Hymenobacter aquaticus (KCTC 52194, JCM 31653, 16F3P)

Name: Hymenobacter aquaticus (KCTC 52194, JCM 31653, 16F3P)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133120

Type strain

Strain Designation 16F3P

Culture col. no. KCTC 52194 JCM 31653 16F3P

NCBI tax ID(s) 1867101

Special Collections JCM KCTC Literature strains

Links

Hymenobacter aquaticus 16F3P is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from water sample collected from the Han River.

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

Name and taxonomic classification

SI-ID 288146

KCTC 52194,JCM 31653

@ref 20215

Last LPSN update 2025-12-16 10:01:41

Domain Pseudomonadati

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Hymenobacter

Species Hymenobacter aquaticus

Full scientific name Hymenobacter aquaticus Lee et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
25296	negative	2.6-3.1 µm	1.0-1.2 µm	rod-shaped
67771				rod-shaped
67771	negative
125438	negative				96.482
125439	negative				94.6

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
25296	reddish-pink	circular	3 days	R2A

Culture and growth conditions

Culture medium

@ref	Name	Growth
25296	Reasoner's 2A agar (R2A)
25296	Nutrient agar (NA)
25296	Trypticase Soy Agar (TSA)
25296	LB (Luria-Bertani) MEDIUM

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
25296	negative	growth	10
25296	positive	growth	30	mesophilic
67770	positive	growth	25	mesophilic
67771	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
25296		growth	5
25296		growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
25296	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
25296
125439		96.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25296	NaCl	positive	growth	0.5 %
25296	NaCl		growth	3 %

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25296		2-oxogluconate	-	assimilation
25296		2-oxogluconate	-	builds acid from
25296	16193 ChEBI	3-hydroxybenzoate	-	assimilation
25296	37054 ChEBI	3-hydroxybutyrate	-	assimilation
25296	17879 ChEBI	4-hydroxybenzoate	+	assimilation
25296	58143 ChEBI	5-dehydro-D-gluconate	-	assimilation
25296	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
25296	30089 ChEBI	acetate	-	assimilation
25296	17128 ChEBI	adipate	-	assimilation
25296	27613 ChEBI	amygdalin	-	builds acid from
25296	18305 ChEBI	arbutin	-	builds acid from
25296	17968 ChEBI	butyrate	-	assimilation
25296	17057 ChEBI	cellobiose	-	builds acid from
25296	16947 ChEBI	citrate	-	assimilation
25296	17108 ChEBI	D-arabinose	-	builds acid from
25296	18333 ChEBI	D-arabitol	-	builds acid from
25296	15824 ChEBI	D-fructose	+	builds acid from
25296	28847 ChEBI	D-fucose	-	builds acid from
25296	12936 ChEBI	D-galactose	-	builds acid from
25296	17634 ChEBI	D-glucose	-	assimilation
25296	62318 ChEBI	D-lyxose	-	builds acid from
25296	16899 ChEBI	D-mannitol	-	assimilation
25296	16899 ChEBI	D-mannitol	-	builds acid from
25296	16024 ChEBI	D-mannose	-	assimilation
25296	16024 ChEBI	D-mannose	-	builds acid from
25296	16988 ChEBI	D-ribose	-	assimilation
25296	16988 ChEBI	D-ribose	-	builds acid from
25296	17924 ChEBI	D-sorbitol	-	assimilation
25296	17924 ChEBI	D-sorbitol	-	builds acid from
25296	16443 ChEBI	D-tagatose	-	builds acid from
25296	65327 ChEBI	D-xylose	+	builds acid from
25296	17113 ChEBI	erythritol	-	builds acid from
25296	4853 ChEBI	esculin	+/-	hydrolysis
25296	4853 ChEBI	esculin	+/-	builds acid from
25296	16813 ChEBI	galactitol	-	builds acid from
25296	5291 ChEBI	gelatin	+	hydrolysis
25296	28066 ChEBI	gentiobiose	+	builds acid from
25296	24265 ChEBI	gluconate	-	assimilation
25296	24265 ChEBI	gluconate	-	builds acid from
25296	17234 ChEBI	glucose	-	fermentation
25296	17754 ChEBI	glycerol	-	builds acid from
25296	28087 ChEBI	glycogen	+	assimilation
25296	28087 ChEBI	glycogen	+	builds acid from
25296	15443 ChEBI	inulin	+	builds acid from
25296	17240 ChEBI	itaconate	-	assimilation
25296	16977 ChEBI	L-alanine	-	assimilation
25296	30849 ChEBI	L-arabinose	-	assimilation
25296	30849 ChEBI	L-arabinose	+	builds acid from
25296	18403 ChEBI	L-arabitol	-	builds acid from
25296	18287 ChEBI	L-fucose	-	assimilation
25296	18287 ChEBI	L-fucose	-	builds acid from
25296	15971 ChEBI	L-histidine	-	assimilation
25296	15589 ChEBI	L-malate	-	assimilation
25296	17203 ChEBI	L-proline	-	assimilation
25296	62345 ChEBI	L-rhamnose	-	assimilation
25296	62345 ChEBI	L-rhamnose	-	builds acid from
25296	17115 ChEBI	L-serine	-	assimilation
25296	65328 ChEBI	L-xylose	-	builds acid from
25296	24996 ChEBI	lactate	+	assimilation
25296	17716 ChEBI	lactose	-	builds acid from
25296	15792 ChEBI	malonate	-	assimilation
25296	17306 ChEBI	maltose	+	assimilation
25296	17306 ChEBI	maltose	+	builds acid from
25296	6731 ChEBI	melezitose	-	builds acid from
25296	28053 ChEBI	melibiose	-	assimilation
25296	28053 ChEBI	melibiose	-	builds acid from
25296	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
25296	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
25296	74863 ChEBI	methyl beta-D-xylopyranoside	+/-	builds acid from
25296	17268 ChEBI	myo-inositol	-	builds acid from
25296	17268 ChEBI	myo-inositol	-	assimilation
25296	506227 ChEBI	N-acetylglucosamine	-	assimilation
25296	506227 ChEBI	N-acetylglucosamine	-	builds acid from
25296	17632 ChEBI	nitrate	-	reduction
25296	18401 ChEBI	phenylacetate	-	assimilation
25296	17272 ChEBI	propionate	-	assimilation
25296	16634 ChEBI	raffinose	+	builds acid from
25296	15963 ChEBI	ribitol	-	builds acid from
25296	17814 ChEBI	salicin	-	assimilation
25296	17814 ChEBI	salicin	-	builds acid from
25296	9300 ChEBI	suberic acid	-	assimilation
25296	17992 ChEBI	sucrose	-	assimilation
25296	17992 ChEBI	sucrose	+	builds acid from
25296	27082 ChEBI	trehalose	+/-	builds acid from
25296	32528 ChEBI	turanose	-	builds acid from
25296	16199 ChEBI	urea	-	hydrolysis
25296	31011 ChEBI	valerate	-	assimilation
25296	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25296	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
25296	acid phosphatase	+/-	3.1.3.2
25296	alkaline phosphatase	+	3.1.3.1
25296	alpha-chymotrypsin	-	3.4.21.1
25296	alpha-fucosidase	-	3.2.1.51
25296	alpha-galactosidase	-	3.2.1.22
25296	alpha-glucosidase	-	3.2.1.20
25296	alpha-mannosidase	-	3.2.1.24
25296	arginine dihydrolase	-	3.5.3.6
25296	beta-galactosidase	-	3.2.1.23
25296	beta-glucosidase	-	3.2.1.21
25296	beta-glucuronidase	-	3.2.1.31
25296	catalase	+	1.11.1.6
25296	cystine arylamidase	+/-	3.4.11.3
25296	cytochrome oxidase	+	1.9.3.1
25296	esterase (C 4)	+/-
25296	esterase Lipase (C 8)	+/-
25296	leucine arylamidase	+	3.4.11.1
25296	lipase (C 14)	-
25296	N-acetyl-beta-glucosaminidase	-	3.2.1.52
25296	naphthol-AS-BI-phosphohydrolase	+/-
25296	trypsin	-	3.4.21.4
25296	urease	-	3.5.1.5
25296	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

25296

Fatty acid	Percentage
C16:0	19.8
C16:1ω7c / C16:1ω6c	15.4
C15:0 iso	13
C18:0	12.5
C16:1ω5c	10.7
C17:1 iso I /C17:1 anteiso B	6.9
C15:0 anteiso	6.3
C17:0 iso 3OH	3
C15:1 iso G	2.5
C15:0 iso 3OH	1.9
C14:0	1.5
C18:1ω9c	1.1
C16:0 3OH	1
C16:1 iso I / C14:0 3OH	1

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
25296	water sample collected from the Han River	Han River, South Korea	Republic of Korea	KOR	Asia	37	126.935 37/126.935
67770	Water from Han River		Republic of Korea	KOR	Asia
67771	From water	Han River, Seoul	Republic of Korea	KOR	Asia	37.5278	126.935 37.5278/126.935

Taxonmaps

69479

Global distribution of 16S sequence KU758879 (>99% sequence identity) for Hymenobacter aquaticus from Microbeatlas

Aquatic Samples	11
Soil Samples	13
Animal Samples	20
Plant Samples
Total Samples	44

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM476560v1 assembly for Hymenobacter aquaticus JCM 31653	contig	GCA_004765605	1867101.3	2895852395	1867101	76.06

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25296	Hymenobacter aquaticus strain 16F3P 16S ribosomal RNA gene, partial sequence	KU758879	1466		1867101

GC content

@ref	GC-content (mol%)	Method
67771	61.9
67770	61.9	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: Hymenobacter aquaticus JCM 31653
NCBI: GCA_004765605

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.30	no
125439	motility	BacteriaNetⓘ	yes	77.70	no
125439	gram_stain	BacteriaNetⓘ	negative	94.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	68.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hymenobacter aquaticus strain JCM 31653
PATRIC: 1867101.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.48	yes
125438	anaerobic	anaerobicⓘ	no	96.91	yes
125438	spore-forming	spore-formingⓘ	no	83.93	yes
125438	aerobic	aerobicⓘ	yes	83.85	yes
125438	thermophilic	thermophileⓘ	no	93.67	yes
125438	flagellated	motile2+ⓘ	no	86.18	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter telluris sp. nov., isolated from soil in South Korea.	Damdintogtokh T, Park Y, Maeng S, Oh HJ, Bang M, Lee YK, Oh J, Bai J, Kim MK	Arch Microbiol	10.1007/s00203-021-02692-x	2022
Phylogeny	Hymenobacter fodinae sp. nov. and Hymenobacter metallicola sp. nov., isolated from abandoned lead-zinc mine.	Feng GD, Zhang J, Chen W, Wang SN, Zhu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004313	2020
Phylogeny	Hymenobacter persicinus sp. nov., a novel member of the family Hymenobacteraceae.	Ten LN, Jeon NY, Li W, Kim MK, Cho YJ, Jung HY	Antonie Van Leeuwenhoek	10.1007/s10482-019-01236-0	2019
Phylogeny	Hymenobacter aquaticus sp. nov., a radiation-resistant bacterium isolated from a river.	Lee JJ, Park SJ, Lee YH, Lee SY, Ten LN, Jung HY	Int J Syst Evol Microbiol	10.1099/ijsem.0.001788	2017

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 )
#25296	J. J. P. Lee, S. J.,Lee, Y. H.,Lee, S. Y.,Ten, L. N.,Jung, H. Y.: Hymenobacter aquaticus sp. nov., a radiation-resistant bacterium isolated from a river. IJSEM 67: 1206 - 1211 2017 ( DOI 10.1099/ijsem.0.001788 , PubMed 28086076 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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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Hymenobacter aquaticus (KCTC 52194, JCM 31653, 16F3P)

Name and taxonomic classification