Name: Chitinophaga arvensicola M64
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17742

Type strain:

Species: Chitinophaga arvensicola

Strain Designation: M64

Culture col. no.: DSM 3695, ATCC 51264, IAM 12650, JCM 2836, NCIB 11855, CECT 358, CIP 104804, IFO 14973, IFO 16136, KCTC 2943, NBRC 14973, NBRC 16136, NCIMB 11855

Strain history: CIP <- 1996, IFO <- 1989, IAM <- H. Oyaizu, Tokyo Univ., Tokyo, Japan <- T. Harada, Osaka Univ., Osaka, Japan: strain M64

NCBI tax ID(s): 29529 (species)

SI-ID 10826

LMG 8359, ATCC 51264, IAM 12650, IFO 14973, JCM 2836, NCIMB 11855, CIP 104804, DSM 3695, NCIB 11855, IFO 16136, KCTC 2943, NBRC 14973, NBRC 16136

Other strains from Chitinophaga arvensicola

C. arvensicola JCM 2837, IAM 12646, IFO 16132, ...
C. arvensicola JCM 2838, IAM 12647, IFO 16133, ...
C. arvensicola JCM 2839, IAM 12648, IFO 16134, ...
C. arvensicola JCM 2869, IAM 12649, IFO 16135, ...
C. arvensicola JCM 2870, IAM 12651, IFO 16137, ...
C. arvensicola JCM 2871, IAM 12653, IFO 16138, ...
C. arvensicola JCM 2872, IAM 12654, IFO 16139, ...

Section

Chitinophaga arvensicola M64 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

Gram-negative
rod-shaped
mesophilic
obligate 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 arvensicola**
	Full Scientific Name (LPSN)	Chitinophaga arvensicola (Oyaizu et al. 1983) Kämpfer et al. 2006

Synonym

Cytophaga arvensicola

Information on morphological and physiological properties Morphology

[Ref.: #116514]	Gram stain	negative

[Ref.: #116514]	Cell shape	rod-shaped

[Ref.: #116514]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1457]

Culture medium

CY-AGAR (DSMZ Medium 67)

[Ref.: #1457]

Culture medium growth

[Ref.: #1457]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1457]

Culture medium composition

expand / minimize

[Ref.: #39104]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #39104]

Culture medium growth

[Ref.: #39104]

Culture medium composition

expand / minimize

[Ref.: #116514]

Culture medium

CIP Medium 251

[Ref.: #116514]

Culture medium growth

[Ref.: #116514]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #116514]

Culture medium

CIP Medium 3

[Ref.: #116514]

Culture medium growth

[Ref.: #116514]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #116514]

Culture medium

CIP Medium 99

[Ref.: #116514]

Culture medium growth

[Ref.: #116514]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #1457]		growth	30 °C
[Ref.: #39104]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #116514]		growth	5-37 °C
[Ref.: #116514]	no	growth	41 °C
[Ref.: #116514]	no	growth	45 °C

[Ref.: #1457]	Temperature range	mesophilic
[Ref.: #39104]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #116514]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #116514]

Oxygen tolerance

obligate aerobe

[Ref.: #1457]

Name of produced compound

succinoglucan depolymerase

	Salt	Tested relation		Salt conc.
[Ref.: #116514]	NaCl		growth	0-2	%
[Ref.: #116514]	NaCl	no	growth	4	%
[Ref.: #116514]	NaCl	no	growth	6	%
[Ref.: #116514]	NaCl	no	growth	8	%
[Ref.: #116514]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #116514]	esculin ChEBI	+	hydrolysis
[Ref.: #116514]	hippurate ChEBI	-	hydrolysis
[Ref.: #116514]	malonate ChEBI	-	assimilation
[Ref.: #116514]	nitrate ChEBI	+	reduction
[Ref.: #116514]	nitrate ChEBI	-	respiration
[Ref.: #116514]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #116514]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	yes	no

	Metabolite production	Metabolite	Production
[Ref.: #116514]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #116514]		acetoin ChEBI	-
[Ref.: #116514]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116514]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #116514]	amylase	-
[Ref.: #116514]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116514]	caseinase	-	3.4.21.50
[Ref.: #116514]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #116514]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #116514]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #116514]	gelatinase	-
[Ref.: #116514]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #116514]	lipase	-
[Ref.: #68382]	lipase (C 14)	+		* from API zym
[Ref.: #116514]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116514]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116514]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #116514]	tryptophan deaminase	-
[Ref.: #116514]	tween esterase	-
[Ref.: #116514]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #116514]	831	not determinedn.d.	+	-	+	+	+	-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	-	-	-	-	-	+	-	-	+	+	-	-	-	+	-	+	-	-	-	-	-	-	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	+	-	-	+	+	-	-	-	-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116514]	8211	-	+	+	+	+	+	+	+	+	-	+	+	-	+	-	+	+	+	-	-

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

[Ref.: #1457]	Sample type/isolated from	soil
[Ref.: #1457]	Country	Japan
[Ref.: #1457]	Country ISO 3 Code	JPN
[Ref.: #1457]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil

[Ref.: #116514]	Sample type/isolated from	Environment, Soil
[Ref.: #116514]	Country	Japan
[Ref.: #116514]	Country ISO 3 Code	JPN
[Ref.: #116514]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM237311 (>99% sequence identity) for Chitinophaga arvensicola from Microbeatlas

Aquatic Samples
Soil Samples	24
Animal Samples
Plant Samples	1
Total Samples	25

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #1457]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116514]	Biosafety level	1	Risk group (French classification)

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.: #20218]	Cytophaga arvensicola partial 16S rRNA gene, type strain DSM 3695T	AM237311	1424	ENA	29529 tax ID	*
[Ref.: #20218]	Cytophaga arvensicola gene for 16S ribosomal RNA, partial sequence	D12657	1263	ENA	29529 tax ID	*
[Ref.: #20218]	Chitinophaga arvensicola gene for 16S rRNA, partial sequence, strain: NBRC 14973	AB680728	1452	ENA	29529 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Chitinophaga arvensicola DSM 3695	GCA_900110835	scaffold	GenBank	29529 tax ID
[Ref.: #66792]	Chitinophaga arvensicola strain DSM 3695	29529.11	wgs	PATRIC	29529 tax ID	*
[Ref.: #66792]	Chitinophaga arvensicola DSM 3695	2636416040	draft	JGI IMG/M	29529 tax ID	*

[Ref.: #1457]	GC-content	46.0 mol%
[Ref.: #67770]	GC-content	46 mol%	thermal denaturation, midpoint method (Tm)

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 arvensicola strain DSM 3695 PATRIC: 29529.11
[Ref.: #69480]	gram-positive	no	97.489	no
[Ref.: #69480]	anaerobic	no	99.342	no
[Ref.: #69480]	halophile	no	93.964	no
[Ref.: #69480]	spore-forming	no	92.459	no
[Ref.: #69480]	glucose-util	yes	87.148	no
[Ref.: #69480]	motile	no	91.24	no
[Ref.: #69480]	flagellated	no	96.856	no
[Ref.: #69480]	aerobic	yes	88.247	no
[Ref.: #69480]	thermophile	no	99.427	yes
[Ref.: #69480]	glucose-ferment	no	85.277	no

Availability in culture collections External links

[Ref.: #1457]

Culture collection no.

DSM 3695, ATCC 51264, IAM 12650, JCM 2836, NCIB 11855, CECT 358, CIP 104804, IFO 14973, IFO 16136, KCTC 2943, NBRC 14973, NBRC 16136, NCIMB 11855

[Ref.: #86732]

SI-ID 10826

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chitinophaga hostae sp. nov., isolated from the rhizosphere soil of Hosta plantaginea.	He SW, Ma R, Zhao YY, An L, Huang JH, Zhang Q, Han JG, Zhang XX	Int J Syst Evol Microbiol	10.1099/ijsem.0.005335	2022	*
Phylogeny	Chitinophaga eiseniae sp. nov., isolated from vermicompost.	Yasir M, Chung EJ, Song GC, Bibi F, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.023028-0	2010	*
Phylogeny	Chitinophaga vermicomposti sp. nov., with antifungal activity, isolated from vermicompost.	Yasir M, Aslam Z, Song GC, Bibi F, Jeon CO, Chung YR	Int J Syst Evol Microbiol	10.1099/ijs.0.013425-0	2009	*
Phylogeny	Isolation of aerobic, gliding, xylanolytic and laminarinolytic bacteria from acidic Sphagnum peatlands and emended description of Chitinophaga arvensicola Kampfer et al. 2006.	Pankratov TA, Kulichevskaya IS, Liesack W, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.64451-0	2006	*

References

#1457

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3695

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#39104 ; Curators of the CIP;

#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;

#68382

Automatically annotated from API zym .

#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) .

#86732

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID10826.1 )

#116514 Collection of Institut Pasteur ; Curators of the CIP; CIP 104804
* These data were automatically processed and therefore are not curated

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Chitinophaga arvensicola strain DSM 3695

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