Name: Hymenobacter rutilus K2-33028
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133390

Type strain:

Species: Hymenobacter rutilus

Strain Designation: K2-33028

Culture col. no.: CCTCC AB 2016091, KCTC 52447

Strain history: <- Myong Chol Kim and Fang Peng, Wuhan Univ.

NCBI tax ID(s): 1867850 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Hymenobacter rutilus K2-33028 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from marine sediment sample.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Hymenobacteraceae*
	Genus	*Hymenobacter*
	Species	**Hymenobacter rutilus**
	Full Scientific Name (LPSN)	Hymenobacter rutilus Kim et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25273]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #25273]	Cell length	1.6-2.4 µm

[Ref.: #25273]	Cell width	0.8-1.0 µm

[Ref.: #25273]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #25273]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #25273]	Colony size	2.0-3.0 mm
[Ref.: #25273]	Colony color	brick-red
[Ref.: #25273]	Colony shape	circular
[Ref.: #25273]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

0.1 x TSB agar

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Culture medium growth

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Culture medium

TSB agar

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Culture medium growth

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Culture medium

PYES agar

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Culture medium growth

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Culture medium

Czapek’s-Dox agar

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Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

		Temperature
[Ref.: #25273]	growth	4-37 °C
[Ref.: #25273]	optimum	28 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #25273]			optimum	7
[Ref.: #25273]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25273]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #25273]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25273]		NaCl	maximum	0	%(w/v)

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Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25273]	2-oxopentanoate ChEBI	+	respiration
[Ref.: #25273]	adipate ChEBI	-	carbon source
[Ref.: #25273]	casein	+	hydrolysis
[Ref.: #25273]	D-glucarate ChEBI	+	respiration
[Ref.: #25273]	D-glucose ChEBI	-	carbon source
[Ref.: #25273]	D-mannitol ChEBI	-	carbon source
[Ref.: #25273]	D-mannose ChEBI	-	carbon source
[Ref.: #25273]	decanoate ChEBI	-	carbon source
[Ref.: #25273]	esculin ChEBI	+	hydrolysis
[Ref.: #25273]	gelatin ChEBI	+	hydrolysis
[Ref.: #25273]	glycerol ChEBI	+	respiration
[Ref.: #25273]	glycyl L-aspartic acid ChEBI	+	respiration
[Ref.: #25273]	inosine ChEBI	+	respiration
[Ref.: #25273]	L-arabinose ChEBI	-	carbon source
[Ref.: #25273]	L-arabinose ChEBI	+	respiration
[Ref.: #25273]	L-fucose ChEBI	+	respiration
[Ref.: #25273]	L-glutamate ChEBI	+	respiration
[Ref.: #25273]	L-serine ChEBI	+	respiration
[Ref.: #25273]	malate ChEBI	-	carbon source
[Ref.: #25273]	maltose ChEBI	-	carbon source
[Ref.: #25273]	methyl pyruvate ChEBI	+	respiration
[Ref.: #25273]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #25273]	nitrate ChEBI	-	reduction
[Ref.: #25273]	phenylacetate ChEBI	-	carbon source
[Ref.: #25273]	potassium gluconate ChEBI	-	carbon source
[Ref.: #25273]	sodium citrate ChEBI	-	carbon source
[Ref.: #25273]	thymidine ChEBI	+	respiration
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #25273]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #25273]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #25273]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #25273]	penicillin g ChEBI	yes	10	Unit (disc)
[Ref.: #25273]	polymyxin b ChEBI				yes	300	Unit (disc)
[Ref.: #25273]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #25273]	vancomycin ChEBI	yes	30	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #25273]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #25273]	acid phosphatase	+	3.1.3.2
[Ref.: #25273]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25273]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #25273]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25273]	alpha-glucosidase	-	3.2.1.20
[Ref.: #25273]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25273]	beta-fucosidase	-
[Ref.: #25273]	beta-galactosidase	-	3.2.1.23
[Ref.: #25273]	beta-glucosidase	-	3.2.1.21
[Ref.: #25273]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25273]	catalase	+	1.11.1.6
[Ref.: #25273]	cystine arylamidase	+	3.4.11.3
[Ref.: #25273]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25273]	esterase (C 4)	+
[Ref.: #25273]	esterase Lipase (C 8)	+
[Ref.: #25273]	leucine arylamidase	+	3.4.11.1
[Ref.: #25273]	lipase (C 14)	-
[Ref.: #25273]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25273]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25273]	trypsin	-	3.4.21.4
[Ref.: #25273]	urease	-	3.5.1.5
[Ref.: #25273]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25273]

Fatty acid	Percentage
C15:0 iso	20.7
C16:1ω7c / C16:1ω6c	15.3
C16:1ω5c	10.6
anteiso-C17:1B / C17:1 I	8.9
C15:0 anteiso	7.6
C16:1 iso H	4.3
C16:0	4.3
C16:0 iso	3.6
C18:0	3.3
C17:0 iso 3OH	3.3
C15:1 iso G	2.7
C15:0 iso 3OH	2.3
C16:0 3OH	1.5
C15:1ω6c	1.4
C17:1ω6c	1.3
iso-C15:1H/C13:0 3-OH	1.3

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

[Ref.: #25273]	Sample type/isolated from	marine sediment sample
[Ref.: #25273]	Geographic location (country and/or sea, region)	Kings Bay, Ny-Ålesund in the Svalbard Archipelago
[Ref.: #25273]	Country	Norway
[Ref.: #25273]	Country ISO 3 Code	NOR
[Ref.: #25273]	Continent	Europe
[Ref.: #25273]	Geographic location	78.0000°/11.8860°
[Ref.: #25273]	Enrichment culture	R2A agar (Becton, Dickinson and Company)
[Ref.: #25273]	Enrichment culture temperature	28 ̊C
[Ref.: #25273]	Isolation/enrichment procedure	standard dilution plating method

[Ref.: #67771]	Sample type/isolated from	From marine sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	near Ny-Alesund, Svalbard Archipelago
[Ref.: #67771]	Country	Norway
[Ref.: #67771]	Country ISO 3 Code	NOR
[Ref.: #67771]	Continent	Europe
[Ref.: #67771]	Geographic location	78.9667°/11.8333°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX139010 (>99% sequence identity) for Hymenobacter rutilus subclade from Microbeatlas

Aquatic Samples	89
Soil Samples	109
Animal Samples	328
Plant Samples	31
Total Samples	557

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.: #25273]	Hymenobacter rutilus strain K2-33028 16S ribosomal RNA gene, partial sequence	KX139010	1507	GenBank ENA	1867850 tax ID

[Ref.: #25273]	GC-content	64.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	64.3 mol%

Availability in culture collections External links

[Ref.: #25273]

Culture collection no.

CCTCC AB 2016091, KCTC 52447

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter jejuensis sp. nov., a UV radiation-tolerant bacterium isolated from Jeju Island.	Maeng S, Kim MK, Subramani G	Antonie Van Leeuwenhoek	10.1007/s10482-019-01363-8	2019	*
Phylogeny	Hymenobacter rutilus sp. nov., isolated from marine sediment in the Arctic.	Kim MC, Kim CM, Kang OC, Zhang Y, Liu Z, Wangmu D, Wei Z, Huang Y, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.001685	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 )

#25273

M. C. K. Kim, C. M.,Kang, O. C.,Zhang, Y.,Liu, Z.,Wangmu, D.,Wei, Z.,Huang, Y.,Peng, F.: Hymenobacter rutilus sp. nov., isolated from marine sediment in the Arctic. IJSEM 67: 856 - 861 2017 ( DOI 10.1099/ijsem.0.001685 , PubMed 27902346 )

#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 .

* These data were automatically processed and therefore are not curated

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