Name: Hymenobacter aquaticus 16F3P
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133120

Type strain:

Species: Hymenobacter aquaticus

Strain Designation: 16F3P

Culture col. no.: KCTC 52194, JCM 31653

Strain history: <- Jung Hee-Young, Kyungpook National Univ.

NCBI tax ID(s): 1867101 (species)

Section

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

colony-forming
Gram-negative
rod-shaped
aerobe
psychrophilic
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	*Cytophagia*
	Order	*Cytophagales*
	Family	*Hymenobacteraceae*
	Genus	*Hymenobacter*
	Species	**Hymenobacter aquaticus**
	Full Scientific Name (LPSN)	Hymenobacter aquaticus Lee et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25296]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #25296]	Cell length	2.6-3.1 µm

[Ref.: #25296]	Cell width	1.0-1.2 µm

[Ref.: #25296]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #25296]	Motility	no
[Ref.: #67771]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.62

[Ref.: #25296]	Colony color	reddish-pink
[Ref.: #25296]	Colony shape	circular
[Ref.: #25296]	Incubation period	3 days
[Ref.: #25296]	Cultivation medium used	R2A

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25296]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #25296]

Culture medium growth

[Ref.: #25296]

Culture medium

Nutrient agar (NA)

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Culture medium growth

[Ref.: #25296]

Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

	Kind of temperature		Temperature
[Ref.: #25296]	no	growth	10 °C
[Ref.: #25296]		growth	30 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #67771]		growth	25 °C

[Ref.: #25296]	Temperature range	psychrophilic
[Ref.: #25296]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25296]		no	growth	5
[Ref.: #25296]		no	growth	10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25296]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #25296]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25296]		NaCl		growth	0.5	%
[Ref.: #25296]		NaCl	no	growth	3	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25296]	2-oxogluconate	-	assimilation
[Ref.: #25296]	2-oxogluconate	-	builds acid from
[Ref.: #25296]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #25296]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #25296]	4-hydroxybenzoate ChEBI	+	assimilation
[Ref.: #25296]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #25296]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #25296]	acetate ChEBI	-	assimilation
[Ref.: #25296]	adipate ChEBI	-	assimilation
[Ref.: #25296]	amygdalin ChEBI	-	builds acid from
[Ref.: #25296]	arbutin ChEBI	-	builds acid from
[Ref.: #25296]	butyrate ChEBI	-	assimilation
[Ref.: #25296]	cellobiose ChEBI	-	builds acid from
[Ref.: #25296]	citrate ChEBI	-	assimilation
[Ref.: #25296]	D-arabinose ChEBI	-	builds acid from
[Ref.: #25296]	D-arabitol ChEBI	-	builds acid from
[Ref.: #25296]	D-fructose ChEBI	+	builds acid from
[Ref.: #25296]	D-fucose ChEBI	-	builds acid from
[Ref.: #25296]	D-galactose ChEBI	-	builds acid from
[Ref.: #25296]	D-glucose ChEBI	-	assimilation
[Ref.: #25296]	D-lyxose ChEBI	-	builds acid from
[Ref.: #25296]	D-mannitol ChEBI	-	assimilation
[Ref.: #25296]	D-mannitol ChEBI	-	builds acid from
[Ref.: #25296]	D-mannose ChEBI	-	assimilation
[Ref.: #25296]	D-mannose ChEBI	-	builds acid from
[Ref.: #25296]	D-ribose ChEBI	-	assimilation
[Ref.: #25296]	D-ribose ChEBI	-	builds acid from
[Ref.: #25296]	D-sorbitol ChEBI	-	assimilation
[Ref.: #25296]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #25296]	D-tagatose ChEBI	-	builds acid from
[Ref.: #25296]	D-xylose ChEBI	+	builds acid from
[Ref.: #25296]	erythritol ChEBI	-	builds acid from
[Ref.: #25296]	esculin ChEBI	+/-	hydrolysis
[Ref.: #25296]	esculin ChEBI	+/-	builds acid from
[Ref.: #25296]	galactitol ChEBI	-	builds acid from
[Ref.: #25296]	gelatin ChEBI	+	hydrolysis
[Ref.: #25296]	gentiobiose ChEBI	+	builds acid from
[Ref.: #25296]	gluconate ChEBI	-	assimilation
[Ref.: #25296]	gluconate ChEBI	-	builds acid from
[Ref.: #25296]	glucose ChEBI	-	fermentation
[Ref.: #25296]	glycerol ChEBI	-	builds acid from
[Ref.: #25296]	glycogen ChEBI	+	assimilation
[Ref.: #25296]	glycogen ChEBI	+	builds acid from
[Ref.: #25296]	inulin ChEBI	+	builds acid from
[Ref.: #25296]	itaconate ChEBI	-	assimilation
[Ref.: #25296]	L-alanine ChEBI	-	assimilation
[Ref.: #25296]	L-arabinose ChEBI	-	assimilation
[Ref.: #25296]	L-arabinose ChEBI	+	builds acid from
[Ref.: #25296]	L-arabitol ChEBI	-	builds acid from
[Ref.: #25296]	L-fucose ChEBI	-	assimilation
[Ref.: #25296]	L-fucose ChEBI	-	builds acid from
[Ref.: #25296]	L-histidine ChEBI	-	assimilation
[Ref.: #25296]	L-malate ChEBI	-	assimilation
[Ref.: #25296]	L-proline ChEBI	-	assimilation
[Ref.: #25296]	L-rhamnose ChEBI	-	assimilation
[Ref.: #25296]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #25296]	L-serine ChEBI	-	assimilation
[Ref.: #25296]	L-xylose ChEBI	-	builds acid from
[Ref.: #25296]	lactate ChEBI	+	assimilation
[Ref.: #25296]	lactose ChEBI	-	builds acid from
[Ref.: #25296]	malonate ChEBI	-	assimilation
[Ref.: #25296]	maltose ChEBI	+	assimilation
[Ref.: #25296]	maltose ChEBI	+	builds acid from
[Ref.: #25296]	melezitose ChEBI	-	builds acid from
[Ref.: #25296]	melibiose ChEBI	-	assimilation
[Ref.: #25296]	melibiose ChEBI	-	builds acid from
[Ref.: #25296]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #25296]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #25296]	methyl beta-D-xylopyranoside ChEBI	+/-	builds acid from
[Ref.: #25296]	myo-inositol ChEBI	-	builds acid from
[Ref.: #25296]	myo-inositol ChEBI	-	assimilation
[Ref.: #25296]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25296]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #25296]	nitrate ChEBI	-	reduction
[Ref.: #25296]	phenylacetate ChEBI	-	assimilation
[Ref.: #25296]	propionate ChEBI	-	assimilation
[Ref.: #25296]	raffinose ChEBI	+	builds acid from
[Ref.: #25296]	ribitol ChEBI	-	builds acid from
[Ref.: #25296]	salicin ChEBI	-	assimilation
[Ref.: #25296]	salicin ChEBI	-	builds acid from
[Ref.: #25296]	suberic acid ChEBI	-	assimilation
[Ref.: #25296]	sucrose ChEBI	-	assimilation
[Ref.: #25296]	sucrose ChEBI	+	builds acid from
[Ref.: #25296]	trehalose ChEBI	+/-	builds acid from
[Ref.: #25296]	turanose ChEBI	-	builds acid from
[Ref.: #25296]	urea ChEBI	-	hydrolysis
[Ref.: #25296]	valerate ChEBI	-	assimilation
[Ref.: #25296]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25296]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #25296]	acid phosphatase	+/-	3.1.3.2
[Ref.: #25296]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25296]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25296]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25296]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25296]	alpha-glucosidase	-	3.2.1.20
[Ref.: #25296]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25296]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25296]	beta-galactosidase	-	3.2.1.23
[Ref.: #25296]	beta-glucosidase	-	3.2.1.21
[Ref.: #25296]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25296]	catalase	+	1.11.1.6
[Ref.: #25296]	cystine arylamidase	+/-	3.4.11.3
[Ref.: #25296]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25296]	esterase (C 4)	+/-
[Ref.: #25296]	esterase Lipase (C 8)	+/-
[Ref.: #25296]	leucine arylamidase	+	3.4.11.1
[Ref.: #25296]	lipase (C 14)	-
[Ref.: #25296]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25296]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #25296]	trypsin	-	3.4.21.4
[Ref.: #25296]	urease	-	3.5.1.5
[Ref.: #25296]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #25296]	Sample type/isolated from	water sample collected from the Han River
[Ref.: #25296]	Geographic location (country and/or sea, region)	Han River, South Korea
[Ref.: #25296]	Country	Republic of Korea
[Ref.: #25296]	Country ISO 3 Code	KOR
[Ref.: #25296]	Continent	Asia
[Ref.: #25296]	Geographic location	37.0000°/126.9350°

[Ref.: #67770]	Sample type/isolated from	Water from Han River
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From water
[Ref.: #67771]	Geographic location (country and/or sea, region)	Han River, Seoul
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	37.5278°/126.9350°
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#River (Creek)

What are isolation sources categories?

[Ref.: #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

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.: #25296]	16S rRNA gene sequences	KU758879	1466	ENA	1867101 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Hymenobacter aquaticus JCM 31653	GCA_004765605	contig	GenBank	1867101 tax ID
[Ref.: #66792]	Hymenobacter aquaticus strain JCM 31653	1867101.3	wgs	PATRIC	1867101 tax ID	*
[Ref.: #66792]	Hymenobacter aquaticus JCM 31653	2895852395	draft	JGI IMG/M	1867101 tax ID	*

[Ref.: #67771]	GC-content	61.9 mol%
[Ref.: #67770]	GC-content	61.9 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: Hymenobacter aquaticus strain JCM 31653 PATRIC: 1867101.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hymenobacter aquaticus strain JCM 31653 PATRIC: 1867101.3
[Ref.: #69480]	motile	no	93.818	no
[Ref.: #69480]	gram-positive	no	97.057	yes
[Ref.: #69480]	anaerobic	no	99.265	no
[Ref.: #69480]	aerobic	yes	92.572	yes
[Ref.: #69480]	halophile	no	94.261	no
[Ref.: #69480]	spore-forming	no	92.394	yes
[Ref.: #69480]	glucose-util	yes	66.98	yes
[Ref.: #69480]	flagellated	no	97.07	no
[Ref.: #69480]	thermophile	no	97.896	yes
[Ref.: #69480]	glucose-ferment	no	90.137	yes

Availability in culture collections External links

[Ref.: #25296]

Culture collection no.

KCTC 52194, JCM 31653

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 )

#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;
#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 .

#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 )

* These data were automatically processed and therefore are not curated

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Hymenobacter aquaticus strain JCM 31653

Hymenobacter aquaticus strain JCM 31653

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