Chitinophaga sedimenti (ACCC 19966, KCTC 52590, TFL-3)

Name: Chitinophaga sedimenti (ACCC 19966, KCTC 52590, TFL-3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140711

Type strain

Strain Designation TFL-3

Culture col. no. ACCC 19966 KCTC 52590 TFL-3

NCBI tax ID(s) 2033606

Special Collections KCTC Literature strains

Links

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

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 24948

KCTC 52590

@ref 20215

Last LPSN update 2025-12-16 10:03:40

Domain Pseudomonadati

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Chitinophaga

Species Chitinophaga sedimenti

Full scientific name Chitinophaga sedimenti Li et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
43486	negative	1.2-8 µm	0.5-0.7 µm	rod-shaped
67771				rod-shaped
67771	negative
125439	negative
125438	negative

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
43486	Orange-Yellow	circular	3 days	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
43486	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
43486	positive	growth	10-40
43486	positive	optimum	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
43486	positive	optimum	7
43486	positive	growth	6-9

Physiology and metabolism

Oxygen tolerance

67771

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation
43486
67771
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43486	NaCl	positive	growth	0-2.5 %
43486	NaCl	positive	optimum	0.5 %

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43486	90259 ChEBI	4-nitrophenyl beta-D-glucopyranoside	+	assimilation
43486	30089 ChEBI	acetate	+	assimilation
43486	13705 ChEBI	acetoacetate	+	assimilation
43486	17128 ChEBI	adipate	-	assimilation
43486	27613 ChEBI	amygdalin	+	fermentation
43486	17057 ChEBI	cellobiose	+	assimilation
43486	17029 ChEBI	chitin	-	hydrolysis
43486	16947 ChEBI	citrate	-	assimilation
43486	15824 ChEBI	D-fructose	+	assimilation
43486	12936 ChEBI	D-galactose	+	assimilation
43486	18024 ChEBI	D-galacturonic acid	+	assimilation
43486	17634 ChEBI	D-glucose	+	assimilation
43486	17634 ChEBI	D-glucose	+	fermentation
43486	15748 ChEBI	D-glucuronate	+	assimilation
43486	16899 ChEBI	D-mannitol	-	fermentation
43486	16024 ChEBI	D-mannose	+	assimilation
43486	63150 ChEBI	D-rhamnose	+	assimilation
43486	17924 ChEBI	D-sorbitol	-	fermentation
43486	27689 ChEBI	decanoate	-	assimilation
43486	23652 ChEBI	dextrin	+	assimilation
43486		esculin ferric citrate	+	hydrolysis
43486	5291 ChEBI	gelatin	+	hydrolysis
43486	28066 ChEBI	gentiobiose	+	assimilation
43486	32323 ChEBI	glucuronamide	+	assimilation
43486	70744 ChEBI	glycine-proline	+	assimilation
43486	30849 ChEBI	L-arabinose	+	fermentation
43486	16467 ChEBI	L-arginine	-	hydrolysis
43486	29991 ChEBI	L-aspartate	+	assimilation
43486	18287 ChEBI	L-fucose	+	assimilation
43486	29985 ChEBI	L-glutamate	+	assimilation
43486	62345 ChEBI	L-rhamnose	-	fermentation
43486	17115 ChEBI	L-serine	+	assimilation
43486	16828 ChEBI	L-tryptophan	-	hydrolysis
43486	17716 ChEBI	lactose	+	assimilation
43486	25115 ChEBI	malate	-	assimilation
43486	17306 ChEBI	maltose	+	assimilation
43486	28053 ChEBI	melibiose	+	assimilation
43486	28053 ChEBI	melibiose	+	fermentation
43486	37657 ChEBI	methyl D-glucoside	+	assimilation
43486	17268 ChEBI	myo-inositol	-	fermentation
43486	28037 ChEBI	N-acetylgalactosamine	+	assimilation
43486	17632 ChEBI	nitrate	-	reduction
43486	17309 ChEBI	pectin	+	assimilation
43486	18401 ChEBI	phenylacetate	-	assimilation
43486	32032 ChEBI	potassium gluconate	-	assimilation
43486	17814 ChEBI	salicin	+	assimilation
43486	53258 ChEBI	sodium citrate	-	assimilation
43486	17992 ChEBI	sucrose	-	fermentation
43486	17992 ChEBI	sucrose	+	assimilation
43486	27082 ChEBI	trehalose	+	assimilation
43486	32528 ChEBI	turanose	+	assimilation
43486	53423 ChEBI	tween 40	+	hydrolysis
43486	16199 ChEBI	urea	-	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite
43486	2637	amikacin
43486	28971	ampicillin
43486	17833	gentamicin
43486	6104	kanamycin
43486	7507	neomycin
43486	9215	spectinomycin
43486	17076	streptomycin

Metabolite production

@ref	Chebi-ID	Metabolite
43486	15688 ChEBI	acetoin
43486	16136 ChEBI	hydrogen sulfide
43486	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
43486	15688 ChEBI	acetoin	+

Enzymes

@ref	Value	Activity	Ec
43486	acid phosphatase	-	3.1.3.2
43486	alkaline phosphatase	-	3.1.3.1
43486	alpha-chymotrypsin	-	3.4.21.1
43486	alpha-fucosidase	-	3.2.1.51
43486	alpha-galactosidase	-	3.2.1.22
43486	alpha-glucosidase	-	3.2.1.20
43486	alpha-mannosidase	-	3.2.1.24
43486	arginine dihydrolase	-	3.5.3.6
43486	beta-galactosidase	+	3.2.1.23
43486	beta-glucosidase	-	3.2.1.21
43486	beta-glucuronidase	-	3.2.1.31
43486	catalase	+	1.11.1.6
43486	cytochrome oxidase	+	1.9.3.1
43486	esterase (C 4)	-
43486	esterase Lipase (C 8)	-
43486	leucine arylamidase	-	3.4.11.1
43486	lipase (C 14)	-
43486	lysine decarboxylase	-	4.1.1.18
43486	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43486	naphthol-AS-BI-phosphohydrolase	-
43486	ornithine decarboxylase	-	4.1.1.17
43486	trypsin	-	3.4.21.4
43486	urease	-	3.5.1.5
43486	valine arylamidase	-

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
43486	sediment collected from the Yangtze River in Nanjing	Nanjing, Jiangsu Province	China	CHN	Asia	32.05	118.76 32.05/118.76
67771	From sediment	the Yangtze River, Nanjing, Jiangsu Province	China	CHN	Asia	32.05	118.767 32.05/118.767

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2315619v1 assembly for Chitinophaga sedimenti KCTC 52590	contig	GCA_023156195	2033606.4	8054171283	2033606	49.47

Genome browser: GCA_023156195

16S sequences

@ref	Description	Accession	Database
43486	Chitinophaga sedimenti 16S ribosomal RNA gene, partial sequence	KX962169

GC content

@ref	GC-content (mol%)	Method
43486	50.5	high performance liquid chromatography (HPLC)
67771	49.5-51.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chitinophaga sedimenti KCTC 52590
NCBI: GCA_023156195

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.40	no
125439	motility	BacteriaNetⓘ	yes	50.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	82.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chitinophaga sedimenti KCTC 52590
NCBI: GCA_023156195.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.14	yes
125438	anaerobic	anaerobicⓘ	no	99.47	yes
125438	aerobic	aerobicⓘ	yes	87.42	no
125438	spore-forming	spore-formingⓘ	no	87.46	yes
125438	thermophilic	thermophileⓘ	no	95.03	yes
125438	flagellated	motile2+ⓘ	no	89.00	yes

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 .
#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 sedimenti (ACCC 19966, KCTC 52590, TFL-3)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile?

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_023156195

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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Fatty acid profile