Erythrobacter ramosus (DSM 8510, IAM 14333, NCIMB 13404)

Name: Erythrobacter ramosus (DSM 8510, IAM 14333, NCIMB 13404)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5387

Type strain

Strain Designation E5

Culture col. no. DSM 8510 IAM 14333 NCIMB 13404 E5 NBRC 102621 3 more

NCBI tax ID(s) 35811

Special Collections DSMZ JCM CIP Literature strains

History DSMZ <- V. Yurkov, E5 JCM <-- E. Yabuuchi EY4223 <-- ATCC 700003 <-- DSM 8510 <-- V. Yurkov E5. CIP <- 2001, IAM <- DSMZ <- V. Yurkov: strain E5

Links

Erythrobacter ramosus E5 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from cyanobacterial mat from a hot spring.

Gram-negative motile rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 93008

ATCC 700003,CIP 106927,IAM 14333,NCIMB 13404,JCM 10282,DSM 8510,NBRC 102621

@ref 20215

Last LPSN update 2026-05-29 08:26:09

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Erythrobacter

Species Erythrobacter ramosus

Full scientific name Erythrobacter ramosus (Yurkov et al. 1994) Xu et al. 2020

Synonyms (1)

Erythromicrobium ramosum

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
23246	negative	1.3-2.5 µm	0.6-1.0 µm	rod-shaped	monotrichous, polar
122135	negative			rod-shaped
125439	negative					98.757
125438	negative					98.208

Colony morphology

@ref	Colony color	Hemolysis ability
23246	orange
122135		0

Pigmentation

@ref	Production	Name
23246		bacteriochlorophyll a
23246		carotenoid pigment

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3291	ERYTHROMICROBIUM AND ROSEOCOCCUS MEDIUM (DSMZ Medium 767)	Medium recipe at MediaDive	Name: ERYTHROMICROBIUM AND ROSEOCOCCUS MEDIUM (DSMZ Medium 767) Composition: Yeast extract 1.0 g/l Na-acetate 1.0 g/l Bacto peptone 1.0 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.3 g/l NH4Cl 0.3 g/l KCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l Na2MoO4 x 2 H2O 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Vitamin B12 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
37252	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122135	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3291	positive	growth	30
23246	positive	optimum	25-30
37252	positive	growth	25
67770	positive	growth	26
122135	positive	growth	15-45
122135	negative	growth	5

Culture pH

@ref	Ability	Type	PH	PH range
23246	positive	optimum	7.08-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.971
122135	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.159
125438		90.965

Halophily

@ref	Salt	Growth	Tested relation	Concentration
122135	NaCl	positive	growth	0-10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23246	30089 ChEBI	acetate	+	growth
23246	22599 ChEBI	arabinose	-	growth
23246	16150 ChEBI	benzoate	-	growth
23246	17968 ChEBI	butyrate	+	growth
23246		casein hydrolysate	+	growth
23246	16947 ChEBI	citrate	+	growth
122135	16947 ChEBI	citrate	-	carbon source
122135	4853 ChEBI	esculin	+	hydrolysis
23246	16236 ChEBI	ethanol	+	growth
23246	15740 ChEBI	formate	-	growth
23246	28757 ChEBI	fructose	+	growth
23246	29806 ChEBI	fumarate	+	growth
23246	5291 ChEBI	gelatin	-	hydrolysis
23246	17234 ChEBI	glucose	+	growth
23246	29987 ChEBI	glutamate	+	growth
23246	17754 ChEBI	glycerol	-	growth
23246	29805 ChEBI	glycolate	-	growth
122135	606565 ChEBI	hippurate	+	hydrolysis
23246	24996 ChEBI	lactate	+	growth
23246	25115 ChEBI	malate	+	growth
122135	15792 ChEBI	malonate	-	assimilation
23246	17306 ChEBI	maltose	+	growth
23246	29864 ChEBI	mannitol	-	growth
23246	17790 ChEBI	methanol	-	assimilation
23246	17790 ChEBI	methanol	-	growth
122135	17632 ChEBI	nitrate	-	builds gas from
122135	17632 ChEBI	nitrate	-	reduction
122135	17632 ChEBI	nitrate	-	respiration
122135	16301 ChEBI	nitrite	-	builds gas from
122135	16301 ChEBI	nitrite	-	reduction
23246	17272 ChEBI	propionate	+	growth
23246	15361 ChEBI	pyruvate	+	growth
23246	33942 ChEBI	ribose	-	growth
23246	28017 ChEBI	starch	-	hydrolysis
23246	30031 ChEBI	succinate	+	growth
23246	17992 ChEBI	sucrose	+	growth
23246	132950 ChEBI	tartrate	+	growth
23246	53426 ChEBI	tween 80	-	hydrolysis
23246		yeast extract	+	growth

Antibiotic resistance

@ref	ChEBI	Group ID	Metabolite	Sensitivity conc.	Resistance conc.
122135			0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
23246	2637	0	amikacin
23246	28971	0	ampicillin
23246	28669	0	bacitracin
23246	17698	0	chloramphenicol	100 µg (disc)
23246	27644	0	chlortetracyclin
23246	48923	0	erythromycin
23246	71321	0	fusidate	0.5 µg (disc)
23246	17833	0	gentamicin
23246	6104	0	kanamycin
23246	100147	0	nalidixic acid
23246	7507	0	neomycin
23246	28368	0	novobiocin
23246	7660	0	nystatin
23246	7660	0	nystatin
23246	17334	0	penicillin		20 Unit (disc)
23246	8309	0	polymyxin b	100 Unit (disc)
23246	17076	0	streptomycin		50 µg (disc)
23246	27902	0	tetracycline
23246	28001	0	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122135	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
122135	15688 ChEBI	acetoin	-
122135	17234 ChEBI	glucose		+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
122135	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
122135	amylase	-
68382	beta-galactosidase	+	3.2.1.23	from API zym
122135	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122135	caseinase	-	3.4.21.50
23246	catalase	+	1.11.1.6
122135	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
23246	cytochrome oxidase	+	1.9.3.1
122135	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
122135	gamma-glutamyltransferase	+	2.3.2.2
122135	gelatinase	+/-
122135	lecithinase	+
68382	leucine arylamidase	-	3.4.11.1	from API zym
122135	lipase	+
68382	lipase (C 14)	-		from API zym
122135	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122135	ornithine decarboxylase	-	4.1.1.17
122135	oxidase	+
122135	protease	+
68382	trypsin	-	3.4.21.4	from API zym
122135	tryptophan deaminase	-
122135	tween esterase	-
122135	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122135	-	-	+	+	-	-	+	-	-	+	-	+	-	+	-	-	+	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
122135	not determinedn.d.	+	+	+	+	+	-	+	+	+	-	+	-	-	-	-	+	+	+	+	+	+	+	+	-	-	-	-	-	-	-	+	+	+	+	+	+	-	-	-	-	-	+	-	-	-	-	-	-	-	+	+	+	-	+	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	+	-	+	-	-	-	+	-	-	+	+	-	-	+	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	#Thermal spring
#Environmental	#Microbial community	#Microbial mat
#Host	#Microbial	#Bacteria
#Condition	#Alkaline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3291	cyanobacterial mat from a hot spring	Lake Baykal region	Russia	RUS	Asia
23246	cyanobacterial mat from an alkaline spring (pH 9.5; 25°C)
67770	Cyanobacterial mat from an alkaline spring
122135	Environment, Cyanobacterial mat from a hot spring	Baykal lake	Russian Federation	RUS	Europe

Taxonmaps

69479

Global distribution of 16S sequence AF465837 (>99% sequence identity) for Erythrobacter from Microbeatlas

Aquatic Samples	430
Soil Samples	88
Animal Samples	276
Plant Samples	31
Total Samples	825

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3291	1	Risk group (German classification) According to TRBA 466
122135	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1419567v1 assembly for Erythrobacter ramosus DSM 8510	contig	GCA_014195675	35811.6	2828010827	35811	71.27
67770	ASM982805v1 assembly for Erythrobacter ramosus JCM 10282	scaffold	GCA_009828055	35811.5	8110311199	35811	71.27
124043	ASM3952274v1 assembly for Erythrobacter ramosus JCM 10282	scaffold	GCA_039522745			35811	58.93

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Erythromicrobium ramosum gene for 16S rRNA	AB013355	1408	35811
20218	Erythromicrobium ramosum strain DSM 8510 16S ribosomal RNA gene, partial sequence	AF465837	1413	35811
20218	E.ramosum gene for 16S rRNA	X72909	1115	35811

GC content

@ref	GC-content (mol%)	Method
67770	64	thermal denaturation, midpoint method (Tm)
67770	64.3	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM982805v1 assembly for Erythrobacter ramosus JCM 10282
BV-BRC: 35811.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.97	no
125439	gram_stain	BacteriaNetⓘ	negative	98.76	no
125439	motility	BacteriaNetⓘ	no	59.93	no
125439	spore_formation	BacteriaNetⓘ	no	99.16	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Erythromicrobium ramosum strain DSM 8510
PATRIC: 35811.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.21	yes
125438	anaerobic	anaerobicⓘ	no	94.47	no
125438	spore-forming	spore-formingⓘ	no	90.97	no
125438	aerobic	aerobicⓘ	yes	85.65	no
125438	thermophilic	thermophileⓘ	no	94.40	no
125438	flagellated	motile2+ⓘ	yes	56.80	yes

Literature

Title	Authors	Journal	DOI	Year
New Multidrug Efflux Systems in a Microcystin-Degrading Bacterium Blastomonas fulva and Its Genomic Feature.	Jin L, Cui C, Zhang C, Ko SR, Li T, Jin FJ, Ahn CY, Oh HM, Lee HG.	Int J Mol Sci	10.3390/ijms231810856	2022
An S-methyltransferase that produces the climate-active gas dimethylsulfide is widespread across diverse marine bacteria.	Zhang Y, Sun C, Guo Z, Liu L, Zhang X, Sun K, Zheng Y, Gates AJ, Todd JD, Zhang XH.	Nat Microbiol	10.1038/s41564-024-01788-6	2024
Abundance, Characterization and Diversity of Culturable Anoxygenic Phototrophic Bacteria in Manitoban Marshlands.	Messner K, Yurkov V.	Microorganisms	10.3390/microorganisms12051007	2024

References

#3291	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 8510
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#23246	VLADIMIR YURKOV, ERKO STACKEBRANDT, ANDREW HOLMES, JOHN A. FUERST, P. HUGENHOLTZ, JOCHEN GOLECKI, NASSER GAD'ON, VLADIMIR M. GORLENKO, ELENA I. KOMPANTSEVA, GERHART DREWS: Phylogenetic Positions of Novel Aerobic, Bacteriochlorophyll a-Containing Bacteria and Description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov.. IJSEM 44: 427 - 434 1994 ( DOI 10.1099/00207713-44-3-427 , PubMed 7520734 )
#37252	; Curators of the CIP;
#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;
#68382	Automatically annotated from API zym .
#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 .
#122135	Collection of Institut Pasteur ; Curators of the CIP; CIP 106927
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Erythrobacter ramosus (DSM 8510, IAM 14333, NCIMB 13404)

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

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014195675

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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