Ruegeria intermedia (DSM 23285, CCM 7758, CCUG 59209)

Name: Ruegeria intermedia (DSM 23285, CCM 7758, CCUG 59209)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24505

Type strain

Strain Designation CC-GIMAT-2

Variant Isotype of BacDive ID 132916 & 130627

Culture col. no. DSM 23285 CCM 7758 CCUG 59209 DSM 104504 DSM 29341 2 more

NCBI tax ID(s) 996115

Special Collections DSMZ CCUG Literature strains

Links

Ruegeria intermedia CC-GIMAT-2 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from coastal hot spring of a volcanic island.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 368608

DSM 29341,DSM 104504,DSM 23285,LMG 25539,CCM 7758,CCUG 59209

@ref 20215

Last LPSN update 2025-12-16 09:52:51

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Ruegeria

Species Ruegeria intermedia

Full scientific name Ruegeria intermedia Kämpfer et al. 2013

BacDive ID	Other strains from **Ruegeria intermedia** (2)	Type strain
130627	R. intermedia CC-GIMAT-2, DSM 29341, CCM 7758, CCUG 59209, ... (type strain)
132916	R. intermedia CC-GIMAT-2, DSM 104504, CCM 7758, CCUG 59209, ... (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30935	negative	3.5 µm	1.1 µm	rod-shaped
125438	negative				99.333
125439	negative				98.5

Pigmentation

30935

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20793	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20793	positive	growth	28	mesophilic
30935	positive	growth	15-55
30935	positive	optimum	41	thermophilic

Culture pH

@ref	Ability	Type	PH	PH range
30935	positive	optimum	8
30935	positive	growth	5.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30935	aerobe
125439	obligate aerobe	92

Spore formation

@ref	Spore formation	Confidence
30935
125438		93.401
125439		98

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30935	NaCl	positive	growth	01-04 %
30935	NaCl	positive	optimum	1.5 %

Observation

30935

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30935	4853 ChEBI	esculin	+	hydrolysis
30935	28260 ChEBI	galactose	+	carbon source
30935	17234 ChEBI	glucose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30935	catalase	+	1.11.1.6
30935	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Environmental	#Terrestrial	#Volcanic
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
20793	coastal hot spring of a volcanic island	Green Island (Lutao) of the Pacific Ocean, off the east coast of Taiwan (22°39' N 121° 29' E)	Taiwan, Province of China	TWN	Asia	22.65	121.483 22.65/121.483

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20793	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2695420938 annotated assembly for Ruegeria intermedia DSM 29341	scaffold	GCA_900129345	996115.4	2695420938	996115	58.3

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20793	Ruegeria intermedia partial 16S rRNA gene, type strain CC-GIMAT-2T	FR832879	1344		996115
124043	Ruegeria intermedia strain DSM 29341 16S ribosomal RNA gene, partial sequence.	MW198103	601		996115

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ruegeria intermedia DSM 29341
NCBI: GCA_900129345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.00	no
125439	motility	BacteriaNetⓘ	yes	62.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ruegeria intermedia DSM 29341
NCBI: GCA_900129345.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.33	no
125438	anaerobic	anaerobicⓘ	no	92.58	yes
125438	aerobic	aerobicⓘ	yes	80.32	no
125438	spore-forming	spore-formingⓘ	no	93.40	yes
125438	thermophilic	thermophileⓘ	no	95.30	yes
125438	flagellated	motile2+ⓘ	no	55.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Prokaryotic viperins produce diverse antiviral molecules.	Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R.	Nature	10.1038/s41586-020-2762-2	2021
Phylogeny	Ruegeria sediminis sp. nov., isolated from tidal flat sediment.	Baek J, Kim JH, Sukhoom A, Kim W	Int J Syst Evol Microbiol	10.1099/ijsem.0.004128	2020
Phylogeny	Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring.	Kampfer P, Arun AB, Rekha PD, Busse HJ, Young CC, Glaeser SP	Int J Syst Evol Microbiol	10.1099/ijs.0.047910-0	2012
Phylogeny	Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea.	Zhang G, Haroon MF, Zhang R, Dong X, Wang D, Liu Y, Xun W, Dong X, Stingl U	Int J Syst Evol Microbiol	10.1099/ijsem.0.002344	2017

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 )
#20793	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23285
#27265	IJSEM 2538 2013 ( DOI 10.1099/ijs.0.047910-0 , PubMed 23243093 )
#30935	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27265
#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) .
#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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Ruegeria intermedia (DSM 23285, CCM 7758, CCUG 59209)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900129345

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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