Name: Rufibacter ruber CCM 8646
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133192

Type strain:

Species: Rufibacter ruber

Culture col. no.: CCM 8646, LMG 29438

NCBI tax ID(s): 1783499 (species)

Section

Rufibacter ruber CCM 8646 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and has a red pigmentation.

colony-forming
Gram-negative
pigmented
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	*Rufibacter*
	Species	**Rufibacter ruber**
	Full Scientific Name (LPSN)	Rufibacter ruber Kýrová et al. 2016

Synonym

Rufibacter quisquiliarum

Information on morphological and physiological properties Morphology

[Ref.: #24988]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.991

[Ref.: #24988]	Cell shape	rod-shaped

[Ref.: #24988]	Type of hemolysis	gamma
[Ref.: #24988]	Colony size	1.0-2.0 mm
[Ref.: #24988]	Colony color	pink-red
[Ref.: #24988]	Colony shape	circular
[Ref.: #24988]	Cultivation medium used	R2A agar (Reasoner's 2A agar)

[Ref.: #24988]	Pigment production	yes
[Ref.: #24988]	Pigmentation color	red

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24988]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #24988]

Culture medium growth

[Ref.: #24988]

Culture medium

plate count agar (Oxoid)

[Ref.: #24988]

Culture medium growth

[Ref.: #24988]

Culture medium

tryptone soya agar (Oxoid)

[Ref.: #24988]

Culture medium growth

[Ref.: #24988]

Culture medium

brain infusion agar (Oxoid)

[Ref.: #24988]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #24988]		growth	10.0-40.0 °C
[Ref.: #24988]	no	growth	5 °C
[Ref.: #24988]	no	growth	42 °C
[Ref.: #24988]		optimum	25 °C

[Ref.: #24988]	Temperature range	psychrophilic
[Ref.: #24988]	Temperature range	thermophilic
[Ref.: #24988]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #24988]			optimum	8
[Ref.: #24988]			growth	7.0-11.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24988]

Oxygen tolerance

aerobe

[Ref.: #24988]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.958

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24988]		NaCl		maximum	1	%(w/v)
[Ref.: #24988]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24988]	casein	-	hydrolysis
[Ref.: #24988]	citrate ChEBI	-	carbon source
[Ref.: #24988]	esculin ChEBI	+	hydrolysis
[Ref.: #24988]	fructose ChEBI	+	builds acid from
[Ref.: #24988]	gelatin ChEBI	+	hydrolysis
[Ref.: #24988]	glucose ChEBI	+	builds acid from
[Ref.: #24988]	lecithin ChEBI	-	hydrolysis
[Ref.: #24988]	maltose ChEBI	+	builds acid from
[Ref.: #24988]	mannitol ChEBI	-	builds acid from
[Ref.: #24988]	nitrate ChEBI	-	reduction
[Ref.: #24988]	nitrite ChEBI	-	reduction
[Ref.: #24988]	O-nitrophenyl-beta-D-galactopyranosid	+	hydrolysis
[Ref.: #24988]	starch ChEBI	+	hydrolysis
[Ref.: #24988]	tween 80 ChEBI	-	hydrolysis
[Ref.: #24988]	tyrosine ChEBI	-	hydrolysis
[Ref.: #24988]	xylose ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Physiological tests	Metabolite	Citrate test
[Ref.: #24988]		citrate ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #24988]	acid phosphatase	+	3.1.3.2
[Ref.: #24988]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24988]	alpha-fucosidase	-	3.2.1.51
[Ref.: #24988]	alpha-galactosidase	+	3.2.1.22
[Ref.: #24988]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24988]	alpha-mannosidase	-	3.2.1.24
[Ref.: #24988]	arginine dihydrolase	-	3.5.3.6
[Ref.: #24988]	beta-galactosidase	-	3.2.1.23
[Ref.: #24988]	beta-glucosidase	-	3.2.1.21
[Ref.: #24988]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24988]	catalase	+	1.11.1.6
[Ref.: #24988]	chymotrypsin	-	3.4.4.5
[Ref.: #24988]	cystine arylamidase	-	3.4.11.3
[Ref.: #24988]	cytochrome oxidase	-	1.9.3.1
[Ref.: #24988]	DNase	+
[Ref.: #24988]	esterase (C 4)	-
[Ref.: #24988]	esterase Lipase (C 8)	+
[Ref.: #24988]	leucine arylamidase	+	3.4.11.1
[Ref.: #24988]	lipase (C 14)	-
[Ref.: #24988]	lysine decarboxylase	-	4.1.1.18
[Ref.: #24988]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #24988]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #24988]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #24988]	trypsin	-	3.4.21.4
[Ref.: #24988]	urease	-	3.5.1.5
[Ref.: #24988]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24988]	Sample type/isolated from	fragmentary rock
[Ref.: #24988]	Geographic location (country and/or sea, region)	James Ross Island
[Ref.: #24988]	Country	Antarctica
[Ref.: #24988]	Country ISO 3 Code	ATA
[Ref.: #24988]	Continent	Australia and Oceania
[Ref.: #24988]	Geographic location	-63.0000°/-57.0000°
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Geologic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU603607 (>99% sequence identity) for Rufibacter from Microbeatlas

Aquatic Samples	721
Soil Samples	450
Animal Samples	1055
Plant Samples	96
Total Samples	2322

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.: #24988]	Rufibacter ruber strain CCM 8646 16S ribosomal RNA gene, partial sequence	KU603607	1500	GenBank	1783499 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rufibacter ruber CCM 8646	GCA_001647275	contig	GenBank	1783499 tax ID	*
[Ref.: #66792]	Rufibacter sp. CCM 8646	1783499.3	wgs	PATRIC	1783499 tax ID	*
[Ref.: #66792]	Rufibacter ruber CCM 8646	2744054599	draft	JGI IMG/M	1783499 tax ID	*

[Ref.: #24988]

GC-content

51.54 mol%

genome sequence analysis

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 sp. CCM 8646 PATRIC: 1783499.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rufibacter sp. CCM 8646 PATRIC: 1783499.3
[Ref.: #69480]	motile	no	89.902	no
[Ref.: #69480]	gram-positive	no	98.027	no
[Ref.: #69480]	anaerobic	no	99.466	yes
[Ref.: #69480]	aerobic	yes	92.454	no
[Ref.: #69480]	halophile	no	93.871	no
[Ref.: #69480]	spore-forming	no	93.832	yes
[Ref.: #69480]	thermophile	no	96.808	no
[Ref.: #69480]	glucose-util	yes	89.985	no
[Ref.: #69480]	flagellated	no	96.549	no
[Ref.: #69480]	glucose-ferment	no	90.825	no

Availability in culture collections External links

[Ref.: #24988]

Culture collection no.

CCM 8646, LMG 29438

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rufibacter ruber sp. nov., isolated from fragmentary rock.	Kyrova K, Sedlacek I, Pantucek R, Kralova S, Holochova P, Maslanova I, Stankova E, Kleinhagauer T, Gelbicova T, Sobotka R, Svec P, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001364	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 )

#24988

K. S. Kýrová, Ivo,Pantucek, Roman,Králová, Stanislava,Holochová, Pavla,Maslanová, Ivana,Stanková, Eva,Kleinhagauer, Tanita,Gelbícová, Tereza,Sobotka, Roman,Svec, Pavel,Busse, Hans-Jürgen: Rufibacter ruber sp. nov., isolated from fragmentary rock. IJSEM 66: 4401 - 4405 2016 ( DOI 10.1099/ijsem.0.001364 , PubMed 27488543 )

#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

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Rufibacter ruber in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Rufibacter sp. CCM 8646

Rufibacter sp. CCM 8646

Change proposal

Change proposal