Rufibacter glacialis (CGMCC 1.9789, NBRC 109705, MDT1-10-3)

Name: Rufibacter glacialis (CGMCC 1.9789, NBRC 109705, MDT1-10-3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158531

Type strain

Strain Designation MDT1-10-3

Culture col. no. CGMCC 1.9789 NBRC 109705 MDT1-10-3

NCBI tax ID(s) 1259555

Special Collections Literature strains

Links

Rufibacter glacialis MDT1-10-3 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil.

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

Name and taxonomic classification

SI-ID 133360

NBRC 109705

@ref 20215

Last LPSN update 2026-05-29 08:43:59

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Rufibacter

Species Rufibacter glacialis

Full scientific name Rufibacter glacialis Liu et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
65208	negative	1.7-1.9 µm	0.9-1.1 µm	rod-shaped
125438	negative				94.482
125439	negative				99.288

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65208	2.0 mm	red	circular	4 days	R2A

Culture and growth conditions

Culture medium

@ref	Name	Growth
65208	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
65208	positive	optimum	18-22
65208	positive	growth	4-25
65208	negative	growth	30

Culture pH

@ref	Ability	Type	PH
65208	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
65208	aerobe
125439	facultative anaerobe	92.668

Spore formation

@ref	Spore formation	Confidence
125439		99.924

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65208	NaCl	positive	growth	0-1.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65208	30916 ChEBI	2-oxoglutarate	-	carbon source
65208	13705 ChEBI	acetoacetate	+	carbon source
65208	17925 ChEBI	alpha-D-glucose	+	carbon source
65208	36219 ChEBI	alpha-lactose	+	carbon source
65208	73706 ChEBI	bromosuccinate	-	carbon source
65208		casein	+	hydrolysis
65208	17057 ChEBI	cellobiose	-	carbon source
65208	16947 ChEBI	citrate	-	assimilation
65208	16947 ChEBI	citrate	+	carbon source
65208	78697 ChEBI	D-fructose 6-phosphate	+	carbon source
65208	12936 ChEBI	D-galactose	+	carbon source
65208	18024 ChEBI	D-galacturonic acid	+	carbon source
65208	15748 ChEBI	D-glucuronate	-	carbon source
65208	16024 ChEBI	D-mannose	-	carbon source
65208	23652 ChEBI	dextrin	+	carbon source
65208	4853 ChEBI	esculin	+	hydrolysis
65208	5291 ChEBI	gelatin	+	carbon source
65208	5291 ChEBI	gelatin	+	hydrolysis
65208	28066 ChEBI	gentiobiose	-	carbon source
65208	17234 ChEBI	glucose	-	fermentation
65208	32323 ChEBI	glucuronamide	+	carbon source
65208	70744 ChEBI	glycine-proline	-	carbon source
65208	16977 ChEBI	L-alanine	-	carbon source
65208	29991 ChEBI	L-aspartate	-	carbon source
65208	17464 ChEBI	L-galactonic acid gamma-lactone	+	carbon source
65208	29985 ChEBI	L-glutamate	-	carbon source
65208	15589 ChEBI	L-malate	-	carbon source
65208	62345 ChEBI	L-rhamnose	-	carbon source
65208	17306 ChEBI	maltose	+	carbon source
65208	506227 ChEBI	N-acetylglucosamine	+	carbon source
65208	17632 ChEBI	nitrate	+	reduction
65208	17309 ChEBI	pectin	+	carbon source
65208	28017 ChEBI	starch	+	hydrolysis
65208	27082 ChEBI	trehalose	+	carbon source
65208	32528 ChEBI	turanose	-	carbon source
65208	53426 ChEBI	tween 80	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite
65208	15688 ChEBI	acetoin
65208	16136 ChEBI	hydrogen sulfide
65208	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
65208	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
65208	acid phosphatase	+	3.1.3.2
65208	alkaline phosphatase	+	3.1.3.1
65208	alpha-chymotrypsin	-	3.4.21.1
65208	alpha-fucosidase	-	3.2.1.51
65208	alpha-galactosidase	-	3.2.1.22
65208	alpha-glucosidase	-	3.2.1.20
65208	alpha-mannosidase	-	3.2.1.24
65208	arginine dihydrolase	-	3.5.3.6
65208	beta-galactosidase	+	3.2.1.23
65208	beta-glucosidase	-	3.2.1.21
65208	beta-glucuronidase	-	3.2.1.31
65208	catalase	+	1.11.1.6
65208	cytochrome oxidase	+	1.9.3.1
65208	esterase (C 4)	+
65208	esterase Lipase (C 8)	+
65208	leucine arylamidase	+	3.4.11.1
65208	lysine decarboxylase	-	4.1.1.18
65208	N-acetyl-beta-glucosaminidase	+	3.2.1.52
65208	naphthol-AS-BI-phosphohydrolase	+
65208	ornithine decarboxylase	-	4.1.1.17
65208	trypsin	+	3.4.21.4
65208	tryptophan deaminase	-	4.1.99.1
65208	urease	-	3.5.1.5
65208	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

65208

Fatty acid	Percentage
C17:1 iso I and/or C17:1 anteiso B	22.3
C16:1ω6c and/or C16:1ω7c	16.4
C17:1ω6c	9.9
C15:0 anteiso	9.8
C15:0 iso	8.9
C16:1ω5c	7.7
C16:1 iso H	3.4
C16:0 iso 3OH	2.4
C16:0 iso	2.4
C17:0 iso 3OH	2.1
C15:1ω6c	2.1
iso-C15:0 I/H and/or C13:0 3-OH	1.8
C15:0 iso 3OH	1.6
C17:0 2OH	1.6
C18:0	1.2

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
65208	soil	Midui glacier in Tibet	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JX949546 (>99% sequence identity) for Rufibacter glacialis subclade from Microbeatlas

Aquatic Samples	4
Soil Samples	60
Animal Samples	66
Plant Samples	1
Total Samples	131

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1464571v1 assembly for Rufibacter glacialis CGMCC 1.9789	scaffold	GCA_014645715	1259555.5	8066105975	1259555	73.98
66792	ASM827174v1 assembly for Rufibacter glacialis MDT1-10-3	scaffold	GCA_008271745	1259555.4	2891128709	1259555	73.34

16S sequences

@ref	Description	Accession	Database
65208	Rufibacter glacialis 16S ribosomal RNA gene, partial sequence	JX949546

GC content

@ref	GC-content (mol%)	Method
65208	49	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: ASM1464571v1 assembly for Rufibacter glacialis CGMCC 1.9789
NCBI: GCA_014645715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.67	no
125439	gram_stain	BacteriaNetⓘ	negative	99.29	no
125439	motility	BacteriaNetⓘ	no	65.42	no
125439	spore_formation	BacteriaNetⓘ	no	99.92	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rufibacter glacialis MDT1-10-3
NCBI: GCA_008271745.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.48	no
125438	anaerobic	anaerobicⓘ	no	97.24	no
125438	aerobic	aerobicⓘ	yes	87.72	yes
125438	spore-forming	spore-formingⓘ	no	82.77	no
125438	thermophilic	thermophileⓘ	no	94.19	no
125438	flagellated	motile2+ⓘ	no	87.25	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodocytophaga rosea sp. nov. and Nibribacter ruber sp. nov., two radiation-resistant bacteria isolated from soil.	Park Y, Maeng S, Han JH, Lee SE, Zhang J, Kim MK, Cha IT, Lee KE, Lee BH, Kim MK	Antonie Van Leeuwenhoek	10.1007/s10482-020-01488-1	2020
Phylogeny	Rufibacter hautae sp. nov., a red-pigmented bacterium from freshwater lake sediment, and proposal of Rufibacter quisquiliarum as a latter heterotypic synonym of Rufibacter ruber.	Zhou J, Ma WW, Qu JH, Li HF, Yang BB, Qu LB, Wang LF	Int J Syst Evol Microbiol	10.1099/ijsem.0.004502	2020
Phylogeny	Rufibacter latericius sp. nov., isolated from Baiyang Lake.	Yang YZ, Chen JF, Huang WR, Zhang RR, Liu S, Wang C, Feng J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004500	2020
Phylogeny	Rufibacter quisquiliarum sp. nov., a new member of the phylum Bacteroidetes isolated from a bioreactor treating landfill leachate.	Felfoldi T, Mentes A, Schumann P, Keki Z, Mathe I, Marialigeti K, Toth EM	Int J Syst Evol Microbiol	10.1099/ijsem.0.001488	2016
Phylogeny	Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil.	Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000717	2015

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 )
#65208	Qing Liu, Hong-Can Liu, Jian-Li Zhang, Yu-Guang Zhou, Yu-Hua Xin: Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil. IJSEM 66: 315 - 318 2016 ( DOI 10.1099/ijsem.0.000717 , PubMed 26510965 )
#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 .
#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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Rufibacter glacialis (CGMCC 1.9789, NBRC 109705, MDT1-10-3)

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

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014645715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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