Arcicella aurantiaca (DSM 22214, BCRC 17969, LMG 25207)

Name: Arcicella aurantiaca (DSM 22214, BCRC 17969, LMG 25207)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3766

Type strain

Strain Designation TNR-18

Culture col. no. DSM 22214 BCRC 17969 LMG 25207 TNR-18

NCBI tax ID(s) 591202

Special Collections DSMZ Literature strains

History <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; TNR-18

Links

Arcicella aurantiaca TNR-18 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from stream water.

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

Name and taxonomic classification

SI-ID 360697

LMG 25207,BCRC 17969,DSM 22214

@ref 20215

Last LPSN update 2026-02-09 11:18:34

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Arcicella

Species Arcicella aurantiaca

Full scientific name Arcicella aurantiaca Sheu et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29806	negative	01-03 µm	0.5-0.6 µm	rod-shaped
125439	negative				99.7
125438	negative				97.283

Pigmentation

29806

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16206	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16206	positive	growth	28
29806	positive	growth	10-30
29806	positive	optimum	25

Culture pH

@ref	Ability	Type	PH	PH range
29806	positive	optimum	7
29806	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29806	aerobe
125439	obligate aerobe	99.3

Spore formation

@ref	Spore formation	Confidence
29806
125439		98.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29806	NaCl	positive	growth	0-0.2 %

Observation

29806

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29806	16449 ChEBI	alanine	+	carbon source
29806	35391 ChEBI	aspartate	+	carbon source
29806	17057 ChEBI	cellobiose	+	carbon source
29806	23652 ChEBI	dextrin	+	carbon source
29806	4853 ChEBI	esculin	+	hydrolysis
29806	28757 ChEBI	fructose	+	carbon source
29806	33984 ChEBI	fucose	+	carbon source
29806	28260 ChEBI	galactose	+	carbon source
29806	17234 ChEBI	glucose	+	carbon source
29806	29987 ChEBI	glutamate	+	carbon source
29806	28087 ChEBI	glycogen	+	carbon source
29806	17716 ChEBI	lactose	+	carbon source
29806	17306 ChEBI	maltose	+	carbon source
29806	37684 ChEBI	mannose	+	carbon source
29806	28053 ChEBI	melibiose	+	carbon source
29806	51850 ChEBI	methyl pyruvate	+	carbon source
29806	17632 ChEBI	nitrate	+	reduction
29806	16634 ChEBI	raffinose	+	carbon source
29806	26546 ChEBI	rhamnose	+	carbon source
29806	17822 ChEBI	serine	+	carbon source
29806	30911 ChEBI	sorbitol	+	carbon source
29806	17992 ChEBI	sucrose	+	carbon source
29806	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29806	catalase	+	1.11.1.6
29806	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	ethanol fermentation	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	kanosamine biosynthesis II	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	quinate degradation	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
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	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	methylglyoxal degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	NAD metabolism	77.78	14 of 18
66794	lipid A biosynthesis	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	leucine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	isoleucine metabolism	75	6 of 8
66794	degradation of sugar alcohols	75	12 of 16
66794	purine metabolism	73.4	69 of 94
66794	flavin biosynthesis	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	pyrimidine metabolism	68.89	31 of 45
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	lysine metabolism	66.67	28 of 42
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	degradation of sugar acids	64	16 of 25
66794	d-xylose degradation	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of hexoses	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	gallate degradation	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	non-pathway related	57.89	22 of 38
66794	tyrosine metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	carotenoid biosynthesis	54.55	12 of 22
66794	sulfate reduction	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	selenocysteine biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	polyamine pathway	47.83	11 of 23
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	metabolism of disaccharids	45.45	5 of 11
66794	oxidative phosphorylation	45.05	41 of 91
66794	phenol degradation	45	9 of 20
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	enterobactin biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	cyanate degradation	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	urea cycle	30.77	4 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin B12 metabolism	23.53	8 of 34
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16206	stream water	Kaohsiung Prefecture	Taiwan, Province of China	TWN	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ593908 (>99% sequence identity) for Arcicella aurantiaca subclade from Microbeatlas

Aquatic Samples	41
Soil Samples
Animal Samples
Plant Samples	4
Total Samples	45

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16206	1	Risk group (German 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	ASM314862v1 assembly for Arcicella aurantiaca DSM 22214	scaffold	GCA_003148625	591202.3	2595698202	591202	57.95

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16206	Arcicella aurantiaca 16S ribosomal RNA gene, partial sequence	FJ593908	1411		591202

GC content

@ref	GC-content (mol%)	Method
16206	39.9	high performance liquid chromatography (HPLC)
29806	39.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arcicella aurantiaca DSM 22214
NCBI: GCA_003148625

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.10	no
125439	motility	BacteriaNetⓘ	no	75.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arcicella aurantiaca DSM 22214
NCBI: GCA_003148625.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.28	no
125438	anaerobic	anaerobicⓘ	no	96.92	yes
125438	aerobic	aerobicⓘ	yes	88.77	no
125438	spore-forming	spore-formingⓘ	no	88.40	no
125438	thermophilic	thermophileⓘ	no	96.93	no
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arcicella rigui sp. nov., isolated from water of a wetland, and emended descriptions of the genus Arcicella, Arcicella aquatica, Arcicella rosea and Arcicella aurantiaca.	Chen WM, Yang SH, Young CC, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijs.0.037242-0	2012
Phylogeny	Arcicella aurantiaca sp. nov., isolated from stream water.	Sheu SY, Yang CS, Chen MH, Arun AB, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.021527-0	2010

References

#16206	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22214
#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 )
#26183	IJSEM 2979 2010 ( DOI 10.1099/ijs.0.021527-0 , PubMed 20118286 )
#29806	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 #26183
#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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Arcicella aurantiaca (DSM 22214, BCRC 17969, LMG 25207)

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_003148625

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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