Name: Hymenobacter gummosus ANT-18
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158673

Type strain:

Species: Hymenobacter gummosus

Strain Designation: ANT-18

Culture col. no.: BCRC 80966, LMG 29477, KCTC 52166

Strain history: <- Wen-Ming Chen, National Kaohsiung Marine Univ., Taiwan

NCBI tax ID(s): 1776032 (species)

Section

Hymenobacter gummosus ANT-18 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from water of the Longtoushan Spring of Maolin Valley.

colony-forming
Gram-negative
motile
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 gummosus**
	Full Scientific Name (LPSN)	Hymenobacter gummosus Chen et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65403]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #65403]	Cell length	2.3-3.0 µm

[Ref.: #65403]	Cell width	0.5-1.0 µm

[Ref.: #65403]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #65403]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #67771]	Flagellum arrangement	gliding

[Ref.: #65403]	Colony size	3.5 mm
[Ref.: #65403]	Colony color	pink
[Ref.: #65403]	Colony shape	circular
[Ref.: #65403]	Incubation period	2 days
[Ref.: #65403]	Cultivation medium used	R2A agar

[Ref.: #65403]	Pigment production	no
[Ref.: #65403]	Pigment name	Flexirubin
[Ref.: #65403]	Pigment production	yes
[Ref.: #65403]	Pigment name	Carotenoid

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65403]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #65403]

Culture medium growth

		Temperature
[Ref.: #65403]	growth	20-37 °C
[Ref.: #65403]	optimum	25 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #65403]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65403]			optimum	7
[Ref.: #65403]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65403]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992
[Ref.: #69481]	Ability of spore formation	no Confidence in %98

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65403]		NaCl		growth	0-1	%

[Ref.: #65403]	Observation	rods that are covered by large capsules
[Ref.: #65403]	Observation	colonies are shiny, slightly sticky, convex and circular with irregular, curled margins
[Ref.: #65403]	Observation	flexirubin-type pigments are not produced
[Ref.: #65403]	Observation	carotenoid pigments are present with maximum absorption at 480 nm
[Ref.: #65403]	Observation	predominant respiratory quinone is MK-7
[Ref.: #65403]	Observation	polar lipid profile consists of phosphatidylethanolamine, one uncharacterized aminolipid, two uncharacterized aminophospholipids, two uncharacterized glycolipids and seven uncharacterized lipids, Homospermidine is the major polyamine
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65403]	(+)-L-ornithine ChEBI	-	aerobic growth
[Ref.: #65403]	adipate ChEBI	-	aerobic growth
[Ref.: #65403]	adipate ChEBI	-	assimilation
[Ref.: #65403]	alpha-D-glucose ChEBI	-	aerobic growth
[Ref.: #65403]	amygdalin ChEBI	-	assimilation
[Ref.: #65403]	arabinose ChEBI	-	assimilation
[Ref.: #65403]	arbutin ChEBI	+	builds acid from
[Ref.: #65403]	beta-gentiobiose ChEBI	-	assimilation
[Ref.: #65403]	casein	+	hydrolysis
[Ref.: #65403]	cellobiose ChEBI	-	aerobic growth
[Ref.: #65403]	cellobiose ChEBI	-	assimilation
[Ref.: #65403]	chitin ChEBI	-	hydrolysis
[Ref.: #65403]	D-arabinose ChEBI	-	assimilation
[Ref.: #65403]	D-arabitol ChEBI	+	builds acid from
[Ref.: #65403]	D-fructose ChEBI	-	aerobic growth
[Ref.: #65403]	D-fructose ChEBI	-	assimilation
[Ref.: #65403]	D-fucose ChEBI	+	builds acid from
[Ref.: #65403]	D-galactose ChEBI	-	aerobic growth
[Ref.: #65403]	D-galactose ChEBI	+	builds acid from
[Ref.: #65403]	D-glucose ChEBI	-	assimilation
[Ref.: #65403]	D-glucose ChEBI	-	builds acid from
[Ref.: #65403]	D-lyxose ChEBI	+	builds acid from
[Ref.: #65403]	D-mannitol ChEBI	-	aerobic growth
[Ref.: #65403]	D-mannitol ChEBI	-	assimilation
[Ref.: #65403]	D-mannose ChEBI	-	aerobic growth
[Ref.: #65403]	D-mannose ChEBI	-	assimilation
[Ref.: #65403]	D-ribose ChEBI	+	builds acid from
[Ref.: #65403]	D-sorbitol ChEBI	-	aerobic growth
[Ref.: #65403]	D-sorbitol ChEBI	-	assimilation
[Ref.: #65403]	D-tagatose ChEBI	+	builds acid from
[Ref.: #65403]	D-xylose ChEBI	+	builds acid from
[Ref.: #65403]	decanoate ChEBI	-	aerobic growth
[Ref.: #65403]	decanoate ChEBI	-	assimilation
[Ref.: #65403]	dextrin ChEBI	-	aerobic growth
[Ref.: #65403]	dna ChEBI	+	hydrolysis
[Ref.: #65403]	erythritol ChEBI	-	assimilation
[Ref.: #65403]	esculin ChEBI	-	hydrolysis
[Ref.: #65403]	esculin ChEBI	+	builds acid from
[Ref.: #65403]	galactitol ChEBI	-	assimilation
[Ref.: #65403]	gelatin ChEBI	+	hydrolysis
[Ref.: #65403]	gluconate ChEBI	-	aerobic growth
[Ref.: #65403]	gluconate ChEBI	-	assimilation
[Ref.: #65403]	glucose ChEBI	-	assimilation
[Ref.: #65403]	glycerol ChEBI	-	assimilation
[Ref.: #65403]	glycogen ChEBI	+	builds acid from
[Ref.: #65403]	histidine ChEBI	-	aerobic growth
[Ref.: #65403]	hydroxyethylcellulose ChEBI	-	hydrolysis
[Ref.: #65403]	inulin ChEBI	-	assimilation
[Ref.: #65403]	isocitrate ChEBI	-	aerobic growth
[Ref.: #65403]	isocitrate ChEBI	-	assimilation
[Ref.: #65403]	L-arabinose ChEBI	-	aerobic growth
[Ref.: #65403]	L-arabinose ChEBI	+	builds acid from
[Ref.: #65403]	L-arabitol ChEBI	+	builds acid from
[Ref.: #65403]	L-fucose ChEBI	-	assimilation
[Ref.: #65403]	L-glutamate ChEBI	-	aerobic growth
[Ref.: #65403]	L-proline ChEBI	-	aerobic growth
[Ref.: #65403]	L-rhamnose ChEBI	-	aerobic growth
[Ref.: #65403]	L-rhamnose ChEBI	-	assimilation
[Ref.: #65403]	L-serine ChEBI	-	aerobic growth
[Ref.: #65403]	L-sorbose ChEBI	-	assimilation
[Ref.: #65403]	L-xylose ChEBI	-	assimilation
[Ref.: #65403]	lactose ChEBI	-	assimilation
[Ref.: #65403]	leucine ChEBI	+	aerobic growth
[Ref.: #65403]	malate ChEBI	-	assimilation
[Ref.: #65403]	malate ChEBI	+	aerobic growth
[Ref.: #65403]	maltose ChEBI	-	assimilation
[Ref.: #65403]	maltose ChEBI	+	aerobic growth
[Ref.: #65403]	maltose ChEBI	+	builds acid from
[Ref.: #65403]	mannitol ChEBI	-	assimilation
[Ref.: #65403]	mannose ChEBI	-	assimilation
[Ref.: #65403]	melezitose ChEBI	-	assimilation
[Ref.: #65403]	melibiose ChEBI	-	assimilation
[Ref.: #65403]	methyl alpha-D-glucopyranoside ChEBI	-	assimilation
[Ref.: #65403]	methyl beta-D-xylopyranoside ChEBI	-	assimilation
[Ref.: #65403]	myo-inositol ChEBI	-	assimilation
[Ref.: #65403]	N-acetylglucosamine ChEBI	-	aerobic growth
[Ref.: #65403]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #65403]	nitrate ChEBI	-	reduction
[Ref.: #65403]	phenylacetate ChEBI	-	assimilation
[Ref.: #65403]	potassium 2-dehydro-D-gluconate	+	builds acid from
[Ref.: #65403]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #65403]	raffinose ChEBI	-	aerobic growth
[Ref.: #65403]	raffinose ChEBI	-	assimilation
[Ref.: #65403]	ribitol ChEBI	-	aerobic growth
[Ref.: #65403]	ribitol ChEBI	-	assimilation
[Ref.: #65403]	salicin ChEBI	-	assimilation
[Ref.: #65403]	sodium acetate ChEBI	+	aerobic growth
[Ref.: #65403]	sodium succinate ChEBI	-	aerobic growth
[Ref.: #65403]	starch ChEBI	+	builds acid from
[Ref.: #65403]	sucrose ChEBI	-	aerobic growth
[Ref.: #65403]	sucrose ChEBI	+	builds acid from
[Ref.: #65403]	trehalose ChEBI	-	aerobic growth
[Ref.: #65403]	trehalose ChEBI	-	assimilation
[Ref.: #65403]	turanose ChEBI	-	assimilation
[Ref.: #65403]	tween 20 ChEBI	+	aerobic growth
[Ref.: #65403]	tween 20 ChEBI	+	hydrolysis
[Ref.: #65403]	tween 40 ChEBI	+	aerobic growth
[Ref.: #65403]	tween 40 ChEBI	+	hydrolysis
[Ref.: #65403]	tween 60 ChEBI	+	aerobic growth
[Ref.: #65403]	tween 60 ChEBI	+	hydrolysis
[Ref.: #65403]	tween 80 ChEBI	+	aerobic growth
[Ref.: #65403]	tween 80 ChEBI	+	hydrolysis
[Ref.: #65403]	xylitol ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #65403]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #65403]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #65403]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #65403]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #65403]	nalidixic acid ChEBI	yes	30	µg (disc)
[Ref.: #65403]	novobiocin ChEBI	yes	30	µg (disc)
[Ref.: #65403]	penicillin g ChEBI	yes	10	Unit
[Ref.: #65403]	rifampicin ChEBI	yes	5	µg (disc)
[Ref.: #65403]	streptomycin ChEBI	yes	10	µg (disc)
[Ref.: #65403]	sulfamethoxazole ChEBI	yes	23.75	µg (disc)
[Ref.: #65403]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #65403]	trimethoprim ChEBI	yes	1.25	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65403]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65403]	acid phosphatase	+	3.1.3.2
[Ref.: #65403]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65403]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65403]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65403]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65403]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65403]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65403]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65403]	beta-galactosidase	+	3.2.1.23
[Ref.: #65403]	beta-glucosidase	-	3.2.1.21
[Ref.: #65403]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65403]	catalase	+	1.11.1.6
[Ref.: #65403]	cystine arylamidase	+	3.4.11.3
[Ref.: #65403]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65403]	esterase (C 4)	-
[Ref.: #65403]	esterase Lipase (C 8)	+
[Ref.: #65403]	leucine arylamidase	+	3.4.11.1
[Ref.: #65403]	lipase	-
[Ref.: #65403]	lipase (C 14)	-
[Ref.: #65403]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65403]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65403]	trypsin	-	3.4.21.4
[Ref.: #65403]	urease	-	3.5.1.5
[Ref.: #65403]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65403]

Fatty acid	Percentage
C15:0 iso	17.1
C15:0 anteiso	10.8
C18:0	10.7
C17:1 iso I and/or C17:1 anteiso B	10
C18:1ω9c	7
C17:0 iso	6.2
C17:0 anteiso	5.3
C17:0 iso 3OH	3
C16:0	2.8
C18:1ω7c	2.7
C16:1ω5c	2.4
C16:1ω7c and/or C16:1ω6c and/or iso-C1	2.2
C14:0 anteiso	2.2
C19:0 anteiso	2.1
C12:0	1.8
C20:0	1.7
iso-C15:03-OH	1.5
C14:0	1.5
C17:0	1.4
C17:1ω6c	1.2
C16:0 iso	1
iso-C15:1 H and/or C13:0 3-OH	1

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

[Ref.: #65403]	Sample type/isolated from	water of the Longtoushan Spring of Maolin Valley
[Ref.: #65403]	Geographic location (country and/or sea, region)	in the vicinity of Kaoshiung city
[Ref.: #65403]	Country	Taiwan
[Ref.: #65403]	Country ISO 3 Code	TWN
[Ref.: #65403]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From freshwater
[Ref.: #67771]	Geographic location (country and/or sea, region)	Longtoushan Spring, Maolin Valley, Kaohsiung City
[Ref.: #67771]	Country	Taiwan
[Ref.: #67771]	Country ISO 3 Code	TWN
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	22.9111°/120.6860°
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Spring

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LN997850 (>99% sequence identity) for Hymenobacter gummosus subclade from Microbeatlas

Aquatic Samples	13
Soil Samples	13
Animal Samples	20
Plant Samples	19
Total Samples	65

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.: #65403]	16S rRNA gene sequence	LN997850		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Hymenobacter gummosus KCTC 52166	GCA_003970915	contig	GenBank	1776032 tax ID	*
[Ref.: #66792]	Hymenobacter gummosus strain KCTC 52166	1776032.3	wgs	PATRIC	1776032 tax ID	*
[Ref.: #66792]	Hymenobacter gummosus KCTC 52166	2895866647	draft	JGI IMG/M	1776032 tax ID	*

[Ref.: #65403]	GC-content	63.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	63.6 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 gummosus strain KCTC 52166 PATRIC: 1776032.3
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hymenobacter gummosus strain KCTC 52166 PATRIC: 1776032.3
[Ref.: #69480]	motile	no	91.735	no
[Ref.: #69480]	gram-positive	no	97.23	yes
[Ref.: #69480]	anaerobic	no	99.508	yes
[Ref.: #69480]	aerobic	yes	92.719	yes
[Ref.: #69480]	halophile	no	95.426	yes
[Ref.: #69480]	spore-forming	no	93.08	no
[Ref.: #69480]	thermophile	no	98.726	no
[Ref.: #69480]	glucose-util	yes	76.854	no
[Ref.: #69480]	flagellated	no	96.356	yes
[Ref.: #69480]	glucose-ferment	no	89.668	no

Availability in culture collections External links

[Ref.: #65403]

Culture collection no.

BCRC 80966, LMG 29477, KCTC 52166

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter edaphi sp. nov., isolated from abandoned arsenic-contaminated farmland soil.	Nie L, Fan X, Xiang D, Liao S, Wang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.003578	2019	*
Phylogeny	Hymenobacter oligotrophus sp. nov., isolated from a contaminated agar plate.	Geng Y, Zhang Y, Tian J, Liu J, Qin K, Huang Y, Wei Z, Peng F	Antonie Van Leeuwenhoek	10.1007/s10482-019-01279-3	2019	*
Phylogeny	Hymenobacter gummosus sp. nov., isolated from a spring.	Chen WM, Chen WT, Young CC, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002372	2017	*
Phylogeny	Hymenobacter busanensis sp. nov., radiation-resistant species isolated from soil in South Korea.	Lee SE, Ten LN, Park Y, Maeng S, Zhang J, Kim MK, Cha IT, Lee KE, Lee BH, Jung H-, Kim MK	Arch Microbiol	10.1007/s00203-020-02080-x	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 )

#65403

Wen-Ming Chen, Wei-Ting Chen, Chiu-Chung Young, Shih-Yi Sheu: Hymenobacter gummosus sp. nov., isolated from a spring. IJSEM 67: 4728 - 4735 2017 ( DOI 10.1099/ijsem.0.002372 , PubMed 28984220 )

#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;

#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 gummosus strain KCTC 52166

Hymenobacter gummosus strain KCTC 52166

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