Kistimonas scapharcae (KACC 16204, JCM 17805, A36)

Name: Kistimonas scapharcae (KACC 16204, JCM 17805, A36)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133798

Type strain

Strain Designation A36

Culture col. no. KACC 16204 JCM 17805 A36

NCBI tax ID(s) 1036133

Special Collections JCM Literature strains

History JCM <-- J.-W. Bae A36.

Links

Kistimonas scapharcae A36 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from Ark clam.

Gram-negative motile rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 132039

JCM 17805

@ref 20215

Last LPSN update 2026-05-29 08:38:10

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Endozoicomonadaceae

Genus Kistimonas

Species Kistimonas scapharcae

Full scientific name Kistimonas scapharcae Lee et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30546	negative	2.25 µm	0.3 µm	rod-shaped

Pigmentation

30546

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30546	positive	growth	10-45
30546	positive	optimum	33.5
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
30546	positive	optimum	8
30546	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

30546

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.888

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30546	NaCl	positive	growth	0-5 %
30546	NaCl	positive	optimum	1 %

Observation

67770

Observationquinones: Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30546	16449 ChEBI	alanine	+	carbon source
30546	22653 ChEBI	asparagine	+	carbon source
30546	35391 ChEBI	aspartate	+	carbon source
30546	29987 ChEBI	glutamate	+	carbon source
30546	18257 ChEBI	ornithine	+	carbon source
30546	17822 ChEBI	serine	+	carbon source
30546	30031 ChEBI	succinate	+	carbon source
30546	53423 ChEBI	tween 40	+	carbon source
30546	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30546	acid phosphatase	+	3.1.3.2
30546	alkaline phosphatase	+	3.1.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Mollusca

Isolation

@ref	Sample type
30546	Ark clam
67770	Dead ark clam on the south coast of Korea

Taxonmaps

69479

Global distribution of 16S sequence JF811908 (>99% sequence identity) for Kistimonas scapharcae from Microbeatlas

Aquatic Samples	1106
Soil Samples	96
Animal Samples	130
Plant Samples	21
Total Samples	1353

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3954097v1 assembly for Kistimonas scapharcae JCM 17805	contig	GCA_039540975	1036133	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30546	Kistimonas scapharcae strain A36 16S ribosomal RNA gene, partial sequence	JF811908	1473		1036133

GC content

@ref	GC-content (mol%)	Method
30546	47.3
67770	47.3	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3954097v1 assembly for Kistimonas scapharcae JCM 17805
NCBI: GCA_039540975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	89.61	no
125439	gram_stain	BacteriaNetⓘ	negative	89.27	no
125439	spore_formation	BacteriaNetⓘ	no	99.89	no
125439	motility	BacteriaNetⓘ	yes	52.82	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and emended description of the genus Kistimonas.	Lee J, Shin NR, Lee HW, Roh SW, Kim MS, Kim YO, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.038422-0	2012

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 )
#26877	IJSEM 2865 2012 ( DOI 10.1099/ijs.0.038422-0 , PubMed 22247211 )
#30546	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 #26877
#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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Kistimonas scapharcae (KACC 16204, JCM 17805, A36)

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_039540975

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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