Strain identifier

BacDive ID: 5719

Type strain: Yes

Species: Christiangramia gaetbulicola

Strain Designation: RA5-111

Strain history: <- SB Kim, Chungnam Univ.

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General

@ref: 16698

BacDive-ID: 5719

DSM-Number: 23082

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

description: Christiangramia gaetbulicola RA5-111 is an aerobe, mesophilic, motile bacterium that was isolated from foreshore soil.

strain history

@refhistory
16698<- S. B. Kim, School Biosci. Biotechnol., Chungnam Natl. Univ., Republic of Korea; RA5-111
67770S. B. Kim RA5-111.
67771<- SB Kim, Chungnam Univ.

doi: 10.13145/bacdive5719.20250331.9.3

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 gaetbulicola
  • full scientific name: Christiangramia gaetbulicola (Cho et al. 2011) Deshmukh and Oren 2023

  • synonyms

    • @ref: 20215
    • synonym: Gramella gaetbulicola

@ref: 16698

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Gramella

species: Gramella gaetbulicola

full scientific name: Gramella gaetbulicola Cho et al. 2011 emend. Panschin et al. 2017

strain designation: RA5-111

type strain: yes

Morphology

cell morphology

@refcell shapemotilityflagellum arrangementgram stainconfidence
67771rod-shapedyesgliding
67771negative
125439negative99.8
125438no92.75
125438negative95.5

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_23082_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23082_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23082_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23082_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23082_5.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_23082_6.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 16698
  • 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; with strain-specific modifications) Composition: NaCl 80.0 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

@refgrowthtypetemperature
16698positivegrowth28
67770positivegrowth30
67771positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
125439no98.9
125438no91

observation

@refobservation
67770quinones: MK-6
67771quinones: MK-6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16698foreshore soilChungnam, Boryeong, Daechon-DongRepublic of KoreaKORAsia
67770Foreshore soil in the Buan areaJeonbukRepublic of KoreaKORAsia
67771From foreshore soilBuan area, JeonbukRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_73761.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_1604;97_1915;98_6856;99_73761&stattab=map
  • Last taxonomy: Gramella gaetbulicola
  • 16S sequence: GQ857650
  • Sequence Identity:
  • Total samples: 34
  • soil counts: 2
  • aquatic counts: 28
  • animal counts: 4

Safety information

risk assessment

  • @ref: 16698
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16698
  • description: Gramella gaetbulicola strain RA5-111 16S ribosomal RNA gene, partial sequence
  • accession: GQ857650
  • length: 1402
  • database: nuccore
  • NCBI tax ID: 703340

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gramella gaetbulicola strain DSM 23082703340.3wgspatric703340
66792Gramella gaetbulicola DSM 230822734482285draftimg703340
67770Christiangramia gaetbulicola DSM 23082GCA_003054225contigncbi703340

GC content

@refGC-contentmethod
1669839.1high performance liquid chromatography (HPLC)
6777139.1

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno95.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.521yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.726no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.404yes
125438motile2+flagellatedAbility to perform flagellated movementno92.75yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.9
125439BacteriaNetmotilityAbility to perform movementno65.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe79.6

External links

@ref: 16698

culture collection no.: DSM 23082, JCM 16528, KCTC 23022, NBRC 106272

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21148671Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil.Cho SH, Chae SH, Cho M, Kim TU, Choi S, Han JH, Kim YT, Joung Y, Joh K, Nedashkovskaya OI, Kim SBInt J Syst Evol Microbiol10.1099/ijs.0.027599-02010Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny26032555Gramella lutea sp. nov., a Novel Species of the Family Flavobacteriaceae Isolated from Marine Sediment.Yoon J, Jo Y, Kim GJ, Choi HCurr Microbiol10.1007/s00284-015-0849-z2015Bacterial Typing Techniques, Base Composition, Fatty Acids/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, Republic of Korea, Seawater/*microbiologyMetabolism
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
Phylogeny32996881Gramella bathymodioli sp. nov., isolated from a mussel inhabiting a hydrothermal field in the Okinawa Trough.Liu L, Wang S, Zhou S, Sun W, Fu T, Zhang Y, Zhang XH, Yu MInt J Syst Evol Microbiol10.1099/ijsem.0.0044882020Animals, Bacterial Typing Techniques, Base Composition, Bivalvia/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Pacific Ocean, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16698Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23082)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23082
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
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1