Name: Hymenobacter rubripertinctus NY03-3-30
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158615

Type strain:

Species: Hymenobacter rubripertinctus

Strain Designation: NY03-3-30

Culture col. no.: CCTCC AB 2017095, KCTC 62163, CCM 8852

Strain history: <- Fan Jiang, Wuhan Univ.

NCBI tax ID(s): 2029981 (species)

Section

Hymenobacter rubripertinctus NY03-3-30 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from From soil.

colony-forming
Gram-negative
rod-shaped
aerobe
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 rubripertinctus**
	Full Scientific Name (LPSN)	Hymenobacter rubripertinctus Jiang et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65337]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #65337]	Cell length	2.1-5.6 µm

[Ref.: #65337]	Cell width	0.8-1 µm

[Ref.: #65337]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #65337]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #65337]	Colony color	red
[Ref.: #65337]	Colony shape	circular
[Ref.: #65337]	Cultivation medium used	R2A

[Ref.: #65337]	Pigment production	no
[Ref.: #65337]	Pigment name	flexirubin-type pigments
[Ref.: #65337]	Pigment production	yes
[Ref.: #65337]	Pigment name	carotinoid pigments

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

0.3 x R2A

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Culture medium growth

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Culture medium

tryptic soy agar

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Culture medium growth

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Culture medium

Marine agar (MA)

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Culture medium growth

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Culture medium

nutriet agar

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Culture medium growth

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

		Temperature
[Ref.: #65337]	growth	4-28 °C
[Ref.: #65337]	optimum	20 °C
[Ref.: #67771]	growth	20 °C

[Ref.: #65337]	Temperature range	psychrophilic
[Ref.: #67771]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #65337]			optimum	7
[Ref.: #65337]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65337]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65337]		NaCl		growth	0-1	%(w/v)
[Ref.: #65337]		NaCl		optimum	0	%(w/v)

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65337]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #65337]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #65337]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #65337]	adipate ChEBI	-	assimilation
[Ref.: #65337]	D-glucose ChEBI	-	fermentation
[Ref.: #65337]	D-mannitol ChEBI	-	assimilation
[Ref.: #65337]	D-mannose ChEBI	-	assimilation
[Ref.: #65337]	D-ribose ChEBI	-	assimilation
[Ref.: #65337]	D-sorbitol ChEBI	-	assimilation
[Ref.: #65337]	decanoate ChEBI	-	assimilation
[Ref.: #65337]	esculin ChEBI	-	hydrolysis
[Ref.: #65337]	gelatin ChEBI	-	hydrolysis
[Ref.: #65337]	glycogen ChEBI	+	assimilation
[Ref.: #65337]	itaconate ChEBI	-	assimilation
[Ref.: #65337]	L-alanine ChEBI	-	assimilation
[Ref.: #65337]	L-arabinose ChEBI	-	assimilation
[Ref.: #65337]	L-fucose ChEBI	-	assimilation
[Ref.: #65337]	L-histidine ChEBI	-	assimilation
[Ref.: #65337]	L-proline ChEBI	-	assimilation
[Ref.: #65337]	L-rhamnose ChEBI	-	assimilation
[Ref.: #65337]	L-serine ChEBI	-	assimilation
[Ref.: #65337]	lactate ChEBI	-	assimilation
[Ref.: #65337]	malate ChEBI	-	assimilation
[Ref.: #65337]	maltose ChEBI	+	assimilation
[Ref.: #65337]	melibiose ChEBI	-	assimilation
[Ref.: #65337]	myo-inositol ChEBI	-	assimilation
[Ref.: #65337]	nitrate ChEBI	+	reduction
[Ref.: #65337]	phenylacetate ChEBI	-	assimilation
[Ref.: #65337]	potassium 2-dehydro-D-gluconate	-	assimilation
[Ref.: #65337]	potassium 5-dehydro-D-gluconate	-	assimilation
[Ref.: #65337]	potassium gluconate ChEBI	-	assimilation
[Ref.: #65337]	propionate ChEBI	-	assimilation
[Ref.: #65337]	salicin ChEBI	-	assimilation
[Ref.: #65337]	sodium acetate ChEBI	-	assimilation
[Ref.: #65337]	sodium citrate ChEBI	-	assimilation
[Ref.: #65337]	sodium malonate ChEBI	-	assimilation
[Ref.: #65337]	suberic acid ChEBI	-	assimilation
[Ref.: #65337]	sucrose ChEBI	-	assimilation
[Ref.: #65337]	valerate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #65337]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #65337]	aztreonam ChEBI	yes	30	µg (disc)
[Ref.: #65337]	ceftriaxone ChEBI	yes	30	µg (disc)
[Ref.: #65337]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #65337]	ciprofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #65337]	erythromycin ChEBI	yes	15	µg (disc)
[Ref.: #65337]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #65337]	polymyxin b ChEBI	yes	30	µg (disc)
[Ref.: #65337]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #65337]	tobramycin ChEBI				yes	10	µg (disc)
[Ref.: #65337]	vancomycin ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65337]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65337]	acid phosphatase	+	3.1.3.2
[Ref.: #65337]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65337]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65337]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65337]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65337]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65337]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65337]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65337]	beta-galactosidase	-	3.2.1.23
[Ref.: #65337]	beta-glucosidase	+	3.2.1.21
[Ref.: #65337]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65337]	catalase	+	1.11.1.6
[Ref.: #65337]	cystine arylamidase	+	3.4.11.3
[Ref.: #65337]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65337]	esterase (C 4)	+
[Ref.: #65337]	esterase Lipase (C 8)	+
[Ref.: #65337]	leucine arylamidase	+	3.4.11.1
[Ref.: #65337]	lipase (C 14)	-
[Ref.: #65337]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65337]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65337]	trypsin	-	3.4.21.4
[Ref.: #65337]	urease	-	3.5.1.5
[Ref.: #65337]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Inexpressible Island, Northern Victoria Land of the Antarctic Ross Orogen, Antarctica
[Ref.: #67771]	Country	Antarctica
[Ref.: #67771]	Country ISO 3 Code	ATA
[Ref.: #67771]	Continent	Australia and Oceania

[Ref.: #65337]	Sample type/isolated from	soil sample
[Ref.: #65337]	Sampling date	2015-02
[Ref.: #65337]	Geographic location (country and/or sea, region)	Inexpressible Island, Northern Victoria Land of the Antarctic Ross Orogen
[Ref.: #65337]	Country	Antarctica
[Ref.: #65337]	Country ISO 3 Code	ATA
[Ref.: #65337]	Continent	Australia and Oceania
[Ref.: #65337]	Geographic location	-74.9169°/163.7160°
[Ref.: #65337]	Enrichment culture	R2A agar
[Ref.: #65337]	Isolation/enrichment procedure	dilution plating technique
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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.: #65337]	16S rRNA gene sequence	MF770258		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Hymenobacter rubripertinctus CCM 8852	GCA_003583925	contig	GenBank	2029981 tax ID	*
[Ref.: #66792]	Hymenobacter rubripertinctus strain CCM 8852	2029981.3	wgs	PATRIC	2029981 tax ID	*
[Ref.: #66792]	Hymenobacter rubripertinctus CCM 8852	2881489277	draft	JGI IMG/M	2029981 tax ID	*

[Ref.: #65337]	GC-content	59.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	59.4 mol%

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 rubripertinctus strain CCM 8852 PATRIC: 2029981.3
[Ref.: #69481]	spore-forming	no	82	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hymenobacter rubripertinctus strain CCM 8852 PATRIC: 2029981.3
[Ref.: #69480]	motile	no	93.939	no
[Ref.: #69480]	gram-positive	no	97.782	yes
[Ref.: #69480]	anaerobic	no	98.99	yes
[Ref.: #69480]	aerobic	yes	90.432	yes
[Ref.: #69480]	halophile	no	93.093	no
[Ref.: #69480]	spore-forming	no	93.879	no
[Ref.: #69480]	glucose-util	yes	75.151	no
[Ref.: #69480]	flagellated	no	97.521	yes
[Ref.: #69480]	thermophile	no	96.533	yes
[Ref.: #69480]	glucose-ferment	no	91.58	yes

Availability in culture collections External links

[Ref.: #65337]

Culture collection no.

CCTCC AB 2017095, KCTC 62163, CCM 8852

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter amundsenii sp. nov. resistant to ultraviolet radiation, isolated from regoliths in Antarctica.	Sedlacek I, Pantucek R, Kralova S, Maslanova I, Holochova P, Stankova E, Vrbovska V, Svec P, Busse HJ	Syst Appl Microbiol	10.1016/j.syapm.2018.12.004	2018	*
Phylogeny	Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil.	Jiang F, Danzeng W, Zhang Y, Zhang Y, Jiang L, Liu J, Lu L, Fan W, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.002563	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 )

#65337

Fan Jiang, Wangmu Danzeng, Yuming Zhang, Yan Zhang, Li Jiang, Jia Liu, Lu Lu, Wei Fan, Fang Peng: Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil. IJSEM 68: 663 - 668 2018 ( DOI 10.1099/ijsem.0.002563 , PubMed 29388548 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 rubripertinctus strain CCM 8852

Hymenobacter rubripertinctus strain CCM 8852

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