Name: Rufibacter glacialis MDT1-10-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158531

Type strain:

Species: Rufibacter glacialis

Strain Designation: MDT1-10-3

Culture col. no.: CGMCC 1.9789, NBRC 109705

NCBI tax ID(s): 1259555 (species)

Section

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

colony-forming
Gram-negative
rod-shaped
aerobe
psychrophilic
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	*Rufibacter*
	Species	**Rufibacter glacialis**
	Full Scientific Name (LPSN)	Rufibacter glacialis Liu et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #65208]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #65208]	Cell length	1.7-1.9 µm

[Ref.: #65208]	Cell width	0.9-1.1 µm

[Ref.: #65208]	Cell shape	rod-shaped

[Ref.: #65208]	Motility	no

[Ref.: #65208]	Colony size	2.0 mm
[Ref.: #65208]	Colony color	red
[Ref.: #65208]	Colony shape	circular
[Ref.: #65208]	Incubation period	4 days
[Ref.: #65208]	Cultivation medium used	R2A

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65208]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #65208]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #65208]		optimum	18-22 °C
[Ref.: #65208]		growth	4-25 °C
[Ref.: #65208]	no	growth	30 °C

[Ref.: #65208]	Temperature range	psychrophilic
[Ref.: #65208]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65208]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65208]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.902
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65208]		NaCl		growth	0-1.0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65208]	2-oxoglutarate ChEBI	-	carbon source
[Ref.: #65208]	acetoacetate ChEBI	+	carbon source
[Ref.: #65208]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #65208]	alpha-lactose ChEBI	+	carbon source
[Ref.: #65208]	bromosuccinate ChEBI	-	carbon source
[Ref.: #65208]	casein	+	hydrolysis
[Ref.: #65208]	cellobiose ChEBI	-	carbon source
[Ref.: #65208]	citrate ChEBI	-	assimilation
[Ref.: #65208]	citrate ChEBI	+	carbon source
[Ref.: #65208]	D-fructose 6-phosphate ChEBI	+	carbon source
[Ref.: #65208]	D-galactose ChEBI	+	carbon source
[Ref.: #65208]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #65208]	D-glucuronate ChEBI	-	carbon source
[Ref.: #65208]	D-mannose ChEBI	-	carbon source
[Ref.: #65208]	dextrin ChEBI	+	carbon source
[Ref.: #65208]	esculin ChEBI	+	hydrolysis
[Ref.: #65208]	gelatin ChEBI	+	carbon source
[Ref.: #65208]	gelatin ChEBI	+	hydrolysis
[Ref.: #65208]	gentiobiose ChEBI	-	carbon source
[Ref.: #65208]	glucose ChEBI	-	fermentation
[Ref.: #65208]	glucuronamide ChEBI	+	carbon source
[Ref.: #65208]	glycine-proline ChEBI	-	carbon source
[Ref.: #65208]	L-alanine ChEBI	-	carbon source
[Ref.: #65208]	L-aspartate ChEBI	-	carbon source
[Ref.: #65208]	L-galactonic acid gamma-lactone ChEBI	+	carbon source
[Ref.: #65208]	L-glutamate ChEBI	-	carbon source
[Ref.: #65208]	L-malate ChEBI	-	carbon source
[Ref.: #65208]	L-rhamnose ChEBI	-	carbon source
[Ref.: #65208]	maltose ChEBI	+	carbon source
[Ref.: #65208]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #65208]	nitrate ChEBI	+	reduction
[Ref.: #65208]	pectin ChEBI	+	carbon source
[Ref.: #65208]	starch ChEBI	+	hydrolysis
[Ref.: #65208]	trehalose ChEBI	+	carbon source
[Ref.: #65208]	turanose ChEBI	-	carbon source
[Ref.: #65208]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #65208]	acetoin ChEBI	no
[Ref.: #65208]	hydrogen sulfide ChEBI	no
[Ref.: #65208]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #65208]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #65208]	acid phosphatase	+	3.1.3.2
[Ref.: #65208]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65208]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65208]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65208]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65208]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65208]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65208]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65208]	beta-galactosidase	+	3.2.1.23
[Ref.: #65208]	beta-glucosidase	-	3.2.1.21
[Ref.: #65208]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65208]	catalase	+	1.11.1.6
[Ref.: #65208]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65208]	esterase (C 4)	+
[Ref.: #65208]	esterase Lipase (C 8)	+
[Ref.: #65208]	leucine arylamidase	+	3.4.11.1
[Ref.: #65208]	lysine decarboxylase	-	4.1.1.18
[Ref.: #65208]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #65208]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65208]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #65208]	trypsin	+	3.4.21.4
[Ref.: #65208]	tryptophan deaminase	-	4.1.99.1
[Ref.: #65208]	urease	-	3.5.1.5
[Ref.: #65208]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #65208]	Sample type/isolated from	soil
[Ref.: #65208]	Geographic location (country and/or sea, region)	Midui glacier in Tibet
[Ref.: #65208]	Country	China
[Ref.: #65208]	Country ISO 3 Code	CHN
[Ref.: #65208]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #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

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.: #65208]	16S rRNA gene sequence	JX949546		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rufibacter glacialis MDT1-10-3	GCA_008271745	scaffold	GenBank	1259555 tax ID	*
[Ref.: #66792]	Rufibacter glacialis CGMCC 1.9789	GCA_014645715	scaffold	GenBank	1259555 tax ID	*
[Ref.: #66792]	Rufibacter glacialis strain CGMCC 1.9789	1259555.5	wgs	PATRIC	1259555 tax ID	*
[Ref.: #66792]	Rufibacter glacialis MDT1-10-3	2891128709	draft	JGI IMG/M	1259555 tax ID	*

[Ref.: #65208]

GC-content

49 mol%

thermal denaturation, midpoint method (Tm)

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: Rufibacter glacialis MDT1-10-3 NCBI: GCA_008271745.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rufibacter glacialis MDT1-10-3 NCBI: GCA_008271745.1
[Ref.: #69480]	motile	no	93.233	yes
[Ref.: #69480]	flagellated	no	97.192	yes
[Ref.: #69480]	gram-positive	no	98.055	no
[Ref.: #69480]	anaerobic	no	99.281	yes
[Ref.: #69480]	aerobic	yes	91.268	yes
[Ref.: #69480]	halophile	no	93.026	yes
[Ref.: #69480]	spore-forming	no	93.239	no
[Ref.: #69480]	glucose-util	yes	90.05	yes
[Ref.: #69480]	thermophile	no	94.731	yes
[Ref.: #69480]	glucose-ferment	no	88.474	no

Availability in culture collections External links

[Ref.: #65208]

Culture collection no.

CGMCC 1.9789, NBRC 109705

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 .

#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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