Ruania albidiflava (DSM 18029, CGMCC 4.3142, JCM 13910)

Name: Ruania albidiflava (DSM 18029, CGMCC 4.3142, JCM 13910)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17801

Type strain

Strain Designation 3-6

Culture col. no. DSM 18029 CGMCC 4.3142 JCM 13910 PCM 2644 3-6 2 more

NCBI tax ID(s) 1123065 366586

Special Collections DSMZ JCM Wink compendium Literature strains CIP

History <- Ying Huang <- Qiang Gu, strain 3-6 Y. Huang 3-6. CIP <- 2007, JCM <- 2006, Y. Huang, Chinese Academy Sciences, Beijing, China: strain 3-6

Links

Ruania albidiflava 3-6 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from soil, farmland.

Gram-positive coccus-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 302773

CGMCC 4.3142,DSM 18029,JCM 13910,AS 4.3142,CIP 109565

@ref 20215

Last LPSN update 2026-02-09 11:22:18

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Ruaniaceae

Genus Ruania

Species Ruania albidiflava

Full scientific name Ruania albidiflava Gu et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell width	Cell shape	Confidence
31908	positive	0.5-0.8 µm	coccus-shaped
125438				94
125439	positive			98.5
116186	positive		coccus-shaped

Colony morphology

@ref	Colony color	Incubation period	Medium used
21406	Cream (9001)	10-14 days	ISP 2
21406	Beige (1001)	10-14 days	ISP 4

Pigmentation

31908

Productionyes

Multimedia

@ref:	66793
multimedia content:	EM_DSM_18029_1.jpg
multimedia.multimedia content:	EM_DSM_18029_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18029_2.jpg
multimedia.multimedia content:	EM_DSM_18029_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18029_3.jpg
multimedia.multimedia content:	EM_DSM_18029_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18029_4.jpg
multimedia.multimedia content:	EM_DSM_18029_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7254	RICH MEDIUM (DSMZ Medium 736)	Medium recipe at MediaDive	Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
21406	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21406	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
36057	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116186	CIP Medium 72	Medium recipe at CIP
116186	CIP Medium 112	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7254	positive	growth	28
31908	positive	growth	20-37
31908	positive	optimum	28
36057	positive	growth	30
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31908	positive	optimum	6.5-10.5
31908	positive	growth	5.5-12.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31908	aerobe
116186	facultative anaerobe
125439	obligate aerobe	99.1

Spore formation

31908

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31908	NaCl	positive	growth	0-10 %
31908	NaCl	positive	optimum	5 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31908	30089 ChEBI	acetate	+	carbon source
31908	16449 ChEBI	alanine	+	carbon source
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
31908	29016 ChEBI	arginine	+	carbon source
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
31908	28757 ChEBI	fructose	+	carbon source
31908	33984 ChEBI	fucose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
31908	17234 ChEBI	glucose	+	carbon source
31908	29987 ChEBI	glutamate	+	carbon source
31908	17754 ChEBI	glycerol	+	carbon source
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
31908	17716 ChEBI	lactose	+	carbon source
31908	17306 ChEBI	maltose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
31908	37657 ChEBI	methyl D-glucoside	+	carbon source
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
31908	17632 ChEBI	nitrate	+	reduction
116186	17632 ChEBI	nitrate	+	reduction
116186	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
31908	26271 ChEBI	proline	+	carbon source
31908	33942 ChEBI	ribose	+	carbon source
31908	30911 ChEBI	sorbitol	+	carbon source
31908	17992 ChEBI	sucrose	+	carbon source
31908	27082 ChEBI	trehalose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116186	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31908	catalase	+	1.11.1.6
116186	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116186	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
116186	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
116186	-	+	+	+	-	+	+	+	+	-	+	+	+	+	-	+	+	+	+	+

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
116186	not determinedn.d.	+/-	-	+/-	+/-	+/-	+/-	-	+/-	+/-	+/-	+/-	+/-	+/-	-	+/-	-	-	-	-	-	-	+/-	-	-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	-	-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	-	-	+/-	+/-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	-
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7254	soil, farmland	Shandong Province	China	CHN	Asia
67770	Farmland soil	Shandong Province	China	CHN	Asia
116186	Environment, Soil, farmland	Shandong	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence DQ343153 (>99% sequence identity) for Ruania albidiflava subclade from Microbeatlas

Aquatic Samples	113
Soil Samples	409
Animal Samples	842
Plant Samples	99
Total Samples	1463

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7254	1	Risk group (German classification) According to TRBA 466
116186	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
67770	ASM42122v1 assembly for Ruania albidiflava DSM 18029	contig	GCA_000421225	1123065.3	2524614511	1123065	66.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7254	Ruania albidiflava strain AS 4.3142 16S ribosomal RNA gene, partial sequence	DQ343153	1454		366586

GC content

@ref	GC-content (mol%)	Method
7254	69.8
67770	69.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ruania albidiflava DSM 18029
NCBI: GCA_000421225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	55.50	no
125439	motility	BacteriaNetⓘ	no	78.20	no
125439	gram_stain	BacteriaNetⓘ	positive	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ruania albidiflava DSM 18029
PATRIC: 1123065.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.60	yes
125438	anaerobic	anaerobicⓘ	no	94.37	yes
125438	spore-forming	spore-formingⓘ	no	72.84	no
125438	aerobic	aerobicⓘ	yes	82.86	no
125438	thermophilic	thermophileⓘ	no	93.94	no
125438	flagellated	motile2+ⓘ	no	94.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ruania albidiflava gen. nov., sp. nov., a novel member of the suborder Micrococcineae.	Gu Q, Pasciak M, Luo H, Gamian A, Liu Z, Huang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64635-0	2007
Phylogeny	Ruania rhizosphaerae sp. nov., a novel actinobacterium isolated from rhizosphere of Suaeda aralocaspica.	Lu WN, Xu YZ, Xie YG, Gao R, Song JQ, Liu DF, Xiao M, Wang HF, Li QL, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.005007	2021
Phylogeny	Identification of Haloactinobacterium kanbiaonis sp. nov. and Ruania zhangjianzhongii sp. nov., two novel species of the family Ruaniaceae isolated from faeces of bats (Hipposideros spp.).	Xu M, Dai Y, Huang Y, Yang J, Lai XH, Jin D, Lu S, Zhou J, Zhang S, Bai Y, Jiao Y, Qiao L, Jiang Y, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004953	2021

References

#7254	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18029
#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 )
#21406	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#28165	IJSEM 809 2007 ( DOI 10.1099/ijs.0.64635-0 , PubMed 17392211 )
#31908	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 #28165
#36057	; Curators of the CIP;
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#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 .
#116186	Collection of Institut Pasteur ; Curators of the CIP; CIP 109565
#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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Ruania albidiflava (DSM 18029, CGMCC 4.3142, JCM 13910)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000421225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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