Name: Clostridium ganghwense HY-42-06
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2842

Type strain:

Species: Clostridium ganghwense

Strain Designation: HY-42-06

Culture col. no.: DSM 18771, IMSNU 40127, JCM 13193, KCTC 5146

Strain history: <- J Chun, SNU, HY-42-06

NCBI tax ID(s): 312089 (species)

SI-ID 232204

KCTC 5146, JCM 13193, DSM 18771

Section

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

Gram-negative
motile
rod-shaped
anaerobe
mesophilic
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Clostridium*
	Species	**Clostridium ganghwense**
	Full Scientific Name (LPSN)	Clostridium ganghwense Kim et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31550]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #31550]	Cell length	04-08 µm

[Ref.: #31550]	Cell width	0.7-0.8 µm

[Ref.: #31550]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31550]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #67771]	Flagellum arrangement	peritrichous

[Ref.: #31550]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7688]

Culture medium

RCM MEDIUM (WITH SEA SALTS) (DSMZ Medium 634b)

[Ref.: #7688]

Culture medium growth

[Ref.: #7688]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7688]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7688]	growth	35 °C
[Ref.: #31550]	growth	15-40 °C
[Ref.: #31550]	optimum	35 °C
[Ref.: #67770]	growth	35 °C
[Ref.: #67771]	growth	35 °C

[Ref.: #7688]	Temperature range	mesophilic
[Ref.: #31550]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31550]			optimum	7.5
[Ref.: #31550]			growth	5.5-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7688]	Oxygen tolerance	anaerobe
[Ref.: #31550]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #31550]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31550]		NaCl		growth	0-5	%
[Ref.: #31550]		NaCl		optimum	0-5	%

[Ref.: #31550]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31550]	cellobiose ChEBI	+	carbon source
[Ref.: #31550]	esculin ChEBI	+	hydrolysis
[Ref.: #31550]	glucose ChEBI	+	carbon source
[Ref.: #31550]	maltose ChEBI	+	carbon source
[Ref.: #31550]	mannose ChEBI	+	carbon source
[Ref.: #31550]	salicin ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #31550]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #31550]		indole ChEBI	+

	Enzymes	Enzyme	Enzyme activity
[Ref.: #31550]		gelatinase	+

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

[Ref.: #7688]	Sample type/isolated from	tidal flat sediment
[Ref.: #7688]	Geographic location (country and/or sea, region)	Ganghwa Island
[Ref.: #7688]	Country	Republic of Korea
[Ref.: #7688]	Country ISO 3 Code	KOR
[Ref.: #7688]	Continent	Asia
[Ref.: #7688]	Geographic location	37.5833°/126.4500°

[Ref.: #67770]	Sample type/isolated from	Tidal flat sediment from Ganghwa Island
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From tidal flat sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	Ganghwa Island
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	37.5886°/126.4540°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #7688]

Biosafety level

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.: #7688]	Clostridium ganghwense strain HY-42-06 16S ribosomal RNA gene, partial sequence	AY903294	1433	ENA	312089 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clostridium ganghwense HY-42-06	GCA_026735165	scaffold	GenBank	312089 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Clostridium ganghwense HY-42-06 NCBI: GCA_026735165.1
[Ref.: #69480]	motile	yes	86.687	yes
[Ref.: #69480]	flagellated	yes	73.744	yes
[Ref.: #69480]	gram-positive	no	52.534	no
[Ref.: #69480]	anaerobic	yes	98.703	no
[Ref.: #69480]	aerobic	no	98.714	no
[Ref.: #69480]	halophile	no	83.266	no
[Ref.: #69480]	spore-forming	yes	92.515	yes
[Ref.: #69480]	glucose-ferment	no	55.682	no
[Ref.: #69480]	thermophile	no	95.176	yes
[Ref.: #69480]	glucose-util	yes	88.163	no

Availability in culture collections External links

[Ref.: #7688]

Culture collection no.

DSM 18771, IMSNU 40127, JCM 13193, KCTC 5146

[Ref.: #72366]

SI-ID 232204

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 .

#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) .

#72366

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-ID232204.1 )

#27841

IJSEM 691 2006 ( DOI 10.1099/ijs.0.63791-0 , PubMed 16585678 )

* These data were automatically processed and therefore are not curated

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