Chitinophaga skermanii (DSM 23857, CCUG 52510, CIP 109140)

Name: Chitinophaga skermanii (DSM 23857, CCUG 52510, CIP 109140)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17748

Type strain

Strain Designation CC SG-1B, CC-SG1B

Culture col. no. DSM 23857 CCUG 52510 CIP 109140 CC SG-1B CC-SG1B

NCBI tax ID(s) 331697

Special Collections DSMZ CCUG CIP

History <- CCUG <- P. Kämpfer, Univ. Giessen, Germany CIP <- 2006, P. Kämpfer, Justus Liebig Univ., Giessen, Germany: strain CC-SG1B

Links

Chitinophaga skermanii CC SG-1B is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from faeces of the millipede .

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

Name and taxonomic classification

SI-ID 297146

CCUG 52510,CIP 109140,DSM 23857

@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 skermanii

Full scientific name Chitinophaga skermanii Kämpfer et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		92.17
125439	negative		91.7
122639	negative	rod-shaped

Colony morphology

122639

Hemolysis ability1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17407	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
34355	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
122639	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
17407	positive	growth	28
34355	positive	growth	30
59573	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
59573	aerobe
122639	obligate aerobe
125439	obligate aerobe	97.8

Spore formation

@ref	Spore formation	Confidence
125439		97.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	+	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
122639	17632 ChEBI	nitrate	-	reduction
122639	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122639	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122639	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	+	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122639	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
122639	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122639	ornithine decarboxylase	-	4.1.1.17
122639	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
122639	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	CMP-KDO biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	acetoin degradation	100	3 of 3
66794	starch degradation	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	biotin biosynthesis	100	4 of 4
66794	kanosamine biosynthesis II	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	NAD metabolism	94.44	17 of 18
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	pentose phosphate pathway	81.82	9 of 11
66794	lipid metabolism	80.65	25 of 31
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	vitamin B1 metabolism	76.92	10 of 13
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	isoprenoid biosynthesis	73.08	19 of 26
66794	proline metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	leucine metabolism	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	histidine metabolism	68.97	20 of 29
66794	formaldehyde oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	tyrosine metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	cysteine metabolism	61.11	11 of 18
66794	coenzyme M biosynthesis	60	6 of 10
66794	non-pathway related	57.89	22 of 38
66794	glutathione metabolism	57.14	8 of 14
66794	carotenoid biosynthesis	54.55	12 of 22
66794	arginine metabolism	54.17	13 of 24
66794	sulfate reduction	53.85	7 of 13
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	resorcinol degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of sugar acids	48	12 of 25
66794	degradation of pentoses	46.43	13 of 28
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	oxidative phosphorylation	46.15	42 of 91
66794	metabolism of disaccharids	45.45	5 of 11
66794	phenol degradation	45	9 of 20
66794	daunorubicin biosynthesis	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	degradation of sugar alcohols	43.75	7 of 16
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	vitamin B12 metabolism	35.29	12 of 34
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	cyanate degradation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	chlorophyll metabolism	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	allantoin degradation	22.22	2 of 9

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122639	-	+	+	+	-	+	+	+	+	-	+	+	+	+	-	+	+	+	-	+

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122639	not determinedn.d.	-	-	+/-	-	-	-	-	-	-	+/-	+	-	+	-	-	-	-	-	-	-	+/-	+	+	+	+	+	+	+	+	+	+/-	+/-	-	-	+/-	+	+/-	+/-	+	+	-	-	-	+	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Arthropoda	#Insecta
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
17407	faeces of the millipede (Arthrosphaera magna)	Arthrosphaera magna	Taiwan, Province of China	TWN	Asia
59573	Millipede feces (Arthrosphaera magna)		Taiwan, Province of China	TWN	Asia
122639	Faeces, millipede Arthrosphaera magna		Taiwan, Province of China	TWN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17407	1	Risk group (German classification) According to TRBA 466
122639	1	Risk group (French 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	ASM325933v1 assembly for Chitinophaga skermanii DSM 23857	scaffold	GCA_003259335	331697.3	2593339293	331697	72.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17407	Chitinophaga skermanii strain CC-SG1B 16S ribosomal RNA, partial sequence	NR_043516	1490		331697

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chitinophaga skermanii DSM 23857
NCBI: GCA_003259335

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.10	no
125439	motility	BacteriaNetⓘ	no	78.10	no
125439	gram_stain	BacteriaNetⓘ	negative	91.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chitinophaga skermanii DSM 23857
NCBI: GCA_003259335.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.17	no
125438	anaerobic	anaerobicⓘ	no	98.86	yes
125438	aerobic	aerobicⓘ	yes	89.75	yes
125438	spore-forming	spore-formingⓘ	no	83.26	no
125438	thermophilic	thermophileⓘ	no	97.08	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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	Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.	Kampfer P, Young CC, Sridhar KR, Arun AB, Lai WA, Shen FT, Rekha PD	Int J Syst Evol Microbiol	10.1099/ijs.0.64359-0	2006

References

#17407	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23857
#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 )
#34355	; Curators of the CIP;
#59573	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52510
#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 )
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#122639	Collection of Institut Pasteur ; Curators of the CIP; CIP 109140
#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 skermanii (DSM 23857, CCUG 52510, CIP 109140)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003259335

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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