Archive BacDiveID:10.13145/bacdive17764.20240916.9.1

Strain identifier

BacDive ID: 17764

Type strain:

Species: Gracilimonas tropica

Strain Designation: CL-CB462

Strain history: <- B. C. Cho, Seoul Natl. Univ., Republic of Korea; CL-CB462

NCBI tax ID(s): 1121930 (strain), 454600 (species)

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

General

@ref: 8156

BacDive-ID: 17764

DSM-Number: 19535

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-negative, rod-shaped

description: Gracilimonas tropica CL-CB462 is an aerobe, spore-forming, Gram-negative bacterium that was isolated from Synechococcus culture established from surface water of the tropical Pacific Ocean.

NCBI tax id

NCBI tax id	Matching level
1121930	strain
454600	species

strain history

@ref: 8156
history: <- B. C. Cho, Seoul Natl. Univ., Republic of Korea; CL-CB462

doi: 10.13145/bacdive17764.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/balneolota
domain: Bacteria
phylum: Balneolota
class: Balneolia
order: Balneolales
family: Balneolaceae
genus: Gracilimonas
species: Gracilimonas tropica
full scientific name: Gracilimonas tropica Choi et al. 2009

@ref: 8156

domain: Bacteria

phylum: Balneolaeota

class: Balneolia

order: Sphingobacteriales

family: Balneolaceae

genus: Gracilimonas

species: Gracilimonas tropica

full scientific name: Gracilimonas tropica Choi et al. 2009

strain designation: CL-CB462

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29073	negative	15.35 µm	0.25 µm	rod-shaped	no
69480	negative					93.278

pigmentation

@ref: 29073
production: yes

multimedia

@ref	multimedia content	caption	intellectual property rights
66793	EM_DSM_19535_1.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_19535_2.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_19535_3.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_19535_4.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_19535_5.jpg	electron microscopic image	© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 8156
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

@ref	growth	type	temperature
8156	positive	growth	28
29073	positive	growth	20-40
29073	positive	optimum	35

culture pH

@ref	ability	type	pH	PH range
29073	positive	growth	06-10	alkaliphile
29073	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref: 29073
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
29073	yes
69481	no	100

halophily

@ref: 29073
salt: NaCl
growth: positive
tested relation: growth
concentration: 1-20 %

observation

@ref: 29073
observation: aggregates in clumps

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29073	35391	aspartate	+	carbon source
29073	28757	fructose	+	carbon source
29073	17234	glucose	+	carbon source
29073	53423	tween 40	+	carbon source
29073	53426	tween 80	+	carbon source

enzymes

@ref	value	activity	ec
29073	acid phosphatase	+	3.1.3.2
29073	alkaline phosphatase	+	3.1.3.1
29073	catalase	+	1.11.1.6
29073	gelatinase	+
29073	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref: 8156
sample type: Synechococcus culture established from surface water of the tropical Pacific Ocean
host species: Synechococcus
country: Republic of Korea
origin.country: KOR
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Lab enrichment
#Environmental	#Aquatic	#Marine
#Host	#Microbial	#Bacteria
#Climate	#Hot	#Tropical

taxonmaps

@ref: 69479
File name: preview.99_6393.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_471;96_3029;97_3723;98_4722;99_6393&stattab=map
Last taxonomy: Gracilimonas tropica subclade
16S sequence: EF988655
Sequence Identity:
Total samples: 1065
soil counts: 120
aquatic counts: 824
animal counts: 118
plant counts: 3

Safety information

risk assessment

@ref: 8156
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 8156
description: Gracilimonas tropica strain CL-CB462 16S ribosomal RNA gene, partial sequence
accession: EF988655
length: 1447
database: nuccore
NCBI tax ID: 454600

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Gracilimonas tropica DSM 19535	GCA_000375425	contig	ncbi	1121930
66792	Gracilimonas tropica DSM 19535	1121930.3	wgs	patric	1121930
66792	Gracilimonas tropica DSM 19535	2515154158	draft	img	1121930

GC content

@ref	GC-content	method
8156	42.7	high performance liquid chromatography (HPLC)
29073	42.7

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69481	spore-forming	spore-forming	Ability to form endo- or exospores	no	100	no
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	no	93.278	yes
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	93.653	no
69480	spore-forming	spore-forming	Ability to form endo- or exospores	no	88.324	no
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	80.53	yes
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	no	90.242	yes
69480	flagellated	motile2+	Ability to perform flagellated movement	no	79.405	yes

External links

@ref: 8156

culture collection no.: DSM 19535, KCCM 90063

straininfo link

@ref: 86755
straininfo: 396773

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19406813	Gracilimonas tropica gen. nov., sp. nov., isolated from a Synechococcus culture.	Choi DH, Zhang GI, Noh JH, Kim WS, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.005512-0	2009	Bacterial Typing Techniques, Bacteroidetes/classification/genetics/isolation & purification/physiology, Base Composition, Culture Media, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Pacific Ocean, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Species Specificity, Synechococcus/*growth & development/isolation & purification	Enzymology
Phylogeny	23710054	Gracilimonas mengyeensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-western China.	Wang YX, Li YP, Liu JH, Xiao W, Lai YH, Li ZY, Ding ZG, Wen ML, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.052043-0	2013	Bacterial Typing Techniques, Bacteroidetes/classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride	Genetics
Phylogeny	23710056	Gracilimonas rosea sp. nov., isolated from tropical seawater, and emended description of the genus Gracilimonas.	Cho Y, Chung H, Jang GI, Choi DH, Noh JH, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.052340-0	2013	Bacterial Typing Techniques, Bacteroidetes/classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micronesia, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Water Microbiology	Genetics
Genetics	26566423	High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture.	Choi DH, Ahn C, Jang GI, Lapidus A, Han J, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Rohde M, Tindall B, Goker M, Woyke T, Klenk HP, Kyrpides NC, Cho BC	Stand Genomic Sci	10.1186/s40793-015-0088-8	2015
Phylogeny	26961808	Aliifodinibius halophilus sp. nov., a moderately halophilic member of the genus Aliifodinibius, and proposal of Balneolaceae fam. nov.	Xia J, Ling SK, Wang XQ, Chen GJ, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001012	2016	Bacterial Typing Techniques, Bacteroidetes/classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gram-Positive Rods/classification/genetics/isolation & purification, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water Microbiology	Enzymology
Phylogeny	28109207	Rhodohalobacter halophilus gen. nov., sp. nov., a moderately halophilic member of the family Balneolaceae.	Xia J, Xie ZH, Dunlap CA, Rooney AP, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001806	2017	Bacterial Typing Techniques, Bacteroidetes/classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water Microbiology	Transcriptome
Phylogeny	29611802	Gracilimonas amylolytica sp. nov., isolated from deep-sea sediment.	Wu YH, Yan J, Fang C, Huo YY, Ma WL, Zhang DM, Wang CS, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002734	2018	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Gram-Negative Aerobic Rods and Cocci/classification/genetics/isolation & purification, Pacific Ocean, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
8156	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19535)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-19535
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
29073	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	25503	28776041
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		28604660	35: 676-683 2017
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
86755	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID396773.1	StrainInfo: A central database for resolving microbial strain identifiers