Hymenobacter rivuli (BCRC 80979, LMG 29559, KCTC 52236)

Name: Hymenobacter rivuli (BCRC 80979, LMG 29559, KCTC 52236)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158705

Type strain

Strain Designation TAPP3

Culture col. no. BCRC 80979 LMG 29559 KCTC 52236 TAPP3

NCBI tax ID(s) 1815561

Special Collections KCTC Literature strains

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Hymenobacter rivuli TAPP3 is an aerobe, Gram-negative, motile prokaryote that forms circular colonies and was isolated from a surface water sample .

Gram-negative motile rod-shaped colony-forming aerobe 16S sequence

Name and taxonomic classification

SI-ID 272530

LMG 29559,KCTC 52236,BCRC 80979

@ref 20215

Last LPSN update 2025-12-16 10:08:05

Domain Pseudomonadati

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Hymenobacter

Species Hymenobacter rivuli

Full scientific name Hymenobacter rivuli Sheu et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement
65447	negative	1.7-3.6 µm	0.6-0.8 µm	rod-shaped	gliding
67771				rod-shaped	gliding
67771	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65447	1.5-2.5 mm	bright red	circular	2 days	Reasoner's 2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
65447	Reasoner's 2A agar

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
65447	positive	growth	20-35
65447	positive	optimum	25-30	mesophilic
67771	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
65447	positive	optimum	7
65447	positive	growth	6.5-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
65447	aerobe
67771	aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65447	NaCl	positive	growth	0-1 %
65447	NaCl	positive	optimum	0 %

Observation

@ref	Observation
65447	rods that were covered by large capsules
65447	the predominant respiratory quinone is MK-7
65447	the polar lipid profile consists of phosphatidylethanolamine, six uncharacterized aminophospholipids and four uncharacterized lipids
65447	homospermidine is the major polyamine
67771	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65447	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
65447	58143 ChEBI	5-dehydro-D-gluconate	+	builds acid from
65447	17128 ChEBI	adipate	+	assimilation
65447	17925 ChEBI	alpha-D-glucose	-	aerobic growth
65447	27613 ChEBI	amygdalin	-	builds acid from
65447	22599 ChEBI	arabinose	+	assimilation
65447	18305 ChEBI	arbutin	-	builds acid from
65447	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
65447		casein	+	hydrolysis
65447	17057 ChEBI	cellobiose	-	builds acid from
65447	17057 ChEBI	cellobiose	+	aerobic growth
65447	17029 ChEBI	chitin	-	hydrolysis
65447	17108 ChEBI	D-arabinose	-	builds acid from
65447	18333 ChEBI	D-arabitol	-	builds acid from
65447	15824 ChEBI	D-fructose	-	aerobic growth
65447	15824 ChEBI	D-fructose	+	builds acid from
65447	28847 ChEBI	D-fucose	-	builds acid from
65447	12936 ChEBI	D-galactose	-	aerobic growth
65447	12936 ChEBI	D-galactose	+	builds acid from
65447	17634 ChEBI	D-glucose	-	builds acid from
65447	62318 ChEBI	D-lyxose	-	builds acid from
65447	16899 ChEBI	D-mannitol	-	aerobic growth
65447	16899 ChEBI	D-mannitol	-	builds acid from
65447	16024 ChEBI	D-mannose	-	aerobic growth
65447	16024 ChEBI	D-mannose	+	builds acid from
65447	16988 ChEBI	D-ribose	-	builds acid from
65447	17924 ChEBI	D-sorbitol	-	aerobic growth
65447	17924 ChEBI	D-sorbitol	-	builds acid from
65447	16443 ChEBI	D-tagatose	-	builds acid from
65447	65327 ChEBI	D-xylose	+	builds acid from
65447	27689 ChEBI	decanoate	+	assimilation
65447	16991 ChEBI	dna	+	hydrolysis
65447	17113 ChEBI	erythritol	-	builds acid from
65447		esculin ferric citrate	-	hydrolysis
65447		esculin ferric citrate	+	builds acid from
65447	16813 ChEBI	galactitol	-	builds acid from
65447	495056 ChEBI	gamma-cyclodextrin	+	aerobic growth
65447	5291 ChEBI	gelatin	+	hydrolysis
65447	28066 ChEBI	gentiobiose	-	builds acid from
65447	24265 ChEBI	gluconate	-	builds acid from
65447	24265 ChEBI	gluconate	+	assimilation
65447	17234 ChEBI	glucose	+	assimilation
65447	17754 ChEBI	glycerol	-	builds acid from
65447	28087 ChEBI	glycogen	+	builds acid from
65447	15443 ChEBI	inulin	-	builds acid from
65447	30849 ChEBI	L-arabinose	+	builds acid from
65447		L-arabito	-	builds acid from
65447	18287 ChEBI	L-fucose	-	builds acid from
65447	62345 ChEBI	L-rhamnose	-	builds acid from
65447	62345 ChEBI	L-rhamnose	+	aerobic growth
65447	17266 ChEBI	L-sorbose	-	builds acid from
65447	65328 ChEBI	L-xylose	-	builds acid from
65447	17716 ChEBI	lactose	+	builds acid from
65447	61995 ChEBI	lecithin	-	hydrolysis
65447	25115 ChEBI	malate	+	assimilation
65447	17306 ChEBI	maltose	-	aerobic growth
65447	17306 ChEBI	maltose	-	builds acid from
65447	17306 ChEBI	maltose	+	assimilation
65447	29864 ChEBI	mannitol	+	assimilation
65447	37684 ChEBI	mannose	+	assimilation
65447	6731 ChEBI	melezitose	-	builds acid from
65447	28053 ChEBI	melibiose	+	builds acid from
65447	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
65447	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
65447	37657 ChEBI	methyl D-glucoside	-	builds acid from
65447	17268 ChEBI	myo-inositol	-	builds acid from
65447	506227 ChEBI	N-acetylglucosamine	-	builds acid from
65447	506227 ChEBI	N-acetylglucosamine	+	assimilation
65447	17632 ChEBI	nitrate	-	reduction
65447	18401 ChEBI	phenylacetate	+	assimilation
65447	16634 ChEBI	raffinose	-	aerobic growth
65447	16634 ChEBI	raffinose	-	builds acid from
65447	15963 ChEBI	ribitol	+	aerobic growth
65447	15963 ChEBI	ribitol	-	builds acid from
65447	17814 ChEBI	salicin	-	builds acid from
65447	53311 ChEBI	sodium alginate	-	hydrolysis
65447	53258 ChEBI	sodium citrate	+	assimilation
65447	28017 ChEBI	starch	+	builds acid from
65447	28017 ChEBI	starch	+	hydrolysis
65447	17992 ChEBI	sucrose	+	aerobic growth
65447	17992 ChEBI	sucrose	+	builds acid from
65447	27082 ChEBI	trehalose	-	aerobic growth
65447	27082 ChEBI	trehalose	-	builds acid from
65447	32528 ChEBI	turanose	-	builds acid from
65447	53424 ChEBI	tween 20	-	hydrolysis
65447	53424 ChEBI	tween 20	+	aerobic growth
65447	53423 ChEBI	tween 40	+	aerobic growth
65447	53423 ChEBI	tween 40	+	hydrolysis
65447	53425 ChEBI	tween 60	+	aerobic growth
65447	53425 ChEBI	tween 60	+	hydrolysis
65447	53426 ChEBI	tween 80	+	aerobic growth
65447	53426 ChEBI	tween 80	+	hydrolysis
65447	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65447	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65447	acid phosphatase	+	3.1.3.2
65447	alkaline phosphatase	+	3.1.3.1
65447	alpha-chymotrypsin	-	3.4.21.1
65447	alpha-fucosidase	-	3.2.1.51
65447	alpha-galactosidase	+	3.2.1.22
65447	alpha-glucosidase	+	3.2.1.20
65447	alpha-mannosidase	-	3.2.1.24
65447	arginine dihydrolase	-	3.5.3.6
65447	beta-galactosidase	+	3.2.1.23
65447	beta-glucosidase	-	3.2.1.21
65447	beta-glucuronidase	-	3.2.1.31
65447	catalase	+	1.11.1.6
65447	cystine arylamidase	+	3.4.11.3
65447	cytochrome oxidase	+	1.9.3.1
65447	esterase (C 4)	+
65447	esterase Lipase (C 8)	+
65447	leucine arylamidase	+	3.4.11.1
65447	lipase	-
65447	lipase (C 14)	+
65447	N-acetyl-beta-glucosaminidase	+	3.2.1.52
65447	naphthol-AS-BI-phosphohydrolase	+
65447	trypsin	-	3.4.21.4
65447	urease	-	3.5.1.5
65447	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

65447

Fatty acid	Percentage
C15:0 iso	33
C16:1ω7c and/or C16:1ω6c	22.6
C16:1ω5c	15.4
C15:0 anteiso	6.6
C16:0	3.4
C14:0	2.8
C16:0 3OH	2.4
C14:0 anteiso	2.2
C18:1ω9c	1.7
iso-C17:1 I and/or ante-iso-C17:1 B	1.7
C18:0	1.7
C15:0 iso 3OH	1.3
C17:0 iso	1.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
65447	a surface water sample (28 C, pH 7, 0 % NaCl)	Wanan Creek in the vicinity of Pingtung County	Taiwan, Province of China	TWN	Asia	R2A agar	3 days	25	collected and then was plated on R2A agar (BD Difco) by using the standard dilution plating method
67771	From freshwater, river	the Wanan Creek, the vicinity of Pingtung County	Taiwan, Province of China	TWN	Asia

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Database
65447	Hymenobacter sp. TAPP3 partial 16S rRNA gene, strain TAPP3	LT223127

GC content

@ref	GC-content (mol%)	Method
65447	62.8	high performance liquid chromatography (HPLC)
67771	62.8

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter rivuli sp. nov., isolated from a freshwater creek.	Sheu SY, Hsieh TY, Kwon SW, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.002657	2018

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 )
#65447	Shih-Yi Sheu, Tsai-Ying Hsieh, Soon-Wo Kwon, Wen-Ming Chen: Hymenobacter rivuli sp. nov., isolated from a freshwater creek. IJSEM 68: 1220 - 1226 2018 ( DOI 10.1099/ijsem.0.002657 , PubMed 29504928 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Hymenobacter rivuli (BCRC 80979, LMG 29559, KCTC 52236)

Name and taxonomic classification