Strain identifier

BacDive ID: 5718

Type strain: Yes

Species: Christiangramia portivictoriae

Strain Designation: UST040801-001

Strain history: S. Lau UST040801-001.

NCBI tax ID(s): 1121932 (strain), 326069 (species)

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General

@ref: 17278

BacDive-ID: 5718

DSM-Number: 23547

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

description: Christiangramia portivictoriae UST040801-001 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment.

NCBI tax id

NCBI tax idMatching level
326069species
1121932strain

strain history

@refhistory
17278<- JCM; JCM 13192 <- S. C. K. Lau
67770S. Lau UST040801-001.

doi: 10.13145/bacdive5718.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Christiangramia
  • species: Christiangramia portivictoriae
  • full scientific name: Christiangramia portivictoriae (Lau et al. 2005) Deshmukh and Oren 2023

  • synonyms

    • @ref: 20215
    • synonym: Gramella portivictoriae

@ref: 17278

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Gramella

species: Gramella portivictoriae

full scientific name: Gramella portivictoriae Lau et al. 2005 emend. Panschin et al. 2016

strain designation: UST040801-001

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityflagellum arrangementconfidence
31567negative2.1 µmrod-shapedyesgliding
69480negative99.898

pigmentation

  • @ref: 31567
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_23547_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23547_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23547_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23547_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23547_5.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23547_6.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23547_7.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23547_8.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23547_9.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 17278
  • 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
17278positivegrowth28mesophilic
31567positivegrowth04-36
31567positiveoptimum29mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31567positivegrowth06-10alkaliphile
31567positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31567
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31567no
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
31567NaClpositivegrowth01-06 %
31567NaClpositiveoptimum3.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3156722599arabinose+carbon source
3156728260galactose+carbon source
3156717234glucose+carbon source
3156717754glycerol+carbon source
3156729864mannitol+carbon source
3156728053melibiose+carbon source
3156730911sorbitol+carbon source
3156717992sucrose+carbon source
3156753424tween 20+carbon source
3156753423tween 40+carbon source
3156753426tween 80+carbon source

enzymes

@refvalueactivityec
31567acid phosphatase+3.1.3.2
31567alkaline phosphatase+3.1.3.1
31567alpha-galactosidase+3.2.1.22
31567catalase+1.11.1.6
31567cytochrome oxidase+1.9.3.1
31567urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17278sedimentVictoria HarbourHong KongHKGAsia
67770Sediment in Victoria HarbourHong KongChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3066.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_1604;97_1915;98_2356;99_3066&stattab=map
  • Last taxonomy: Gramella portivictoriae
  • 16S sequence: AB681471
  • Sequence Identity:
  • Total samples: 406
  • soil counts: 24
  • aquatic counts: 353
  • animal counts: 28
  • plant counts: 1

Safety information

risk assessment

  • @ref: 17278
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gramella portivictoriae gene for 16S rRNA, partial sequence, strain: NBRC 101534AB6814711455ena326069
17278Gramella portivictoriae strain UST040801-001 16S ribosomal RNA gene, partial sequenceDQ0028711468ena326069

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gramella portivictoriae DSM 235471121932.6wgspatric1121932
66792Gramella portivictoriae DSM 235472524614725draftimg1121932
67770Christiangramia portivictoriae DSM 23547GCA_000423045scaffoldncbi1121932

GC content

@refGC-contentmethod
1727839.9±0.2high performance liquid chromatography (HPLC)
3156739.9
6777039.7-40.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.641no
flagellatedno94.243yes
gram-positiveno97.759yes
anaerobicno99.501yes
halophileyes64.521no
spore-formingno96.539yes
thermophileno99.23yes
glucose-utilyes86.512no
aerobicyes91.881yes
glucose-fermentno91.018no

External links

@ref: 17278

culture collection no.: DSM 23547, JCM 13192, NBRC 101534, NRRL B-41137, CIP 109020, KCTC 22434

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280516Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment.Lau SCK, Tsoi MMY, Li X, Plakhotnikova I, Dobretsov S, Wong PK, Qian PYInt J Syst Evol Microbiol10.1099/ijs.0.63824-02005DNA, Bacterial/analysis, Fatty Acids/analysis, Flavobacteriaceae/chemistry/classification/genetics/*isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Water MicrobiologyGenetics
27274783Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005.Panschin I, Huang S, Meier-Kolthoff JP, Tindall BJ, Rohde M, Verbarg S, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Goker M, Klenk HP, Kyrpides NC, Hahnke RLStand Genomic Sci10.1186/s40793-016-0163-92016
Phylogeny27902319Description of Gramella forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of Gramella gaetbulicola Cho et al. 2011.Panschin I, Becher M, Verbarg S, Sproer C, Rohde M, Schuler M, Amann RI, Harder J, Tindall BJ, Hahnke RLInt J Syst Evol Microbiol10.1099/ijsem.0.0017002017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Germany, North Sea, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
17278Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23547)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23547
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31567Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127857
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 life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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