Name: Chitinophaga sedimenti TFL-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140711

Type strain:

Species: Chitinophaga sedimenti

Strain Designation: TFL-3

Culture col. no.: ACCC 19966, KCTC 52590

Strain history: <- Jiang He, Nanjing Agricultural Univ.

NCBI tax ID(s): 2033606 (species)

Section

Chitinophaga sedimenti TFL-3 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from sediment collected from the Yangtze River in Nanjing.

colony-forming
Gram-negative
rod-shaped
aerobe
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 sedimenti**
	Full Scientific Name (LPSN)	Chitinophaga sedimenti Li et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43486]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #43486]	Cell length	1.2-8 µm

[Ref.: #43486]	Cell width	0.5-0.7 µm

[Ref.: #43486]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #43486]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #43486]	Colony color	Orange-Yellow
[Ref.: #43486]	Colony shape	circular
[Ref.: #43486]	Incubation period	3 days
[Ref.: #43486]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43486]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43486]

Culture medium growth

		Temperature
[Ref.: #43486]	growth	10-40 °C
[Ref.: #43486]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #43486]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43486]			optimum	7
[Ref.: #43486]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #43486]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43486]		NaCl		growth	0-2.5	%
[Ref.: #43486]		NaCl		optimum	0.5	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43486]	4-nitrophenyl beta-D-glucopyranoside ChEBI	+	assimilation
[Ref.: #43486]	acetate ChEBI	+	assimilation
[Ref.: #43486]	acetoacetate ChEBI	+	assimilation
[Ref.: #43486]	adipate ChEBI	-	assimilation
[Ref.: #43486]	amygdalin ChEBI	+	fermentation
[Ref.: #43486]	cellobiose ChEBI	+	assimilation
[Ref.: #43486]	chitin ChEBI	-	hydrolysis
[Ref.: #43486]	citrate ChEBI	-	assimilation
[Ref.: #43486]	D-fructose ChEBI	+	assimilation
[Ref.: #43486]	D-galactose ChEBI	+	assimilation
[Ref.: #43486]	D-galacturonic acid ChEBI	+	assimilation
[Ref.: #43486]	D-glucose ChEBI	+	assimilation
[Ref.: #43486]	D-glucose ChEBI	+	fermentation
[Ref.: #43486]	D-glucuronate ChEBI	+	assimilation
[Ref.: #43486]	D-mannitol ChEBI	-	fermentation
[Ref.: #43486]	D-mannose ChEBI	+	assimilation
[Ref.: #43486]	D-rhamnose ChEBI	+	assimilation
[Ref.: #43486]	D-sorbitol ChEBI	-	fermentation
[Ref.: #43486]	decanoate ChEBI	-	assimilation
[Ref.: #43486]	dextrin ChEBI	+	assimilation
[Ref.: #43486]	esculin ferric citrate	+	hydrolysis
[Ref.: #43486]	gelatin ChEBI	+	hydrolysis
[Ref.: #43486]	gentiobiose ChEBI	+	assimilation
[Ref.: #43486]	glucuronamide ChEBI	+	assimilation
[Ref.: #43486]	glycine-proline ChEBI	+	assimilation
[Ref.: #43486]	L-arabinose ChEBI	+	fermentation
[Ref.: #43486]	L-arginine ChEBI	-	hydrolysis
[Ref.: #43486]	L-aspartate ChEBI	+	assimilation
[Ref.: #43486]	L-fucose ChEBI	+	assimilation
[Ref.: #43486]	L-glutamate ChEBI	+	assimilation
[Ref.: #43486]	L-rhamnose ChEBI	-	fermentation
[Ref.: #43486]	L-serine ChEBI	+	assimilation
[Ref.: #43486]	L-tryptophan ChEBI	-	hydrolysis
[Ref.: #43486]	lactose ChEBI	+	assimilation
[Ref.: #43486]	malate ChEBI	-	assimilation
[Ref.: #43486]	maltose ChEBI	+	assimilation
[Ref.: #43486]	melibiose ChEBI	+	assimilation
[Ref.: #43486]	melibiose ChEBI	+	fermentation
[Ref.: #43486]	methyl D-glucoside ChEBI	+	assimilation
[Ref.: #43486]	myo-inositol ChEBI	-	fermentation
[Ref.: #43486]	N-acetylgalactosamine ChEBI	+	assimilation
[Ref.: #43486]	nitrate ChEBI	-	reduction
[Ref.: #43486]	pectin ChEBI	+	assimilation
[Ref.: #43486]	phenylacetate ChEBI	-	assimilation
[Ref.: #43486]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43486]	salicin ChEBI	+	assimilation
[Ref.: #43486]	sodium citrate ChEBI	-	assimilation
[Ref.: #43486]	sucrose ChEBI	-	fermentation
[Ref.: #43486]	sucrose ChEBI	+	assimilation
[Ref.: #43486]	trehalose ChEBI	+	assimilation
[Ref.: #43486]	turanose ChEBI	+	assimilation
[Ref.: #43486]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43486]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic resistance
[Ref.: #43486]	amikacin ChEBI	yes
[Ref.: #43486]	ampicillin ChEBI	yes
[Ref.: #43486]	gentamicin ChEBI	yes
[Ref.: #43486]	kanamycin ChEBI	yes
[Ref.: #43486]	neomycin ChEBI	yes
[Ref.: #43486]	spectinomycin ChEBI	yes
[Ref.: #43486]	streptomycin ChEBI	yes

	Metabolite	Production
[Ref.: #43486]	acetoin ChEBI	yes
[Ref.: #43486]	hydrogen sulfide ChEBI	no
[Ref.: #43486]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #43486]		acetoin ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #43486]	acid phosphatase	-	3.1.3.2
[Ref.: #43486]	alkaline phosphatase	-	3.1.3.1
[Ref.: #43486]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43486]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43486]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43486]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43486]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43486]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43486]	beta-galactosidase	+	3.2.1.23
[Ref.: #43486]	beta-glucosidase	-	3.2.1.21
[Ref.: #43486]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43486]	catalase	+	1.11.1.6
[Ref.: #43486]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43486]	esterase (C 4)	-
[Ref.: #43486]	esterase Lipase (C 8)	-
[Ref.: #43486]	leucine arylamidase	-	3.4.11.1
[Ref.: #43486]	lipase (C 14)	-
[Ref.: #43486]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43486]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43486]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #43486]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43486]	trypsin	-	3.4.21.4
[Ref.: #43486]	urease	-	3.5.1.5
[Ref.: #43486]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43486]

Fatty acid	Percentage
C15:0 iso	35.7
C16:1ω5c	22
C16:1ω6c / C16:1ω7c	20.2
C17:0 iso 3OH	4.8
C16:0	3.3
C16:0 iso 3OH	2.9
C14:0	2.4
C15:0 iso 3OH	2.4
C15:0 anteiso	1.2
C17:0 anteiso	0.8
C16:0 iso	0.7

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

[Ref.: #43486]	Sample type/isolated from	sediment collected from the Yangtze River in Nanjing
[Ref.: #43486]	Geographic location (country and/or sea, region)	Nanjing, Jiangsu Province
[Ref.: #43486]	Country	China
[Ref.: #43486]	Country ISO 3 Code	CHN
[Ref.: #43486]	Continent	Asia
[Ref.: #43486]	Geographic location	32.0500°/118.7600°

[Ref.: #67771]	Sample type/isolated from	From sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	the Yangtze River, Nanjing, Jiangsu Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	32.0500°/118.7670°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX962169 (>99% sequence identity) for Chitinophaga sedimenti subclade from Microbeatlas

Aquatic Samples	652
Soil Samples	1550
Animal Samples	215
Plant Samples	392
Total Samples	2809

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.: #43486]	16S rRNA sequence	KX962169		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chitinophaga sedimenti KCTC 52590	GCA_023156195	contig	GenBank	2033606 tax ID	*

[Ref.: #43486]	GC-content	50.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	49.5-51.5 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chitinophaga sedimenti KCTC 52590 NCBI: GCA_023156195.1
[Ref.: #69480]	flagellated	no	97.993	no
[Ref.: #69480]	gram-positive	no	97.878	no
[Ref.: #69480]	anaerobic	no	98.962	yes
[Ref.: #69480]	aerobic	yes	91.798	yes
[Ref.: #69480]	halophile	no	94.224	yes
[Ref.: #69480]	spore-forming	no	93.093	yes
[Ref.: #69480]	motile	no	92.41	yes
[Ref.: #69480]	glucose-ferment	no	78.164	yes
[Ref.: #69480]	thermophile	no	98.993	yes
[Ref.: #69480]	glucose-util	yes	89.025	yes

Availability in culture collections External links

[Ref.: #43486]

Culture collection no.

ACCC 19966, KCTC 52590

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga sedimenti sp. nov., isolated from sediment.	Li N, Chen T, Cheng D, Xu XJ, He J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002150	2017	*

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 )

#43486

Na Li, Tao Chen, Dan Cheng, Xun-Jun Xu, Jian He: Chitinophaga sedimenti sp. nov., isolated from sediment. IJSEM 67: 3485 - 3489 2017 ( DOI 10.1099/ijsem.0.002150 , PubMed 28857037 )

#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 .

#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) .

* These data were automatically processed and therefore are not curated

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Chitinophaga sedimenti KCTC 52590

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