Clostridium ganghwense (DSM 18771, IMSNU 40127, JCM 13193)

Name: Clostridium ganghwense (DSM 18771, IMSNU 40127, JCM 13193)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2842

Type strain

Strain Designation HY-42-06

Culture col. no. DSM 18771 IMSNU 40127 JCM 13193 KCTC 5146 HY-42-06

NCBI tax ID(s) 312089

Special Collections DSMZ JCM KCTC Literature strains

Links

Clostridium ganghwense HY-42-06 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from tidal flat sediment.

Gram-negative motile rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 232204

KCTC 5146,JCM 13193,DSM 18771

@ref 20215

Last LPSN update 2025-12-16 09:47:24

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium ganghwense

Full scientific name Clostridium ganghwense Kim et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement
31550	negative	04-08 µm	0.7-0.8 µm	rod-shaped
67771				rod-shaped	peritrichous
67771	negative

Pigmentation

31550

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7688	RCM MEDIUM (WITH SEA SALTS) (DSMZ Medium 634b)		Medium recipe at MediaDive	Name: RCM MEDIUM (with Sea Salts) (DSMZ Medium 634b) Composition: dehydrated RCM medium 38.0 g/l Sea salts 30.0 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7688	positive	growth	35	mesophilic
31550	positive	growth	15-40
31550	positive	optimum	35	mesophilic
67770	positive	growth	35	mesophilic
67771	positive	growth	35	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31550	positive	optimum	7.5
31550	positive	growth	5.5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7688	anaerobe
31550	anaerobe
67771	anaerobe
125439	facultative anaerobe	98.1

Spore formation

@ref	Spore formation	Confidence
31550
125439		97.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31550	NaCl	positive	growth	0-5 %
31550	NaCl	positive	optimum	0-5 %

Observation

31550

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31550	17057 ChEBI	cellobiose	+	carbon source
31550	4853 ChEBI	esculin	+	hydrolysis
31550	17234 ChEBI	glucose	+	carbon source
31550	17306 ChEBI	maltose	+	carbon source
31550	37684 ChEBI	mannose	+	carbon source
31550	17814 ChEBI	salicin	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31550	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
31550	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity
31550	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
7688	tidal flat sediment	Ganghwa Island	Republic of Korea	KOR	Asia	37.5833	126.45 37.5833/126.45
67770	Tidal flat sediment from Ganghwa Island		Republic of Korea	KOR	Asia
67771	From tidal flat sediment	Ganghwa Island	Republic of Korea	KOR	Asia	37.5886	126.454 37.5886/126.454

Taxonmaps

69479

Global distribution of 16S sequence AY903294 (>99% sequence identity) for Clostridium ganghwense subclade from Microbeatlas

Aquatic Samples	120
Soil Samples	3
Animal Samples	34
Plant Samples
Total Samples	157

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7688	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2673516v1 assembly for Clostridium ganghwense HY-42-06	scaffold	GCA_026735165	312089.3	8048799138	312089	70.31

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7688	Clostridium ganghwense strain HY-42-06 16S ribosomal RNA gene, partial sequence	AY903294	1433		312089

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium ganghwense HY-42-06
NCBI: GCA_026735165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	97.30	no
125439	motility	BacteriaNetⓘ	yes	87.30	no
125439	gram_stain	BacteriaNetⓘ	positive	86.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	98.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium ganghwense HY-42-06
NCBI: GCA_026735165.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	62.49	yes
125438	anaerobic	anaerobicⓘ	yes	79.79	no
125438	aerobic	aerobicⓘ	no	94.18	no
125438	spore-forming	spore-formingⓘ	yes	55.40	yes
125438	thermophilic	thermophileⓘ	no	86.64	no
125438	flagellated	motile2+ⓘ	yes	85.99	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov.	Morotomi M, Nagai F, Watanabe Y	Int J Syst Evol Microbiol	10.1099/ijs.0.026989-0	2011
Phylogeny	Clostridium aestuarii sp. nov., from tidal flat sediment.	Kim S, Jeong H, Chun J	Int J Syst Evol Microbiol	10.1099/ijs.0.64428-0	2007
Phylogeny	Clostridium ganghwense sp. nov., isolated from tidal flat sediment.	Kim S, Jeong H, Kim S, Chun J	Int J Syst Evol Microbiol	10.1099/ijs.0.63791-0	2006

References

#7688	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18771
#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 )
#31550	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 #27841 (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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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 )

Rate our new design

Content

About us

Clostridium ganghwense (DSM 18771, IMSNU 40127, JCM 13193)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_026735165

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media