Rufibacter ruber (CCM 8646, LMG 29438)

Name: Rufibacter ruber (CCM 8646, LMG 29438)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133192

Type strain

Culture col. no. CCM 8646 LMG 29438

NCBI tax ID(s) 1783499

Special Collections Literature strains

Links

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

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

Name and taxonomic classification

SI-ID 272735

LMG 29438

@ref 20215

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

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Hymenobacteraceae

Genus Rufibacter

Species Rufibacter ruber

Full scientific name Rufibacter ruber Kýrová et al. 2016

Synonyms (1)

Rufibacter quisquiliarum

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
24988	negative	rod-shaped
125439	negative		99.6
125438	negative		95.982

Colony morphology

@ref	Type of hemolysis	Colony size	Colony color	Colony shape	Medium used
24988	gamma	1.0-2.0 mm	pink-red	circular	R2A agar (Reasoner's 2A agar)

Pigmentation

@ref	Production	Color
24988		red

Culture and growth conditions

Culture medium

@ref	Name	Growth
24988	Reasoner's 2A agar (R2A)
24988	plate count agar (Oxoid)
24988	tryptone soya agar (Oxoid)
24988	brain infusion agar (Oxoid)

Culture temp

@ref	Growth	Type	Temperature (°C)
24988	positive	growth	10.0-40.0
24988	negative	growth	5
24988	negative	growth	42
24988	positive	optimum	25

Culture pH

@ref	Ability	Type	PH	PH range
24988	positive	optimum	8
24988	positive	growth	7.0-11.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

24988

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
24988
125439		99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
24988	NaCl	positive	maximum	1 %(w/v)
24988	NaCl		optimum	0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
24988		casein	-	hydrolysis
24988	16947 ChEBI	citrate	-	carbon source
24988	4853 ChEBI	esculin	+	hydrolysis
24988	28757 ChEBI	fructose	+	builds acid from
24988	5291 ChEBI	gelatin	+	hydrolysis
24988	17234 ChEBI	glucose	+	builds acid from
24988	61995 ChEBI	lecithin	-	hydrolysis
24988	17306 ChEBI	maltose	+	builds acid from
24988	29864 ChEBI	mannitol	-	builds acid from
24988	17632 ChEBI	nitrate	-	reduction
24988	16301 ChEBI	nitrite	-	reduction
24988		O-nitrophenyl-beta-D-galactopyranosid	+	hydrolysis
24988	28017 ChEBI	starch	+	hydrolysis
24988	53426 ChEBI	tween 80	-	hydrolysis
24988	18186 ChEBI	tyrosine	-	hydrolysis
24988	18222 ChEBI	xylose	+	builds acid from

Metabolite tests

@ref	Chebi-ID	Metabolite	Citrate test
24988	16947 ChEBI	citrate	-

Enzymes

@ref	Value	Activity	Ec
24988	acid phosphatase	+	3.1.3.2
24988	alkaline phosphatase	+	3.1.3.1
24988	alpha-fucosidase	-	3.2.1.51
24988	alpha-galactosidase	+	3.2.1.22
24988	alpha-glucosidase	+	3.2.1.20
24988	alpha-mannosidase	-	3.2.1.24
24988	arginine dihydrolase	-	3.5.3.6
24988	beta-galactosidase	-	3.2.1.23
24988	beta-glucosidase	-	3.2.1.21
24988	beta-glucuronidase	-	3.2.1.31
24988	catalase	+	1.11.1.6
24988	chymotrypsin	-	3.4.4.5
24988	cystine arylamidase	-	3.4.11.3
24988	cytochrome oxidase	-	1.9.3.1
24988	DNase	+
24988	esterase (C 4)	-
24988	esterase Lipase (C 8)	+
24988	leucine arylamidase	+	3.4.11.1
24988	lipase (C 14)	-
24988	lysine decarboxylase	-	4.1.1.18
24988	N-acetyl-beta-glucosaminidase	+	3.2.1.52
24988	naphthol-AS-BI-phosphohydrolase	-
24988	ornithine decarboxylase	-	4.1.1.17
24988	trypsin	-	3.4.21.4
24988	urease	-	3.5.1.5
24988	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24988	fragmentary rock	James Ross Island	Antarctica	ATA	Australia and Oceania	-63	-57 -63/-57

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM164727v1 assembly for Rufibacter ruber CCM 8646	contig	GCA_001647275	1783499.3	2744054599	1783499	43.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24988	Rufibacter ruber strain CCM 8646 16S ribosomal RNA gene, partial sequence	KU603607	1500		1783499

GC content

@ref	GC-content (mol%)	Method
24988	51.54	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rufibacter ruber CCM 8646
NCBI: GCA_001647275

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	no	53.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	67.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rufibacter sp. CCM 8646
PATRIC: 1783499.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.98	yes
125438	anaerobic	anaerobicⓘ	no	97.22	yes
125438	spore-forming	spore-formingⓘ	no	86.19	no
125438	aerobic	aerobicⓘ	yes	89.58	yes
125438	thermophilic	thermophileⓘ	no	96.96	yes
125438	flagellated	motile2+ⓘ	no	88.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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 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 .
#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 ruber (CCM 8646, LMG 29438)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001647275

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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