Name: Hymenobacter coccineus P5239
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140596

Type strain:

Species: Hymenobacter coccineus

Strain Designation: P5239

Culture col. no.: LMG 29441, CCM 8649

NCBI tax ID(s): 1908235 (species)

Section

Hymenobacter coccineus P5239 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and has a red pigmentation.

colony-forming
Gram-negative
pigmented
rod-shaped
aerobe
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 coccineus**
	Full Scientific Name (LPSN)	Hymenobacter coccineus Sedlá?ek et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43239]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #43239]	Cell shape	rod-shaped

[Ref.: #43239]	Motility	no

[Ref.: #43239]	Colony size	1-2 mm
[Ref.: #43239]	Colony color	reddish
[Ref.: #43239]	Colony shape	circular
[Ref.: #43239]	Incubation period	3 days
[Ref.: #43239]	Cultivation medium used	R2A

[Ref.: #43239]	Pigment production	yes
[Ref.: #43239]	Pigmentation color	red
[Ref.: #43239]	Pigment name	carotenoide
[Ref.: #43239]	Pigment production	no
[Ref.: #43239]	Pigment name	flexirubin-type 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

PCA

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Culture medium growth

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Culture medium

Trypticase Soy Agar (TSA)

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Culture medium growth

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Culture medium

BHI

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Culture medium growth

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Culture medium

MacConcey agar

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #43239]		no	growth	25 °C
[Ref.: #43239]			growth	5-20 °C

[Ref.: #43239]	Temperature range	mesophilic
[Ref.: #43239]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #43239]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43239]

Oxygen tolerance

aerobe

[Ref.: #43239]	Type of spore	spore
[Ref.: #43239]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.979

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43239]		NaCl		growth	0.5	%(w/v)
[Ref.: #43239]		NaCl	no	growth	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43239]	2,3-butanediol ChEBI	-	respiration
[Ref.: #43239]	2-hydroxybutyrate ChEBI	-	respiration
[Ref.: #43239]	2-oxobutanoate ChEBI	-	respiration
[Ref.: #43239]	2-oxogluconate	-	builds acid from
[Ref.: #43239]	2-oxoglutarate ChEBI	-	respiration
[Ref.: #43239]	2-oxopentanoate ChEBI	-	respiration
[Ref.: #43239]	3-hydroxybutyrate ChEBI	-	respiration
[Ref.: #43239]	4-hydroxy-L-proline ChEBI	-	respiration
[Ref.: #43239]	4-hydroxybutyrate ChEBI	-	respiration
[Ref.: #43239]	4-hydroxyphenylacetic acid ChEBI	-	respiration
[Ref.: #43239]	5-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #43239]	acetamide ChEBI	-	assimilation
[Ref.: #43239]	acetate ChEBI	+	respiration
[Ref.: #43239]	alpha-cyclodextrin ChEBI	-	respiration
[Ref.: #43239]	alpha-D-glucose ChEBI	+	respiration
[Ref.: #43239]	alpha-lactose ChEBI	+	respiration
[Ref.: #43239]	amygdalin ChEBI	-	builds acid from
[Ref.: #43239]	arbutin ChEBI	-	builds acid from
[Ref.: #43239]	bromosuccinate ChEBI	-	respiration
[Ref.: #43239]	casein	-	hydrolysis
[Ref.: #43239]	cellobiose ChEBI	+	builds acid from
[Ref.: #43239]	cellobiose ChEBI	+	respiration
[Ref.: #43239]	cis-aconitate ChEBI	-	respiration
[Ref.: #43239]	citrate ChEBI	-	carbon source
[Ref.: #43239]	citrate ChEBI	-	respiration
[Ref.: #43239]	D-alanine ChEBI	-	respiration
[Ref.: #43239]	D-arabinose ChEBI	+	builds acid from
[Ref.: #43239]	D-arabitol ChEBI	-	builds acid from
[Ref.: #43239]	D-arabitol ChEBI	-	respiration
[Ref.: #43239]	D-fructose ChEBI	-	builds acid from
[Ref.: #43239]	D-fructose ChEBI	-	respiration
[Ref.: #43239]	D-fucose ChEBI	-	builds acid from
[Ref.: #43239]	D-galactonic acid lactone ChEBI	-	respiration
[Ref.: #43239]	D-galactose ChEBI	-	respiration
[Ref.: #43239]	D-galacturonic acid ChEBI	-	respiration
[Ref.: #43239]	D-glucarate ChEBI	-	respiration
[Ref.: #43239]	D-gluconate ChEBI	-	respiration
[Ref.: #43239]	D-glucosaminic acid ChEBI	-	respiration
[Ref.: #43239]	D-glucose ChEBI	+	builds acid from
[Ref.: #43239]	D-glucose 6-phosphate ChEBI	-	respiration
[Ref.: #43239]	D-glucuronate ChEBI	-	respiration
[Ref.: #43239]	D-lyxose ChEBI	-	builds acid from
[Ref.: #43239]	D-mannitol ChEBI	-	respiration
[Ref.: #43239]	D-mannose ChEBI	+	builds acid from
[Ref.: #43239]	D-mannose ChEBI	-	respiration
[Ref.: #43239]	D-psicose ChEBI	-	respiration
[Ref.: #43239]	D-serine ChEBI	-	respiration
[Ref.: #43239]	D-sorbitol ChEBI	+	respiration
[Ref.: #43239]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43239]	D-xylose ChEBI	-	builds acid from
[Ref.: #43239]	dextrin ChEBI	+	respiration
[Ref.: #43239]	DL-carnitine ChEBI	-	respiration
[Ref.: #43239]	dna ChEBI	-	hydrolysis
[Ref.: #43239]	erythritol ChEBI	-	builds acid from
[Ref.: #43239]	erythritol ChEBI	-	respiration
[Ref.: #43239]	esculin ChEBI	+	hydrolysis
[Ref.: #43239]	ethanolamine ChEBI	-	respiration
[Ref.: #43239]	formate ChEBI	-	respiration
[Ref.: #43239]	galactitol ChEBI	-	builds acid from
[Ref.: #43239]	galactose ChEBI	+	builds acid from
[Ref.: #43239]	gamma-aminobutyric acid ChEBI	-	respiration
[Ref.: #43239]	gelatin ChEBI	-	hydrolysis
[Ref.: #43239]	gentiobiose ChEBI	+	builds acid from
[Ref.: #43239]	gentiobiose ChEBI	+	respiration
[Ref.: #43239]	gluconate ChEBI	-	builds acid from
[Ref.: #43239]	glucose ChEBI	-	fermentation
[Ref.: #43239]	glucose 1-phosphate ChEBI	-	respiration
[Ref.: #43239]	glucuronamide ChEBI	-	respiration
[Ref.: #43239]	glycerol ChEBI	-	builds acid from
[Ref.: #43239]	glycerol ChEBI	-	respiration
[Ref.: #43239]	glycerol 1-phosphate ChEBI	-	respiration
[Ref.: #43239]	glycogen ChEBI	-	builds acid from
[Ref.: #43239]	glycogen ChEBI	-	respiration
[Ref.: #43239]	glycyl L-aspartic acid ChEBI	-	respiration
[Ref.: #43239]	glycyl-l-glutamate ChEBI	-	respiration
[Ref.: #43239]	inosine ChEBI	-	respiration
[Ref.: #43239]	inulin ChEBI	-	builds acid from
[Ref.: #43239]	itaconate ChEBI	-	respiration
[Ref.: #43239]	L-alaninamide ChEBI	-	respiration
[Ref.: #43239]	L-alanine ChEBI	-	respiration
[Ref.: #43239]	L-alanylglycine ChEBI	-	respiration
[Ref.: #43239]	L-arabinose ChEBI	-	respiration
[Ref.: #43239]	L-arabitol ChEBI	-	builds acid from
[Ref.: #43239]	L-asparagine ChEBI	-	respiration
[Ref.: #43239]	L-aspartate ChEBI	-	respiration
[Ref.: #43239]	L-fucose ChEBI	-	builds acid from
[Ref.: #43239]	L-fucose ChEBI	-	respiration
[Ref.: #43239]	L-glutamate ChEBI	-	respiration
[Ref.: #43239]	L-histidine ChEBI	-	respiration
[Ref.: #43239]	L-leucine ChEBI	-	respiration
[Ref.: #43239]	L-ornithine ChEBI	-	respiration
[Ref.: #43239]	L-phenylalanine ChEBI	-	respiration
[Ref.: #43239]	L-proline ChEBI	-	respiration
[Ref.: #43239]	L-pyroglutamic acid ChEBI	-	respiration
[Ref.: #43239]	L-rhamnose ChEBI	-	respiration
[Ref.: #43239]	L-serine ChEBI	-	respiration
[Ref.: #43239]	L-threonine ChEBI	-	respiration
[Ref.: #43239]	L-xylose ChEBI	-	builds acid from
[Ref.: #43239]	lactate ChEBI	-	respiration
[Ref.: #43239]	lactose ChEBI	+	builds acid from
[Ref.: #43239]	lactulose ChEBI	+	respiration
[Ref.: #43239]	lecithin ChEBI	-	hydrolysis
[Ref.: #43239]	malonate ChEBI	-	assimilation
[Ref.: #43239]	malonate ChEBI	-	respiration
[Ref.: #43239]	maltose ChEBI	+	builds acid from
[Ref.: #43239]	maltose ChEBI	+	respiration
[Ref.: #43239]	mannitol ChEBI	-	builds acid from
[Ref.: #43239]	melezitose ChEBI	-	builds acid from
[Ref.: #43239]	melibiose ChEBI	-	builds acid from
[Ref.: #43239]	melibiose ChEBI	-	respiration
[Ref.: #43239]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #43239]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #43239]	methyl beta-D-glucopyranoside ChEBI	+	respiration
[Ref.: #43239]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #43239]	methyl pyruvate ChEBI	-	respiration
[Ref.: #43239]	monomethyl succinate ChEBI	-	respiration
[Ref.: #43239]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43239]	myo-inositol ChEBI	-	respiration
[Ref.: #43239]	N-acetylgalactosamine ChEBI	-	respiration
[Ref.: #43239]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #43239]	N-acetylglucosamine ChEBI	-	respiration
[Ref.: #43239]	nitrate ChEBI	-	reduction
[Ref.: #43239]	nitrite ChEBI	-	reduction
[Ref.: #43239]	phenylethylamine ChEBI	-	respiration
[Ref.: #43239]	propionate ChEBI	-	respiration
[Ref.: #43239]	putrescine ChEBI	-	respiration
[Ref.: #43239]	quinate ChEBI	-	respiration
[Ref.: #43239]	raffinose ChEBI	-	builds acid from
[Ref.: #43239]	raffinose ChEBI	-	respiration
[Ref.: #43239]	rhamnose ChEBI	-	builds acid from
[Ref.: #43239]	ribitol ChEBI	-	builds acid from
[Ref.: #43239]	ribitol ChEBI	-	respiration
[Ref.: #43239]	ribose ChEBI	-	builds acid from
[Ref.: #43239]	salicin ChEBI	+	builds acid from
[Ref.: #43239]	sebacic acid ChEBI	-	respiration
[Ref.: #43239]	sorbitol ChEBI	-	builds acid from
[Ref.: #43239]	sorbose ChEBI	-	builds acid from
[Ref.: #43239]	starch ChEBI	-	hydrolysis
[Ref.: #43239]	starch ChEBI	-	builds acid from
[Ref.: #43239]	succinamate ChEBI	-	respiration
[Ref.: #43239]	succinate ChEBI	-	respiration
[Ref.: #43239]	sucrose ChEBI	+	builds acid from
[Ref.: #43239]	sucrose ChEBI	+	respiration
[Ref.: #43239]	thymidine ChEBI	-	respiration
[Ref.: #43239]	trehalose ChEBI	+	builds acid from
[Ref.: #43239]	trehalose ChEBI	+	respiration
[Ref.: #43239]	turanose ChEBI	-	builds acid from
[Ref.: #43239]	turanose ChEBI	+	respiration
[Ref.: #43239]	tween 40 ChEBI	-	respiration
[Ref.: #43239]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43239]	tween 80 ChEBI	-	respiration
[Ref.: #43239]	tyrosine ChEBI	-	hydrolysis
[Ref.: #43239]	uridine ChEBI	-	respiration
[Ref.: #43239]	urocanic acid ChEBI	-	respiration
[Ref.: #43239]	xylitol ChEBI	-	builds acid from
[Ref.: #43239]	xylitol ChEBI	-	respiration
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43239]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #43239]	aztreonam ChEBI				yes	30	µg (disc)
[Ref.: #43239]	carbenicillin ChEBI	yes	100	µg (disc)
[Ref.: #43239]	cefalotin ChEBI	yes	30	µg (disc)
[Ref.: #43239]	cefixime ChEBI				yes	5	µg (disc)
[Ref.: #43239]	ceftazidime ChEBI				yes	10	µg (disc)
[Ref.: #43239]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #43239]	ciprofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #43239]	co-trimoxazole ChEBI	yes	25	µg (disc)
[Ref.: #43239]	gentamicin ChEBI				yes	10	µg (disc)
[Ref.: #43239]	imipenem ChEBI	yes	10	µg (disc)
[Ref.: #43239]	kanamycin ChEBI				yes	30	µg (disc)
[Ref.: #43239]	piperacillin ChEBI	yes	30	µg (disc)
[Ref.: #43239]	polymyxin b ChEBI	yes	300	Unit
[Ref.: #43239]	streptomycin ChEBI	yes	10	µg (disc)
[Ref.: #43239]	tetracycline ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #43239]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43239]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43239]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43239]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43239]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43239]	beta-galactosidase	+	3.2.1.23
[Ref.: #43239]	beta-glucosidase	+	3.2.1.21
[Ref.: #43239]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43239]	catalase	+	1.11.1.6
[Ref.: #43239]	chymotrypsin	-	3.4.4.5
[Ref.: #43239]	cystine arylamidase	-	3.4.11.3
[Ref.: #43239]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43239]	esterase (C 4)	-
[Ref.: #43239]	esterase Lipase (C 8)	-
[Ref.: #43239]	leucine arylamidase	+	3.4.11.1
[Ref.: #43239]	lipase (C 14)	-
[Ref.: #43239]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43239]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43239]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #43239]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43239]	phosphatase	+
[Ref.: #43239]	trypsin	-	3.4.21.4
[Ref.: #43239]	urease	-	3.5.1.5
[Ref.: #43239]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43239]

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	39
C16:1ω5c	20
C15:0 iso	14

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

[Ref.: #43239]	Sample type/isolated from	lichens on stone
[Ref.: #43239]	Geographic location (country and/or sea, region)	Panorama Pass, James Ross Island, Antarctica
[Ref.: #43239]	Country	Antarctica
[Ref.: #43239]	Country ISO 3 Code	ATA
[Ref.: #43239]	Continent	Australia and Oceania
[Ref.: #43239]	Geographic location	-63.0000°/-57.0000°
[Ref.: #43239]	Isolation date	2013
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Geologic
#Host	#Other	#Lichen

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX611463 (>99% sequence identity) for Hymenobacter coccineus subclade from Microbeatlas

Aquatic Samples	12
Soil Samples	32
Animal Samples	33
Plant Samples	13
Total Samples	90

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.: #43239]	16S rRNA gene sequences	KX611463	1502	ENA	1908235 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Hymenobacter coccineus CCM 8649	GCA_001816125	contig	GenBank	1908235 tax ID	*
[Ref.: #66792]	Hymenobacter sp. CCM 8649	1884790.3	wgs	PATRIC	1908235 tax ID	*
[Ref.: #66792]	Hymenobacter coccineus CCM 8649	2791355030	draft	JGI IMG/M	1908235 tax ID	*

[Ref.: #43239]

GC-content

63.1 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 sp. CCM 8649 PATRIC: 1884790.3
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hymenobacter sp. CCM 8649 PATRIC: 1884790.3
[Ref.: #69480]	motile	no	93.934	no
[Ref.: #69480]	gram-positive	no	96.827	yes
[Ref.: #69480]	anaerobic	no	99.431	yes
[Ref.: #69480]	aerobic	yes	89.429	yes
[Ref.: #69480]	halophile	no	93.678	no
[Ref.: #69480]	spore-forming	no	94.068	yes
[Ref.: #69480]	glucose-util	yes	87.147	yes
[Ref.: #69480]	flagellated	no	96.484	yes
[Ref.: #69480]	thermophile	no	97.981	yes
[Ref.: #69480]	glucose-ferment	no	90.264	yes

Availability in culture collections External links

[Ref.: #43239]

Culture collection no.

LMG 29441, CCM 8649

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter caeli sp. nov., an airborne bacterium isolated from King George Island, Antarctica.	Roldan DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB, Kralova S, Sedlacek I, Busse HJ, Menes RJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004838	2021	*
Phylogeny	Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica.	Sedlacek I, Kralova S, Kyrova K, Maslanova I, Busse HJ, Stankova E, Vrbovska V, Nemec M, Bartak M, Holochova P, Svec P, Pantucek R	Int J Syst Evol Microbiol	10.1099/ijsem.0.001898	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 )

#43239

Ivo Sedlácek, Stanislava Králová, Kamila Kýrová, Ivana Malanová, Hans-Jürgen Busse, Eva Stanková, Veronika Vrbovská, Miroslav Nemec, Milo Barták, Pavla Holochová, Pavel and Roman Pantucek: Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica. IJSEM 67: 1975 - 1983 2017 ( DOI 10.1099/ijsem.0.001898 , PubMed 28629503 )

#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) .

#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 .

#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 sp. CCM 8649

Hymenobacter sp. CCM 8649

Change proposal

Change proposal