Chitinophaga rhizosphaerae (KACC 18790, JCM 31600, T16R-86)

Name: Chitinophaga rhizosphaerae (KACC 18790, JCM 31600, T16R-86)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140710

Type strain

Strain Designation T16R-86

Culture col. no. KACC 18790 JCM 31600 T16R-86

NCBI tax ID(s) 1864947

Special Collections JCM Literature strains

History S.-W. Kwon; KACC, South Korea; T16R-86.

Links

Chitinophaga rhizosphaerae T16R-86 is an aerobe, Gram-negative, rod-shaped bacterium that forms irregular colonies and was isolated from rhizosphere of a tomato plant collected from a farm on Buyeo-gun.

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

Name and taxonomic classification

SI-ID 391100

JCM 31600

@ref 20215

Last LPSN update 2026-02-09 11:33:41

Domain Bacteria

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Chitinophaga

Species Chitinophaga rhizosphaerae

Full scientific name Chitinophaga rhizosphaerae Kim et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
43485	negative	1.2-3 µm	0.5-0.6 µm	rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Medium used
43485	Yellow	irregular	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
43485	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
43485	positive	growth	10-37
43485	positive	optimum	28
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
43485	positive	optimum	7
43485	positive	growth	6-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

43485

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
43485
125439		97.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43485	NaCl	positive	growth	0-2 %(w/v)

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43485	16193 ChEBI	3-hydroxybenzoate	-	assimilation
43485	37054 ChEBI	3-hydroxybutyrate	-	assimilation
43485	17879 ChEBI	4-hydroxybenzoate	-	assimilation
43485	17128 ChEBI	adipate	-	assimilation
43485	85146 ChEBI	carboxymethylcellulose	+	hydrolysis
43485		casein	+	hydrolysis
43485	17029 ChEBI	chitin	-	hydrolysis
43485	17634 ChEBI	D-glucose	+	assimilation
43485	16899 ChEBI	D-mannitol	-	assimilation
43485	16024 ChEBI	D-mannose	+	assimilation
43485	16988 ChEBI	D-ribose	+	assimilation
43485	17924 ChEBI	D-sorbitol	-	assimilation
43485	27689 ChEBI	decanoate	-	assimilation
43485	16991 ChEBI	dna	-	hydrolysis
43485	4853 ChEBI	esculin	+	hydrolysis
43485	5291 ChEBI	gelatin	+	hydrolysis
43485	17234 ChEBI	glucose	-	fermentation
43485	28087 ChEBI	glycogen	-	assimilation
43485	17368 ChEBI	hypoxanthine	-	hydrolysis
43485	17240 ChEBI	itaconate	-	assimilation
43485	16977 ChEBI	L-alanine	-	assimilation
43485	30849 ChEBI	L-arabinose	-	assimilation
43485	18287 ChEBI	L-fucose	-	assimilation
43485	15971 ChEBI	L-histidine	+	assimilation
43485	17203 ChEBI	L-proline	-	assimilation
43485	62345 ChEBI	L-rhamnose	-	assimilation
43485	17115 ChEBI	L-serine	+	assimilation
43485	24996 ChEBI	lactate	-	assimilation
43485	25115 ChEBI	malate	-	assimilation
43485	17306 ChEBI	maltose	+	assimilation
43485	28053 ChEBI	melibiose	+	assimilation
43485	17268 ChEBI	myo-inositol	-	assimilation
43485	506227 ChEBI	N-acetylglucosamine	+	assimilation
43485	17632 ChEBI	nitrate	-	reduction
43485	18401 ChEBI	phenylacetate	-	assimilation
43485		potassium 2-dehydro-D-gluconate	-	assimilation
43485		potassium 5-dehydro-D-gluconate	-	assimilation
43485	32032 ChEBI	potassium gluconate	-	assimilation
43485	17272 ChEBI	propionate	-	assimilation
43485	17814 ChEBI	salicin	+	assimilation
43485	32954 ChEBI	sodium acetate	-	assimilation
43485	53258 ChEBI	sodium citrate	-	assimilation
43485	62983 ChEBI	sodium malonate	-	assimilation
43485	28017 ChEBI	starch	-	hydrolysis
43485	9300 ChEBI	suberic acid	-	assimilation
43485	17992 ChEBI	sucrose	+	assimilation
43485	53426 ChEBI	tween 80	-	hydrolysis
43485	18186 ChEBI	tyrosine	-	hydrolysis
43485	16199 ChEBI	urea	-	hydrolysis
43485	31011 ChEBI	valerate	-	assimilation
43485	15318 ChEBI	xanthine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43485	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43485	acid phosphatase	+	3.1.3.2
43485	alkaline phosphatase	+	3.1.3.1
43485	alpha-chymotrypsin	-	3.4.21.1
43485	alpha-fucosidase	+	3.2.1.51
43485	alpha-galactosidase	+	3.2.1.22
43485	alpha-glucosidase	+	3.2.1.20
43485	alpha-mannosidase	-	3.2.1.24
43485	arginine dihydrolase	-	3.5.3.6
43485	beta-galactosidase	+	3.2.1.23
43485	beta-glucosidase	+	3.2.1.21
43485	beta-glucuronidase	-	3.2.1.31
43485	catalase	+	1.11.1.6
43485	cystine arylamidase	+	3.4.11.3
43485	cytochrome oxidase	+	1.9.3.1
43485	esterase (C 4)	+
43485	esterase Lipase (C 8)	+
43485	leucine arylamidase	+	3.4.11.1
43485	lipase (C 14)	-
43485	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43485	naphthol-AS-BI-phosphohydrolase	+
43485	trypsin	+	3.4.21.4
43485	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

43485

Fatty acid	Percentage	ECL
C15:0 iso	37.9
C16:1ω5c	20.5
C17:0 iso 3OH	18.9
C15:0 iso 3OH	4.9
C16:0	3.6
C15:0 iso 2OH / C16:1ω7c	2.7
C16:0 iso	1.9
C16:1ω11c	1.8
Unknown ECL 16.582	1.4	16582
C17:0 3OH	1.2
C17:0 2OH	1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Plantation
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
43485	rhizosphere of a tomato plant collected from a farm on Buyeo-gun	Buyeo-gun, Chungcheongnam-do	Republic of Korea	KOR	Asia	36.293	126.931 36.293/126.931
67770	Rhizosphere soil of a tomato plant from a farm on Buyeo-gun	Chungcheongnam-do	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KX417377 (>99% sequence identity) for Chitinophaga from Microbeatlas

Aquatic Samples	347
Soil Samples	2519
Animal Samples	203
Plant Samples	579
Total Samples	3648

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM395864v1 assembly for Chitinophaga rhizosphaerae T16R-86	contig	GCA_003958645	1864947.3	2883068021	1864947	72.7

16S sequences

@ref	Description	Accession	Database
43485	Chitinophaga rhizosphaerae 16S ribosomal RNA gene, partial sequence	KX417377

GC content

@ref	GC-content (mol%)	Method
43485	53.6	Thermal denaturation, fluorometry
67770	53.6	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chitinophaga rhizosphaerae T16R-86
NCBI: GCA_003958645

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.10	no
125439	motility	BacteriaNetⓘ	no	80.50	no
125439	gram_stain	BacteriaNetⓘ	negative	78.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	88.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga deserti sp. nov., isolated from desert soil.	Kong XK, Chen D, Huang JW, Cheng XK, Jiang JD	Int J Syst Evol Microbiol	10.1099/ijsem.0.003395	2019
Phylogeny	Chitinophaga rhizosphaerae sp. nov., isolated from rhizosphere soil of a tomato plant.	Kim SJ, Cho H, Ahn JH, Weon HY, Joa JH, Hong SB, Seok SJ, Kim JS, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002134	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 )
#43485	Soo-Jin Kim, Hayoung Cho, Jae-Hyung Ahn, Hang-Yeon Weon, Jae-Ho Joa, Seung-Beom Hong, Soon-Ja Seok, Jeong-Seon Kim, Soon-Wo Kwon: Chitinophaga rhizosphaerae sp. nov., isolated from rhizosphere soil of a tomato plant. IJSEM 67: 3435 - 3439 2017 ( DOI 10.1099/ijsem.0.002134 , PubMed 28875897 )
#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) .
#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 .
#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 rhizosphaerae (KACC 18790, JCM 31600, T16R-86)

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

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_003958645

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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