Strain identifier

BacDive ID: 130813

Type strain: Yes

Species: Gallaecimonas xiamenensis

Strain Designation: 3-C-1

Strain history: <- LMG <- Q. Lai, Key Lab. Marine Biogenetic Resources <- L. Wang, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen, China

NCBI tax ID(s): 1207039 (species)

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General

@ref: 22073

BacDive-ID: 130813

DSM-Number: 100312

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

description: Gallaecimonas xiamenensis 3-C-1 is a mesophilic, Gram-negative, motile bacterium that was isolated from surface seawater.

NCBI tax id

  • NCBI tax id: 1207039
  • Matching level: species

strain history

  • @ref: 22073
  • history: <- LMG <- Q. Lai, Key Lab. Marine Biogenetic Resources <- L. Wang, Key Lab. Marine Biogenetic Resources, Third Institute of Oceanography, Xiamen, China

doi: 10.13145/bacdive130813.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Gallaecimonadaceae
  • genus: Gallaecimonas
  • species: Gallaecimonas xiamenensis
  • full scientific name: Gallaecimonas xiamenensis Wang et al. 2013

@ref: 22073

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Gammaproteobacteria, not assigned to family

genus: Gallaecimonas

species: Gallaecimonas xiamenensis

full scientific name: Gallaecimonas xiamenensis Wang et al. 2013

strain designation: 3-C-1

type strain: yes

Morphology

cell morphology

  • @ref: 30697
  • gram stain: negative
  • cell length: 3.15 µm
  • cell width: 0.55 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 30697
  • production: no

Culture and growth conditions

culture medium

  • @ref: 22073
  • 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
22073positivegrowth28mesophilic
30697positivegrowth10-42
30697positiveoptimum27.5mesophilic

culture pH

@refabilitytypepHPH range
30697positivegrowth05-10alkaliphile
30697positiveoptimum7

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
30697NaClpositivegrowth0-12 %
30697NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3069721217L-alaninamide+carbon source
3069716449alanine+carbon source
3069740585alpha-cyclodextrin+carbon source
3069722599arabinose+carbon source
3069722653asparagine+carbon source
3069735391aspartate+carbon source
3069717057cellobiose+carbon source
3069716947citrate+carbon source
3069723652dextrin+carbon source
3069724175galacturonate+carbon source
3069717234glucose+carbon source
3069732323glucuronamide+carbon source
3069729987glutamate+carbon source
3069715428glycine+carbon source
3069728087glycogen+carbon source
3069727570histidine+carbon source
3069717596inosine+carbon source
3069725017leucine+carbon source
3069715792malonate+carbon source
3069717306maltose+carbon source
3069751850methyl pyruvate+carbon source
30697506227N-acetylglucosamine+carbon source
3069726271proline+carbon source
3069717272propionate+carbon source
3069717822serine+carbon source
3069730031succinate+carbon source
3069726986threonine+carbon source
3069753423tween 40+carbon source
3069753426tween 80+carbon source
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30697catalase+1.11.1.6
30697cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
22073------+-++--++-+-++-+

Isolation, sampling and environmental information

isolation

  • @ref: 22073
  • sample type: surface seawater
  • geographic location: near Xiamen Island
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_2567.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_11;96_1378;97_1638;98_1990;99_2567&stattab=map
  • Last taxonomy: Gallaecimonas xiamenensis subclade
  • 16S sequence: JQ666155
  • Sequence Identity:
  • Total samples: 1006
  • soil counts: 36
  • aquatic counts: 348
  • animal counts: 587
  • plant counts: 35

Safety information

risk assessment

  • @ref: 22073
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22073
  • description: Gallaecimonas xiamenensis 3-C-1 16S ribosomal RNA gene, partial sequence
  • accession: JQ666155
  • length: 1506
  • database: ena
  • NCBI tax ID: 745411

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gallaecimonas xiamenensis 3-C-1GCA_000299915contigncbi745411
66792Gallaecimonas xiamenensis 3-C-1745411.6wgspatric745411
66792Gallaecimonas xiamenensis 3-C-12565956799draftimg745411

GC content

  • @ref: 30697
  • GC-content: 61.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes94.614yes
flagellatedyes89.241no
gram-positiveno98.851yes
anaerobicno97.504no
aerobicyes88.329no
halophileno73.995no
spore-formingno93.34no
thermophileno98.79no
glucose-utilyes91.432no
glucose-fermentno77.467yes

External links

@ref: 22073

culture collection no.: DSM 100312, CCTCC AB 209060, LMG 25226, MCCC 1A01354

straininfo link

  • @ref: 89301
  • straininfo: 362601

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22659502Gallaecimonas xiamenensis sp. nov., isolated from seawater.Wang J, Lai Q, Duan X, Fu Y, Wang L, Wang W, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.042283-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Water MicrobiologyGenetics
Genetics23209203Genome sequence of Gallaecimonas xiamenensis type strain 3-C-1.Lai Q, Wang L, Wang W, Shao ZJ Bacteriol10.1128/JB.01854-122012Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, DNA, Bacterial/genetics, DNA, Ribosomal, Gammaproteobacteria/*genetics/isolation & purification, *Genome, Bacterial, Microbial Consortia, Molecular Sequence Data, Petroleum, RNA, Ribosomal, 16S, Seawater/*microbiology, Sequence Analysis, DNAPhylogeny
Phylogeny29637394Gallaecimonas mangrovi sp. nov., a novel bacterium isolated from mangrove sediment.Zhang WY, Yuan Y, Su DQ, He XP, Han SB, Epstein SS, He S, Wu MAntonie Van Leeuwenhoek10.1007/s10482-018-1076-y2018Acanthaceae/*microbiology, *Environmental Microbiology, Gammaproteobacteria/chemistry/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Metabolomics/methods, Molecular Typing, Phenotype, Phylogeny, RNA, Ribosomal, 16S/geneticsPhenotype

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
22073Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100312Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100312)
30697Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172702828776041
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
68369Automatically annotated from API 20NE
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/
89301Reimer, 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-ID362601.1