Hymenobacter glacieicola (B1909, JCM 30596, CGMCC 1.12990)

Name: Hymenobacter glacieicola (B1909, JCM 30596, CGMCC 1.12990)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133140

Type strain

Strain Designation B1909

Culture col. no. B1909 JCM 30596 CGMCC 1.12990

NCBI tax ID(s) 1562124

Special Collections JCM Literature strains

History Y. Liu; Inst. of Tibetan Plateau Res., CAS, China; B1909.

Links

Hymenobacter glacieicola B1909 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from ice core drilled from; the Muztagh Glacier.

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

Name and taxonomic classification

SI-ID 132220

JCM 30596

@ref 20215

Last LPSN update 2026-02-09 11:31:53

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Hymenobacter

Species Hymenobacter glacieicola

Full scientific name Hymenobacter glacieicola Liu et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
24906	negative	3.5 µm	1.1 µm	rod-shaped
125438	negative				93.951
125439	negative				97.5

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
24906	0.5-1.5 mm	red-pink	circular	7 days	R2A

Culture and growth conditions

Culture medium

@ref	Name	Growth
24906	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
24906	positive	growth	4-30
24906	positive	optimum	10
67770	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
24906	positive	optimum	6
24906	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
24906	aerobe
125438	aerobe	90.179

Spore formation

@ref	Spore formation	Confidence
125439		97.4

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
24906	4853 ChEBI	esculin	+	hydrolysis
24906	5291 ChEBI	gelatin	+	hydrolysis
24906	17234 ChEBI	glucose	-	builds acid from
24906	17632 ChEBI	nitrate	-	reduction
24906	16301 ChEBI	nitrite	-	reduction
24906	27897 ChEBI	tryptophan	-	energy source

Antibiotic resistance

@ref	ChEBI	Metabolite
24906	28971	ampicillin
24906	17698	chloramphenicol
24906	100241	ciprofloxacin
24906	3745	clindamycin
24906	48923	erythromycin
24906	17833	gentamicin
24906	7507	neomycin
24906	18208	penicillin g
24906	28077	rifampicin
24906	27902	tetracycline
24906	28001	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
24906	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
24906	35581 ChEBI	indole	-

Enzymes

@ref	Value	Activity	Ec
24906	acid phosphatase	+	3.1.3.2
24906	alkaline phosphatase	+	3.1.3.1
24906	alpha-chymotrypsin	-	3.4.21.1
24906	alpha-fucosidase	-	3.2.1.51
24906	alpha-galactosidase	+	3.2.1.22
24906	alpha-glucosidase	+	3.2.1.20
24906	alpha-mannosidase	-	3.2.1.24
24906	beta-galactosidase	-	3.2.1.23
24906	beta-glucosidase	+	3.2.1.21
24906	beta-glucuronidase	-	3.2.1.31
24906	catalase	+	1.11.1.6
24906	cystine arylamidase	+	3.4.11.3
24906	cytochrome oxidase	+	1.9.3.1
24906	esterase (C 4)	+
24906	esterase lipase (C 8)	+
24906	leucine arylamidase	+	3.4.11.1
24906	lipase (C 14)	-
24906	N-acetyl-beta-glucosaminidase	+	3.2.1.52
24906	naphthol-AS-BI-phosphohydrolase	+
24906	trypsin	+	3.4.21.4
24906	tryptophan deaminase	-	4.1.99.1
24906	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Glacier
#Environmental	#Aquatic	#Ice
#Environmental	#Terrestrial	#Core sample

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24906	ice core drilled from the Muztagh Glacier	Tibetan Plateau	China	CHN	Asia
67770	Ice core drilled from Muztagh Glacier on the Tibetan Plateau		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KM203869 (>99% sequence identity) for Hymenobacter glacieicola subclade from Microbeatlas

Aquatic Samples	88
Soil Samples	75
Animal Samples	287
Plant Samples	76
Total Samples	526

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1464031v1 assembly for Hymenobacter glacieicola CGMCC 1.12990	scaffold	GCA_014640315	1562124.3	2995860656	1562124	71.21

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24906	Hymenobacter glacieicola strain B1909 16S ribosomal RNA gene, partial sequence	KM203869	1480		1562124

GC content

@ref	GC-content (mol%)	Method
24906	59	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hymenobacter glacieicola CGMCC 1.12990
NCBI: GCA_014640315

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.40	no
125439	motility	BacteriaNetⓘ	yes	64.60	no
125439	gram_stain	BacteriaNetⓘ	negative	97.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	85.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hymenobacter glacieicola CGMCC 1.12990
NCBI: GCA_014640315.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.95	no
125438	anaerobic	anaerobicⓘ	no	96.13	no
125438	aerobic	aerobicⓘ	yes	90.18	yes
125438	spore-forming	spore-formingⓘ	no	85.22	no
125438	thermophilic	thermophileⓘ	no	95.63	no
125438	flagellated	motile2+ⓘ	no	85.03	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter glacieicola sp. nov., isolated from glacier ice.	Liu K, Liu Y, Wang N, Gu Z, Shen L, Xu B, Zhou Y, Liu H, Jiao N	Int J Syst Evol Microbiol	10.1099/ijsem.0.001266	2016

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 )
#24906	K. L. Liu, Yongqin,Wang, Ninglian,Gu, Zhengquan,Shen, Liang,Xu, Baiqing,Zhou, Yuguang,Liu, Hongcan,Jiao, Nianzhi: Hymenobacter glacieicola sp. nov., isolated from glacier ice. IJSEM 66: 3793 - 3798 2016 ( DOI 10.1099/ijsem.0.001266 , PubMed 27374800 )
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )

Rate our new design

Content

About us

Hymenobacter glacieicola (B1909, JCM 30596, CGMCC 1.12990)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014640315

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media