Acetobacterium bakii (DSM 8239, Z-4391, Z-S11)

Name: Acetobacterium bakii (DSM 8239, Z-4391, Z-S11)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5409

Type strain

Strain Designation Z-4391, Z-S11

Culture col. no. DSM 8239 Z-4391 Z-S11

NCBI tax ID(s) 52689

Special Collections DSMZ

History <- A. N. Nozhevnikova, Institute of Microbiology, Russ. Academy of Sciences, Moscow, Russia; Z-S11

Links

Acetobacterium bakii Z-4391 is an anaerobe bacterium that was isolated from anaerobic sediment, paper mill waste water polluted pond.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 43182

ATCC 51794,DSM 8239

@ref 20215

Last LPSN update 2026-02-09 11:18:57

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Eubacteriaceae

Genus Acetobacterium

Species Acetobacterium bakii

Full scientific name Acetobacterium bakii Kotsyurbenko et al. 1997

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3216	ACETOBACTERIUM TUNDRAE MEDIUM (DSMZ Medium 900)		Medium recipe at MediaDive	Name: ACETOBACTERIUM TUNDRAE MEDIUM (DSMZ Medium 900) Composition: D-Fructose 4.99002 g/l Na2CO3 1.49701 g/l Yeast extract 0.998004 g/l MgCl2 x 6 H2O 0.518962 g/l KCl 0.329341 g/l NH4Cl 0.329341 g/l KH2PO4 0.329341 g/l CaCl2 x 2 H2O 0.299401 g/l Na2S x 9 H2O 0.299401 g/l L-Cysteine HCl x H2O 0.299401 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l Pyridoxine hydrochloride 0.000299401 g/l Nicotinic acid 0.000199601 g/l Thiamine-HCl x 2 H2O 0.000199601 g/l CoCl2 x 6 H2O 0.000189621 g/l Calcium pantothenate 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l Vitamin B12 9.98004e-05 g/l p-Aminobenzoic acid 7.98403e-05 g/l ZnCl2 6.98603e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l D-(+)-biotin 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
3216	positive	growth	20

Physiology and metabolism

Oxygen tolerance

3216

Oxygen toleranceanaerobe

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	starch degradation	100	10 of 10
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	acetoin degradation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	90.91	20 of 22
66794	threonine metabolism	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glycolysis	82.35	14 of 17
66794	flavin biosynthesis	80	12 of 15
66794	vitamin B12 metabolism	79.41	27 of 34
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
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	leucine metabolism	76.92	10 of 13
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	pyrimidine metabolism	73.33	33 of 45
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	purine metabolism	72.34	68 of 94
66794	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	degradation of sugar alcohols	68.75	11 of 16
66794	methane metabolism	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	d-mannose degradation	66.67	6 of 9
66794	histidine metabolism	65.52	19 of 29
66794	alanine metabolism	65.52	19 of 29
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lysine metabolism	64.29	27 of 42
66794	ketogluconate metabolism	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	oxidative phosphorylation	60.44	55 of 91
66794	factor 420 biosynthesis	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	non-pathway related	57.89	22 of 38
66794	tryptophan metabolism	57.89	22 of 38
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	citric acid cycle	57.14	8 of 14
66794	polyamine pathway	56.52	13 of 23
66794	nitrate assimilation	55.56	5 of 9
66794	proline metabolism	54.55	6 of 11
66794	CMP-KDO biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	lactate fermentation	50	2 of 4
66794	sulfopterin metabolism	50	2 of 4
66794	gluconeogenesis	50	4 of 8
66794	toluene degradation	50	2 of 4
66794	acetate fermentation	50	2 of 4
66794	glutathione metabolism	50	7 of 14
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	lipid metabolism	45.16	14 of 31
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	tyrosine metabolism	42.86	6 of 14
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	glycine metabolism	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	degradation of hexoses	38.89	7 of 18
66794	metabolism of disaccharids	36.36	4 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	Entner Doudoroff pathway	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	androgen and estrogen metabolism	25	4 of 16
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	arachidonic acid metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Industrial wastewater
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3216	anaerobic sediment, paper mill waste water polluted pond	Middle Ural, near Syktyvkar	Russia	RUS	Europe

Taxonmaps

69479

Global distribution of 16S sequence X96960 (>99% sequence identity) for Acetobacterium bakii subclade from Microbeatlas

Aquatic Samples	1219
Soil Samples	837
Animal Samples	209
Plant Samples	21
Total Samples	2286

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3216	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	ASM808662v1 assembly for Acetobacterium bakii DSM 8239	contig	GCA_008086625	52689.11	8118826493	52689	69.29
66792	ASM126335v1 assembly for Acetobacterium bakii DSM 8239	scaffold	GCA_001263355	52689.10	2654587740	52689	57.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3216	A.bakii 16S rRNA gene	X96960	1459		52689

GC content

@ref	GC-content (mol%)	Method
3216	41.2	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acetobacterium bakii DSM 8239
NCBI: GCA_001263355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	78.60	no
125439	motility	BacteriaNetⓘ	yes	73.30	no
125439	gram_stain	BacteriaNetⓘ	variable	82.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	73.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acetobacterium bakii DSM 8239
NCBI: GCA_001263355.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	60.73	no
125438	anaerobic	anaerobicⓘ	yes	84.80	yes
125438	aerobic	aerobicⓘ	no	92.66	no
125438	spore-forming	spore-formingⓘ	yes	52.83	no
125438	thermophilic	thermophileⓘ	no	88.61	yes
125438	flagellated	motile2+ⓘ	yes	71.03	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome-scale analysis of Acetobacterium bakii reveals the cold adaptation of psychrotolerant acetogens by post-transcriptional regulation.	Shin J, Song Y, Jin S, Lee JK, Kim DR, Kim SC, Cho S, Cho BK.	RNA	10.1261/rna.068239.118	2018
	Electron bifurcation and fluoride efflux systems implicated in defluorination of perfluorinated unsaturated carboxylic acids by Acetobacterium spp.	Yu Y, Xu F, Zhao W, Thoma C, Che S, Richman JE, Jin B, Zhu Y, Xing Y, Wackett L, Men Y.	Sci Adv	10.1126/sciadv.ado2957	2024
	Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria.	Rosenbaum FP, Muller V.	Extremophiles	10.1007/s00792-021-01241-0	2021
Metabolism	The Sporomusa type Nfn is a novel type of electron-bifurcating transhydrogenase that links the redox pools in acetogenic bacteria.	Kremp F, Roth J, Muller V.	Sci Rep	10.1038/s41598-020-71038-2	2020
Metabolism	Using gas mixtures of CO, CO₂ and H₂ as microbial substrates: the do's and don'ts of successful technology transfer from laboratory to production scale.	Takors R, Kopf M, Mampel J, Bluemke W, Blombach B, Eikmanns B, Bengelsdorf FR, Weuster-Botz D, Durre P.	Microb Biotechnol	10.1111/1751-7915.13270	2018
Genetics	Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood-Ljungdahl pathway.	Esposito A, Tamburini S, Triboli L, Ambrosino L, Chiusano ML, Jousson O	Microbiologyopen	10.1002/mbo3.938	2019
Genetics	Draft Genome Sequence of Acetobacterium bakii DSM 8239, a Potential Psychrophilic Chemical Producer through Syngas Fermentation.	Hwang S, Song Y, Cho BK	Genome Announc	10.1128/genomeA.01070-15	2015

References

#3216	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 8239
#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 )

Rate our new design

Content

About us

Acetobacterium bakii (DSM 8239, Z-4391, Z-S11)

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_008086625

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media