Strain identifier

BacDive ID: 131557

Type strain: Yes

Species: Photobacterium galatheae

Strain Designation: S2753

Strain history: <- H. Machado, Technical University of Denmark, Systems Biology, Kgs. Lyngby, Denmark; S2753 <- L. Gram, Systems Biology, Technical University Denmark

NCBI tax ID(s): 1654360 (species)

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General

@ref: 22784

BacDive-ID: 131557

DSM-Number: 100496

keywords: genome sequence, 16S sequence, Bacteria

description: Photobacterium galatheae S2753 is a bacterium that was isolated from surface of a mussel.

NCBI tax id

  • NCBI tax id: 1654360
  • Matching level: species

strain history

  • @ref: 22784
  • history: <- H. Machado, Technical University of Denmark, Systems Biology, Kgs. Lyngby, Denmark; S2753 <- L. Gram, Systems Biology, Technical University Denmark

doi: 10.13145/bacdive131557.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Photobacterium
  • species: Photobacterium galatheae
  • full scientific name: Photobacterium galatheae Machado et al. 2015

@ref: 22784

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium galatheae

full scientific name: Photobacterium galatheae Machado et al. 2015

strain designation: S2753

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22784MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514f.pdf
22784R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830; with strain-specific modifications) Composition: NaCl 30.0 g/l Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l Na-pyruvate 0.3 g/l K2HPO4 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

  • @ref: 22784
  • growth: positive
  • type: growth
  • temperature: 28

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate+reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose+fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase+1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
22784----+-----++--------++-
22784----+-----++--------+

Isolation, sampling and environmental information

isolation

  • @ref: 22784
  • sample type: surface of a mussel
  • geographic location: Solomon Sea (9° 06.480' S 156° 51.570' E)
  • country: Solomon Islands
  • origin.country: SLB
  • continent: Australia and Oceania
  • latitude: -9.108
  • longitude: 156.859

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Mollusca

taxonmaps

  • @ref: 69479
  • File name: preview.99_55762.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_2475;97_19130;98_32249;99_55762&stattab=map
  • Last taxonomy: Photobacterium galatheae subclade
  • 16S sequence: KR704916
  • Sequence Identity:
  • Total samples: 73
  • soil counts: 12
  • aquatic counts: 57
  • animal counts: 2
  • plant counts: 2

Safety information

risk assessment

  • @ref: 22784
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22784
  • description: Photobacterium galatheae strain S2753 16S ribosomal RNA gene, partial sequence
  • accession: KR704916
  • length: 1540
  • database: nuccore
  • NCBI tax ID: 1654360

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium galatheae S2753GCA_000695255contigncbi1654360
66792Photobacterium galatheae S27532711768099draftimg1654360
66792Photobacterium galatheae DSM 100496GCA_023653475contigncbi1654360

GC content

  • @ref: 22784
  • GC-content: 49.5

External links

@ref: 22784

culture collection no.: DSM 100496, LMG 28894

straininfo link

  • @ref: 89971
  • straininfo: 398605

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26374506Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea.Machado H, Giubergia S, Mateiu RV, Gram LInt J Syst Evol Microbiol10.1099/ijsem.0.0006032015Animals, Bacterial Typing Techniques, Base Composition, Bivalvia/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Melanesia, Molecular Sequence Data, Photobacterium/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Enzymology27999269Biological Potential of Chitinolytic Marine Bacteria.Paulsen SS, Andersen B, Gram L, Machado HMar Drugs10.3390/md141202302016Antifungal Agents/*isolation & purification/pharmacology, Chitin/*metabolism, Chitinases/*metabolism, Marine Biology, Pseudoalteromonas/*enzymology/genetics, Vibrionaceae/*enzymology/geneticsMetabolism
Transcriptome28066819Growth on Chitin Impacts the Transcriptome and Metabolite Profiles of Antibiotic-Producing Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753.Giubergia S, Phippen C, Nielsen KF, Gram LmSystems10.1128/mSystems.00141-162017
Phylogeny31693472Photobacterium salinisoli sp. nov., isolated from a sulfonylurea herbicide-degrading consortium enriched with saline soil.Li M, Kong D, Wang Y, Ma Q, Han X, Zhou Y, Jiang X, Zhang Y, Ruan Z, Zhang QInt J Syst Evol Microbiol10.1099/ijsem.0.0037052019Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Herbicides/*metabolism, Nucleic Acid Hybridization, Phospholipids/chemistry, Photobacterium/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sulfonylurea Compounds/*metabolism, Ubiquinone/chemistryMetabolism
Metabolism33771780Holomycin, an Antibiotic Secondary Metabolite, Is Required for Biofilm Formation by the Native Producer Photobacterium galatheae S2753.Zhang SD, Isbrandt T, Lindqvist LL, Larsen TO, Gram LAppl Environ Microbiol10.1128/AEM.00169-212021Anti-Bacterial Agents/biosynthesis/*metabolism, Bacterial Proteins/*genetics/metabolism, Biofilms/*growth & development, Lactams/*metabolism, Mutation, Photobacterium/*physiology
Metabolism36000852Solonamides, a Group of Cyclodepsipeptides, Influence Motility in the Native Producer Photobacterium galatheae S2753.Zhang SD, Lindqvist LL, Isbrandt T, Borre IL, Wibowo M, Nielsen MW, Ding L, Larsen TO, Gram LAppl Environ Microbiol10.1128/aem.01105-222022Bacterial Proteins/genetics/metabolism, Biofilms, Cyclic GMP/metabolism, *Depsipeptides/genetics, Gene Expression Regulation, Bacterial, Photobacterium/genetics, Proteomics, Virulence/genetics

Reference

@idauthorstitledoi/urlcatalogue
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
22784Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100496Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100496)
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
68368Automatically annotated from API 20E
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/
89971Reimer, 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-ID398605.1