Name: Chitinophaga oryziterrae YC7001
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133769

Type strain:

Species: Chitinophaga oryziterrae

Strain Designation: YC7001

Culture col. no.: KACC 14533, JCM 16595, NBRC 109756

Strain history: Y. R. Chung YC7001.

NCBI tax ID(s): 1031224 (species)

Section

Chitinophaga oryziterrae YC7001 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

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 oryziterrae**
	Full Scientific Name (LPSN)	Chitinophaga oryziterrae Chung et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30453]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.987

[Ref.: #30453]	Cell length	4.1 µm

[Ref.: #30453]	Cell width	0.35 µm

[Ref.: #30453]	Cell shape	rod-shaped

[Ref.: #30453]	Motility	no

[Ref.: #30453]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30453]	growth	15-40 °C
[Ref.: #30453]	optimum	27.5 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #30453]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30453]			growth	4.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30453]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.938

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30453]	asparagine ChEBI	+	carbon source
[Ref.: #30453]	aspartate ChEBI	+	carbon source
[Ref.: #30453]	dextrin ChEBI	+	carbon source
[Ref.: #30453]	fucose ChEBI	+	carbon source
[Ref.: #30453]	galactose ChEBI	+	carbon source
[Ref.: #30453]	glucose ChEBI	+	carbon source
[Ref.: #30453]	glutamate ChEBI	+	carbon source
[Ref.: #30453]	glycerol ChEBI	+	carbon source
[Ref.: #30453]	glycogen ChEBI	+	carbon source
[Ref.: #30453]	L-arabitol ChEBI	+	carbon source
[Ref.: #30453]	lactose ChEBI	+	carbon source
[Ref.: #30453]	leucine ChEBI	+	carbon source
[Ref.: #30453]	phenylalanine ChEBI	+	carbon source
[Ref.: #30453]	proline ChEBI	+	carbon source
[Ref.: #30453]	putrescine ChEBI	+	carbon source
[Ref.: #30453]	serine ChEBI	+	carbon source
[Ref.: #30453]	succinate ChEBI	+	carbon source
[Ref.: #30453]	sucrose ChEBI	+	carbon source
[Ref.: #30453]	threonine ChEBI	+	carbon source
[Ref.: #30453]	thymidine ChEBI	+	carbon source
[Ref.: #30453]	trehalose ChEBI	+	carbon source
[Ref.: #30453]	uridine ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30453]	acid phosphatase	+	3.1.3.2
[Ref.: #30453]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30453]	alpha-galactosidase	+	3.2.1.22
[Ref.: #30453]	catalase	+	1.11.1.6
[Ref.: #30453]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30453]	gelatinase	+

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

[Ref.: #30453]	Sample type/isolated from	soil

[Ref.: #67770]	Sample type/isolated from	Rhizosphere soil from a rice field at Jinju
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JF710262 (>99% sequence identity) for Chitinophaga oryziterrae subclade from Microbeatlas

Aquatic Samples	60
Soil Samples	1117
Animal Samples	39
Plant Samples	114
Total Samples	1330

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.: #30453]	Chitinophaga oryziterrae strain YC7001 16S ribosomal RNA gene, partial sequence	JF710262	1491	GenBank	1031224 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Chitinophaga oryziterrae JCM 16595	GCA_009758125	contig	GenBank	1031224 tax ID
[Ref.: #66792]	Chitinophaga oryziterrae strain JCM 16595	1031224.3	wgs	PATRIC	1031224 tax ID	*

[Ref.: #30453]	GC-content	41.3 mol%
[Ref.: #67770]	GC-content	41.3 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Chitinophaga oryziterrae strain JCM 16595 PATRIC: 1031224.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chitinophaga oryziterrae strain JCM 16595 PATRIC: 1031224.3
[Ref.: #69480]	motile	no	93.499	yes
[Ref.: #69480]	flagellated	no	97.345	yes
[Ref.: #69480]	gram-positive	no	96.952	yes
[Ref.: #69480]	anaerobic	no	98.755	yes
[Ref.: #69480]	aerobic	yes	83.904	no
[Ref.: #69480]	halophile	no	96.638	no
[Ref.: #69480]	spore-forming	no	89.156	no
[Ref.: #69480]	thermophile	no	99.352	no
[Ref.: #69480]	glucose-util	yes	87.607	yes
[Ref.: #69480]	glucose-ferment	no	82.048	no

Availability in culture collections External links

[Ref.: #30453]

Culture collection no.

KACC 14533, JCM 16595, NBRC 109756

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga tropicalis sp. nov., isolated from forest soil.	Zhang XJ, Feng GD, Yao Q, Zhang J, Phuong LTB, Zhu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004248	2020	*
Phylogeny	Chitinophaga silvisoli sp. nov., isolated from forest soil.	Wang C, Lv Y, Li A, Feng G, Bao G, Zhu H, Tan Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.003212	2019	*
Phylogeny	Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.).	Chung EJ, Park TS, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.036442-0	2012	*

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 )

#30453

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26788 (see below)

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#26788

IJSEM 3030 2012 ( DOI 10.1099/ijs.0.036442-0 , PubMed 22307507 )

* These data were automatically processed and therefore are not curated

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Chitinophaga oryziterrae strain JCM 16595

Chitinophaga oryziterrae strain JCM 16595

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