Chitinophaga filiformis (CCUG 12809, CIP 106401, DSM 527)

Name: Chitinophaga filiformis (CCUG 12809, CIP 106401, DSM 527)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17744

Type strain

Strain Designation Fx e1

Culture col. no. CCUG 12809 CIP 106401 DSM 527 ATCC 29495 IAM 14320 8 more

NCBI tax ID(s) 104663

Special Collections DSMZ CCUG JCM CIP

History <- H. Reichenbach, Fx e1 (Flexibacter elegans) IAM 14320 <-- IFO 15056 <-- DSM 527 ("Myxococcus filiformis") <-- H. Reichenbach Fx e1 ("Flexibacter elegans"). CIP <- 2000, J.F. Bernardet, INRA, Jouy-en-Josas, France <- ATCC <- DSMZ <- H. Reichenbach: strain Fx e1, Flexibacter elegans

Links

Chitinophaga filiformis Fx e1 is an obligate aerobe, mesophilic, Gram-negative prokaryote that was isolated from soil.

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

Name and taxonomic classification

SI-ID 10279

LMG 10391,ATCC 29495,DSM 527,IFO 15056,CCUG 12809,CIP 106401,IAM 14320,VKM B-1400,NBRC 15056,HAMBI 1966,NCIMB 13250,LMG 23482,JCM 21160

@ref 20215

Last LPSN update 2025-12-16 09:51:10

Domain Pseudomonadati

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Chitinophaga

Species Chitinophaga filiformis

Full scientific name Chitinophaga filiformis (Reichenbach 1989 ex Solntseva 1940) Kämpfer et al. 2006

Synonyms (1)

Flexibacter filiformis

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		92.065
125439	negative		91.1
119348	negative	rod-shaped

Colony morphology

@ref	Incubation period
45832	1-2 days
119348

Pigmentation

@ref	Production	Name
119348		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
125	EX-LM MEDIUM (DSMZ Medium 1550)	Medium recipe at MediaDive	Name: EX-LM MEDIUM (DSMZ Medium 1550) Composition: Yeast extract 5.0 g/l Casitone 5.0 g/l MgSO4 x 7 H2O 2.0 g/l Distilled water
40297	MEDIUM 342 - for Flexibacter filiformis		Distilled water make up to (1000.000 ml);Calcium chloride dihydrate (1.360g);Agar (15.000 g);Casitone (3.000 g)
119348	CIP Medium 35	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
125	positive	growth	30	mesophilic
40297	positive	growth	30	mesophilic
45832	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
119348	positive	growth	15-41
119348	negative	growth	5
119348	negative	growth	45

Physiology and metabolism

Oxygen tolerance

119348

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		95.4

Compound production

@ref	Compound
125	5 chloroflexirubin
125	flexirubin

Halophily

@ref	Salt	Tested relation	Concentration
119348	NaCl	growth	2 %
119348	NaCl	growth	4 %
119348	NaCl	growth	6 %
119348	NaCl	growth	8 %
119348	NaCl	growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119348	4853 ChEBI	esculin	+	hydrolysis
119348	15792 ChEBI	malonate	-	assimilation
119348	17632 ChEBI	nitrate	+	reduction
119348	17632 ChEBI	nitrate	-	respiration
119348	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119348	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
119348	15688 ChEBI	acetoin	-
119348	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119348	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
119348	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
119348	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
119348	caseinase	+	3.4.21.50
119348	catalase	-	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
119348	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
119348	gamma-glutamyltransferase	+	2.3.2.2
119348	gelatinase	+
119348	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119348	lipase	-
68382	lipase (C 14)	-		from API zym
119348	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
119348	ornithine decarboxylase	-	4.1.1.17
119348	phenylalanine ammonia-lyase	-	4.3.1.24
119348	protease	-
68382	trypsin	+	3.4.21.4	from API zym
119348	tryptophan deaminase	-
119348	tween esterase	-
119348	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
119348	-	+	-	-	-	+	+	+	+	-	+	+	-	+	-	+	+	+	-	+

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
119348	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	+	-	+	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	+	+	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
125	soil	Samoa, Upolu, Apia
45832	Soil	Apia,Upolu	Samoa	WSM	Australia and Oceania
67770	Soil on the island of Upolu		Samoa	WSM	Australia and Oceania
119348	Environment, Soil	Upolu, Apia	Samoa	WSM	Australia and Oceania	1966

Taxonmaps

69479

Global distribution of 16S sequence AB680761 (>99% sequence identity) for Chitinophaga from Microbeatlas

Aquatic Samples	4
Soil Samples	315
Animal Samples	15
Plant Samples	58
Total Samples	392

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
125	1	Risk group (German classification) According to TRBA 466
119348	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 2634166296 annotated assembly for Chitinophaga filiformis DSM 527	scaffold	GCA_900102545	104663.4	2634166296	104663	69.49

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Flexibacter elegans 16S ribosomal RNA	M58782	1481	997
20218	Flexibacter filiformis gene for 16S rRNA, strain:IFO 15056	AB078049	1481	104663
20218	Chitinophaga filiformis gene for 16S rRNA, partial sequence, strain: NBRC 15056	AB680761	1451	104663
124043	Chitinophaga filiformis partial 16S rRNA gene, strain HAMBI 1966	LT899941	1507	104663

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chitinophaga filiformis DSM 527
NCBI: GCA_900102545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.40	no
125439	motility	BacteriaNetⓘ	no	68.20	no
125439	gram_stain	BacteriaNetⓘ	negative	91.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	78.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chitinophaga filiformis strain DSM 527
PATRIC: 104663.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.07	no
125438	anaerobic	anaerobicⓘ	no	97.88	yes
125438	spore-forming	spore-formingⓘ	no	68.52	no
125438	aerobic	aerobicⓘ	yes	88.84	yes
125438	thermophilic	thermophileⓘ	no	95.97	yes
125438	flagellated	motile2+ⓘ	no	89.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	LolA and LolB are conserved in Bacteroidota and are crucial for gliding motility and Type IX secretion.	De Smet T, Baland E, Giovannercole F, Mignon J, Lizen L, Dugauquier R, Lauber F, Dieu M, Lima-Mendez G, Michaux C, Devos D, Renzi F.	Commun Biol	10.1038/s42003-025-07817-2	2025
Phylogeny	Chitinophaga agri sp. nov., a bacterium isolated from soil of reclaimed land.	Lee SA, Heo J, Kim TW, Sang MK, Song J, Kwon SW, Weon HY	Arch Microbiol	10.1007/s00203-020-02066-9	2020
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

#125	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 527
#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 )
#40297	; Curators of the CIP;
#45832	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 12809
#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 .
#119348	Collection of Institut Pasteur ; Curators of the CIP; CIP 106401
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 filiformis (CCUG 12809, CIP 106401, DSM 527)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Halophily

Metabolite utilization

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_900102545

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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