Hymenobacter rufus (KCTC 52736, JCM 32196, S1-2-2-6)

Name: Hymenobacter rufus (KCTC 52736, JCM 32196, S1-2-2-6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159745

Type strain

Strain Designation S1-2-2-6

Culture col. no. KCTC 52736 JCM 32196 S1-2-2-6

NCBI tax ID(s) 2025508

Special Collections JCM KCTC Literature strains

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Hymenobacter rufus S1-2-2-6 is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from soil sample.

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

Name and taxonomic classification

SI-ID 25019

KCTC 52736,JCM 32196

@ref 20215

Last LPSN update 2025-12-16 10:08:20

Domain Pseudomonadati

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Hymenobacter

Species Hymenobacter rufus

Full scientific name Hymenobacter rufus Ohn et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
66663	negative	1.3-4.4 µm	0.8-1.7 µm	rod-shaped
67771				rod-shaped
67771	negative

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
66663	red to pink	circular	3 days	R2A medium

Culture and growth conditions

Culture medium

@ref	Name	Growth
66663	Nutrient agar (NA)
66663	Reasoner's 2A agar (R2A)
66663	LB (Luria-Bertani) agar
66663	tryptic soy agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
66663	negative	growth	1
66663	positive	optimum	25	mesophilic
66663	negative	growth	37
66663	positive	growth	4-30
67770	positive	growth	25	mesophilic
67771	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
66663	positive	optimum	7
66663	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
66663	aerobe
67771	aerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66663	NaCl	positive	growth	0-0.5 %

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66663	16193 ChEBI	3-hydroxybenzoate	-	assimilation
66663	37054 ChEBI	3-hydroxybutyrate	-	assimilation
66663	17879 ChEBI	4-hydroxybenzoate	+	assimilation
66663	17128 ChEBI	adipate	+	assimilation
66663	27613 ChEBI	amygdalin	+	builds acid from
66663	18305 ChEBI	arbutin	-	builds acid from
66663	17057 ChEBI	cellobiose	-	builds acid from
66663	17108 ChEBI	D-arabinose	-	builds acid from
66663	18333 ChEBI	D-arabitol	-	builds acid from
66663	15824 ChEBI	D-fructose	-	builds acid from
66663	28847 ChEBI	D-fucose	-	builds acid from
66663	12936 ChEBI	D-galactose	-	builds acid from
66663	17634 ChEBI	D-glucose	-	assimilation
66663	17634 ChEBI	D-glucose	-	builds acid from
66663	62318 ChEBI	D-lyxose	-	builds acid from
66663	16899 ChEBI	D-mannitol	-	assimilation
66663	16899 ChEBI	D-mannitol	-	builds acid from
66663	16024 ChEBI	D-mannose	-	assimilation
66663	16024 ChEBI	D-mannose	-	builds acid from
66663	16988 ChEBI	D-ribose	-	assimilation
66663	16988 ChEBI	D-ribose	-	builds acid from
66663	17924 ChEBI	D-sorbitol	-	assimilation
66663	17924 ChEBI	D-sorbitol	-	builds acid from
66663	16443 ChEBI	D-tagatose	-	builds acid from
66663	65327 ChEBI	D-xylose	+	builds acid from
66663	27689 ChEBI	decanoate	-	assimilation
66663	17113 ChEBI	erythritol	-	builds acid from
66663	4853 ChEBI	esculin	+	hydrolysis
66663		esculin ferric citrate	-	builds acid from
66663	16813 ChEBI	galactitol	-	builds acid from
66663	5291 ChEBI	gelatin	-	hydrolysis
66663	28066 ChEBI	gentiobiose	-	builds acid from
66663	17234 ChEBI	glucose	-	fermentation
66663	17754 ChEBI	glycerol	-	builds acid from
66663	28087 ChEBI	glycogen	+	assimilation
66663	28087 ChEBI	glycogen	+	builds acid from
66663	15443 ChEBI	inulin	-	builds acid from
66663	17240 ChEBI	itaconate	-	assimilation
66663	16977 ChEBI	L-alanine	-	assimilation
66663	30849 ChEBI	L-arabinose	-	assimilation
66663	30849 ChEBI	L-arabinose	-	builds acid from
66663	18403 ChEBI	L-arabitol	-	builds acid from
66663	18287 ChEBI	L-fucose	-	assimilation
66663	18287 ChEBI	L-fucose	-	builds acid from
66663	15971 ChEBI	L-histidine	-	assimilation
66663	17203 ChEBI	L-proline	-	assimilation
66663	62345 ChEBI	L-rhamnose	-	assimilation
66663	62345 ChEBI	L-rhamnose	-	builds acid from
66663	17115 ChEBI	L-serine	-	assimilation
66663	17266 ChEBI	L-sorbose	-	builds acid from
66663	65328 ChEBI	L-xylose	-	builds acid from
66663	24996 ChEBI	lactate	-	assimilation
66663	17716 ChEBI	lactose	-	builds acid from
66663	25115 ChEBI	malate	-	assimilation
66663	17306 ChEBI	maltose	-	assimilation
66663	17306 ChEBI	maltose	-	builds acid from
66663	6731 ChEBI	melezitose	-	builds acid from
66663	28053 ChEBI	melibiose	-	assimilation
66663	28053 ChEBI	melibiose	-	builds acid from
66663	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
66663	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
66663	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
66663	17268 ChEBI	myo-inositol	-	assimilation
66663	17268 ChEBI	myo-inositol	-	builds acid from
66663	59640 ChEBI	N-acetylglucosamine	-	assimilation
66663	59640 ChEBI	N-acetylglucosamine	-	builds acid from
66663	17632 ChEBI	nitrate	-	reduction
66663	18401 ChEBI	phenylacetate	-	assimilation
66663		potassium 2-dehydro-D-gluconate	-	assimilation
66663		potassium 2-dehydro-D-gluconate	-	builds acid from
66663		potassium 5-dehydro-D-gluconate	-	assimilation
66663		potassium 5-dehydro-D-gluconate	-	builds acid from
66663	32032 ChEBI	potassium gluconate	-	assimilation
66663	32032 ChEBI	potassium gluconate	-	builds acid from
66663	17272 ChEBI	propionate	-	assimilation
66663	16634 ChEBI	raffinose	+	builds acid from
66663	15963 ChEBI	ribitol	-	builds acid from
66663	17814 ChEBI	salicin	-	assimilation
66663	17814 ChEBI	salicin	-	builds acid from
66663	32954 ChEBI	sodium acetate	-	assimilation
66663	53258 ChEBI	sodium citrate	-	assimilation
66663	62983 ChEBI	sodium malonate	-	assimilation
66663	28017 ChEBI	starch	-	builds acid from
66663	9300 ChEBI	suberic acid	-	assimilation
66663	17992 ChEBI	sucrose	-	assimilation
66663	17992 ChEBI	sucrose	-	builds acid from
66663	27082 ChEBI	trehalose	-	builds acid from
66663	32528 ChEBI	turanose	-	builds acid from
66663	31011 ChEBI	valerate	-	assimilation
66663	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66663	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
66663	acid phosphatase	+	3.1.3.2
66663	alkaline phosphatase	+	3.1.3.1
66663	alpha-chymotrypsin	-	3.4.21.1
66663	alpha-fucosidase	-	3.2.1.51
66663	alpha-galactosidase	+	3.2.1.22
66663	alpha-glucosidase	+	3.2.1.20
66663	alpha-mannosidase	-	3.2.1.24
66663	arginine dihydrolase	-	3.5.3.6
66663	beta-galactosidase	+	3.2.1.23
66663	beta-glucosidase	-	3.2.1.21
66663	beta-glucuronidase	-	3.2.1.31
66663	catalase	+	1.11.1.6
66663	cystine arylamidase	+	3.4.11.3
66663	cytochrome oxidase	+	1.9.3.1
66663	esterase (C 4)	+
66663	esterase Lipase (C 8)	+
66663	leucine arylamidase	+	3.4.11.1
66663	lipase (C 14)	-
66663	N-acetyl-beta-glucosaminidase	-	3.2.1.52
66663	naphthol-AS-BI-phosphohydrolase	+
66663	trypsin	+	3.4.21.4
66663	urease	-	3.5.1.5
66663	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

66663

Fatty acid	Percentage
C15:0 iso	27.1
C15:0 anteiso	21.8
C16:1 w7c and/or C16:1 w6c and/or C15:1 iso 2OH,	19.5
C16:1 w5c	5.6
C17:1 anteiso B and/or C17:1 iso I	5.1
C15:1 iso G	3.1
C16:1 iso H	2.7
C16:0	2.7
C15:1 anteiso A	1.8
C17:0 2OH	1.5
C17:0 iso 3OH	1.4
C17:0 iso	1.3
C15:0 iso 3OH	1.3
C16:0 iso 3OH	1.2
C16:0 iso	1.1
C14:0 iso	1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
66663	soil sample	2017-01	Jeollabuk-do province	Republic of Korea	KOR	Asia	35.6845	127.432 35.6845/127.432	R2A agar	1 week	25	serial dilution technique
67770	Soil in Jeollabuk-do Province			Republic of Korea	KOR	Asia
67771	From soil		Baegam-ri, Baegun-myeon, Jinan-gun, Jeollabuk-do province	Republic of Korea	KOR	Asia	35.6846	127.432 35.6846/127.432

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66663	Hymenobacter rufus gene for 16S ribosomal RNA, partial sequence	LC315610	1425		2025508

GC content

@ref	GC-content (mol%)	Method
66663	60.7	high performance liquid chromatography (HPLC)
67771	60.7

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter terricola sp. nov., isolated from Antarctic soil.	Chen Y, Zhu L, Bai P, Cui S, Xin Y, Zhang Y, Zhang J	Int J Syst Evol Microbiol	10.1099/ijsem.0.005205	2022
Phylogeny	Hymenobacter rufus sp. nov., a bacterium isolated from soil.	Ohn JE, Ten LN, Kim BO, Cho YJ, Jung HY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002934	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 )
#66663	Jeong-Eun Ohn, Leonid N. Ten, Byung-Oh Kim, Young-Je Cho, Hee-Young Jung: Hymenobacter rufus sp. nov., a bacterium isolated from soil. IJSEM 68: 2983 - 2989 2018 ( DOI 10.1099/ijsem.0.002934 , PubMed 30028287 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 rufus (KCTC 52736, JCM 32196, S1-2-2-6)

Name and taxonomic classification