Gracilimonas tropica CL-CB462 | Type strain | DSM 19535, KCCM 90063 | BacDiveID:17764

Strain identifier

BacDive ID: 17764

Type strain:

Species: Gracilimonas tropica

Strain Designation: CL-CB462

Culture col. no.: DSM 19535, KCCM 90063

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

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

SI-ID 396773

DSM 19535

Special Collections

Section

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.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Balneolota*
	Class	*Balneolia*
	Order	*Balneolales*
	Family	*Balneolaceae*
	Genus	*Gracilimonas*
	Species	**Gracilimonas tropica**
	Full Scientific Name (LPSN)	Gracilimonas tropica Choi et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29073]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %93.278

[Ref.: #29073]	Cell length	15.35 µm

[Ref.: #29073]	Cell width	0.25 µm

[Ref.: #29073]	Cell shape	rod-shaped

[Ref.: #29073]	Motility	no

Pigment production

yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #8156]			growth	28 °C
[Ref.: #29073]			growth	20-40 °C
[Ref.: #29073]			optimum	35 °C

	pH	Kind of pH		pH
[Ref.: #29073]			optimum	7.5
[Ref.: #29073]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

[Ref.: #29073]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29073]		NaCl		growth	1-20	%

Observation

aggregates in clumps

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29073]		aspartate ChEBI	+	carbon source
[Ref.: #29073]		fructose ChEBI	+	carbon source
[Ref.: #29073]		glucose ChEBI	+	carbon source
[Ref.: #29073]		tween 40 ChEBI	+	carbon source
[Ref.: #29073]		tween 80 ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29073]		acid phosphatase	+	3.1.3.2
[Ref.: #29073]		alkaline phosphatase	+	3.1.3.1
[Ref.: #29073]		catalase	+	1.11.1.6
[Ref.: #29073]		cytochrome oxidase	+	1.9.3.1
[Ref.: #29073]		gelatinase	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #8156]	Sample type/isolated from	Synechococcus culture established from surface water of the tropical Pacific Ocean
[Ref.: #8156]	Host species	Synechococcus
[Ref.: #8156]	Country	Republic of Korea
[Ref.: #8156]	Country ISO 3 Code	KOR
[Ref.: #8156]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Global distribution of 16S sequence EF988655 (>99% sequence identity) for Gracilimonas tropica subclade from Microbeatlas

Aquatic Samples	824
Soil Samples	120
Animal Samples	118
Plant Samples	3
Total Samples	1065

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

Biosafety level

1

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #8156]	Gracilimonas tropica strain CL-CB462 16S ribosomal RNA gene, partial sequence	EF988655	1447	GenBank ENA	454600 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Gracilimonas tropica DSM 19535	GCA_000375425	contig	GenBank ENA	1121930 tax ID	*
[Ref.: #66792]	Gracilimonas tropica DSM 19535	1121930.3	wgs	PATRIC	1121930 tax ID	*
[Ref.: #66792]	Gracilimonas tropica DSM 19535	2515154158	draft	JGI IMG/M	1121930 tax ID	*

[Ref.: #8156]	GC-content	42.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29073]	GC-content	42.7 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Gracilimonas tropica DSM 19535 PATRIC: 1121930.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gracilimonas tropica DSM 19535 PATRIC: 1121930.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	93.278	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.653	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.324	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	80.53	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	90.242	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	79.405	yes

Availability in culture collections External links

Culture collection no.

DSM 19535, KCCM 90063

SI-ID 396773

*

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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	*
Phylogeny	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	*
Phylogeny	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	*
Genetics	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	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	*
Phylogeny	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	*
Phylogeny	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	*

References

#8156

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19535

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#29073

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25503 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86755

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID396773.1 )

#25503

IJSEM 1167 2009 ( DOI 10.1099/ijs.0.005512-0 , PubMed 19406813 )

* These data were automatically processed and therefore are not curated

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