Name: Chitinophaga ginsengisegetis M1-09
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17747

Type strain:

Species: Chitinophaga ginsengisegetis

Strain Designation: M1-09

Culture col. no.: DSM 18108, KCTC 12654, Gsoil 040

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 393003 (species)

SI-ID 290946

LMG 23601, DSM 18108, KCTC 12654

Section

Chitinophaga ginsengisegetis M1-09 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of ginseng field.

Gram-negative
rod-shaped
aerobe
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	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Chitinophaga*
	Species	**Chitinophaga ginsengisegetis**
	Full Scientific Name (LPSN)	Chitinophaga ginsengisegetis Lee et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31941]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.962

[Ref.: #31941]	Cell length	1.2 µm

[Ref.: #31941]	Cell width	0.5 µm

[Ref.: #31941]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31941]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #31941]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7398]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7398]

Culture medium growth

[Ref.: #7398]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7398]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7398]	growth	30 °C
[Ref.: #31941]	growth	04-42 °C
[Ref.: #31941]	optimum	23 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #7398]	Temperature range	mesophilic
[Ref.: #31941]	Temperature range	psychrophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31941]			optimum	7
[Ref.: #31941]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31941]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31941]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.524

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31941]		NaCl		growth	0-2	%
[Ref.: #31941]		NaCl		optimum	1	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31941]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #31941]	alanine ChEBI	+	carbon source
[Ref.: #31941]	arabinose ChEBI	+	carbon source
[Ref.: #31941]	fucose ChEBI	+	carbon source
[Ref.: #31941]	gluconate ChEBI	+	carbon source
[Ref.: #31941]	glucose ChEBI	+	carbon source
[Ref.: #31941]	histidine ChEBI	+	carbon source
[Ref.: #31941]	leucine ChEBI	+	carbon source
[Ref.: #31941]	maltose ChEBI	+	carbon source
[Ref.: #31941]	mannose ChEBI	+	carbon source
[Ref.: #31941]	melibiose ChEBI	+	carbon source
[Ref.: #31941]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31941]	proline ChEBI	+	carbon source
[Ref.: #31941]	rhamnose ChEBI	+	carbon source
[Ref.: #31941]	salicin ChEBI	+	carbon source
[Ref.: #31941]	serine ChEBI	+	carbon source
[Ref.: #31941]	sorbitol ChEBI	+	carbon source
[Ref.: #31941]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31941]		urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	lipid metabolism	83.87	26 of 31
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	61.54	8 of 13
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	oxidative phosphorylation	47.25	43 of 91
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	daunorubicin biosynthesis	44.44	4 of 9
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7398]	Sample type/isolated from	soil of ginseng field
[Ref.: #7398]	Country	Republic of Korea
[Ref.: #7398]	Country ISO 3 Code	KOR
[Ref.: #7398]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil, ginseng field
[Ref.: #67771]	Geographic location (country and/or sea, region)	Pocheon province
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB264798 (>99% sequence identity) for Chitinophaga ginsengisegetis from Microbeatlas

Aquatic Samples	35
Soil Samples	321
Animal Samples	11
Plant Samples	39
Total Samples	406

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

[Ref.: #7398]

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.: #31941]	Chitinophaga ginsengisegetis gene for 16S rRNA, partial sequence	AB264798	1521	GenBank	393003 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chitinophaga ginsengisegetis DSM 18108	GCA_900168065	scaffold	GenBank	393003 tax ID	*
[Ref.: #66792]	Chitinophaga ginsengisegetis strain DSM 18108	393003.3	wgs	PATRIC	393003 tax ID	*
[Ref.: #66792]	Chitinophaga ginsengisegetis DSM 18108	2595698247	draft	JGI IMG/M	393003 tax ID	*

[Ref.: #31941]

GC-content

47.1 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Chitinophaga ginsengisegetis DSM 18108 NCBI: GCA_900168065.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chitinophaga ginsengisegetis DSM 18108 NCBI: GCA_900168065.1
[Ref.: #69480]	motile	no	92.641	yes
[Ref.: #69480]	flagellated	no	96.879	yes
[Ref.: #69480]	gram-positive	no	98.013	no
[Ref.: #69480]	anaerobic	no	99.203	yes
[Ref.: #69480]	aerobic	yes	89.181	yes
[Ref.: #69480]	halophile	no	95.39	no
[Ref.: #69480]	spore-forming	no	92.734	no
[Ref.: #69480]	thermophile	no	99.282	no
[Ref.: #69480]	glucose-util	yes	88.577	yes
[Ref.: #69480]	glucose-ferment	no	84.072	no

Availability in culture collections External links

[Ref.: #7398]

Culture collection no.

DSM 18108, KCTC 12654, Gsoil 040

[Ref.: #86738]

SI-ID 290946

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga hostae sp. nov., isolated from the rhizosphere soil of Hosta plantaginea.	He SW, Ma R, Zhao YY, An L, Huang JH, Zhang Q, Han JG, Zhang XX	Int J Syst Evol Microbiol	10.1099/ijsem.0.005335	2022	*
Phylogeny	Chitinophaga taiwanensis sp. nov., isolated from the rhizosphere of Arabidopsis thaliana.	Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Huang HI, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.054452-0	2013	*
Phylogeny	Chitinophaga eiseniae sp. nov., isolated from vermicompost.	Yasir M, Chung EJ, Song GC, Bibi F, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.023028-0	2010	*
Phylogeny	Chitinophaga vermicomposti sp. nov., with antifungal activity, isolated from vermicompost.	Yasir M, Aslam Z, Song GC, Bibi F, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.013425-0	2009	*
Phylogeny	Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.	Lee HG, An DS, Im WT, Liu QM, Na JR, Cho DH, Jin CW, Lee ST, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.64688-0	2007	*

References

#7398

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18108

#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 )

#31941

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 #28197 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86738

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-ID290946.1 )

#28197

IJSEM 1396 2007 ( DOI 10.1099/ijs.0.64688-0 , PubMed 17625164 )

* These data were automatically processed and therefore are not curated

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Chitinophaga ginsengisegetis DSM 18108

Chitinophaga ginsengisegetis DSM 18108

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