Nibrella viscosa (KACC 16447, JCM 17925, GYR3121)

Name: Nibrella viscosa (KACC 16447, JCM 17925, GYR3121)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134054

Type strain

Strain Designation GYR3121

Culture col. no. KACC 16447 JCM 17925 GYR3121

NCBI tax ID(s) 1084524

Special Collections JCM Literature strains

History JCM <-- K. Y. Jahng GYR3121.

Links

Nibrella viscosa GYR3121 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 390872

JCM 17925

@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 viscosa

Full scientific name Nibrella viscosa Kang et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31145	negative	9.1 µm	0.95 µm	rod-shaped
125439	negative					99.361

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	5.5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	93.461

Spore formation

@ref	Spore formation	Confidence
125439		99.824

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31145	NaCl	positive	growth	0-1.0 %

Observation

31145

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31145	16449 ChEBI	alanine	+	carbon source
31145	17057 ChEBI	cellobiose	+	carbon source
31145	4853 ChEBI	esculin	+	hydrolysis
31145	28757 ChEBI	fructose	+	carbon source
31145	28260 ChEBI	galactose	+	carbon source
31145	24265 ChEBI	gluconate	+	carbon source
31145	17234 ChEBI	glucose	+	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	17716 ChEBI	lactose	+	carbon source
31145	17306 ChEBI	maltose	+	carbon source
31145	37684 ChEBI	mannose	+	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	16634 ChEBI	raffinose	+	carbon source
31145	17992 ChEBI	sucrose	+	carbon source
31145	27082 ChEBI	trehalose	+	carbon source
31145	53423 ChEBI	tween 40	+	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 JN607161 (>99% sequence identity) for Nibrella viscosa subclade from Microbeatlas

Aquatic Samples	88
Soil Samples	181
Animal Samples	41
Plant Samples	71
Total Samples	381

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3954187v1 assembly for Nibrella viscosa JCM 17925	scaffold	GCA_039541875	1084524	65.12

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31145	Nibrella viscosa strain GYR3121 16S ribosomal RNA gene, partial sequence	JN607161	1358		1084524

GC content

31145

GC-content (mol%)54.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3954187v1 assembly for Nibrella viscosa JCM 17925
NCBI: GCA_039541875

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	93.46	no
125439	gram_stain	BacteriaNetⓘ	negative	99.36	no
125439	motility	BacteriaNetⓘ	yes	60.24	no
125439	spore_formation	BacteriaNetⓘ	no	99.82	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 viscosa (KACC 16447, JCM 17925, GYR3121)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

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_039541875

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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