Chitinophaga arvensicola (DSM 3695, ATCC 51264, IAM 12650)

Name: Chitinophaga arvensicola (DSM 3695, ATCC 51264, IAM 12650)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17742

Type strain

Strain Designation M64

Culture col. no. DSM 3695 ATCC 51264 IAM 12650 JCM 2836 NCIB 11855 9 more

NCBI tax ID(s) 29529

Special Collections DSMZ JCM KCTC CIP

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

Links

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

Gram-negative rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2026-02-09 11:22:18

Domain Bacteria

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Chitinophaga

Species Chitinophaga arvensicola

Full scientific name Chitinophaga arvensicola (Oyaizu et al. 1983) Kämpfer et al. 2006

Synonyms (1)

Cytophaga arvensicola

BacDive ID	Other strains from **Chitinophaga arvensicola** (7)	Type strain
163507	C. arvensicola JCM 2837, IAM 12646, IFO 16132, NBRC 16132
163508	C. arvensicola JCM 2838, IAM 12647, IFO 16133, NBRC 16133
163509	C. arvensicola JCM 2839, IAM 12648, IFO 16134, NBRC 16134
163564	C. arvensicola JCM 2869, IAM 12649, IFO 16135, NBRC 16135
163567	C. arvensicola JCM 2870, IAM 12651, IFO 16137, NBRC 16137
163570	C. arvensicola JCM 2871, IAM 12653, IFO 16138, NBRC 16138
163578	C. arvensicola JCM 2872, IAM 12654, IFO 16139, NBRC 16139

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		97.139
125439	negative		98.7
116514	negative	rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1457	CY-AGAR (DSMZ Medium 67)	Medium recipe at MediaDive	Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
39104	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
116514	CIP Medium 251	Medium recipe at CIP
116514	CIP Medium 3	Medium recipe at CIP
116514	CIP Medium 99	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1457	positive	growth	30
39104	positive	growth	30
67770	positive	growth	30
116514	positive	growth	5-37
116514	negative	growth	41
116514	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
116514	obligate aerobe
125439	obligate aerobe	90.2

Spore formation

@ref	Spore formation	Confidence
125439		98.7

Compound production

1457

Compoundsuccinoglucan depolymerase

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116514	NaCl	positive	growth	0-2 %
116514	NaCl		growth	4 %
116514	NaCl		growth	6 %
116514	NaCl		growth	8 %
116514	NaCl		growth	10 %

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
116514	4853 ChEBI	esculin	+	hydrolysis
116514	606565 ChEBI	hippurate	-	hydrolysis
116514	15792 ChEBI	malonate	-	assimilation
116514	17632 ChEBI	nitrate	+	reduction
116514	17632 ChEBI	nitrate	-	respiration
116514	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
116514	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116514	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
116514	15688 ChEBI	acetoin	-
116514	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116514	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
116514	amylase	-
68382	beta-galactosidase	+	3.2.1.23	from API zym
116514	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116514	caseinase	-	3.4.21.50
116514	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
116514	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116514	gamma-glutamyltransferase	+	2.3.2.2
116514	gelatinase	-
116514	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
116514	lipase	-
68382	lipase (C 14)	+		from API zym
116514	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116514	ornithine decarboxylase	-	4.1.1.17
116514	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
116514	tryptophan deaminase	-
116514	tween esterase	-
116514	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
116514	-	+	+	+	+	+	+	+	+	-	+	+	-	+	-	+	+	+	-	-

API biotype100

@ref	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
116514	not determinedn.d.	+	-	+	+	+	-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	-	-	-	-	-	+	-	-	+	+	-	-	-	+	-	+	-	-	-	-	-	-	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	+	-	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
1457	soil	Japan	JPN	Asia
67770	Soil
116514	Environment, Soil	Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1457	1	Risk group (German classification) According to TRBA 466
116514	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2636416040 annotated assembly for Chitinophaga arvensicola DSM 3695	scaffold	GCA_900110835	29529.11	2636416040	29529	74.9

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Cytophaga arvensicola partial 16S rRNA gene, type strain DSM 3695T	AM237311	1424	29529
20218	Cytophaga arvensicola gene for 16S ribosomal RNA, partial sequence	D12657	1263	29529
20218	Chitinophaga arvensicola gene for 16S rRNA, partial sequence, strain: NBRC 14973	AB680728	1452	29529

GC content

@ref	GC-content (mol%)	Method
1457	46.0
67770	46	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 arvensicola DSM 3695
NCBI: GCA_900110835

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	yes	58.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chitinophaga arvensicola strain DSM 3695
PATRIC: 29529.11

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.14	no
125438	anaerobic	anaerobicⓘ	no	97.72	no
125438	spore-forming	spore-formingⓘ	no	83.89	no
125438	aerobic	aerobicⓘ	yes	89.34	yes
125438	thermophilic	thermophileⓘ	no	96.99	no
125438	flagellated	motile2+ⓘ	no	85.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Detection of antibiotics synthetized in microfluidic picolitre-droplets by various actinobacteria.	Mahler L, Wink K, Beulig RJ, Scherlach K, Tovar M, Zang E, Martin K, Hertweck C, Belder D, Roth M.	Sci Rep	10.1038/s41598-018-31263-2	2018
	Microbial consortia degrade several widely used organic UV filters, but a number of hydrophobic filters remain recalcitrant to biodegradation.	Fagervold SK, Rohee C, Lebaron P.	Environ Sci Pollut Res Int	10.1007/s11356-023-31063-w	2023
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
	Chitinophaga nivalis sp. nov., isolated from forest soil in Pyeongchang, Republic of Korea.	Trinh NH, Kim J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005981	2023
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

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;
#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 .
#116514	Collection of Institut Pasteur ; Curators of the CIP; CIP 104804
#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 arvensicola (DSM 3695, ATCC 51264, IAM 12650)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900110835

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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