Nibrella saemangeumensis (KACC 16453, JCM 17927, GCR0103)

Name: Nibrella saemangeumensis (KACC 16453, JCM 17927, GCR0103)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134053

Type strain

Strain Designation GCR0103

Culture col. no. KACC 16453 JCM 17927 GCR0103

NCBI tax ID(s) 1084526

Special Collections JCM Literature strains

History JCM <-- K. Y. Jahng GCR0103.

Links

Nibrella saemangeumensis GCR0103 is a Gram-negative, rod-shaped bacterium that was isolated from seawater.

Gram-negative rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 133116

JCM 17927

@ref 20215

Last LPSN update 2026-05-29 08:38:14

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Nibrella

Species Nibrella saemangeumensis

Full scientific name Nibrella saemangeumensis Kang et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31145	negative	7.3 µm	1.15 µm	rod-shaped
125439	negative					92.641

Pigmentation

31145

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
31145	positive	growth	15-37
31145	positive	optimum	25
67770	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
31145	positive	optimum	7.5
31145	positive	growth	6.5-10.0	alkaliphile

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		98.954

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31145	NaCl	positive	growth	0-0.4 %

Observation

31145

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31145	16449 ChEBI	alanine	+	carbon source
31145	22599 ChEBI	arabinose	+	carbon source
31145	4853 ChEBI	esculin	+	hydrolysis
31145	24265 ChEBI	gluconate	+	carbon source
31145	29987 ChEBI	glutamate	+	carbon source
31145	28087 ChEBI	glycogen	+	carbon source
31145	21217 ChEBI	L-alaninamide	+	carbon source
31145	24996 ChEBI	lactate	+	carbon source
31145	25017 ChEBI	leucine	+	carbon source
31145	28053 ChEBI	melibiose	+	carbon source
31145	37657 ChEBI	methyl D-glucoside	+	carbon source
31145	51850 ChEBI	methyl pyruvate	+	carbon source
31145	506227 ChEBI	N-acetylglucosamine	+	carbon source
31145	30031 ChEBI	succinate	+	carbon source
31145	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31145	acid phosphatase	+	3.1.3.2
31145	alkaline phosphatase	+	3.1.3.1
31145	alpha-galactosidase	+	3.2.1.22
31145	catalase	+	1.11.1.6
31145	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
31145	seawater
67770	Seawater of the Saemangeum Embankment in Jeollabuk-do	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence JN607159 (>99% sequence identity) for Nibrella saemangeumensis subclade from Microbeatlas

Aquatic Samples	308
Soil Samples	790
Animal Samples	326
Plant Samples	121
Total Samples	1545

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3954191v1 assembly for Nibrella saemangeumensis JCM 17927	contig	GCA_039541915	1084526	62.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31145	Nibrella saemangeumensis strain GCR0103 16S ribosomal RNA gene, partial sequence	JN607159	1343		1084526

GC content

31145

GC-content (mol%)56

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3954191v1 assembly for Nibrella saemangeumensis JCM 17927
NCBI: GCA_039541915

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	67.89	no
125439	motility	BacteriaNetⓘ	no	67.34	no
125439	gram_stain	BacteriaNetⓘ	negative	92.64	no
125439	spore_formation	BacteriaNetⓘ	no	98.95	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nibrella saemangeumensis gen. nov., sp. nov. and Nibrella viscosa sp. nov., novel members of the family Cytophagaceae, isolated from seawater.	Kang JY, Chun J, Choi A, Cho JC, Jahng KY	Int J Syst Evol Microbiol	10.1099/ijs.0.053439-0	2013

References

#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 )
#27473	IJSEM 4508 2013 ( DOI 10.1099/ijs.0.053439-0 , PubMed 23907222 )
#31145	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 #27473
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Nibrella saemangeumensis (KACC 16453, JCM 17927, GCR0103)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_039541915

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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