Archive BacDiveID:10.13145/bacdive5719.20230509.8.1

Strain identifier

BacDive ID: 5719

Type strain:

Species: Christiangramia gaetbulicola

Strain Designation: RA5-111

Strain history: <- SB Kim, Chungnam Univ.

NCBI tax ID(s): 703340 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

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.

NCBI tax id

NCBI tax id: 703340
Matching level: species

strain history

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

doi: 10.13145/bacdive5719.20230509.8.1

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 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

@ref	cell shape	motility	flagellum arrangement	gram stain	confidence
67771	rod-shaped	yes	gliding
67771				negative
69480				negative	99.97

multimedia

@ref	multimedia content	caption	intellectual property rights
66793	EM_DSM_23082_1.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_23082_2.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_23082_3.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_23082_4.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_23082_5.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_23082_6.jpg	electron 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

@ref	growth	type	temperature	range
16698	positive	growth	28	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 67771
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.999

observation

@ref	observation
67770	quinones: MK-6
67771	quinones: MK-6

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
16698	foreshore soil	Chungnam, Boryeong, Daechon-Dong	Republic of Korea	KOR	Asia
67770	Foreshore soil in the Buan area	Jeonbuk	Republic of Korea	KOR	Asia
67771	From foreshore soil	Buan area, Jeonbuk	Republic of Korea	KOR	Asia

isolation source categories

Cat1	Cat2	Cat3
#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: ena
NCBI tax ID: 703340

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Gramella gaetbulicola strain DSM 23082	703340.3	wgs	patric	703340
66792	Gramella gaetbulicola DSM 23082	2734482285	draft	img	703340
67770	Christiangramia gaetbulicola DSM 23082	GCA_003054225	contig	ncbi	703340

GC content

@ref	GC-content	method
16698	39.1	high performance liquid chromatography (HPLC)
67771	39.1

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
gram-positive	no	97.805	yes
anaerobic	no	99.072	no
halophile	yes	52.856	no
spore-forming	no	96.104	no
glucose-util	yes	88.741	no
flagellated	no	94.691	yes
thermophile	no	98.888	yes
aerobic	yes	88.826	yes
glucose-ferment	no	89.314	no
motile	no	89.012	no

External links

@ref: 16698

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

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	21148671	Gramella 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 SB	Int J Syst Evol Microbiol	10.1099/ijs.0.027599-0	2010	Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Flavobacteriaceae/classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology	Metabolism
Phylogeny	26032555	Gramella lutea sp. nov., a Novel Species of the Family Flavobacteriaceae Isolated from Marine Sediment.	Yoon J, Jo Y, Kim GJ, Choi H	Curr Microbiol	10.1007/s00284-015-0849-z	2015	Bacterial Typing Techniques, Base Composition, Fatty Acids/metabolism, Flavobacteriaceae/classification/genetics/isolation & purification/metabolism, Geologic Sediments/microbiology, Molecular Sequence Data, Phylogeny, Republic of Korea, Seawater/microbiology	Metabolism
Phylogeny	27902319	Description 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 RL	Int J Syst Evol Microbiol	10.1099/ijsem.0.001700	2017	Bacterial 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/chemistry	Transcriptome
Phylogeny	32996881	Gramella 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 M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004488	2020	Animals, 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/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
16698	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23082)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-23082
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
67771	Curators of the KCTC		https://kctc.kribb.re.kr/En/Kctc
69479	João 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
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

multimedia

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

oxygen tolerance

spore formation

observation

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

literature

Reference