Hymenobacter gummosus (BCRC 80966, LMG 29477, KCTC 52166)

Name: Hymenobacter gummosus (BCRC 80966, LMG 29477, KCTC 52166)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158673

Type strain

Strain Designation ANT-18

Culture col. no. BCRC 80966 LMG 29477 KCTC 52166 ANT-18

NCBI tax ID(s) 1776032

Special Collections KCTC Literature strains

Links

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

Gram-negative motile rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 272153

LMG 29477,BCRC 80966,KCTC 52166

@ref 20215

Last LPSN update 2025-12-16 10:08:05

Domain Pseudomonadati

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Hymenobacter

Species Hymenobacter gummosus

Full scientific name Hymenobacter gummosus Chen et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
65403	negative	2.3-3.0 µm	0.5-1.0 µm	rod-shaped
67771				rod-shaped	gliding
67771	negative
125438	negative					94.437

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65403	3.5 mm	pink	circular	2 days	R2A agar

Pigmentation

@ref	Production	Name
65403		Flexirubin
65403		Carotenoid

Culture and growth conditions

Culture medium

@ref	Name	Growth
65403	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
65403	positive	growth	20-37
65403	positive	optimum	25	mesophilic
67771	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
65403	positive	optimum	7
65403	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65403	aerobe
67771	aerobe
125439	obligate aerobe	95.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65403	NaCl	positive	growth	0-1 %

Observation

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65403	15729 ChEBI	(+)-L-ornithine	-	aerobic growth
65403	17128 ChEBI	adipate	-	aerobic growth
65403	17128 ChEBI	adipate	-	assimilation
65403	17925 ChEBI	alpha-D-glucose	-	aerobic growth
65403	27613 ChEBI	amygdalin	-	assimilation
65403	22599 ChEBI	arabinose	-	assimilation
65403	18305 ChEBI	arbutin	+	builds acid from
65403	71422 ChEBI	beta-gentiobiose	-	assimilation
65403		casein	+	hydrolysis
65403	17057 ChEBI	cellobiose	-	aerobic growth
65403	17057 ChEBI	cellobiose	-	assimilation
65403	17029 ChEBI	chitin	-	hydrolysis
65403	17108 ChEBI	D-arabinose	-	assimilation
65403	18333 ChEBI	D-arabitol	+	builds acid from
65403	15824 ChEBI	D-fructose	-	aerobic growth
65403	15824 ChEBI	D-fructose	-	assimilation
65403	28847 ChEBI	D-fucose	+	builds acid from
65403	12936 ChEBI	D-galactose	-	aerobic growth
65403	12936 ChEBI	D-galactose	+	builds acid from
65403	17634 ChEBI	D-glucose	-	assimilation
65403	17634 ChEBI	D-glucose	-	builds acid from
65403	62318 ChEBI	D-lyxose	+	builds acid from
65403	16899 ChEBI	D-mannitol	-	aerobic growth
65403	16899 ChEBI	D-mannitol	-	assimilation
65403	16024 ChEBI	D-mannose	-	aerobic growth
65403	16024 ChEBI	D-mannose	-	assimilation
65403	16988 ChEBI	D-ribose	+	builds acid from
65403	17924 ChEBI	D-sorbitol	-	aerobic growth
65403	17924 ChEBI	D-sorbitol	-	assimilation
65403	16443 ChEBI	D-tagatose	+	builds acid from
65403	65327 ChEBI	D-xylose	+	builds acid from
65403	27689 ChEBI	decanoate	-	aerobic growth
65403	27689 ChEBI	decanoate	-	assimilation
65403	23652 ChEBI	dextrin	-	aerobic growth
65403	16991 ChEBI	dna	+	hydrolysis
65403	17113 ChEBI	erythritol	-	assimilation
65403	4853 ChEBI	esculin	-	hydrolysis
65403	4853 ChEBI	esculin	+	builds acid from
65403	16813 ChEBI	galactitol	-	assimilation
65403	5291 ChEBI	gelatin	+	hydrolysis
65403	24265 ChEBI	gluconate	-	aerobic growth
65403	24265 ChEBI	gluconate	-	assimilation
65403	17234 ChEBI	glucose	-	assimilation
65403	17754 ChEBI	glycerol	-	assimilation
65403	28087 ChEBI	glycogen	+	builds acid from
65403	27570 ChEBI	histidine	-	aerobic growth
65403	85249 ChEBI	hydroxyethylcellulose	-	hydrolysis
65403	15443 ChEBI	inulin	-	assimilation
65403	16087 ChEBI	isocitrate	-	aerobic growth
65403	16087 ChEBI	isocitrate	-	assimilation
65403	30849 ChEBI	L-arabinose	-	aerobic growth
65403	30849 ChEBI	L-arabinose	+	builds acid from
65403	18403 ChEBI	L-arabitol	+	builds acid from
65403	18287 ChEBI	L-fucose	-	assimilation
65403	29985 ChEBI	L-glutamate	-	aerobic growth
65403	17203 ChEBI	L-proline	-	aerobic growth
65403	62345 ChEBI	L-rhamnose	-	aerobic growth
65403	62345 ChEBI	L-rhamnose	-	assimilation
65403	17115 ChEBI	L-serine	-	aerobic growth
65403	17266 ChEBI	L-sorbose	-	assimilation
65403	65328 ChEBI	L-xylose	-	assimilation
65403	17716 ChEBI	lactose	-	assimilation
65403	25017 ChEBI	leucine	+	aerobic growth
65403	25115 ChEBI	malate	-	assimilation
65403	25115 ChEBI	malate	+	aerobic growth
65403	17306 ChEBI	maltose	-	assimilation
65403	17306 ChEBI	maltose	+	aerobic growth
65403	17306 ChEBI	maltose	+	builds acid from
65403	29864 ChEBI	mannitol	-	assimilation
65403	37684 ChEBI	mannose	-	assimilation
65403	6731 ChEBI	melezitose	-	assimilation
65403	28053 ChEBI	melibiose	-	assimilation
65403	320061 ChEBI	methyl alpha-D-glucopyranoside	-	assimilation
65403	74863 ChEBI	methyl beta-D-xylopyranoside	-	assimilation
65403	17268 ChEBI	myo-inositol	-	assimilation
65403	506227 ChEBI	N-acetylglucosamine	-	aerobic growth
65403	506227 ChEBI	N-acetylglucosamine	-	assimilation
65403	17632 ChEBI	nitrate	-	reduction
65403	18401 ChEBI	phenylacetate	-	assimilation
65403		potassium 2-dehydro-D-gluconate	+	builds acid from
65403		potassium 5-dehydro-D-gluconate	+	builds acid from
65403	16634 ChEBI	raffinose	-	aerobic growth
65403	16634 ChEBI	raffinose	-	assimilation
65403	15963 ChEBI	ribitol	-	aerobic growth
65403	15963 ChEBI	ribitol	-	assimilation
65403	17814 ChEBI	salicin	-	assimilation
65403	32954 ChEBI	sodium acetate	+	aerobic growth
65403	63675 ChEBI	sodium succinate	-	aerobic growth
65403	28017 ChEBI	starch	+	builds acid from
65403	17992 ChEBI	sucrose	-	aerobic growth
65403	17992 ChEBI	sucrose	+	builds acid from
65403	27082 ChEBI	trehalose	-	aerobic growth
65403	27082 ChEBI	trehalose	-	assimilation
65403	32528 ChEBI	turanose	-	assimilation
65403	53424 ChEBI	tween 20	+	aerobic growth
65403	53424 ChEBI	tween 20	+	hydrolysis
65403	53423 ChEBI	tween 40	+	aerobic growth
65403	53423 ChEBI	tween 40	+	hydrolysis
65403	53425 ChEBI	tween 60	+	aerobic growth
65403	53425 ChEBI	tween 60	+	hydrolysis
65403	53426 ChEBI	tween 80	+	aerobic growth
65403	53426 ChEBI	tween 80	+	hydrolysis
65403	17151 ChEBI	xylitol	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.
65403	28971	ampicillin	10 µg (disc)
65403	17698	chloramphenicol	30 µg (disc)
65403	17833	gentamicin	10 µg (disc)
65403	6104	kanamycin	30 µg (disc)
65403	100147	nalidixic acid	30 µg (disc)
65403	28368	novobiocin	30 µg (disc)
65403	18208	penicillin g	10 Unit
65403	28077	rifampicin	5 µg (disc)
65403	17076	streptomycin	10 µg (disc)
65403	9332	sulfamethoxazole	23.75 µg (disc)
65403	27902	tetracycline	30 µg (disc)
65403	45924	trimethoprim	1.25 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65403	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
65403	acid phosphatase	+	3.1.3.2
65403	alkaline phosphatase	+	3.1.3.1
65403	alpha-chymotrypsin	-	3.4.21.1
65403	alpha-fucosidase	-	3.2.1.51
65403	alpha-galactosidase	-	3.2.1.22
65403	alpha-glucosidase	+	3.2.1.20
65403	alpha-mannosidase	-	3.2.1.24
65403	arginine dihydrolase	-	3.5.3.6
65403	beta-galactosidase	+	3.2.1.23
65403	beta-glucosidase	-	3.2.1.21
65403	beta-glucuronidase	-	3.2.1.31
65403	catalase	+	1.11.1.6
65403	cystine arylamidase	+	3.4.11.3
65403	cytochrome oxidase	+	1.9.3.1
65403	esterase (C 4)	-
65403	esterase Lipase (C 8)	+
65403	leucine arylamidase	+	3.4.11.1
65403	lipase	-
65403	lipase (C 14)	-
65403	N-acetyl-beta-glucosaminidase	+	3.2.1.52
65403	naphthol-AS-BI-phosphohydrolase	+
65403	trypsin	-	3.4.21.4
65403	urease	-	3.5.1.5
65403	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Spring

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
65403	water of the Longtoushan Spring of Maolin Valley	in the vicinity of Kaoshiung city	Taiwan, Province of China	TWN	Asia
67771	From freshwater	Longtoushan Spring, Maolin Valley, Kaohsiung City	Taiwan, Province of China	TWN	Asia	22.9111	120.686 22.9111/120.686

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM397091v1 assembly for Hymenobacter gummosus KCTC 52166	contig	GCA_003970915	1776032.3	2895866647	1776032	61.78

16S sequences

@ref	Description	Accession	Database
65403	Hymenobacter sp. ANT-18 partial 16S rRNA gene, strain ANT-18	LN997850

GC content

@ref	GC-content (mol%)	Method
65403	63.3	high performance liquid chromatography (HPLC)
67771	63.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hymenobacter gummosus KCTC 52166
NCBI: GCA_003970915

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	71.20	no
125439	motility	BacteriaNetⓘ	yes	50.20	no
125439	gram_stain	BacteriaNetⓘ	positive	70.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hymenobacter gummosus strain KCTC 52166
PATRIC: 1776032.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.44	yes
125438	anaerobic	anaerobicⓘ	no	96.59	no
125438	spore-forming	spore-formingⓘ	no	82.05	no
125438	aerobic	aerobicⓘ	yes	86.77	no
125438	thermophilic	thermophileⓘ	no	94.64	yes
125438	flagellated	motile2+ⓘ	no	85.78	yes

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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Hymenobacter gummosus (BCRC 80966, LMG 29477, KCTC 52166)

Name and taxonomic classification