Name: Flavobacterium aquicola TMd3a3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132986

Type strain:

Species: Flavobacterium aquicola

Strain Designation: TMd3a3

Culture col. no.: DSM 100880, JCM 30987, BCRC 81042

Strain history: K. Hatayama; Sagami Chem. Res. Inst., Japan; TMd3a3.

NCBI tax ID(s): 1682742 (species)

SI-ID 406973

DSM 100880

Section

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

colony-forming
Gram-negative
motile
rod-shaped
facultative anaerobe
mesophilic
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	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Flavobacterium*
	Species	**Flavobacterium aquicola**
	Full Scientific Name (LPSN)	Flavobacterium aquicola Hatayama et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43092]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.992

[Ref.: #43092]	Cell length	4-11 µm

[Ref.: #43092]	Cell width	0.5-0.6 µm

[Ref.: #43092]	Cell shape	rod-shaped

[Ref.: #43092]	Motility	yes

[Ref.: #43092]	Flagellum arrangement	gliding

[Ref.: #43092]	Colony color	light yellow
[Ref.: #43092]	Colony shape	irregular
[Ref.: #43092]	Incubation period	3 days
[Ref.: #43092]	Cultivation medium used	R2A

[Ref.: #43092]	Pigment production	yes
[Ref.: #43092]	Pigment name	Flexirubin-type pigment

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43092]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43092]

Culture medium growth

[Ref.: #43092]

Culture medium

IPM

[Ref.: #43092]

Culture medium growth

[Ref.: #43092]

Culture medium composition

expand / minimize

[Ref.: #43092]

Culture medium

trypticase soy agar (TSA)

[Ref.: #43092]

Culture medium growth

[Ref.: #43092]

Culture medium

nutritient agar (NA)

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Culture medium growth

[Ref.: #24774]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #24774]

Culture medium growth

[Ref.: #24774]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24774]

Culture medium composition

expand / minimize

[Ref.: #43092]

Culture medium

Marine agar (MA)

[Ref.: #43092]

Culture medium growth

		Temperature
[Ref.: #24774]	growth	25 °C
[Ref.: #43092]	optimum	25 °C
[Ref.: #43092]	growth	4-30 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #24774]	Temperature range	mesophilic
[Ref.: #43092]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43092]			optimum	6.0-7.0
[Ref.: #43092]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43092]

Oxygen tolerance

facultative anaerobe

[Ref.: #43092]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.987

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43092]		NaCl		growth	0-1	%(w/v)
[Ref.: #43092]		NaCl		optimum	0	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43092]	2,3-butanediol ChEBI	-	oxidation
[Ref.: #43092]	2-hydroxybutyrate ChEBI	-	oxidation
[Ref.: #43092]	2-oxobutanoate ChEBI	-	oxidation
[Ref.: #43092]	2-oxoglutarate ChEBI	-	oxidation
[Ref.: #43092]	2-oxopentanoate ChEBI	-	oxidation
[Ref.: #43092]	4-hydroxy-L-proline ChEBI	-	oxidation
[Ref.: #43092]	4-hydroxybutyrate ChEBI	-	oxidation
[Ref.: #43092]	4-hydroxyphenylacetic acid ChEBI	-	oxidation
[Ref.: #43092]	acetate ChEBI	-	oxidation
[Ref.: #43092]	adipate ChEBI	-	assimilation
[Ref.: #43092]	alpha-cyclodextrin ChEBI	+	oxidation
[Ref.: #43092]	alpha-D-glucose ChEBI	+	oxidation
[Ref.: #43092]	alpha-lactose ChEBI	+	oxidation
[Ref.: #43092]	amygdalin ChEBI	-	fermentation
[Ref.: #43092]	beta-hydroxybutyrate ChEBI	-	oxidation
[Ref.: #43092]	bromosuccinate ChEBI	-	oxidation
[Ref.: #43092]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #43092]	casein	+	hydrolysis
[Ref.: #43092]	cellobiose ChEBI	+	oxidation
[Ref.: #43092]	chitin ChEBI	-	hydrolysis
[Ref.: #43092]	cis-aconitate ChEBI	-	oxidation
[Ref.: #43092]	citrate ChEBI	-	assimilation
[Ref.: #43092]	citrate ChEBI	-	oxidation
[Ref.: #43092]	D-alanine ChEBI	-	oxidation
[Ref.: #43092]	D-arabitol ChEBI	-	oxidation
[Ref.: #43092]	D-fructose ChEBI	-	oxidation
[Ref.: #43092]	D-galactonic acid lactone ChEBI	-	oxidation
[Ref.: #43092]	D-galactose ChEBI	+	oxidation
[Ref.: #43092]	D-galacturonic acid ChEBI	-	oxidation
[Ref.: #43092]	D-gluconate ChEBI	-	oxidation
[Ref.: #43092]	D-glucosaminic acid ChEBI	-	oxidation
[Ref.: #43092]	D-glucose ChEBI	+	assimilation
[Ref.: #43092]	D-glucose 6-phosphate ChEBI	-	oxidation
[Ref.: #43092]	D-glucuronate ChEBI	-	oxidation
[Ref.: #43092]	D-mannitol ChEBI	-	assimilation
[Ref.: #43092]	D-mannitol ChEBI	-	fermentation
[Ref.: #43092]	D-mannitol ChEBI	-	oxidation
[Ref.: #43092]	D-mannose ChEBI	+	assimilation
[Ref.: #43092]	D-mannose ChEBI	+	oxidation
[Ref.: #43092]	D-psicose ChEBI	-	oxidation
[Ref.: #43092]	D-saccharate ChEBI	-	oxidation
[Ref.: #43092]	D-serine ChEBI	-	oxidation
[Ref.: #43092]	D-sorbitol ChEBI	-	fermentation
[Ref.: #43092]	D-sorbitol ChEBI	-	oxidation
[Ref.: #43092]	decanoate ChEBI	-	assimilation
[Ref.: #43092]	dextrin ChEBI	+	oxidation
[Ref.: #43092]	DL-carnitine ChEBI	-	oxidation
[Ref.: #43092]	dna ChEBI	-	hydrolysis
[Ref.: #43092]	egg yolk	-	hydrolysis
[Ref.: #43092]	erythritol ChEBI	-	oxidation
[Ref.: #43092]	ethanolamine ChEBI	-	oxidation
[Ref.: #43092]	formate ChEBI	-	oxidation
[Ref.: #43092]	gamma-aminobutyric acid ChEBI	-	oxidation
[Ref.: #43092]	gelatin ChEBI	-	hydrolysis
[Ref.: #43092]	gentiobiose ChEBI	+	oxidation
[Ref.: #43092]	glucose ChEBI	-	fermentation
[Ref.: #43092]	glucose 1-phosphate ChEBI	-	oxidation
[Ref.: #43092]	glucuronamide ChEBI	-	oxidation
[Ref.: #43092]	glycerol ChEBI	-	oxidation
[Ref.: #43092]	glycogen ChEBI	+	oxidation
[Ref.: #43092]	glycyl L-aspartic acid ChEBI	+	oxidation
[Ref.: #43092]	glycyl-l-glutamate ChEBI	+	oxidation
[Ref.: #43092]	inosine ChEBI	-	oxidation
[Ref.: #43092]	itaconate ChEBI	-	oxidation
[Ref.: #43092]	L-alaninamide ChEBI	-	oxidation
[Ref.: #43092]	L-alanine ChEBI	-	oxidation
[Ref.: #43092]	L-alanylglycine ChEBI	-	oxidation
[Ref.: #43092]	L-arabinose ChEBI	+	assimilation
[Ref.: #43092]	L-arabinose ChEBI	-	fermentation
[Ref.: #43092]	L-arabinose ChEBI	+	oxidation
[Ref.: #43092]	L-asparagine ChEBI	-	oxidation
[Ref.: #43092]	L-aspartate ChEBI	-	oxidation
[Ref.: #43092]	L-fucose ChEBI	-	oxidation
[Ref.: #43092]	L-glutamate ChEBI	+	oxidation
[Ref.: #43092]	L-histidine ChEBI	-	oxidation
[Ref.: #43092]	L-leucine ChEBI	-	oxidation
[Ref.: #43092]	L-ornithine ChEBI	-	oxidation
[Ref.: #43092]	L-phenylalanine ChEBI	-	oxidation
[Ref.: #43092]	L-proline ChEBI	-	oxidation
[Ref.: #43092]	L-pyroglutamic acid ChEBI	-	oxidation
[Ref.: #43092]	L-rhamnose ChEBI	-	fermentation
[Ref.: #43092]	L-rhamnose ChEBI	-	oxidation
[Ref.: #43092]	L-serine ChEBI	-	oxidation
[Ref.: #43092]	L-threonine ChEBI	-	oxidation
[Ref.: #43092]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #43092]	lactate ChEBI	-	oxidation
[Ref.: #43092]	lactulose ChEBI	-	oxidation
[Ref.: #43092]	malate ChEBI	-	assimilation
[Ref.: #43092]	malonate ChEBI	-	oxidation
[Ref.: #43092]	maltose ChEBI	+	assimilation
[Ref.: #43092]	maltose ChEBI	+	oxidation
[Ref.: #43092]	melibiose ChEBI	-	fermentation
[Ref.: #43092]	melibiose ChEBI	-	oxidation
[Ref.: #43092]	methyl beta-D-glucopyranoside ChEBI	-	oxidation
[Ref.: #43092]	methyl pyruvate ChEBI	-	oxidation
[Ref.: #43092]	monomethyl succinate ChEBI	-	oxidation
[Ref.: #43092]	myo-inositol ChEBI	-	fermentation
[Ref.: #43092]	myo-inositol ChEBI	-	oxidation
[Ref.: #43092]	N-acetylgalactosamine ChEBI	-	oxidation
[Ref.: #43092]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43092]	N-acetylglucosamine ChEBI	-	oxidation
[Ref.: #43092]	nitrate ChEBI	+	reduction
[Ref.: #43092]	pectin ChEBI	-	hydrolysis
[Ref.: #43092]	phenylacetate ChEBI	-	assimilation
[Ref.: #43092]	phenylethylamine ChEBI	-	oxidation
[Ref.: #43092]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43092]	propionate ChEBI	-	oxidation
[Ref.: #43092]	putrescine ChEBI	-	oxidation
[Ref.: #43092]	quinate ChEBI	-	oxidation
[Ref.: #43092]	raffinose ChEBI	-	oxidation
[Ref.: #43092]	ribitol ChEBI	-	oxidation
[Ref.: #43092]	sebacic acid ChEBI	-	oxidation
[Ref.: #43092]	sodium citrate ChEBI	-	assimilation
[Ref.: #43092]	starch ChEBI	+	hydrolysis
[Ref.: #43092]	succinamate ChEBI	-	oxidation
[Ref.: #43092]	succinate ChEBI	-	oxidation
[Ref.: #43092]	sucrose ChEBI	-	fermentation
[Ref.: #43092]	sucrose ChEBI	-	oxidation
[Ref.: #43092]	thymidine ChEBI	-	oxidation
[Ref.: #43092]	trehalose ChEBI	-	oxidation
[Ref.: #43092]	turanose ChEBI	-	oxidation
[Ref.: #43092]	tween 40 ChEBI	-	oxidation
[Ref.: #43092]	tween 80 ChEBI	-	oxidation
[Ref.: #43092]	uridine ChEBI	-	oxidation
[Ref.: #43092]	urocanic acid ChEBI	-	oxidation
[Ref.: #43092]	xylitol ChEBI	-	oxidation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43092]	acetoin ChEBI	no
[Ref.: #43092]	hydrogen sulfide ChEBI	no
[Ref.: #43092]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #43092]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #43092]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43092]	beta-galactosidase	+	3.2.1.23
[Ref.: #43092]	beta-glucosidase	+	3.2.1.21
[Ref.: #43092]	catalase	+	1.11.1.6
[Ref.: #43092]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43092]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43092]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43092]	tryptophan deaminase	-	4.1.99.1
[Ref.: #43092]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #24774]	Sample type/isolated from	fresh water from a river
[Ref.: #24774]	Geographic location (country and/or sea, region)	Kanagawa, Atsugi, Tamagawa River
[Ref.: #24774]	Country	Japan
[Ref.: #24774]	Country ISO 3 Code	JPN
[Ref.: #24774]	Continent	Asia

[Ref.: #43092]	Sample type/isolated from	freshwater sample
[Ref.: #43092]	Geographic location (country and/or sea, region)	Tamagawa River, Atsugi, Kanagawa
[Ref.: #43092]	Country	Japan
[Ref.: #43092]	Country ISO 3 Code	JPN
[Ref.: #43092]	Continent	Asia
[Ref.: #43092]	Enrichment culture	IPM plates
[Ref.: #43092]	Enrichment culture duration	2-7 days
[Ref.: #43092]	Enrichment culture temperature	25 ̊C

[Ref.: #67770]	Sample type/isolated from	Freshwater sample collected from the Tamagawa River
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#River (Creek)

What are isolation sources categories?

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

[Ref.: #24774]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #24774]	Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence	LC065662	1436	ENA	1682742 tax ID
[Ref.: #24774]	Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C1	LC120818	1436	ENA	1682742 tax ID
[Ref.: #24774]	Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C2	LC120819	1436	ENA	1682742 tax ID
[Ref.: #24774]	Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C3	LC120820	1436	ENA	1682742 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium aquicola DSM 100880	GCA_003385115	scaffold	GenBank	1682742 tax ID	*
[Ref.: #66792]	Flavobacterium aquicola strain DSM 100880	1682742.3	wgs	PATRIC	1682742 tax ID	*
[Ref.: #66792]	Flavobacterium aquicola DSM 100880 (v2)	2739367662	draft	JGI IMG/M	1682742 tax ID	*

[Ref.: #24774]

GC-content

36.5 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: Flavobacterium aquicola DSM 100880 NCBI: GCA_003385115.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flavobacterium aquicola DSM 100880 NCBI: GCA_003385115.1
[Ref.: #69480]	motile	no	90.273	no
[Ref.: #69480]	flagellated	no	95.001	yes
[Ref.: #69480]	gram-positive	no	97.839	yes
[Ref.: #69480]	anaerobic	no	99.625	no
[Ref.: #69480]	aerobic	yes	90.336	no
[Ref.: #69480]	halophile	no	96.835	yes
[Ref.: #69480]	spore-forming	no	94.376	yes
[Ref.: #69480]	glucose-util	yes	87.658	no
[Ref.: #69480]	thermophile	no	99.659	yes
[Ref.: #69480]	glucose-ferment	no	90.195	yes

Availability in culture collections External links

[Ref.: #24774]

Culture collection no.

DSM 100880, JCM 30987, BCRC 81042

[Ref.: #91262]

SI-ID 406973

Literature:

Topic	Title	Authors	Journal	DOI	Year
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;

#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 )

#91262

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-ID406973.1 )

* These data were automatically processed and therefore are not curated

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Flavobacterium aquicola DSM 100880

Flavobacterium aquicola DSM 100880

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