Chitinophaga varians (GDMCC 1.1252, KACC 19415, KCTC 52926)

Name: Chitinophaga varians (GDMCC 1.1252, KACC 19415, KCTC 52926)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159706

Type strain

Strain Designation 10-7W-9003

Culture col. no. GDMCC 1.1252 KACC 19415 KCTC 52926 10-7W-9003

NCBI tax ID(s) 2202339

Special Collections KCTC Literature strains

History KCTC <- Yingying Lv, Guangdong institute of Microbiology

Links

Chitinophaga varians 10-7W-9003 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from forest soil.

Gram-negative motile filament-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 286117

KCTC 52926

@ref 20215

Last LPSN update 2026-05-29 08:44:15

Domain Bacteria

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Chitinophaga

Species Chitinophaga varians

Full scientific name Chitinophaga varians Lv et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
66554	negative	5-10 µm	0.4-0.5 µm	filament-shaped	gliding
66554	negative	1.0-1.5 µm	0.5-0.7 µm	rod-shaped	gliding
67771				rod-shaped
67771	negative
125438	negative					92.741

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
66554	yellow	circular	2 days	Reasoner's 2A agar (R2A)

Pigmentation

@ref	Production	Name
66554		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth
66554	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
66554	positive	growth	10-42
66554	positive	optimum	28-30
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
66554	positive	optimum	6.5-7.5
66554	positive	growth	6-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
66554	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.671

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66554	NaCl	positive	optimum	0-0.5 %(w/v)
66554	NaCl	positive	other	>2.5 %(w/v)

Observation

@ref	Observation
66554	Young cultures of the type strain contain long filamentous cells which divide into rods
67771	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66554	30796 ChEBI	(R)-malic acid	+	carbon source
66554	16651 ChEBI	(S)-lactate	+	carbon source
66554	30797 ChEBI	(S)-malic acid	+	carbon source
66554		1 % sodium lactate	+	carbon source
66554	64552 ChEBI	2-hydroxybutyrate	+	carbon source
66554	16763 ChEBI	2-oxobutanoate	-	carbon source
66554	16810 ChEBI	2-oxoglutarate	+	carbon source
66554	37054 ChEBI	3-hydroxybutyrate	+	carbon source
66554	73918 ChEBI	3-O-methyl-D-glucose	+	carbon source
66554	18101 ChEBI	4-hydroxyphenylacetic acid	+	carbon source
66554	16411 ChEBI	acetic acid	+	carbon source
66554	13705 ChEBI	acetoacetate	+	carbon source
66554	17925 ChEBI	alpha-D-glucose	+	carbon source
66554	161680 ChEBI	aztreonam	+	carbon source
66554	73706 ChEBI	bromosuccinate	+	carbon source
66554	17057 ChEBI	cellobiose	+	carbon source
66554	53258 ChEBI	citric acid	+	carbon source
66554	18333 ChEBI	D-arabitol	+	carbon source
66554	29990 ChEBI	D-aspartate	+	carbon source
66554	15824 ChEBI	D-fructose	+	carbon source
66554	78697 ChEBI	D-fructose 6-phosphate	-	carbon source
66554	28847 ChEBI	D-fucose	+	carbon source
66554	12936 ChEBI	D-galactose	+	carbon source
66554	18024 ChEBI	D-galacturonic acid	+	carbon source
66554	30612 ChEBI	D-glucarate	+	carbon source
66554	14314 ChEBI	D-glucose 6-phosphate	+	carbon source
66554	15748 ChEBI	D-glucuronate	+	carbon source
66554	16899 ChEBI	D-mannitol	+	carbon source
66554	16024 ChEBI	D-mannose	+	carbon source
66554	16523 ChEBI	D-serine	+	carbon source
66554	17924 ChEBI	D-sorbitol	+	carbon source
66554	16551 ChEBI	D-trehalose	+	carbon source
66554	23652 ChEBI	dextrin	+	carbon source
66554	15740 ChEBI	formate	+	carbon source
66554	71321 ChEBI	fusidate	+	carbon source
66554	16537 ChEBI	galactarate	+	carbon source
66554	16865 ChEBI	gamma-aminobutyric acid	+	carbon source
66554	5291 ChEBI	gelatin	+	carbon source
66554	28066 ChEBI	gentiobiose	+	carbon source
66554	32323 ChEBI	glucuronamide	+	carbon source
66554	17754 ChEBI	glycerol	+	carbon source
66554	70744 ChEBI	glycine-proline	+	carbon source
66554	17596 ChEBI	inosine	+	carbon source
66554	16977 ChEBI	L-alanine	+	carbon source
66554	16467 ChEBI	L-arginine	+	carbon source
66554	29991 ChEBI	L-aspartate	+	carbon source
66554	18287 ChEBI	L-fucose	+	carbon source
66554	17464 ChEBI	L-galactonic acid gamma-lactone	+	carbon source
66554	29985 ChEBI	L-glutamate	+	carbon source
66554	15971 ChEBI	L-histidine	+	carbon source
66554	18183 ChEBI	L-pyroglutamic acid	+	carbon source
66554	62345 ChEBI	L-rhamnose	+	carbon source
66554	17115 ChEBI	L-serine	+	carbon source
66554	17716 ChEBI	lactose	+	carbon source
66554	48607 ChEBI	lithium chloride	+	carbon source
66554	17306 ChEBI	maltose	+	carbon source
66554	28053 ChEBI	melibiose	+	carbon source
66554	74611 ChEBI	methyl (R)-lactate	+	carbon source
66554	320055 ChEBI	methyl beta-D-glucopyranoside	+	carbon source
66554	51850 ChEBI	methyl pyruvate	+	carbon source
66554	17268 ChEBI	myo-inositol	+	carbon source
66554	63153 ChEBI	N-acetyl-D-mannosamine	+	carbon source
66554	28800 ChEBI	N-acetylgalactosamine	+	carbon source
66554	59640 ChEBI	N-acetylglucosamine	+	carbon source
66554	35418 ChEBI	n-acetylneuraminate	-	carbon source
66554	100147 ChEBI	nalidixic acid	+	carbon source
66554	17309 ChEBI	pectin	+	carbon source
66554	75248 ChEBI	potassium tellurite	+	carbon source
66554	17272 ChEBI	propionate	+	carbon source
66554	26490 ChEBI	quinate	+	carbon source
66554	16634 ChEBI	raffinose	-	carbon source
66554	17814 ChEBI	salicin	+	carbon source
66554	75229 ChEBI	sodium bromate	+	carbon source
66554	64103 ChEBI	sodium butyrate	+	carbon source
66554	17164 ChEBI	stachyose	+	carbon source
66554	17992 ChEBI	sucrose	+	carbon source
66554	32528 ChEBI	turanose	+	carbon source
66554	53423 ChEBI	tween 40	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66554	72813 ChEBI	exopolysaccharide

Enzymes

@ref	Value	Activity	Ec
66554	acid phosphatase	+	3.1.3.2
66554	alkaline phosphatase	+	3.1.3.1
66554	alpha-chymotrypsin	-	3.4.21.1
66554	alpha-galactosidase	-	3.2.1.22
66554	alpha-glucosidase	+	3.2.1.20
66554	alpha-mannosidase	-	3.2.1.24
66554	beta-D-fucosidase	-	3.2.1.38
66554	beta-galactosidase	+	3.2.1.23
66554	beta-glucosidase	+	3.2.1.21
66554	beta-glucuronidase	-	3.2.1.31
66554	catalase	+	1.11.1.6
66554	cystine arylamidase	+	3.4.11.3
66554	cytochrome oxidase	+	1.9.3.1
66554	esterase (C 4)	-
66554	esterase Lipase (C 8)	-
66554	leucine arylamidase	+	3.4.11.1
66554	lipase (C 14)	-
66554	N-acetyl-beta-glucosaminidase	+	3.2.1.52
66554	naphthol-AS-BI-phosphohydrolase	+
66554	trypsin	+	3.4.21.4
66554	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

66554

Fatty acid	Percentage
C15:0 iso	33.3
C16:1 w5c	28.7
C17:0 iso 3OH	10.9
C16:0	7.5
C16:1 iso w7c and/or C16:1 w6c	4.5
C15:0 iso 3OH	4.1
C16:1 w11c	2.6
C16:0 3OH	2.2
C14:0	1.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
66554	forest soil	2016-09-14	Limushan National Forest Park, Hainan Province	China	CHN	Asia	19.1783	109.746 19.1783/109.746	WCX agar	(1 g CaCl2 x 2H2O, 15 g agar, 1 l H2O, pH 7.2)	5 days	28	Five grams of soil was soaked in 10 ml aseptic water with cycloheximide (100 µg ml-1) for 12 h. Subsequently, the soaked wet soil was put onto the WCX plate for 5 days at 28°C
67771	From forest soil		Limushan National Forest Park	China	CHN	Asia	19.1783	109.746 19.1783/109.746

Taxonmaps

69479

Global distribution of 16S sequence MF685226 (>99% sequence identity) for Chitinophaga from Microbeatlas

Aquatic Samples	49
Soil Samples	67
Animal Samples	29
Plant Samples	45
Total Samples	190

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1452994v1 assembly for Chitinophaga varians KACC 19415	contig	GCA_014529945	2202339.7	3003163278	2202339	63.95

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66554	Chitinophaga varians strain 10-7W-9003 16S ribosomal RNA gene, partial sequence	MF685226	1448		2202339

GC content

@ref	GC-content (mol%)	Method
66554	50.7	high performance liquid chromatography (HPLC)
67771	50.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1452994v1 assembly for Chitinophaga varians KACC 19415
NCBI: GCA_014529945

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	89.69	no
125439	gram_stain	BacteriaNetⓘ	negative	86.94	no
125439	motility	BacteriaNetⓘ	no	61.82	no
125439	spore_formation	BacteriaNetⓘ	no	99.67	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chitinophaga varians strain KACC 19415
PATRIC: 2202339.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.74	yes
125438	anaerobic	anaerobicⓘ	no	96.82	no
125438	spore-forming	spore-formingⓘ	no	76.40	no
125438	aerobic	aerobicⓘ	yes	89.63	yes
125438	thermophilic	thermophileⓘ	no	97.97	yes
125438	flagellated	motile2+ⓘ	no	86.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga varians sp. nov., isolated from forest soil.	Lv YY, Zhang XJ, Li AZ, Zou WL, Feng GD, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002700	2018

References

#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 )
#66554	Ying-ying Lv, Xian-jiao Zhang, An-zhang Li, Wei-ling Zou, Guang-da Feng, Hong-hui Zhu: Chitinophaga varians sp. nov., isolated from forest soil. IJSEM 68: 2139 - 2144 2018 ( DOI 10.1099/ijsem.0.002700 , PubMed 29775176 )
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 varians (GDMCC 1.1252, KACC 19415, KCTC 52926)

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

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014529945

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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