Name: Hymenobacter baengnokdamensis BRD72
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 164676

Type strain:

Species: Hymenobacter baengnokdamensis

Strain Designation: BRD72

Culture col. no.: JCM 33837, KCTC 72649

Strain history: S. Lim; Korea Atomic Energy Res. Inst., South Korea; BRD72.

NCBI tax ID(s): 2615203 (species)

Section

Hymenobacter baengnokdamensis BRD72 is a mesophilic, 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.

colony-forming
Gram-negative
rod-shaped
mesophilic
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 baengnokdamensis**
	Full Scientific Name (LPSN)	Hymenobacter baengnokdamensis Lee et al. 2021

Information on morphological and physiological properties Morphology

[Ref.: #68320]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #68320]	Cell length	2.9-5.3 µm

[Ref.: #68320]	Cell width	1-1.2 µm

[Ref.: #68320]	Cell shape	rod-shaped

[Ref.: #68320]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.398

[Ref.: #68320]	Colony size	1-2 mm
[Ref.: #68320]	Colony color	pink
[Ref.: #68320]	Colony shape	circular
[Ref.: #68320]	Incubation period	5 days
[Ref.: #68320]	Cultivation medium used	Reasoner's 2A agar (R2A)

[Ref.: #68320]	Pigment production	yes
[Ref.: #68320]	Pigment name	Carotenoid pigment
[Ref.: #68320]	Pigment production	no
[Ref.: #68320]	Pigment name	Flexirubin type pigments

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #67770]	growth	25 °C
[Ref.: #68320]	growth	10-30 °C
[Ref.: #68320]	optimum	25-30 °C

[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #68320]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #68320]			optimum	7-8
[Ref.: #68320]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #68320]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.988
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #68320]		NaCl		growth	0-0.5	%(w/v)
[Ref.: #68320]		NaCl		optimum	0	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68320]	amygdalin ChEBI	-	builds acid from
[Ref.: #68320]	arbutin ChEBI	-	builds acid from
[Ref.: #68320]	arginine ChEBI	-	hydrolysis
[Ref.: #68320]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #68320]	casein	-	hydrolysis
[Ref.: #68320]	cellobiose ChEBI	-	builds acid from
[Ref.: #68320]	D-arabinose ChEBI	-	builds acid from
[Ref.: #68320]	D-arabitol ChEBI	-	builds acid from
[Ref.: #68320]	D-fructose ChEBI	-	builds acid from
[Ref.: #68320]	D-fucose ChEBI	-	builds acid from
[Ref.: #68320]	D-galactose ChEBI	-	builds acid from
[Ref.: #68320]	D-glucose ChEBI	-	builds acid from
[Ref.: #68320]	D-lyxose ChEBI	-	builds acid from
[Ref.: #68320]	D-mannitol ChEBI	-	builds acid from
[Ref.: #68320]	D-mannose ChEBI	-	builds acid from
[Ref.: #68320]	D-ribose ChEBI	-	builds acid from
[Ref.: #68320]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #68320]	D-tagatose ChEBI	-	builds acid from
[Ref.: #68320]	D-xylose ChEBI	-	builds acid from
[Ref.: #68320]	erythritol ChEBI	-	builds acid from
[Ref.: #68320]	esculin ChEBI	+	hydrolysis
[Ref.: #68320]	esculin ferric citrate	+	builds acid from
[Ref.: #68320]	galactitol ChEBI	-	builds acid from
[Ref.: #68320]	gelatin ChEBI	-	hydrolysis
[Ref.: #68320]	gentiobiose ChEBI	-	builds acid from
[Ref.: #68320]	glycerol ChEBI	-	builds acid from
[Ref.: #68320]	glycogen ChEBI	-	builds acid from
[Ref.: #68320]	inulin ChEBI	-	builds acid from
[Ref.: #68320]	L-arabinose ChEBI	-	builds acid from
[Ref.: #68320]	L-arabitol ChEBI	-	builds acid from
[Ref.: #68320]	L-fucose ChEBI	-	builds acid from
[Ref.: #68320]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #68320]	L-sorbose ChEBI	-	builds acid from
[Ref.: #68320]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #68320]	L-xylose ChEBI	-	builds acid from
[Ref.: #68320]	lactose ChEBI	-	builds acid from
[Ref.: #68320]	lecithin ChEBI	-	hydrolysis
[Ref.: #68320]	maltose ChEBI	-	builds acid from
[Ref.: #68320]	melezitose ChEBI	-	builds acid from
[Ref.: #68320]	melibiose ChEBI	-	builds acid from
[Ref.: #68320]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #68320]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #68320]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #68320]	myo-inositol ChEBI	-	builds acid from
[Ref.: #68320]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #68320]	nitrate ChEBI	-	reduction
[Ref.: #68320]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #68320]	potassium 5-dehydro-D-gluconate	-	builds acid from
[Ref.: #68320]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #68320]	raffinose ChEBI	-	builds acid from
[Ref.: #68320]	ribitol ChEBI	-	builds acid from
[Ref.: #68320]	salicin ChEBI	-	builds acid from
[Ref.: #68320]	starch ChEBI	-	hydrolysis
[Ref.: #68320]	starch ChEBI	-	builds acid from
[Ref.: #68320]	sucrose ChEBI	-	builds acid from
[Ref.: #68320]	trehalose ChEBI	-	builds acid from
[Ref.: #68320]	turanose ChEBI	-	builds acid from
[Ref.: #68320]	tween 20 ChEBI	-	hydrolysis
[Ref.: #68320]	tween 80 ChEBI	+	hydrolysis
[Ref.: #68320]	urea ChEBI	-	hydrolysis
[Ref.: #68320]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68320]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68320]	acid phosphatase	+	3.1.3.2
[Ref.: #68320]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68320]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68320]	alpha-glucosidase	+/-	3.2.1.20
[Ref.: #68320]	beta-galactosidase	+/-	3.2.1.23
[Ref.: #68320]	beta-glucosidase	+	3.2.1.21
[Ref.: #68320]	catalase	+	1.11.1.6
[Ref.: #68320]	cystine arylamidase	+	3.4.11.3
[Ref.: #68320]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68320]	esterase (C 4)	+
[Ref.: #68320]	esterase Lipase (C 8)	+/-
[Ref.: #68320]	leucine arylamidase	+	3.4.11.1
[Ref.: #68320]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #68320]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68320]	trypsin	+	3.4.21.4
[Ref.: #68320]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #67770]	Sample type/isolated from	Soil from a crater lake (Baengnokdam) at the top of Mt. Hallasan in the Republic of Korea

[Ref.: #68320]	Sample type/isolated from	soil
[Ref.: #68320]	Sampling date	2002-01-01
[Ref.: #68320]	Geographic location (country and/or sea, region)	Baengnokdam, Mt. Hallasan
[Ref.: #68320]	Country	Republic of Korea
[Ref.: #68320]	Country ISO 3 Code	KOR
[Ref.: #68320]	Continent	Asia
[Ref.: #68320]	Geographic location	33.3622°/126.5330°
[Ref.: #68320]	Enrichment culture	R2A agar
[Ref.: #68320]	Enrichment culture duration	7 days
[Ref.: #68320]	Enrichment culture temperature	30 ̊C
* marker position based on {}

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.: #68320]	Hymenobacter sp. strain BRD72 16S ribosomal RNA gene, partial sequence	MK752551	1458	ENA	2615203 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Hymenobacter baengnokdamensis BRD72	GCA_008728635	complete	GenBank	2615203 tax ID	*

[Ref.: #68320]

GC-content

59.8 mol%

genome sequence analysis

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 baengnokdamensis BRD72 NCBI: GCA_008728635.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hymenobacter baengnokdamensis BRD72 NCBI: GCA_008728635.1
[Ref.: #69480]	motile	no	94.533	yes
[Ref.: #69480]	flagellated	no	97.258	yes
[Ref.: #69480]	gram-positive	no	97.481	no
[Ref.: #69480]	anaerobic	no	99.241	no
[Ref.: #69480]	aerobic	yes	93.118	no
[Ref.: #69480]	halophile	no	91.382	yes
[Ref.: #69480]	spore-forming	no	94.344	yes
[Ref.: #69480]	thermophile	no	96.413	yes
[Ref.: #69480]	glucose-util	yes	83.893	no
[Ref.: #69480]	glucose-ferment	no	91.455	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 33837, KCTC 72649

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 )

#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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