Name: Chitinophaga niabensis JS13-10
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17750

Type strain:

Species: Chitinophaga niabensis

Strain Designation: JS13-10

Culture col. no.: DSM 24787, JCM 15440, KACC 12952, NBRC 106412, UCCCB101

Strain history: 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

NCBI tax ID(s): 536979 (species)

SI-ID 403112

DSM 24787

Section

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

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 niabensis**
	Full Scientific Name (LPSN)	Chitinophaga niabensis Weon et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29045]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.852

[Ref.: #29045]	Cell length	4 µm

[Ref.: #29045]	Cell width	0.6 µm

[Ref.: #29045]	Cell shape	rod-shaped

[Ref.: #29045]	Motility	no

[Ref.: #17773]

Incubation period

2-3 days

[Ref.: #29045]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17773]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17773]

Culture medium growth

[Ref.: #17773]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17773]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17773]	growth	28 °C
[Ref.: #29045]	growth	05-40 °C
[Ref.: #29045]	optimum	29 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67772]	optimum	28-30 °C
[Ref.: #67772]	minimum	5 °C
[Ref.: #67772]	maximum	40 °C

[Ref.: #17773]	Temperature range	mesophilic
[Ref.: #29045]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67772]	Temperature range	mesophilic
[Ref.: #67772]	Temperature range	psychrophilic
[Ref.: #67772]	Temperature range	thermophilic

		pH
[Ref.: #67772]	maximum	9.0
[Ref.: #67772]	minimum	6.0
[Ref.: #29045]	optimum	7
[Ref.: #67772]	optimum	7.0
[Ref.: #29045]	growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29045]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.94

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29045]		NaCl		growth	0-2	%
[Ref.: #29045]		NaCl		optimum	1	%

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29045]	arabinose ChEBI	+	carbon source
[Ref.: #29045]	fucose ChEBI	+	carbon source
[Ref.: #29045]	rhamnose ChEBI	+	carbon source
[Ref.: #29045]	salicin ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #29045]	alpha-galactosidase	+	3.2.1.22
[Ref.: #29045]	catalase	+	1.11.1.6
[Ref.: #29045]	cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	O-antigen biosynthesis	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	lipid metabolism	80.65	25 of 31
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	purine metabolism	64.89	61 of 94
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	daunorubicin biosynthesis	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		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.: #17773]	Sample type/isolated from	soil

[Ref.: #67770]	Sample type/isolated from	Soil from Jeju Island
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67772]	Sample type/isolated from	Soil sample
[Ref.: #67772]	Geographic location (country and/or sea, region)	Jeju Special Autonomous Province, Jeju Island
[Ref.: #67772]	Country	Republic of Korea
[Ref.: #67772]	Country ISO 3 Code	KOR
[Ref.: #67772]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #17773]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #67772]	Biosafety level	1

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.: #17773]	Chitinophaga niabensis strain JS13-10 16S ribosomal RNA gene, partial sequence	EU714259	1402	ENA	536979 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Chitinophaga niabensis DSM 24787	GCA_900129465	scaffold	GenBank	536979 tax ID
[Ref.: #66792]	Chitinophaga niabensis strain DSM 24787	536979.4	wgs	PATRIC	536979 tax ID	*
[Ref.: #66792]	Chitinophaga niabensis DSM 24787	2636416022	draft	JGI IMG/M	536979 tax ID	*

[Ref.: #29045]	GC-content	47 mol%
[Ref.: #67770]	GC-content	47 mol%	high performance liquid chromatography (HPLC)

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 niabensis DSM 24787 NCBI: GCA_900129465.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chitinophaga niabensis strain DSM 24787 PATRIC: 536979.4
[Ref.: #69480]	gram-positive	no	96.895	yes
[Ref.: #69480]	anaerobic	no	99.563	yes
[Ref.: #69480]	halophile	no	95.681	yes
[Ref.: #69480]	spore-forming	no	94.796	no
[Ref.: #69480]	glucose-util	yes	90.065	no
[Ref.: #69480]	thermophile	no	99.003	no
[Ref.: #69480]	aerobic	yes	91.66	yes
[Ref.: #69480]	motile	no	92.77	yes
[Ref.: #69480]	glucose-ferment	no	87.4	no
[Ref.: #69480]	flagellated	no	97.556	yes

Availability in culture collections External links

[Ref.: #17773]

Culture collection no.

DSM 24787, JCM 15440, KACC 12952, NBRC 106412, UCCCB101

[Ref.: #86741]

SI-ID 403112

Literature:

Only first 10 entries are displayed. Click here to see all.

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 )

#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 (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 )

#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 .

#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 )

#86741

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-ID403112.1 )

#25475

IJSEM 1297 2009 ( DOI 10.1099/ijs.0.004804-0 , PubMed 19502299 )

* These data were automatically processed and therefore are not curated

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Chitinophaga niabensis DSM 24787

Chitinophaga niabensis strain DSM 24787

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