Chitinophaga niabensis (DSM 24787, JCM 15440, KACC 12952)

Name: Chitinophaga niabensis (DSM 24787, JCM 15440, KACC 12952)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17750

Type strain

Strain Designation JS13-10

Culture col. no. DSM 24787 JCM 15440 KACC 12952 JS13-10 NBRC 106412 1 more

NCBI tax ID(s) 536979

Special Collections DSMZ JCM Literature strains UCCCB

History <- KACC <- H.-Y. Weon, Applied Microbiology Division, National Institute of Agricultural Science and Technology, RDA, Republic of Korea; JS13-10 S.-W. Kwon JS13-10. Weon, H.-Y. National Institute of Agricultural Science and Technology, Rural Development Administration [Proenca DN, Nobre MF, Morais PV. Chitinophaga costaii sp. nov., an endophyte of Pinus pinaster, and emended description of Chitinophaga niabensis. Int

Links

Chitinophaga niabensis JS13-10 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

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

Name and taxonomic classification

SI-ID 403112

JCM 15440,DSM 24787

@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 niabensis

Full scientific name Chitinophaga niabensis Weon et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29045	negative	4 µm	0.6 µm	rod-shaped
125438					90.5
125438	negative				93.635
125439	negative				99.6

Colony morphology

17773

Incubation period2-3 days

Pigmentation

29045

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17773	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
17773	positive	growth	28
29045	positive	growth	05-40
29045	positive	optimum	29
67770	positive	growth	30
67772	positive	optimum	28-30
67772	positive	minimum	5
67772	positive	maximum	40

Culture pH

@ref	Ability	Type	PH	PH range
67772	positive	maximum	9.0
67772	positive	minimum	6.0
29045	positive	optimum	7
67772	positive	optimum	7.0
29045	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

29045

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29045	NaCl	positive	growth	0-2 %
29045	NaCl	positive	optimum	1 %

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29045	22599 ChEBI	arabinose	+	carbon source
29045	33984 ChEBI	fucose	+	carbon source
29045	26546 ChEBI	rhamnose	+	carbon source
29045	17814 ChEBI	salicin	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29045	alpha-galactosidase	+	3.2.1.22
29045	catalase	+	1.11.1.6
29045	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	CMP-KDO biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	O-antigen biosynthesis	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	sulfopterin metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	suberin monomers biosynthesis	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	proline metabolism	81.82	9 of 11
66794	lipid metabolism	80.65	25 of 31
66794	glycogen metabolism	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	propanol degradation	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	tryptophan metabolism	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	threonine metabolism	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	leucine metabolism	69.23	9 of 13
66794	degradation of pentoses	67.86	19 of 28
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	purine metabolism	64.89	61 of 94
66794	tyrosine metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	lysine metabolism	64.29	27 of 42
66794	degradation of sugar acids	64	16 of 25
66794	vitamin B6 metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	alanine metabolism	62.07	18 of 29
66794	degradation of hexoses	61.11	11 of 18
66794	cysteine metabolism	61.11	11 of 18
66794	vitamin K metabolism	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	pyrimidine metabolism	57.78	26 of 45
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	methionine metabolism	57.69	15 of 26
66794	non-pathway related	55.26	21 of 38
66794	arginine metabolism	54.17	13 of 24
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	butanoate fermentation	50	2 of 4
66794	sphingosine metabolism	50	3 of 6
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	oxidative phosphorylation	45.05	41 of 91
66794	arachidonic acid metabolism	44.44	8 of 18
66794	daunorubicin biosynthesis	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	D-cycloserine biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	urea cycle	38.46	5 of 13
66794	metabolism of disaccharids	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	chlorophyll metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	allantoin degradation	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9
66794	vitamin B12 metabolism	20.59	7 of 34

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
17773	soil
67770	Soil from Jeju Island		Republic of Korea	KOR	Asia
67772	Soil sample	Jeju Special Autonomous Province, Jeju Island	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU714259 (>99% sequence identity) for Chitinophaga from Microbeatlas

Aquatic Samples	954
Soil Samples	2344
Animal Samples	371
Plant Samples	389
Total Samples	4058

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17773	1	Risk group (German classification) According to TRBA 466
67772	1

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2636416022 annotated assembly for Chitinophaga niabensis DSM 24787	scaffold	GCA_900129465	536979.4	2636416022	536979	77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17773	Chitinophaga niabensis strain JS13-10 16S ribosomal RNA gene, partial sequence	EU714259	1402		536979
124043	Chitinophaga niabensis gene for 16S rRNA, partial sequence, strain: NBRC 106412.	AB682428	1452		536979

GC content

@ref	GC-content (mol%)	Method
29045	47
67770	47	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chitinophaga niabensis DSM 24787
NCBI: GCA_900129465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.60	no
125439	motility	BacteriaNetⓘ	no	73.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	79.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chitinophaga niabensis strain DSM 24787
PATRIC: 536979.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.64	yes
125438	anaerobic	anaerobicⓘ	no	99.34	no
125438	spore-forming	spore-formingⓘ	no	86.03	no
125438	aerobic	aerobicⓘ	yes	88.58	yes
125438	thermophilic	thermophileⓘ	no	97.97	yes
125438	flagellated	motile2+ⓘ	no	90.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga deserti sp. nov., isolated from desert soil.	Kong XK, Chen D, Huang JW, Cheng XK, Jiang JD	Int J Syst Evol Microbiol	10.1099/ijsem.0.003395	2019
Phylogeny	Chitinophaga humicola sp. nov., isolated from oil-contaminated soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002577	2018
Phylogeny	Rurimicrobium arvi gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from farmland soil.	Dahal RH, Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002452	2017
Phylogeny	Chitinophaga barathri sp. nov., isolated from mountain soil.	Zhang L, Liao S, Tan Y, Wang G, Wang D, Zheng S	Int J Syst Evol Microbiol	10.1099/ijsem.0.000566	2015
Phylogeny	Chitinophaga costaii sp. nov., an endophyte of Pinus pinaster, and emended description of Chitinophaga niabensis.	Proenca DN, Nobre MF, Morais PV	Int J Syst Evol Microbiol	10.1099/ijs.0.053454-0	2014
Phylogeny	Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.).	Chung EJ, Park TS, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.036442-0	2012
Phylogeny	Chitinophaga niabensis sp. nov. and Chitinophaga niastensis sp. nov., isolated from soil.	Weon HY, Yoo SH, Kim YJ, Son JA, Kim BY, Kwon SW, Koo BS	Int J Syst Evol Microbiol	10.1099/ijs.0.004804-0	2009

References

#17773	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24787
#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 )
#25475	IJSEM 1297 2009 ( DOI 10.1099/ijs.0.004804-0 , PubMed 19502299 )
#29045	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 #25475
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67772	The University of Coimbra Bacteria Culture Collection (UCCCB) ; Curators of the UCCCB;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 niabensis (DSM 24787, JCM 15440, KACC 12952)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

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_900129465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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