Chitinophaga rupis (DSM 21039, KCTC 22170, CS5-B1)

Name: Chitinophaga rupis (DSM 21039, KCTC 22170, CS5-B1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17752

Type strain

Strain Designation CS5-B1

Culture col. no. DSM 21039 KCTC 22170 CS5-B1

NCBI tax ID(s) 573321

Special Collections DSMZ KCTC Literature strains

History <- S. D. Lee, Cheju National Univ., Rep. of Korea; CS5-B1

Links

Chitinophaga rupis CS5-B1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil of a cliff.

Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405939

KCTC 22170,DSM 21039

@ref 20215

Last LPSN update 2026-02-09 11:22:18

Domain Bacteria

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Chitinophaga

Species Chitinophaga rupis

Full scientific name Chitinophaga rupis Lee et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29339	negative	1.45 µm	0.55 µm	rod-shaped
125439	negative				99.7
125438	negative				93.506

Pigmentation

29339

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15532	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
15532	positive	growth	30
29339	positive	growth	20-37

Culture pH

@ref	Ability	Type	PH	PH range
29339	positive	growth	5.1-10.1	alkaliphile

Physiology and metabolism

Oxygen tolerance

29339

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29339	NaCl	positive	growth	<1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29339	18240 ChEBI	4-hydroxy-L-proline	+	carbon source
29339	30089 ChEBI	acetate	+	carbon source
29339	22599 ChEBI	arabinose	+	carbon source
29339	22653 ChEBI	asparagine	+	carbon source
29339	35391 ChEBI	aspartate	+	carbon source
29339	17057 ChEBI	cellobiose	+	carbon source
29339	23652 ChEBI	dextrin	+	carbon source
29339	4853 ChEBI	esculin	+	hydrolysis
29339	28757 ChEBI	fructose	+	carbon source
29339	33984 ChEBI	fucose	+	carbon source
29339	24148 ChEBI	galactonate	+	carbon source
29339	28260 ChEBI	galactose	+	carbon source
29339	17234 ChEBI	glucose	+	carbon source
29339	29987 ChEBI	glutamate	+	carbon source
29339	17754 ChEBI	glycerol	+	carbon source
29339	21217 ChEBI	L-alaninamide	+	carbon source
29339	24996 ChEBI	lactate	+	carbon source
29339	17716 ChEBI	lactose	+	carbon source
29339	17306 ChEBI	maltose	+	carbon source
29339	37684 ChEBI	mannose	+	carbon source
29339	28053 ChEBI	melibiose	+	carbon source
29339	37657 ChEBI	methyl D-glucoside	+	carbon source
29339	51850 ChEBI	methyl pyruvate	+	carbon source
29339	506227 ChEBI	N-acetylglucosamine	+	carbon source
29339	17632 ChEBI	nitrate	+	reduction
29339	26271 ChEBI	proline	+	carbon source
29339	16634 ChEBI	raffinose	+	carbon source
29339	26546 ChEBI	rhamnose	+	carbon source
29339	17992 ChEBI	sucrose	+	carbon source
29339	27082 ChEBI	trehalose	+	carbon source
29339	53423 ChEBI	tween 40	+	carbon source
29339	53426 ChEBI	tween 80	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29339	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
29339	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
29339	acid phosphatase	+	3.1.3.2
29339	alkaline phosphatase	+	3.1.3.1
29339	alpha-galactosidase	+	3.2.1.22
29339	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	starch degradation	100	10 of 10
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	acetoin degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	formaldehyde oxidation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	phenylalanine metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	alanine metabolism	82.76	24 of 29
66794	pentose phosphate pathway	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	flavin biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	serine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	urea cycle	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	pyrimidine metabolism	75.56	34 of 45
66794	glutamate and glutamine metabolism	75	21 of 28
66794	ketogluconate metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	degradation of sugar acids	72	18 of 25
66794	citric acid cycle	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	methionine metabolism	69.23	18 of 26
66794	vitamin B1 metabolism	69.23	9 of 13
66794	leucine metabolism	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	degradation of sugar alcohols	68.75	11 of 16
66794	degradation of pentoses	67.86	19 of 28
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	glutathione metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	ascorbate metabolism	63.64	14 of 22
66794	vitamin B6 metabolism	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of hexoses	61.11	11 of 18
66794	coenzyme M biosynthesis	60	6 of 10
66794	arginine metabolism	58.33	14 of 24
66794	oxidative phosphorylation	58.24	53 of 91
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	carotenoid biosynthesis	50	11 of 22
66794	myo-inositol biosynthesis	50	5 of 10
66794	catecholamine biosynthesis	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	arachidonic acid metabolism	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	vitamin K metabolism	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	D-cycloserine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	cholesterol biosynthesis	36.36	4 of 11
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	chlorophyll metabolism	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	vitamin B12 metabolism	32.35	11 of 34
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15532	soil of a cliff	Jeju, Mara island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence FM865977 (>99% sequence identity) for Chitinophaga rupis subclade from Microbeatlas

Aquatic Samples	153
Soil Samples	4639
Animal Samples	240
Plant Samples	2092
Total Samples	7124

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15532	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	IMG-taxon 2622736599 annotated assembly for Chitinophaga rupis DSM 21039	scaffold	GCA_900109685	573321.3	2622736599	573321	72.56

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15532	Chitinophaga rupis partial 16S rRNA gene, type strain CS5-B1T	FM865977	1415		573321

GC content

@ref	GC-content (mol%)	Method
15532	48.7	high performance liquid chromatography (HPLC)
29339	48.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chitinophaga rupis DSM 21039
NCBI: GCA_900109685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.10	no
125439	motility	BacteriaNetⓘ	no	62.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	82.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chitinophaga rupis DSM 21039
NCBI: GCA_900109685.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.51	yes
125438	anaerobic	anaerobicⓘ	no	98.61	yes
125438	aerobic	aerobicⓘ	yes	88.67	yes
125438	spore-forming	spore-formingⓘ	no	79.15	no
125438	thermophilic	thermophileⓘ	no	96.45	no
125438	flagellated	motile2+ⓘ	no	87.25	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Identification of novel toxins associated with the extracellular contractile injection system using machine learning.	Danov A, Pollin I, Moon E, Ho M, Wilson BA, Papathanos PA, Kaplan T, Levy A.	Mol Syst Biol	10.1038/s44320-024-00053-6	2024
Phylogeny	Chitinophaga caeni sp. nov., isolated from activated sludge.	Jin D, Kong X, Wang J, Sun J, Yu X, Zhuang X, Deng Y, Bai Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.002811	2018
Phylogeny	Chitinophaga ginsengihumi sp. nov., isolated from soil of ginseng rhizosphere.	Lee JC, Whang KS	Int J Syst Evol Microbiol	10.1099/ijs.0.062612-0	2014
Phylogeny	Chitinophaga rupis sp. nov., isolated from soil.	Lee DW, Lee JE, Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.011163-0	2009

References

#15532	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21039
#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 )
#25751	IJSEM 2830 2009 ( DOI 10.1099/ijs.0.011163-0 , PubMed 19628608 )
#29339	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 #25751
#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 )
#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 )

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Chitinophaga rupis (DSM 21039, KCTC 22170, CS5-B1)

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

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900109685

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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