Name: Acetobacter nitrogenifigens RG1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 20

Type strain:

Species: Acetobacter nitrogenifigens

Strain Designation: RG1

Culture col. no.: DSM 23921, LMG 23498, MTCC 6912, JCM 33644, BCC 33377, BCRC 80095, NBRC 105050, NRIC 0976, TBRC 15

Strain history: NRIC 0976 <-- NBRC 105050 <-- LMG 23498 <-- R. Gachhui; Jadavpur Univ., India; RG1 <-- D. Dutta; Jadavpur Univ., India.

NCBI tax ID(s): 1120919 (strain), 285268 (species)

SI-ID 290409

LMG 23498

Special Collections

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Acetobacteraceae*
	Genus	*Acetobacter*
	Species	**Acetobacter nitrogenifigens**
	Full Scientific Name (LPSN)	Acetobacter nitrogenifigens Dutta and Gachhui 2006

Information on morphological and physiological properties Morphology

[Ref.: #23235]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96.333

[Ref.: #23235]	Cell length	1.5-2.0 µm

[Ref.: #23235]	Cell width	0.1-0.2 µm

[Ref.: #23235]	Cell shape	rod-shaped

[Ref.: #23235]	Motility	yes

[Ref.: #23235]	Flagellum arrangement	polar

[Ref.: #23235]	Colony size	2-3 mm
[Ref.: #23235]	Colony color	transparent
[Ref.: #23235]	Colony shape	circular
[Ref.: #23235]	Incubation period	5 days
[Ref.: #23235]	Cultivation medium used	nitrogen-free LGI

[Ref.: #23235]	Colony color	dark yellow
[Ref.: #23235]	Cultivation medium used	LGI agar

[Ref.: #23235]	Colony color	light brown
[Ref.: #23235]	Cultivation medium used	potato agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #23235]

Culture medium

LGI agar

[Ref.: #23235]

Culture medium growth

[Ref.: #23235]

Culture medium composition

expand / minimize

[Ref.: #23235]

Culture medium

nitrogen-free LGI

[Ref.: #23235]

Culture medium growth

[Ref.: #23235]

Culture medium

potato agar

[Ref.: #23235]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23235]

Oxygen tolerance

aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %91.758
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #67770]

Observation

quinones: Q-9

[Ref.: #23235]	Name of tolerated compound	Sucrose
[Ref.: #23235]	Tolerance percentage	30
[Ref.: #23235]	Name of tolerated compound	Glucose
[Ref.: #23235]	Tolerance percentage	30
[Ref.: #23235]	Name of tolerated compound	Ethanol
[Ref.: #23235]	Tolerance percentage	10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23235]	ammonium ChEBI	+	growth
[Ref.: #23235]	D-arabinose ChEBI	+	carbon source
[Ref.: #23235]	D-fructose ChEBI	+	carbon source
[Ref.: #23235]	D-galactose ChEBI	+	carbon source
[Ref.: #23235]	D-mannitol ChEBI	+	carbon source
[Ref.: #23235]	D-sorbitol ChEBI	+	carbon source
[Ref.: #23235]	D-xylose ChEBI	+	carbon source
[Ref.: #23235]	ethanol ChEBI	+	oxidation
[Ref.: #23235]	L-alanine ChEBI	+	carbon source
[Ref.: #23235]	L-cysteine ChEBI	+	carbon source
[Ref.: #23235]	L-phenylalanine ChEBI	+	carbon source
[Ref.: #23235]	L-threonine ChEBI	-	carbon source
[Ref.: #23235]	L-threonine ChEBI	-	nitrogen source
[Ref.: #23235]	methanol ChEBI	-	assimilation
[Ref.: #23235]	nitrate ChEBI	-	reduction
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #23235]		4h-pyran-4-one ChEBI	yes
[Ref.: #23235]		dihydroxyacetone ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #23235]		catalase	+	1.11.1.6
[Ref.: #23235]		cytochrome oxidase	-	1.9.3.1

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #17427]	Sample type/isolated from	Kombucha tea
[Ref.: #17427]	Country	India
[Ref.: #17427]	Country ISO 3 Code	IND
[Ref.: #17427]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Kombucha tea
* marker position based on {}

Isolation sources categories

#Engineered	#Food production	#Fermented
#Engineered	#Food production	#Beverage

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #17427]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #17427]	Acetobacter nitrogenifigens strain RG1 16S ribosomal RNA gene, partial sequence	AY669513	1451	GenBank ENA	1120919 tax ID
[Ref.: #67770]	Acetobacter nitrogenifigens gene for 16S rRNA, partial sequence, strain: NBRC 105050	AB682235	1415	GenBank ENA	1120919 tax ID
[Ref.: #20218]	Acetobacter nitrogenifigens partial 16S rRNA gene, strain LMG 23498	HG424425	1421	GenBank ENA	1120919 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Acetobacter nitrogenifigens DSM 23921 = NBRC 105050	GCA_000429165	scaffold	GenBank ENA	1120919 tax ID
[Ref.: #67770]	Acetobacter nitrogenifigens DSM 23921 = NBRC 105050	GCA_007991375	contig	GenBank ENA	1120919 tax ID
[Ref.: #66792]	Acetobacter nitrogenifigens DSM 23921	1120919.3	wgs	PATRIC	1120919 tax ID	*
[Ref.: #66792]	Acetobacter nitrogenifigens DSM 23921 = LMG 23498 strain NBRC 105050	1120919.6	wgs	PATRIC	1120919 tax ID	*
[Ref.: #66792]	Acetobacter nitrogenifigens NBRC 105050	2927201423	draft	JGI IMG/M	1120919 tax ID	*
[Ref.: #66792]	Acetobacter nitrogenifigens DSM 23921	2522572157	draft	JGI IMG/M	1120919 tax ID	*

[Ref.: #17427]	GC-content	64.1 mol%
[Ref.: #23235]	GC-content	64.10 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Acetobacter nitrogenifigens DSM 23921 = LMG 23498 strain NBRC 105050 PATRIC: 1120919.6
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Acetobacter nitrogenifigens DSM 23921 PATRIC: 1120919.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96.333	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.745	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.758	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.367	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.977	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	77.575	yes

Availability in culture collections External links

[Ref.: #17427]

Culture collection no.

DSM 23921, LMG 23498, MTCC 6912, JCM 33644, BCC 33377, BCRC 80095, NBRC 105050, NRIC 0976, TBRC 15

[Ref.: #69704]

SI-ID 290409

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#69704

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID290409.1 )

* These data were automatically processed and therefore are not curated

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Acetobacter nitrogenifigens DSM 23921 = LMG 23498 strain NBRC 105050

Acetobacter nitrogenifigens DSM 23921

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