Hymenobacter baengnokdamensis (KCTC 72649, JCM 33837, BRD72)

Name: Hymenobacter baengnokdamensis (KCTC 72649, JCM 33837, BRD72)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164676

Type strain

Strain Designation BRD72

Culture col. no. KCTC 72649 JCM 33837 BRD72

NCBI tax ID(s) 2615203

Special Collections JCM KCTC Literature strains

History S. Lim; Korea Atomic Energy Res. Inst., South Korea; BRD72.

Links

Hymenobacter baengnokdamensis BRD72 is a Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Soil from a crater lake at the top of Mt. Hallasan in the Republic of Korea.

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

Name and taxonomic classification

SI-ID 25153

KCTC 72649,JCM 33837

@ref 20215

Last LPSN update 2026-02-09 11:39:55

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Hymenobacter

Species Hymenobacter baengnokdamensis

Full scientific name Hymenobacter baengnokdamensis Lee et al. 2021

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
68320	negative	2.9-5.3 µm	1-1.2 µm	rod-shaped
125438	negative					96.844

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
68320	1-2 mm	pink	circular	5 days	Reasoner's 2A agar (R2A)

Pigmentation

@ref	Production	Name
68320		carotenoid pigment
68320		flexirubin type pigments

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
67770	positive	growth	25
68320	positive	growth	10-30
68320	positive	optimum	25-30

Culture pH

@ref	Ability	Type	PH
68320	positive	optimum	7-8
68320	positive	growth	6-8

Physiology and metabolism

Spore formation

68320

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68320	NaCl	positive	growth	0-0.5 %(w/v)
68320	NaCl	positive	optimum	0 %(w/v)

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68320	27613 ChEBI	amygdalin	-	builds acid from
68320	18305 ChEBI	arbutin	-	builds acid from
68320	29016 ChEBI	arginine	-	hydrolysis
68320	85146 ChEBI	carboxymethylcellulose	+	hydrolysis
68320		casein	-	hydrolysis
68320	17057 ChEBI	cellobiose	-	builds acid from
68320	17108 ChEBI	D-arabinose	-	builds acid from
68320	18333 ChEBI	D-arabitol	-	builds acid from
68320	15824 ChEBI	D-fructose	-	builds acid from
68320	28847 ChEBI	D-fucose	-	builds acid from
68320	12936 ChEBI	D-galactose	-	builds acid from
68320	17634 ChEBI	D-glucose	-	builds acid from
68320	62318 ChEBI	D-lyxose	-	builds acid from
68320	16899 ChEBI	D-mannitol	-	builds acid from
68320	16024 ChEBI	D-mannose	-	builds acid from
68320	16988 ChEBI	D-ribose	-	builds acid from
68320	17924 ChEBI	D-sorbitol	-	builds acid from
68320	16443 ChEBI	D-tagatose	-	builds acid from
68320	65327 ChEBI	D-xylose	-	builds acid from
68320	17113 ChEBI	erythritol	-	builds acid from
68320	4853 ChEBI	esculin	+	hydrolysis
68320		esculin ferric citrate	+	builds acid from
68320	16813 ChEBI	galactitol	-	builds acid from
68320	5291 ChEBI	gelatin	-	hydrolysis
68320	28066 ChEBI	gentiobiose	-	builds acid from
68320	17754 ChEBI	glycerol	-	builds acid from
68320	28087 ChEBI	glycogen	-	builds acid from
68320	15443 ChEBI	inulin	-	builds acid from
68320	30849 ChEBI	L-arabinose	-	builds acid from
68320	18403 ChEBI	L-arabitol	-	builds acid from
68320	18287 ChEBI	L-fucose	-	builds acid from
68320	62345 ChEBI	L-rhamnose	-	builds acid from
68320	17266 ChEBI	L-sorbose	-	builds acid from
68320	17895 ChEBI	L-tyrosine	-	hydrolysis
68320	65328 ChEBI	L-xylose	-	builds acid from
68320	17716 ChEBI	lactose	-	builds acid from
68320	61995 ChEBI	lecithin	-	hydrolysis
68320	17306 ChEBI	maltose	-	builds acid from
68320	6731 ChEBI	melezitose	-	builds acid from
68320	28053 ChEBI	melibiose	-	builds acid from
68320	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
68320	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
68320	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
68320	17268 ChEBI	myo-inositol	-	builds acid from
68320	59640 ChEBI	N-acetylglucosamine	-	builds acid from
68320	17632 ChEBI	nitrate	-	reduction
68320		potassium 2-dehydro-D-gluconate	-	builds acid from
68320		potassium 5-dehydro-D-gluconate	-	builds acid from
68320	32032 ChEBI	potassium gluconate	-	builds acid from
68320	16634 ChEBI	raffinose	-	builds acid from
68320	15963 ChEBI	ribitol	-	builds acid from
68320	17814 ChEBI	salicin	-	builds acid from
68320	28017 ChEBI	starch	-	hydrolysis
68320	28017 ChEBI	starch	-	builds acid from
68320	17992 ChEBI	sucrose	-	builds acid from
68320	27082 ChEBI	trehalose	-	builds acid from
68320	32528 ChEBI	turanose	-	builds acid from
68320	53424 ChEBI	tween 20	-	hydrolysis
68320	53426 ChEBI	tween 80	+	hydrolysis
68320	16199 ChEBI	urea	-	hydrolysis
68320	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68320	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68320	acid phosphatase	+	3.1.3.2
68320	alkaline phosphatase	+	3.1.3.1
68320	alpha-galactosidase	+	3.2.1.22
68320	alpha-glucosidase	+/-	3.2.1.20
68320	beta-galactosidase	+/-	3.2.1.23
68320	beta-glucosidase	+	3.2.1.21
68320	catalase	+	1.11.1.6
68320	cystine arylamidase	+	3.4.11.3
68320	cytochrome oxidase	-	1.9.3.1
68320	esterase (C 4)	+
68320	esterase Lipase (C 8)	+/-
68320	leucine arylamidase	+	3.4.11.1
68320	N-acetyl-beta-glucosaminidase	+	3.2.1.52
68320	naphthol-AS-BI-phosphohydrolase	+
68320	trypsin	+	3.4.21.4
68320	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

68320

Fatty acid	Percentage
C16:1 w7c/C16:1 w6c	21.6
C15:0 iso	17.9
C15:0 anteiso	13.3
C17:1 iso I / C17:1 anteiso B	11.3
C16:1 w5c	6.9
C16:1 iso H	3.2
C16:0 iso 3OH	3
C14:0 iso	2.7
C15:0 iso 3OH	2.6
C17:0 iso	2.5
C16:0	2.2
C17:1 w6c	2
C16:0 iso	1.7
C17:0 iso 3OH	1.3
C15:0 iso H / C13:0	1.1

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
67770	Soil from a crater lake (Baengnokdam) at the top of Mt. Hallasan in the Republic of Korea
68320	soil	2002-01-01	Baengnokdam, Mt. Hallasan	Republic of Korea	KOR	Asia	33.3622	126.533 33.3622/126.533	R2A agar	7 days	30

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM872863v1 assembly for Hymenobacter baengnokdamensis BRD72	complete	GCA_008728635	2615203.3	3003075576	2615203	92.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
68320	Hymenobacter baengnokdamensis strain BRD72 16S ribosomal RNA gene, partial sequence	MK752551	1458		2615203

GC content

@ref	GC-content (mol%)	Method
68320	59.8	genome sequence analysis

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hymenobacter baengnokdamensis BRD72
NCBI: GCA_008728635.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.84	no
125438	anaerobic	anaerobicⓘ	no	97.69	no
125438	aerobic	aerobicⓘ	yes	88.56	no
125438	spore-forming	spore-formingⓘ	no	88.92	yes
125438	thermophilic	thermophileⓘ	no	93.97	no
125438	flagellated	motile2+ⓘ	no	84.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter baengnokdamensis sp. nov., Isolated from the Soil of a Crater Lake in Korea.	Lee JH, Kim MK, Jung JH, Seo HS, Zhang J, Choe HN, Choi S, Seong CN, Lim S	Curr Microbiol	10.1007/s00284-020-02225-7	2020

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 )
#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;
#68320	Ji Hee Lee, Min-Kyu Kim, Jong-Hyun Jung, Ho Seong Seo, Jing Zhang, Han Na Choe, Seon Choi, Chi Nam Seong & Sangyong Lim: Hymenobacter baengnokdamensis sp. nov., Isolated from the Soil of a Crater Lake in Korea. Curr Microbiol 77: 4167 - 4173 2020 ( DOI 10.1007/s00284-020-02225-7 )
#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 )
#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 baengnokdamensis (KCTC 72649, JCM 33837, BRD72)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_008728635

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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