Acetobacter nitrogenifigens (DSM 23921, LMG 23498, MTCC 6912)

Name: Acetobacter nitrogenifigens (DSM 23921, LMG 23498, MTCC 6912)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 20

Type strain

Strain Designation RG1

Culture col. no. DSM 23921 LMG 23498 MTCC 6912 RG1 TBRC 15 5 more

NCBI tax ID(s) 1120919 285268

Special Collections DSMZ JCM Literature strains

History <- R. Gachhui, Jadavpur Univ., Kolkata, India; RG1 <- D. Dutta NRIC 0976 <-- NBRC 105050 <-- LMG 23498 <-- R. Gachhui; Jadavpur Univ., India; RG1 <-- D. Dutta; Jadavpur Univ., India.

Links

Acetobacter nitrogenifigens RG1 is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from Kombucha tea.

Gram-negative motile rod-shaped colony-forming aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 24741

BCRC 80095,NBRC 105050

@ref 20215

Last LPSN update 2026-02-09 11:17:46

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodospirillales

Family Acetobacteraceae

Genus Acetobacter

Species Acetobacter nitrogenifigens

Full scientific name Acetobacter nitrogenifigens Dutta and Gachhui 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
23235	negative	1.5-2.0 µm	0.1-0.2 µm	rod-shaped	polar
125438	negative					96.333
125439	negative					99.5

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23235	2-3 mm	transparent	circular	5 days	nitrogen-free LGI
23235		dark yellow			LGI agar
23235		light brown			potato agar

Culture and growth conditions

Culture medium

@ref	Name	Composition
23235	LGI agar	supplemented with 0.001% bromothymol blue
23235	nitrogen-free LGI
23235	potato agar

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23235	aerobe
125439	obligate aerobe	91.1

Spore formation

@ref	Spore formation	Confidence
125438		91.758
125439		99.3

Observation

67770

Observationquinones: Q-9

Tolerance

@ref	Compound	Percentage
23235	Sucrose	30
23235	Glucose	30
23235	Ethanol	10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23235	28938 ChEBI	ammonium	+	growth
23235	17108 ChEBI	D-arabinose	+	carbon source
23235	15824 ChEBI	D-fructose	+	carbon source
23235	12936 ChEBI	D-galactose	+	carbon source
23235	16899 ChEBI	D-mannitol	+	carbon source
23235	17924 ChEBI	D-sorbitol	+	carbon source
23235	65327 ChEBI	D-xylose	+	carbon source
23235	16236 ChEBI	ethanol	+	oxidation
23235	16977 ChEBI	L-alanine	+	carbon source
23235	17561 ChEBI	L-cysteine	+	carbon source
23235	17295 ChEBI	L-phenylalanine	+	carbon source
23235	16857 ChEBI	L-threonine	-	carbon source
23235	16857 ChEBI	L-threonine	-	nitrogen source
23235	17790 ChEBI	methanol	-	assimilation
23235	17632 ChEBI	nitrate	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
23235	37966 ChEBI	4h-pyran-4-one
23235	16016 ChEBI	dihydroxyacetone

Enzymes

@ref	Value	Activity	Ec
23235	catalase	+	1.11.1.6
23235	cytochrome oxidase	-	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	cyanate degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	propanol degradation	100	7 of 7
66794	ethanol fermentation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	quinate degradation	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	95.45	21 of 22
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	NAD metabolism	88.89	16 of 18
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	methionine metabolism	80.77	21 of 26
66794	gallate degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	purine metabolism	79.79	75 of 94
66794	alanine metabolism	79.31	23 of 29
66794	citric acid cycle	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	isoleucine metabolism	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	arginine metabolism	75	18 of 24
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	glutathione metabolism	71.43	10 of 14
66794	Entner Doudoroff pathway	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	non-pathway related	68.42	26 of 38
66794	tryptophan metabolism	68.42	26 of 38
66794	acetoin degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	octane oxidation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	glycolysis	64.71	11 of 17
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	phenol degradation	60	12 of 20
66794	glycogen metabolism	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	lipid metabolism	54.84	17 of 31
66794	metabolism of disaccharids	54.55	6 of 11
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	glycogen biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of sugar alcohols	50	8 of 16
66794	lactate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	degradation of pentoses	50	14 of 28
66794	cyclohexanol degradation	50	2 of 4
66794	sulfate reduction	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	arachidonic acid metabolism	44.44	8 of 18
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	degradation of sugar acids	44	11 of 25
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	factor 420 biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	cholesterol biosynthesis	36.36	4 of 11
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Fermented
#Engineered	#Food production	#Beverage

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
17427	Kombucha tea	India	IND	Asia
67770	Kombucha tea

Taxonmaps

69479

Global distribution of 16S sequence HG424425 (>99% sequence identity) for Acetobacter from Microbeatlas

Aquatic Samples	132
Soil Samples	133
Animal Samples	499
Plant Samples	124
Total Samples	888

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17427	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
67770	ASM42916v1 assembly for Acetobacter nitrogenifigens DSM 23921 = NBRC 105050	scaffold	GCA_000429165	1120919.3	2522572157	1120919	68.83
67770	ASM799137v1 assembly for Acetobacter nitrogenifigens DSM 23921 = NBRC 105050	contig	GCA_007991375	1120919.6	2927201423	1120919	55.36
124043	ASM2599563v1 assembly for Acetobacter nitrogenifigens DSM 23921 = NBRC 105050 LMG 23498	contig	GCA_025995635	1120919.7	8119175672	1120919	35.81

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Acetobacter nitrogenifigens partial 16S rRNA gene, strain LMG 23498	HG424425	1421	1120919
17427	Acetobacter nitrogenifigens strain RG1 16S ribosomal RNA gene, partial sequence	AY669513	1451	1120919
67770	Acetobacter nitrogenifigens gene for 16S rRNA, partial sequence, strain: NBRC 105050	AB682235	1415	1120919

GC content

@ref	GC-content (mol%)
17427	64.1
23235	64.10

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acetobacter nitrogenifigens DSM 23921 = NBRC 105050
NCBI: GCA_000429165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	motility	BacteriaNetⓘ	yes	89.90	no
125439	spore_formation	BacteriaNetⓘ	no	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acetobacter nitrogenifigens DSM 23921
PATRIC: 1120919.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.33	yes
125438	anaerobic	anaerobicⓘ	no	96.75	yes
125438	spore-forming	spore-formingⓘ	no	91.76	no
125438	aerobic	aerobicⓘ	yes	88.37	yes
125438	thermophilic	thermophileⓘ	no	97.98	yes
125438	flagellated	motile2+ⓘ	yes	77.58	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	A genomic investigation of ecological differentiation between free-living and Drosophila-associated bacteria.	Winans NJ, Walter A, Chouaia B, Chaston JM, Douglas AE, Newell PD.	Mol Ecol	10.1111/mec.14232	2017
Metabolism	GqqA, a novel protein in Komagataeibacter europaeus involved in bacterial quorum quenching and cellulose formation.	Valera MJ, Mas A, Streit WR, Mateo E.	Microb Cell Fact	10.1186/s12934-016-0482-y	2016
Pathogenicity	Structural and magnetic properties of cobalt-doped iron oxide nanoparticles prepared by solution combustion method for biomedical applications.	Venkatesan K, Rajan Babu D, Kavya Bai MP, Supriya R, Vidya R, Madeswaran S, Anandan P, Arivanandhan M, Hayakawa Y.	Int J Nanomedicine	10.2147/ijn.s82210	2015
	Entomotherapy as an alternative treatment for diseases due to Gram-negative bacteria in Burkina Faso.	Ouango M, Cisse H, Romba R, Drabo SF, Semde R, Savadogo A, Gnankine O.	Sci Rep	10.1038/s41598-023-50622-2	2024
	Microbiological and Physicochemical Composition of Various Types of Homemade Kombucha Beverages Using Alternative Kinds of Sugars.	Kluz MI, Pietrzyk K, Pastuszczak M, Kacaniova M, Kita A, Kapusta I, Zagula G, Zagrobelna E, Strus K, Marciniak-Lukasiak K, Stanek-Tarkowska J, Timar AV, Puchalski C.	Foods	10.3390/foods11101523	2022
Genetics	Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes.	Rappaport HB, Senewiratne NPJ, Lucas SK, Wolfe BE, Oliverio AM.	mSystems	10.1128/msystems.00537-24	2024
Metabolism	Drosophila Antimicrobial Peptides and Lysozymes Regulate Gut Microbiota Composition and Abundance.	Marra A, Hanson MA, Kondo S, Erkosar B, Lemaitre B.	mBio	10.1128/mbio.00824-21	2021
	Effect of inoculated azotobacteria and Phanerochaete chrysosporium on the composting of olive pomace: Microbial community dynamics and phenols evolution.	Milanovic V, Osimani A, Cardinali F, Taccari M, Garofalo C, Clementi F, Ashoor S, Mozzon M, Foligni R, Canonico L, Ciani M, Aquilanti L.	Sci Rep	10.1038/s41598-019-53313-z	2019
	Probiotic Limosilactobacillus Reuteri (Lactobacillus Reuteri) Extends the Lifespan of Drosophila Melanogaster through Insulin/IGF-1 Signaling.	Lee HY, Lee JH, Kim SH, Jo SY, Min KJ.	Aging Dis	10.14336/ad.2023.0122	2023
Metabolism	Recent advances in nitrogen-fixing acetic acid bacteria.	Pedraza RO.	Int J Food Microbiol	10.1016/j.ijfoodmicro.2007.11.079	2008
	Application of indigenous Saccharomyces cerevisiae to improve the black raspberry (Rubus coreanus Miquel) vinegar fermentation process and its microbiological and physicochemical analysis.	Song NE, Jeong DY, Baik SH.	Food Sci Biotechnol	10.1007/s10068-018-0489-8	2019
Phylogeny	Pinus flexilis and Picea engelmannii share a simple and consistent needle endophyte microbiota with a potential role in nitrogen fixation.	Carrell AA, Frank AC.	Front Microbiol	10.3389/fmicb.2014.00333	2014
	Nitrogen fixing bacteria in the family Acetobacteraceae and their role in agriculture.	Reis VM, Teixeira KR.	J Basic Microbiol	10.1002/jobm.201400898	2015
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
	Acetobacter sacchari sp. nov., for a plant growth-promoting acetic acid bacterium isolated in Vietnam	Vu HTL, Yukphan P, Bui VTT, Charoenyingcharoen P, Malimas S, Nguyen LK, Muramatsu Y, Tanaka N, Tanasupawat S, Le BT, Nakagawa Y, Yamada Y.	Ann Microbiol		2019
Phylogeny	Novel acetic acid bacteria from cider fermentations: Acetobacter conturbans sp. nov. and Acetobacter fallax sp. nov.	Sombolestani AS, Cleenwerck I, Cnockaert M, Borremans W, Wieme AD, De Vuyst L, Vandamme P.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004511	2020
Phylogeny	Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis.	Li L, Wieme A, Spitaels F, Balzarini T, Nunes OC, Manaia CM, Van Landschoot A, De Vuyst L, Cleenwerck I, Vandamme P.	Int J Syst Evol Microbiol	10.1099/ijs.0.058354-0	2014
Phylogeny	Novel nitrogen-fixing Acetobacter nitrogenifigens sp. nov., isolated from Kombucha tea.	Dutta D, Gachhui R	Int J Syst Evol Microbiol	10.1099/ijs.0.64101-0	2006

References

#17427	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23921
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#23235	Debasree Dutta, Ratan Gachhui: Novel nitrogen-fixing Acetobacter nitrogenifigens sp. nov., isolated from Kombucha tea. IJSEM 56: 1899 - 1903 2006 ( DOI 10.1099/ijs.0.64101-0 , PubMed 16902028 )
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Acetobacter nitrogenifigens (DSM 23921, LMG 23498, MTCC 6912)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Tolerance

Metabolite utilization

Metabolite production

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_000429165

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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