Cite this strain

Chitinophaga niastensis (DSM 24859, JCM 15441, KACC 12954)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17751

Type strain

Strain Designation JS16-4

Culture col. no. DSM 24859 JCM 15441 KACC 12954 JS16-4

NCBI tax ID(s) 536980

Special Collections DSMZ JCM Literature strains

Links

Name and taxonomic classification

Chitinophaga niastensis JS16-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

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

SI-ID 403274

DSM 24859

Last LPSN update 2024-12-09 10:45:04

Domain Bacteria

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Chitinophaga

Species Chitinophaga niastensis

Full scientific name Chitinophaga niastensis Weon et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
29045	negative	7 µm	0.65 µm	rod-shaped
125439	negative
125438	negative

Colony morphology

17789

Incubation period3-7 days

Pigmentation

29045

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17789	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)	Range
17789	positive	growth	28	mesophilic
29045	positive	growth	05-30
29045	positive	optimum	28	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
29045	positive	optimum	6.5
29045	positive	growth	5.0-9.0

Physiology and metabolism

Halophily

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

Observation

67770

Observationquinones: MK-7

Spore formation

@ref	Spore formation	Confidence
125439		98.4

Enzymes

@ref	Value	Activity	Ec
29045	catalase	+	1.11.1.6
29045	cytochrome oxidase	+	1.9.3.1
29045	urease	+	3.5.1.5

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29045	17814 ChEBI	salicin	+	carbon source
29045	53426 ChEBI	tween 80	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	acetoin degradation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	kanosamine biosynthesis II	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	gluconeogenesis	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ethanol fermentation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	vitamin K metabolism	80	4 of 5
66794	glycogen metabolism	80	4 of 5
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	tyrosine metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	degradation of sugar acids	72	18 of 25
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	lysine metabolism	69.05	29 of 42
66794	alanine metabolism	68.97	20 of 29
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	histidine metabolism	65.52	19 of 29
66794	pyrimidine metabolism	64.44	29 of 45
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate 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	phenylacetate degradation (aerobic)	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	arginine metabolism	58.33	14 of 24
66794	non-pathway related	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	butanoate fermentation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenol degradation	50	10 of 20
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	vitamin E metabolism	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	lactate fermentation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	cyclohexanol degradation	50	2 of 4
66794	polyamine pathway	47.83	11 of 23
66794	oxidative phosphorylation	47.25	43 of 91
66794	sulfate reduction	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	arachidonic acid metabolism	44.44	8 of 18
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	ascorbate metabolism	40.91	9 of 22
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	carnitine metabolism	37.5	3 of 8
66794	cyanate degradation	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	degradation of sugar alcohols	31.25	5 of 16
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	mevalonate metabolism	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	allantoin degradation	22.22	2 of 9

Oxygen tolerance

@ref	Oxygen tolerance
29045	aerobe
125439	obligate aerobe

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
17789	soil	Jeju Island	Republic of Korea	KOR	Asia
67770	Soil from Jeju Island		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU714260 (>99% sequence identity) for Chitinophaga niastensis subclade from Microbeatlas

Aquatic Samples
Soil Samples	12
Animal Samples	3
Plant Samples	10
Total Samples	25

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
17789	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
17789	43	high performance liquid chromatography (HPLC)
29045	43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17789	Chitinophaga niastensis strain JS16-4 16S ribosomal RNA gene, partial sequence	EU714260	1402		536980

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Chitinophaga niastensis DSM 24859	GCA_003014755	contig		536980
66792	Chitinophaga niastensis strain DSM 24859	536980.3	wgs	PATRIC	536980
66792	Chitinophaga niastensis DSM 24859	2728369470	draft	JGI IMG/M	536980

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Chitinophaga niastensis DSM 24859
NCBI: GCA_003014755

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.40	no
125439	motility	BacteriaNetⓘ	no	59.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.60	no

Predictions from Diaspora project based on:
Chitinophaga niastensis strain DSM 24859
PATRIC: 536980.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.01	yes
125438	anaerobic	anaerobicⓘ	no	97.82	no
125438	spore-forming	spore-formingⓘ	no	77.46	no
125438	aerobic	aerobicⓘ	yes	88.29	yes
125438	thermophilic	thermophileⓘ	no	97.31	no
125438	flagellated	motile2+ⓘ	no	86.25	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga solisilvae sp. nov., isolated from forest soil.	Ping W, Zhang Y, Pang H, Zhang J, Li D, Li Y, Zhang J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004350	2020
Phylogeny	Aurantisolimonas haloimpatiens gen. nov., sp. nov., a bacterium isolated from soil.	Liu MJ, Jin CZ, Asem MD, Ju YJ, Park DJ, Salam N, Xiao M, Li WJ, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002709	2018
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 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

Straininfo Link

@ref	Straininfo	Culture collections
86742	403274	DSM 24859

Culture collection no.

Culture collection no.
DSM 24859
JCM 15441
KACC 12954
JS16-4

References

#17789	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24859
#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;
#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 .
#86742	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-ID403274.1 )
#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 .

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