Flavobacterium aquicola (DSM 100880, JCM 30987, TMd3a3)

Name: Flavobacterium aquicola (DSM 100880, JCM 30987, TMd3a3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132986

Type strain

Strain Designation TMd3a3

Culture col. no. DSM 100880 JCM 30987 TMd3a3 BCRC 81042

NCBI tax ID(s) 1682742

Special Collections DSMZ JCM Literature strains

Links

Flavobacterium aquicola TMd3a3 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that forms irregular colonies and was isolated from fresh water from a river.

Gram-negative motile rod-shaped colony-forming facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406973

JCM 30987,DSM 100880

@ref 20215

Last LPSN update 2025-12-16 10:01:39

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Flavobacterium

Species Flavobacterium aquicola

Full scientific name Flavobacterium aquicola Hatayama et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
43092	negative	4-11 µm	0.5-0.6 µm	rod-shaped	gliding
125439	negative					99.9
125438						91.5
125438	negative					96.727

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
43092	light yellow	irregular	3 days	R2A

Pigmentation

@ref	Production	Name
43092		Flexirubin-type pigment

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43092	Reasoner's 2A agar (R2A)
43092	IPM		0.5 g/l yeast extract, 0.5 g/l proteose peptone no. 3, 0.5 g/l tryptone, 0.5 g/l sucrose, 0.3 g/l sodium pyruvate, 0.3 g/l K2HPO4, 0.3 g/l MgSO4x7H2O, 0.3 g/l CaCl2x2H2O, 15 g/l gellan gum, pH 6.6
43092	trypticase soy agar (TSA)
43092	nutritient agar (NA)
24774	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
43092	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24774	positive	growth	25	mesophilic
43092	positive	optimum	25	mesophilic
43092	positive	growth	4-30
67770	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
43092	positive	optimum	6.0-7.0
43092	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43092	facultative anaerobe
125439	obligate aerobe	95.6

Spore formation

@ref	Spore formation	Confidence
43092
125439		99.6
125438		90.945

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43092	NaCl	positive	growth	0-1 %(w/v)
43092	NaCl	positive	optimum	0 %(w/v)

Observation

67770

Observationquinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43092	62064 ChEBI	2,3-butanediol	-	oxidation
43092	64552 ChEBI	2-hydroxybutyrate	-	oxidation
43092	16763 ChEBI	2-oxobutanoate	-	oxidation
43092	30916 ChEBI	2-oxoglutarate	-	oxidation
43092	28644 ChEBI	2-oxopentanoate	-	oxidation
43092	18240 ChEBI	4-hydroxy-L-proline	-	oxidation
43092	16724 ChEBI	4-hydroxybutyrate	-	oxidation
43092	18101 ChEBI	4-hydroxyphenylacetic acid	-	oxidation
43092	30089 ChEBI	acetate	-	oxidation
43092	17128 ChEBI	adipate	-	assimilation
43092	40585 ChEBI	alpha-cyclodextrin	+	oxidation
43092	17925 ChEBI	alpha-D-glucose	+	oxidation
43092	36219 ChEBI	alpha-lactose	+	oxidation
43092	27613 ChEBI	amygdalin	-	fermentation
43092	8295 ChEBI	beta-hydroxybutyrate	-	oxidation
43092	73706 ChEBI	bromosuccinate	-	oxidation
43092	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
43092		casein	+	hydrolysis
43092	17057 ChEBI	cellobiose	+	oxidation
43092	17029 ChEBI	chitin	-	hydrolysis
43092	16383 ChEBI	cis-aconitate	-	oxidation
43092	16947 ChEBI	citrate	-	assimilation
43092	16947 ChEBI	citrate	-	oxidation
43092	15570 ChEBI	D-alanine	-	oxidation
43092	18333 ChEBI	D-arabitol	-	oxidation
43092	15824 ChEBI	D-fructose	-	oxidation
43092	15895 ChEBI	D-galactonic acid lactone	-	oxidation
43092	12936 ChEBI	D-galactose	+	oxidation
43092	18024 ChEBI	D-galacturonic acid	-	oxidation
43092	8391 ChEBI	D-gluconate	-	oxidation
43092	17784 ChEBI	D-glucosaminic acid	-	oxidation
43092	17634 ChEBI	D-glucose	+	assimilation
43092	14314 ChEBI	D-glucose 6-phosphate	-	oxidation
43092	15748 ChEBI	D-glucuronate	-	oxidation
43092	16899 ChEBI	D-mannitol	-	assimilation
43092	16899 ChEBI	D-mannitol	-	fermentation
43092	16899 ChEBI	D-mannitol	-	oxidation
43092	16024 ChEBI	D-mannose	+	assimilation
43092	16024 ChEBI	D-mannose	+	oxidation
43092	27605 ChEBI	D-psicose	-	oxidation
43092	33801 ChEBI	D-saccharate	-	oxidation
43092	16523 ChEBI	D-serine	-	oxidation
43092	17924 ChEBI	D-sorbitol	-	fermentation
43092	17924 ChEBI	D-sorbitol	-	oxidation
43092	27689 ChEBI	decanoate	-	assimilation
43092	23652 ChEBI	dextrin	+	oxidation
43092	17126 ChEBI	DL-carnitine	-	oxidation
43092	16991 ChEBI	dna	-	hydrolysis
43092		egg yolk	-	hydrolysis
43092	17113 ChEBI	erythritol	-	oxidation
43092	16000 ChEBI	ethanolamine	-	oxidation
43092	15740 ChEBI	formate	-	oxidation
43092	16865 ChEBI	gamma-aminobutyric acid	-	oxidation
43092	5291 ChEBI	gelatin	-	hydrolysis
43092	28066 ChEBI	gentiobiose	+	oxidation
43092	17234 ChEBI	glucose	-	fermentation
43092	29042 ChEBI	glucose 1-phosphate	-	oxidation
43092	32323 ChEBI	glucuronamide	-	oxidation
43092	17754 ChEBI	glycerol	-	oxidation
43092	28087 ChEBI	glycogen	+	oxidation
43092	73804 ChEBI	glycyl L-aspartic acid	+	oxidation
43092	73784 ChEBI	glycyl-l-glutamate	+	oxidation
43092	17596 ChEBI	inosine	-	oxidation
43092	17240 ChEBI	itaconate	-	oxidation
43092	21217 ChEBI	L-alaninamide	-	oxidation
43092	16977 ChEBI	L-alanine	-	oxidation
43092	73786 ChEBI	L-alanylglycine	-	oxidation
43092	30849 ChEBI	L-arabinose	+	assimilation
43092	30849 ChEBI	L-arabinose	-	fermentation
43092	30849 ChEBI	L-arabinose	+	oxidation
43092	17196 ChEBI	L-asparagine	-	oxidation
43092	29991 ChEBI	L-aspartate	-	oxidation
43092	18287 ChEBI	L-fucose	-	oxidation
43092	29985 ChEBI	L-glutamate	+	oxidation
43092	15971 ChEBI	L-histidine	-	oxidation
43092	15603 ChEBI	L-leucine	-	oxidation
43092	15729 ChEBI	L-ornithine	-	oxidation
43092	17295 ChEBI	L-phenylalanine	-	oxidation
43092	17203 ChEBI	L-proline	-	oxidation
43092	18183 ChEBI	L-pyroglutamic acid	-	oxidation
43092	62345 ChEBI	L-rhamnose	-	fermentation
43092	62345 ChEBI	L-rhamnose	-	oxidation
43092	17115 ChEBI	L-serine	-	oxidation
43092	16857 ChEBI	L-threonine	-	oxidation
43092	17895 ChEBI	L-tyrosine	-	hydrolysis
43092	24996 ChEBI	lactate	-	oxidation
43092	6359 ChEBI	lactulose	-	oxidation
43092	25115 ChEBI	malate	-	assimilation
43092	15792 ChEBI	malonate	-	oxidation
43092	17306 ChEBI	maltose	+	assimilation
43092	17306 ChEBI	maltose	+	oxidation
43092	28053 ChEBI	melibiose	-	fermentation
43092	28053 ChEBI	melibiose	-	oxidation
43092	320055 ChEBI	methyl beta-D-glucopyranoside	-	oxidation
43092	51850 ChEBI	methyl pyruvate	-	oxidation
43092	75146 ChEBI	monomethyl succinate	-	oxidation
43092	17268 ChEBI	myo-inositol	-	fermentation
43092	17268 ChEBI	myo-inositol	-	oxidation
43092	28037 ChEBI	N-acetylgalactosamine	-	oxidation
43092	506227 ChEBI	N-acetylglucosamine	-	assimilation
43092	506227 ChEBI	N-acetylglucosamine	-	oxidation
43092	17632 ChEBI	nitrate	+	reduction
43092	17309 ChEBI	pectin	-	hydrolysis
43092	18401 ChEBI	phenylacetate	-	assimilation
43092	50048 ChEBI	phenylethylamine	-	oxidation
43092	32032 ChEBI	potassium gluconate	-	assimilation
43092	17272 ChEBI	propionate	-	oxidation
43092	17148 ChEBI	putrescine	-	oxidation
43092	26490 ChEBI	quinate	-	oxidation
43092	16634 ChEBI	raffinose	-	oxidation
43092	15963 ChEBI	ribitol	-	oxidation
43092	41865 ChEBI	sebacic acid	-	oxidation
43092	53258 ChEBI	sodium citrate	-	assimilation
43092	28017 ChEBI	starch	+	hydrolysis
43092	143136 ChEBI	succinamate	-	oxidation
43092	30031 ChEBI	succinate	-	oxidation
43092	17992 ChEBI	sucrose	-	fermentation
43092	17992 ChEBI	sucrose	-	oxidation
43092	17748 ChEBI	thymidine	-	oxidation
43092	27082 ChEBI	trehalose	-	oxidation
43092	32528 ChEBI	turanose	-	oxidation
43092	53423 ChEBI	tween 40	-	oxidation
43092	53426 ChEBI	tween 80	-	oxidation
43092	16704 ChEBI	uridine	-	oxidation
43092	27248 ChEBI	urocanic acid	-	oxidation
43092	17151 ChEBI	xylitol	-	oxidation

Metabolite production

@ref	Chebi-ID	Metabolite
43092	15688 ChEBI	acetoin
43092	16136 ChEBI	hydrogen sulfide
43092	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
43092	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
43092	arginine dihydrolase	-	3.5.3.6
43092	beta-galactosidase	+	3.2.1.23
43092	beta-glucosidase	+	3.2.1.21
43092	catalase	+	1.11.1.6
43092	cytochrome oxidase	+	1.9.3.1
43092	lysine decarboxylase	-	4.1.1.18
43092	ornithine decarboxylase	-	4.1.1.17
43092	tryptophan deaminase	-	4.1.99.1
43092	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

@ref

43092

Fatty acid	Percentage
C15:0 iso	23.3
C16:1ω6c / C16:1ω7c	17.7
C17:0 iso 3OH	7.6
C16:0 iso 3OH	6.8
iso C15:1 G	5.8
C15:0 anteiso	5.7
C15:1ω6c	5
C15:0 iso 3OH	3.8
C13:0 iso	2.9
C14:0 iso	2.7
C17:1 iso ω9c / C16:0 10-methyl	2.4
C16:0 iso	2.4
C16:0 3OH	2.2
C17:1ω6c	1.9
C16:0	1.5
C16:1 iso H	1.2
C15:0 3OH	1.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
24774	fresh water from a river	Kanagawa, Atsugi, Tamagawa River	Japan	JPN	Asia
43092	freshwater sample	Tamagawa River, Atsugi, Kanagawa	Japan	JPN	Asia	IPM plates	2-7 days	25
67770	Freshwater sample collected from the Tamagawa River		Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24774	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM338511v1 assembly for Flavobacterium aquicola DSM 100880	scaffold	GCA_003385115	1682742.3	2739367662	1682742	68.15

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
24774	Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence	LC065662	1436	1682742
24774	Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C1	LC120818	1436	1682742
24774	Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C2	LC120819	1436	1682742
24774	Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C3	LC120820	1436	1682742

GC content

@ref	GC-content (mol%)	Method
24774	36.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium aquicola DSM 100880
NCBI: GCA_003385115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	yes	50.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Flavobacterium aquicola DSM 100880
NCBI: GCA_003385115.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.73	yes
125438	anaerobic	anaerobicⓘ	no	96.19	yes
125438	aerobic	aerobicⓘ	yes	71.39	yes
125438	spore-forming	spore-formingⓘ	no	90.95	yes
125438	thermophilic	thermophileⓘ	no	98.97	no
125438	flagellated	motile2+ⓘ	no	91.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Validation of a Loop-Mediated Isothermal Amplification-Based Kit for the Detection of Legionella pneumophila in Environmental Samples According to ISO/TS 12869:2012.	Caruso G, Coniglio MA, Lagana P, Fasciana T, Arcoleo G, Arrigo I, Di Carlo P, Palermo M, Giammanco A.	Microorganisms	10.3390/microorganisms12050961	2024
Genetics	Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen.	Laanto E, Ravantti JJ, Sundberg LR.	Microorganisms	10.3390/microorganisms8121919	2020
	Flavobacterium aestuarii sp. nov., a novel species isolated from the Pearl River Estuary.	Li Q, Peng ZQ, Wang HC, Dong L, Guo DY, Wang PD, Luo XQ, Luo ZH, Yang ZW, Li WJ.	Antonie Van Leeuwenhoek	10.1007/s10482-025-02109-5	2025
Phylogeny	Flavobacterium aquicola sp. nov., isolated from river water.	Hatayama K, Ushida A, Kuno T	Int J Syst Evol Microbiol	10.1099/ijsem.0.001057	2016

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 )
#24774	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100880
#43092	Kouta Hatayama, Ayako Ushida, Teruaki Kuno: Flavobacterium aquicola sp. nov., isolated from river water. IJSEM 66: 2789 - 2796 2016 ( DOI 10.1099/ijsem.0.001057 , PubMed 27045592 )
#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;
#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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Flavobacterium aquicola (DSM 100880, JCM 30987, TMd3a3)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile?

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003385115

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media

Fatty acid profile