Propionispira arboris (DSM 2179, ATCC 33732, 12B4)

Name: Propionispira arboris (DSM 2179, ATCC 33732, 12B4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17148

Type strain

Strain Designation 12B4

Culture col. no. DSM 2179 ATCC 33732 12B4

NCBI tax ID(s) 1123002 84035

Special Collections DSMZ

History <- J.G. Zeikus, 12B4

Links

Propionispira arboris 12B4 is an anaerobe, mesophilic prokaryote that was isolated from wetwood, Cotton Wood tree.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 40656

ATCC 33732,DSM 2179

@ref 20215

Last LPSN update 2026-02-09 11:22:08

Domain Bacteria

Phylum Bacillota

Class Negativicutes

Order Selenomonadales

Family Selenomonadaceae

Genus Propionispira

Species Propionispira arboris

Full scientific name Propionispira arboris Schink et al. 1983

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
996	PROPIONISPIRA MEDIUM (DSMZ Medium 207)		Medium recipe at MediaDive	Name: PROPIONISPIRA MEDIUM (DSMZ Medium 207) Composition: Na-lactate 5.0 g/l NaHCO3 4.0 g/l Na2HPO4 x 12 H2O 2.1 g/l Yeast extract 2.0 g/l NH4Cl 1.0 g/l Na2S x 9 H2O 0.5 g/l KH2PO4 0.3 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.128 g/l NaCl 0.01 g/l FeCl2 x 4 H2O 0.002 g/l CoCl2 x 6 H2O 0.0017 g/l FeSO4 x 7 H2O 0.0015 g/l MnCl2 x 4 H2O 0.001 g/l Resazurin 0.001 g/l ZnCl2 0.001 g/l CaCl2 x 2 H2O 0.001 g/l Na2SeO3 x 5 H2O 0.0003 g/l NiCl2 x 6 H2O 0.0003 g/l CuCl2 0.0002 g/l H3BO3 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l Pyridoxine hydrochloride 5e-05 g/l Calcium D-(+)-pantothenate 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l Riboflavin 2.5e-05 g/l (DL)-alpha-Lipoic acid 2.5e-05 g/l Thiamine HCl 2.5e-05 g/l p-Aminobenzoic acid 2.5e-05 g/l Folic acid 1e-05 g/l Biotin 1e-05 g/l Vitamin B12 5e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
996	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
996	anaerobe
125439	facultative anaerobe	94.3

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	methylglyoxal degradation	100	5 of 5
66794	acetoin degradation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	95.45	21 of 22
66794	degradation of sugar alcohols	93.75	15 of 16
66794	vitamin B1 metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	propanol degradation	85.71	6 of 7
66794	vitamin B12 metabolism	85.29	29 of 34
66794	alanine metabolism	82.76	24 of 29
66794	glycolysis	82.35	14 of 17
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	glycogen metabolism	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	purine metabolism	78.72	74 of 94
66794	citric acid cycle	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine 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	sulfopterin metabolism	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	photosynthesis	71.43	10 of 14
66794	myo-inositol biosynthesis	70	7 of 10
66794	oxidative phosphorylation	69.23	63 of 91
66794	degradation of pentoses	67.86	19 of 28
66794	degradation of hexoses	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	heme metabolism	64.29	9 of 14
66794	degradation of sugar acids	64	16 of 25
66794	d-xylose degradation	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	urea cycle	61.54	8 of 13
66794	leucine metabolism	61.54	8 of 13
66794	tryptophan metabolism	60.53	23 of 38
66794	factor 420 biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	nitrate assimilation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	non-pathway related	55.26	21 of 38
66794	metabolism of disaccharids	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	kanosamine biosynthesis II	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	lysine metabolism	50	21 of 42
66794	vitamin E metabolism	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	tyrosine metabolism	50	7 of 14
66794	quinate degradation	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	proline metabolism	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	allantoin degradation	44.44	4 of 9
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	coenzyme M biosynthesis	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	polyamine pathway	34.78	8 of 23
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	glutathione metabolism	28.57	4 of 14
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	phenol degradation	25	5 of 20
66794	cyclohexanol degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	methanogenesis from CO2	25	3 of 12

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
996	wetwood, Cotton Wood tree	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence Y18190 (>99% sequence identity) for Propionispira arboris from Microbeatlas

Aquatic Samples	55
Soil Samples	85
Animal Samples	32
Plant Samples
Total Samples	172

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
996	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	IMG-taxon 2602042026 annotated assembly for Propionispira arboris DSM 2179	contig	GCA_900109225	84035.3	2602042026	84035	68.25

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
996	Propionispira arboris 16S rRNA gene, partial, strain DSM 2179	Y18190	1470		84035

GC content

996

GC-content (mol%)36.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Propionispira arboris DSM 2179
NCBI: GCA_900109225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	78.30	no
125439	motility	BacteriaNetⓘ	yes	72.40	no
125439	gram_stain	BacteriaNetⓘ	positive	84.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	94.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Propionispira arboris strain DSM 2179
PATRIC: 84035.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	83.42	no
125438	anaerobic	anaerobicⓘ	yes	79.97	yes
125438	aerobic	aerobicⓘ	no	88.62	no
125438	spore-forming	spore-formingⓘ	no	54.38	no
125438	thermophilic	thermophileⓘ	no	87.97	yes
125438	flagellated	motile2+ⓘ	yes	72.16	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Regulation of carbon and electron flow in Propionispira arboris: relationship of catabolic enzyme levels to carbon substrates fermented during propionate formation via the methylmalonyl coenzyme A pathway.	Thompson TE, Zeikus JG.	J Bacteriol	10.1128/jb.170.9.3996-4000.1988	1988

References

#996	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2179
#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 )
#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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Propionispira arboris (DSM 2179, ATCC 33732, 12B4)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900109225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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