Name: Komagataeibacter medellinensis NBRC 3288
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133875

Type strain:

Species: Komagataeibacter medellinensis

Culture col. no.: NBRC 3288, Kondo 51, LMG 1693

NCBI tax ID(s): 634177 (strain), 1177712 (species)

SI-ID 14545

IFO 3288, BCRC 11682, CCRC 11682, LMG 1693, NBRC 3288

Section

Komagataeibacter medellinensis NBRC 3288 is a Gram-negative, rod-shaped bacterium that was isolated from food product.

Gram-negative
rod-shaped
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	*Komagataeibacter*
	Species	**Komagataeibacter medellinensis**
	Full Scientific Name (LPSN)	Komagataeibacter medellinensis (Castro et al. 2013) Yamada 2014

Synonym

Gluconacetobacter medellinensis

Information on morphological and physiological properties Morphology

[Ref.: #30737]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.988

[Ref.: #30737]	Cell length	2 µm

[Ref.: #30737]	Cell width	0.65 µm

[Ref.: #30737]	Cell shape	rod-shaped

[Ref.: #30737]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.078

[Ref.: #30737]

Pigment production

yes

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30737]	ethanol ChEBI	+	carbon source
[Ref.: #30737]	fructose ChEBI	+	carbon source
[Ref.: #30737]	gluconate ChEBI	+	carbon source
[Ref.: #30737]	maltose ChEBI	+	carbon source
[Ref.: #30737]	mannitol ChEBI	+	carbon source
[Ref.: #30737]	ribose ChEBI	+	carbon source
[Ref.: #30737]	sorbitol ChEBI	+	carbon source
[Ref.: #30737]	sucrose ChEBI	+	carbon source
[Ref.: #30737]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30737]		catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	vitamin B12 metabolism	91.18	31 of 34
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor 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]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[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]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	degradation of sugar acids	28	7 of 25
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #30737]	Sample type/isolated from	food product
* marker position based on {}

Isolation sources categories

#Engineered

#Food production

#Food

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JX013852 (>99% sequence identity) for Komagataeibacter from Microbeatlas

Aquatic Samples	523
Soil Samples	662
Animal Samples	2327
Plant Samples	555
Total Samples	4067

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.: #30737]	Gluconacetobacter medellensis strain LMG 1693 16S ribosomal RNA gene, partial sequence	JX013852	1443	GenBank	634177 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.: #66792]	Komagataeibacter medellinensis NBRC 3288	2513237191	complete	JGI IMG/M	634177 tax ID	*
[Ref.: #66792]	Gluconacetobacter xylinus NBRC 3288	634177.7	complete	PATRIC	634177 tax ID	*
[Ref.: #66792]	Komagataeibacter medellinensis NBRC 3288	634177.18	plasmid	PATRIC	634177 tax ID	*
[Ref.: #66792]	Komagataeibacter medellinensis NBRC 3288	634177.17	plasmid	PATRIC	634177 tax ID	*
[Ref.: #66792]	Komagataeibacter medellinensis NBRC 3288	634177.14	plasmid	PATRIC	634177 tax ID	*
[Ref.: #66792]	Komagataeibacter medellinensis NBRC 3288	634177.16	plasmid	PATRIC	634177 tax ID	*

[Ref.: #30737]

GC-content

60.7 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Komagataeibacter medellinensis NBRC 3288 NBRC 3288 NCBI: GCA_000182745.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Komagataeibacter medellinensis NBRC 3288 NBRC 3288 NCBI: GCA_000182745.1
[Ref.: #69480]	motile	no	84.057	yes
[Ref.: #69480]	flagellated	no	96.939	no
[Ref.: #69480]	gram-positive	no	96.252	yes
[Ref.: #69480]	anaerobic	no	96.911	no
[Ref.: #69480]	aerobic	yes	83.882	no
[Ref.: #69480]	halophile	no	93.103	no
[Ref.: #69480]	spore-forming	no	96.382	no
[Ref.: #69480]	thermophile	no	97.13	no
[Ref.: #69480]	glucose-util	yes	88.499	no
[Ref.: #69480]	glucose-ferment	no	84.972	no

Availability in culture collections External links

[Ref.: #30737]

Culture collection no.

NBRC 3288, Kondo 51, LMG 1693

[Ref.: #91627]

SI-ID 14545

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Adaptive mutation related to cellulose producibility in Komagataeibacter medellinensis (Gluconacetobacter xylinus) NBRC 3288.	Matsutani M, Ito K, Azuma Y, Ogino H, Shirai M, Yakushi T, Matsushita K	Appl Microbiol Biotechnol	10.1007/s00253-015-6598-x	2015	*
Phylogeny	Transfer of Gluconacetobacter kakiaceti, Gluconacetobacter medellinensis and Gluconacetobacter maltaceti to the genus Komagataeibacter as Komagataeibacter kakiaceti comb. nov., Komagataeibacter medellinensis comb. nov. and Komagataeibacter maltaceti comb. nov.	Yamada Y	Int J Syst Evol Microbiol	10.1099/ijs.0.054494-0	2014	*
Phylogeny	Gluconacetobacter medellinensis sp. nov., cellulose- and non-cellulose-producing acetic acid bacteria isolated from vinegar.	Castro C, Cleenwerck I, Trcek J, Zuluaga R, De Vos P, Caro G, Aguirre R, Putaux JL, Ganan P	Int J Syst Evol Microbiol	10.1099/ijs.0.043414-0	2012	*
Stress	Mutations in degP and spoT Genes Mediate Response to Fermentation Stress in Thermally Adapted Strains of Acetic Acid Bacterium Komagataeibacter medellinensis NBRC 3288.	Kataoka N, Matsutani M, Matsumoto N, Oda M, Mizumachi Y, Ito K, Tanaka S, Kanesaki Y, Yakushi T, Matsushita K	Front Microbiol	10.3389/fmicb.2022.802010	2022	*
Genetics	Genome sequence and characterization of the bcs clusters for the production of nanocellulose from the low pH resistant strain Komagataeibacter medellinensis ID13488.	Hernandez-Arriaga AM, Del Cerro C, Urbina L, Eceiza A, Corcuera MA, Retegi A, Auxiliadora Prieto M	Microb Biotechnol	10.1111/1751-7915.13376	2019	*
Enzymology	Identifying membrane-bound quinoprotein glucose dehydrogenase from acetic acid bacteria that produce lactobionic and cellobionic acids.	Kiryu T, Kiso T, Koma D, Tanaka S, Murakami H	Biosci Biotechnol Biochem	10.1080/09168451.2019.1580136	2019	*

References

#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 )

#30737

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 #27068 (see below)

#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 .

#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 )

#91627

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-ID14545.1 )

#27068

IJSEM 1119 2013 ( DOI 10.1099/ijs.0.043414-0 , PubMed 22729025 )

* These data were automatically processed and therefore are not curated

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Komagataeibacter medellinensis NBRC 3288 NBRC 3288

Komagataeibacter medellinensis NBRC 3288 NBRC 3288

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