Fodinibius roseus (DSM 21986, ACCC 10715, KCTC 23442)

Name: Fodinibius roseus (DSM 21986, ACCC 10715, KCTC 23442)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24787

Type strain

Culture col. no. DSM 21986 ACCC 10715 KCTC 23442 YIM D15

NCBI tax ID(s) 1194090

Special Collections DSMZ KCTC Literature strains

History DSMZ <- X.-L. Cui, YIM; YIM D15 <- J.-H. Liu and Y.-X. Wang

Links

Fodinibius roseus DSM 21986 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from sediment from a salt mine.

Gram-negative rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407464

KCTC 23442,DSM 21986

@ref 20215

Last LPSN update 2026-05-29 08:30:41

Domain Bacteria

Phylum Balneolota

Class Balneolia

Order Balneolales

Family Balneolaceae

Genus Fodinibius

Species Fodinibius roseus

Full scientific name Fodinibius roseus (Wang et al. 2013) Galisteo et al. 2023

Synonyms (1)

Aliifodinibius roseus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30765	negative	0.55 µm	0.3 µm	rod-shaped

Pigmentation

30765

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21259	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 100.0 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)
21259	positive	growth	28
30765	positive	growth	20-42
30765	positive	optimum	28

Culture pH

@ref	Ability	Type	PH
30765	positive	optimum	7
30765	positive	growth	6.5-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30765	facultative anaerobe
125439	facultative anaerobe	92.352

Spore formation

30765

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30765	NaCl	positive	growth	04-20 %
30765	NaCl	positive	optimum	8 %

Observation

30765

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30765	30089 ChEBI	acetate	+	carbon source
30765	35391 ChEBI	aspartate	+	carbon source
30765	4853 ChEBI	esculin	+	hydrolysis
30765	28260 ChEBI	galactose	+	carbon source
30765	17234 ChEBI	glucose	+	carbon source
30765	17754 ChEBI	glycerol	+	carbon source
30765	17306 ChEBI	maltose	+	carbon source
30765	37684 ChEBI	mannose	+	carbon source
30765	30911 ChEBI	sorbitol	+	carbon source
30765	17992 ChEBI	sucrose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30765	acid phosphatase	+	3.1.3.2
30765	alkaline phosphatase	+	3.1.3.1
30765	alpha-galactosidase	+	3.2.1.22
30765	catalase	+	1.11.1.6
30765	cytochrome oxidase	+	1.9.3.1
30765	gelatinase	+
30765	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	vitamin K metabolism	100	5 of 5
66794	glycine betaine biosynthesis	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gallate degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	quinate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	heme metabolism	92.86	13 of 14
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	cellulose degradation	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	pyrimidine metabolism	75.56	34 of 45
66794	purine metabolism	75.53	71 of 94
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	tryptophan metabolism	73.68	28 of 38
66794	vitamin B6 metabolism	72.73	8 of 11
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	degradation of pentoses	71.43	20 of 28
66794	starch degradation	70	7 of 10
66794	coenzyme M biosynthesis	70	7 of 10
66794	degradation of sugar alcohols	68.75	11 of 16
66794	degradation of sugar acids	68	17 of 25
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	methionine metabolism	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	glutathione metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	lysine metabolism	61.9	26 of 42
66794	cysteine metabolism	61.11	11 of 18
66794	glycogen metabolism	60	3 of 5
66794	histidine metabolism	58.62	17 of 29
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	arginine metabolism	58.33	14 of 24
66794	citric acid cycle	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	nitrate assimilation	55.56	5 of 9
66794	degradation of hexoses	55.56	10 of 18
66794	proline metabolism	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	tyrosine metabolism	50	7 of 14
66794	ribulose monophosphate pathway	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	ascorbate metabolism	45.45	10 of 22
66794	metabolism of disaccharids	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	oxidative phosphorylation	42.86	39 of 91
66794	carotenoid biosynthesis	40.91	9 of 22
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	phenol degradation	35	7 of 20
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	butanoate fermentation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Condition	#Saline	-
#Environmental	#Terrestrial	#Sediment
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
21259	sediment from a salt mine	Yunnan Province, Fenggang salt mine (23° 28' N 100° 43' E)	China	CHN	Asia	23.4667	100.717 23.4667/100.717

Taxonmaps

69479

Global distribution of 16S sequence JQ923475 (>99% sequence identity) for Aliifodinibius roseus subclade from Microbeatlas

Aquatic Samples	24
Soil Samples	19
Animal Samples	1
Plant Samples	0
Total Samples	44

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21259	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 2695420936 annotated assembly for Fodinibius roseus DSM 21986	contig	GCA_900129315	1194090.4	2695420936	1194090	65.51

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21259	Aliifodinibius roseus strain YIM D15 16S ribosomal RNA gene, partial sequence	JQ923475	1466		1194090

GC content

@ref	GC-content (mol%)	Method
21259	49.0	high performance liquid chromatography (HPLC)
30765	49

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2695420936 annotated assembly for Fodinibius roseus DSM 21986
NCBI: GCA_900129315

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.35	no
125439	motility	BacteriaNetⓘ	yes	52.25	no
125439	gram_stain	BacteriaNetⓘ	variable	55.64	no
125439	spore_formation	BacteriaNetⓘ	yes	64.29	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Aliifodinibius roseus strain DSM 21986
PATRIC: 1194090.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	89.63	yes
125438	anaerobic	anaerobicⓘ	no	95.88	yes
125438	spore-forming	spore-formingⓘ	no	84.37	yes
125438	aerobic	aerobicⓘ	yes	76.22	no
125438	thermophilic	thermophileⓘ	no	87.35	no
125438	flagellated	motile2+ⓘ	no	56.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Lipids	A biosynthetic pathway for ornithine lipid formation dependent on a GH3 (Gretchen Hagen 3)-like enzyme in planctomycetes.	Rivera-Najera LY, Cruz-Aguilar EM, Vences-Guzman MA, Rivas-Marin E, Valdez IRV, Escobedo-Hinojosa W, Guan Z, Farias-Rico JA, Devos DP, Sohlenkamp C.	J Biol Chem	10.1016/j.jbc.2025.110634	2025
Phylogeny	Fodinibius alkaliphilus sp. nov., a moderately halophilic and alkaliphilic bacterium isolated from an inland saltern in central Portugal and reclassification of Aliifodinibius salipaludis as Fodinibius salipaludis sp. nov.	He Y, Simoes MF, de la Haba RR, Santos-Pereira C, Sousa J, Gomes JS, Silverio SC, Rodrigues LR, Antunes A.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006840	2025
Genetics	Biotin pathway in novel Fodinibius salsisoli sp. nov., isolated from hypersaline soils and reclassification of the genus Aliifodinibius as Fodinibius.	Galisteo C, de la Haba RR, Sanchez-Porro C, Ventosa A.	Front Microbiol	10.3389/fmicb.2022.1101464	2022
Phylogeny	Aliifodinibius salipaludis sp. nov., Isolated from Saline-Alkaline Soil.	Zhao X, Miao S, Sun Y, Gong Q, Zhao J, Wang J, Zhang G	Curr Microbiol	10.1007/s00284-019-01863-w	2020
Phylogeny	Aliifodinibius halophilus sp. nov., a moderately halophilic member of the genus Aliifodinibius, and proposal of Balneolaceae fam. nov.	Xia J, Ling SK, Wang XQ, Chen GJ, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001012	2016
Phylogeny	Aliifodinibius roseus gen. nov., sp. nov., and Aliifodinibius sediminis sp. nov., two moderately halophilic bacteria isolated from salt mine samples.	Wang YX, Liu JH, Xiao W, Ma XL, Lai YH, Li ZY, Ji KY, Wen ML, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.043869-0	2013

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 )
#21259	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21986
#27096	IJSEM 2907 2013 ( DOI 10.1099/ijs.0.043869-0 , PubMed 23334882 )
#30765	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 #27096
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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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Fodinibius roseus (DSM 21986, ACCC 10715, KCTC 23442)

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

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900129315

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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