannose+carbon source
3241618257ornithine+carbon source
3241617272propionate+carbon source
3241630911sorbitol+carbon source
3241630031succinate+carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 8300
  • sample type: Coral mucus Fungia granulosa
  • host species: Fungia granulosa
  • geographic location: Red Sea, Gulf of Eilat
  • country: Israel
  • origin.country: ISR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Cnidaria (Corals)
#Host Body Product#Oral cavity and Airways#Mucus

taxonmaps

  • @ref: 69479
  • File name: preview.99_5132.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2498;97_3049;98_3827;99_5132&stattab=map
  • Last taxonomy: Amorphus coralli subclade
  • 16S sequence: DQ097300
  • Sequence Identity:
  • Total samples: 1398
  • soil counts: 296
  • aquatic counts: 899
  • animal counts: 119
  • plant counts: 84

Safety information

risk assessment

  • @ref: 8300
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8300
  • description: Amorphus coralli strain RS.Sph.026 16S ribosomal RNA gene, partial sequence
  • accession: DQ097300
  • length: 1438
  • database: ena
  • NCBI tax ID: 340680

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amorphus coralli DSM 19760GCA_000374525scaffoldncbi1120983
66792Amorphus coralli DSM 197601120983.3wgspatric1120983
66792Amorphus coralli DSM 197602517572147draftimg1120983

GC content

@refGC-contentmethod
830062.1fluorimetric
830067.1thermal denaturation, midpoint method (Tm)
3241667.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.934yes
flagellatedno95.213yes
gram-positiveno98.18no
anaerobicno96.066yes
aerobicyes88.902yes
halophileno69.72no
spore-formingno96.426yes
glucose-utilyes88.623yes
thermophileno93.877yes
glucose-fermentno93.157no

External links

@ref: 8300

culture collection no.: DSM 19760, LMG 24307

straininfo link

  • @ref: 86862
  • straininfo: 310961

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19060044Amorphus coralli gen. nov., sp. nov., a marine bacterium isolated from coral mucus, belonging to the order Rhizobiales.Zeevi Ben Yosef D, Ben-Dov E, Kushmaro AInt J Syst Evol Microbiol10.1099/ijs.0.65462-02008Alphaproteobacteria/chemistry/*classification/genetics/*physiology/ultrastructure, Animals, Anthozoa/*microbiology, Fatty Acids/analysis, Microscopy, Electron, Transmission, Molecular Sequence Data, Mucus/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny19749037Amorphus orientalis sp. nov., an exopolysaccharide-producing bacterium isolated from salt mine sediment.Wang YX, Liu JH, Chen YG, Zhang XX, Wang ZG, Chen Y, Tian SP, Hu B, Cui XLInt J Syst Evol Microbiol10.1099/ijs.0.015735-02009Alphaproteobacteria/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, Polysaccharides, Bacterial/*metabolism, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*metabolismMetabolism
Phylogeny23687061Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima.Hwang JM, Chung EJ, Park JA, Jeong JH, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.048959-02013Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8300Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19760)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19760
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
32416Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2863928776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
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
86862Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310961.1StrainInfo: A central database for resolving microbial strain identifiers