Name: Chitinophaga varians 10-7W-9003
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 159706

Type strain:

Species: Chitinophaga varians

Strain Designation: 10-7W-9003

Culture col. no.: GDMCC 1.1252, KACC 19415, KCTC 52926

Strain history: <- Yingying Lv, Guangdong institute of Microbiology

NCBI tax ID(s): 2202339 (species)

Special Collections

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Chitinophaga*
	Species	**Chitinophaga varians**
	Full Scientific Name (LPSN)	Chitinophaga varians Lv et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66554]	Gram stain	negative
[Ref.: #66554]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %94.8
[Ref.: #125438]	Gram stain	negative Confidence in %92.741

[Ref.: #66554]	Cell length	5-10 µm
[Ref.: #66554]	Cell length	1.0-1.5 µm

[Ref.: #66554]	Cell width	0.4-0.5 µm
[Ref.: #66554]	Cell width	0.5-0.7 µm

[Ref.: #66554]	Cell shape	filament-shaped
[Ref.: #66554]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #66554]	Motility	yes
[Ref.: #66554]	Motility	yes
[Ref.: #67771]	Motility	no

[Ref.: #66554]	Flagellum arrangement	gliding
[Ref.: #66554]	Flagellum arrangement	gliding

[Ref.: #66554]	Colony color	yellow
[Ref.: #66554]	Colony shape	circular
[Ref.: #66554]	Incubation period	2 days
[Ref.: #66554]	Cultivation medium used	Reasoner's 2A agar (R2A)

[Ref.: #66554]	Pigment production	yes
[Ref.: #66554]	Pigment name	flexirubin-type

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66554]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #66554]

Culture medium growth

		Temperature
[Ref.: #66554]	growth	10-42 °C
[Ref.: #66554]	optimum	28-30 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #66554]			optimum	6.5-7.5
[Ref.: #66554]			growth	6-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66554]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #125439]

Ability of spore formation

no Confidence in %98.7

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66554]		NaCl		optimum	0-0.5	%(w/v)
[Ref.: #66554]		NaCl		other	>2.5	%(w/v)

[Ref.: #66554]	Observation	Young cultures of the type strain contain long filamentous cells which divide into rods
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66554]	(R)-malic acid ChEBI	+	carbon source
[Ref.: #66554]	(S)-lactate ChEBI	+	carbon source
[Ref.: #66554]	(S)-malic acid ChEBI	+	carbon source
[Ref.: #66554]	1 % sodium lactate	+	carbon source
[Ref.: #66554]	2-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #66554]	2-oxobutanoate ChEBI	-	carbon source
[Ref.: #66554]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #66554]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #66554]	3-O-methyl-D-glucose ChEBI	+	carbon source
[Ref.: #66554]	4-hydroxyphenylacetic acid ChEBI	+	carbon source
[Ref.: #66554]	acetic acid ChEBI	+	carbon source
[Ref.: #66554]	acetoacetate ChEBI	+	carbon source
[Ref.: #66554]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #66554]	aztreonam ChEBI	+	carbon source
[Ref.: #66554]	bromosuccinate ChEBI	+	carbon source
[Ref.: #66554]	cellobiose ChEBI	+	carbon source
[Ref.: #66554]	citric acid ChEBI	+	carbon source
[Ref.: #66554]	D-arabitol ChEBI	+	carbon source
[Ref.: #66554]	D-aspartate ChEBI	+	carbon source
[Ref.: #66554]	D-fructose ChEBI	+	carbon source
[Ref.: #66554]	D-fructose 6-phosphate ChEBI	-	carbon source
[Ref.: #66554]	D-fucose ChEBI	+	carbon source
[Ref.: #66554]	D-galactose ChEBI	+	carbon source
[Ref.: #66554]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #66554]	D-glucarate ChEBI	+	carbon source
[Ref.: #66554]	D-glucose 6-phosphate ChEBI	+	carbon source
[Ref.: #66554]	D-glucuronate ChEBI	+	carbon source
[Ref.: #66554]	D-mannitol ChEBI	+	carbon source
[Ref.: #66554]	D-mannose ChEBI	+	carbon source
[Ref.: #66554]	D-serine ChEBI	+	carbon source
[Ref.: #66554]	D-sorbitol ChEBI	+	carbon source
[Ref.: #66554]	D-trehalose ChEBI	+	carbon source
[Ref.: #66554]	dextrin ChEBI	+	carbon source
[Ref.: #66554]	formate ChEBI	+	carbon source
[Ref.: #66554]	fusidate ChEBI	+	carbon source
[Ref.: #66554]	galactarate ChEBI	+	carbon source
[Ref.: #66554]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #66554]	gelatin ChEBI	+	carbon source
[Ref.: #66554]	gentiobiose ChEBI	+	carbon source
[Ref.: #66554]	glucuronamide ChEBI	+	carbon source
[Ref.: #66554]	glycerol ChEBI	+	carbon source
[Ref.: #66554]	glycine-proline ChEBI	+	carbon source
[Ref.: #66554]	inosine ChEBI	+	carbon source
[Ref.: #66554]	L-alanine ChEBI	+	carbon source
[Ref.: #66554]	L-arginine ChEBI	+	carbon source
[Ref.: #66554]	L-aspartate ChEBI	+	carbon source
[Ref.: #66554]	L-fucose ChEBI	+	carbon source
[Ref.: #66554]	L-galactonic acid gamma-lactone ChEBI	+	carbon source
[Ref.: #66554]	L-glutamate ChEBI	+	carbon source
[Ref.: #66554]	L-histidine ChEBI	+	carbon source
[Ref.: #66554]	L-pyroglutamic acid ChEBI	+	carbon source
[Ref.: #66554]	L-rhamnose ChEBI	+	carbon source
[Ref.: #66554]	L-serine ChEBI	+	carbon source
[Ref.: #66554]	lactose ChEBI	+	carbon source
[Ref.: #66554]	lithium chloride ChEBI	+	carbon source
[Ref.: #66554]	maltose ChEBI	+	carbon source
[Ref.: #66554]	melibiose ChEBI	+	carbon source
[Ref.: #66554]	methyl (R)-lactate ChEBI	+	carbon source
[Ref.: #66554]	methyl beta-D-glucopyranoside ChEBI	+	carbon source
[Ref.: #66554]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #66554]	myo-inositol ChEBI	+	carbon source
[Ref.: #66554]	N-acetyl-D-mannosamine ChEBI	+	carbon source
[Ref.: #66554]	N-acetylgalactosamine ChEBI	+	carbon source
[Ref.: #66554]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #66554]	n-acetylneuraminate ChEBI	-	carbon source
[Ref.: #66554]	nalidixic acid ChEBI	+	carbon source
[Ref.: #66554]	pectin ChEBI	+	carbon source
[Ref.: #66554]	potassium tellurite ChEBI	+	carbon source
[Ref.: #66554]	propionate ChEBI	+	carbon source
[Ref.: #66554]	quinate ChEBI	+	carbon source
[Ref.: #66554]	raffinose ChEBI	-	carbon source
[Ref.: #66554]	salicin ChEBI	+	carbon source
[Ref.: #66554]	sodium bromate ChEBI	+	carbon source
[Ref.: #66554]	sodium butyrate ChEBI	+	carbon source
[Ref.: #66554]	stachyose ChEBI	+	carbon source
[Ref.: #66554]	sucrose ChEBI	+	carbon source
[Ref.: #66554]	turanose ChEBI	+	carbon source
[Ref.: #66554]	tween 40 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66554]		exopolysaccharide ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #66554]	acid phosphatase	+	3.1.3.2
[Ref.: #66554]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66554]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #66554]	alpha-galactosidase	-	3.2.1.22
[Ref.: #66554]	alpha-glucosidase	+	3.2.1.20
[Ref.: #66554]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66554]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #66554]	beta-galactosidase	+	3.2.1.23
[Ref.: #66554]	beta-glucosidase	+	3.2.1.21
[Ref.: #66554]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66554]	catalase	+	1.11.1.6
[Ref.: #66554]	cystine arylamidase	+	3.4.11.3
[Ref.: #66554]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66554]	esterase (C 4)	-
[Ref.: #66554]	esterase Lipase (C 8)	-
[Ref.: #66554]	leucine arylamidase	+	3.4.11.1
[Ref.: #66554]	lipase (C 14)	-
[Ref.: #66554]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #66554]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66554]	trypsin	+	3.4.21.4
[Ref.: #66554]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #66554]	Sample type/isolated from	forest soil
[Ref.: #66554]	Sampling date	2016-09-14
[Ref.: #66554]	Geographic location (country and/or sea, region)	Limushan National Forest Park, Hainan Province
[Ref.: #66554]	Country	China
[Ref.: #66554]	Country ISO 3 Code	CHN
[Ref.: #66554]	Continent	Asia
[Ref.: #66554]	Geographic location	19.1783°/109.7460°
[Ref.: #66554]	Enrichment culture	WCX agar
[Ref.: #66554]	Enrichment culture composition	(1 g CaCl2 x 2H2O, 15 g agar, 1 l H2O, pH 7.2)
[Ref.: #66554]	Enrichment culture duration	5 days
[Ref.: #66554]	Enrichment culture temperature	28 ̊C
[Ref.: #66554]	Isolation/enrichment procedure	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

[Ref.: #67771]	Sample type/isolated from	From forest soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Limushan National Forest Park
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	19.1783°/109.7460°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #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

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.: #66554]	Chitinophaga varians strain 10-7W-9003 16S ribosomal RNA gene, partial sequence	MF685226	1448	GenBank ENA	2202339 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chitinophaga varians KACC 19415	GCA_014529945	contig	GenBank ENA	2202339 tax ID	*
[Ref.: #66792]	Chitinophaga varians strain KACC 19415	2202339.7	wgs	PATRIC	2202339 tax ID	*

[Ref.: #66554]	GC-content	50.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	50.7 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	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.: #125438]	gram-positive	gram-positiveⓘ	no	92.741	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.822	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	76.403	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	89.631	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.972	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	86.75	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chitinophaga varians KACC 19415 NCBI: GCA_014529945
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	52.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	94.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	76.9

Availability in culture collections External links

[Ref.: #66554]

Culture collection no.

GDMCC 1.1252, KACC 19415, KCTC 52926

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 .

* These data were automatically processed and therefore are not curated

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Chitinophaga varians strain KACC 19415

Chitinophaga varians KACC 19415

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