Archive BacDiveID:10.13145/bacdive92.20230509.8.1

Strain identifier

BacDive ID: 92

Type strain:

Species: Komagataeibacter intermedius

Strain Designation: TF2

Strain history: CIP <- 1998, ZIM <- C. Boesch, Zürich, Switzerland: strain TF2

NCBI tax ID(s): 66229 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 4493

BacDive-ID: 92

DSM-Number: 11804

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Komagataeibacter intermedius TF2 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from tea fungus beverage .

NCBI tax id

NCBI tax id: 66229
Matching level: species

strain history

@ref	history
4493	<- C. Boesch, ETH; TF2
67770	DSM 11804 <-- C. Boesch TF2.
120151	CIP <- 1998, ZIM <- C. Boesch, Zürich, Switzerland: strain TF2

doi: 10.13145/bacdive92.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Rhodospirillales
family: Acetobacteraceae
genus: Komagataeibacter
species: Komagataeibacter intermedius
full scientific name: Komagataeibacter intermedius (Boesch et al. 1998) Yamada et al. 2013
synonyms
@ref synonym
20215 Komagatabacter intermedius
20215 Acetobacter intermedius
20215 Gluconacetobacter intermedius

@ref	synonym
20215	Komagatabacter intermedius
20215	Acetobacter intermedius
20215	Gluconacetobacter intermedius

@ref: 4493

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Komagataeibacter

species: Komagataeibacter intermedius

full scientific name: Komagataeibacter intermedius (Boesch et al. 1998) Yamada et al. 2013

strain designation: TF2

type strain: yes

Morphology

cell morphology

@ref: 120151
gram stain: negative
cell shape: rod-shaped
motility: no

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
4493	ALTERNATIVE ACETOBACTER INTERMEDIUS MEDIUM (DSMZ Medium 850)	yes	https://mediadive.dsmz.de/medium/850	Name: ALTERNATIVE ACETOBACTER INTERMEDIUS MEDIUM (DSMZ Medium 850) Composition: Agar 12.0 g/l Glucose 5.0 g/l Yeast extract 3.0 g/l Distilled water
4493	AE MEDIUM (DSMZ Medium 849)	yes	https://mediadive.dsmz.de/medium/849	Name: AE MEDIUM (DSMZ Medium 849) Composition: Agar 9.0 g/l Glucose 5.0 g/l Peptone 4.0 g/l Yeast extract 3.0 g/l Glacial acetic acid Absolute ethanol Distilled water
4493	MRS MEDIUM (DSMZ Medium 11)	yes	https://mediadive.dsmz.de/medium/11	Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
39826	MEDIUM 289 - for Acetobacter intermedius	yes		Distilled water make up to (940.000 ml);Agar (8.000 g);Glucose (7.500 g);Yeast extract (3.000 g);Peptone (4.000 g);Acetic acid (30.000 ml);Ethanol (30.000 ml)
120151	CIP Medium 289	yes	https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=289

culture temp

@ref	growth	type	temperature	range
4493	positive	growth	30	mesophilic
39826	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
120151	positive	growth	22-30
120151	no	growth	37	mesophilic
120151	no	growth	45	thermophilic

Physiology and metabolism

metabolite utilization

@ref	metabolite	utilization activity	kind of utilization tested	Chebi-ID
68371	Potassium 5-ketogluconate	-	builds acid from
68371	Potassium 2-ketogluconate	-	builds acid from
68371	gluconate	-	builds acid from	24265
68371	L-arabitol	-	builds acid from	18403
68371	D-arabitol	-	builds acid from	18333
68371	L-fucose	-	builds acid from	18287
68371	D-fucose	-	builds acid from	28847
68371	D-tagatose	-	builds acid from	16443
68371	D-lyxose	-	builds acid from	62318
68371	turanose	-	builds acid from	32528
68371	gentiobiose	-	builds acid from	28066
68371	xylitol	-	builds acid from	17151
68371	glycogen	-	builds acid from	28087
68371	starch	-	builds acid from	28017
68371	raffinose	-	builds acid from	16634
68371	melezitose	-	builds acid from	6731
68371	inulin	-	builds acid from	15443
68371	trehalose	-	builds acid from	27082
68371	sucrose	-	builds acid from	17992
68371	melibiose	-	builds acid from	28053
68371	lactose	-	builds acid from	17716
68371	maltose	-	builds acid from	17306
68371	cellobiose	-	builds acid from	17057
68371	salicin	-	builds acid from	17814
68371	esculin	-	builds acid from	4853
68371	arbutin	-	builds acid from	18305
68371	amygdalin	-	builds acid from	27613
68371	N-acetylglucosamine	-	builds acid from	59640
68371	methyl alpha-D-glucopyranoside	-	builds acid from	320061
68371	methyl alpha-D-mannoside	-	builds acid from	43943
68371	D-sorbitol	-	builds acid from	17924
68371	D-mannitol	-	builds acid from	16899
68371	myo-inositol	-	builds acid from	17268
68371	galactitol	-	builds acid from	16813
68371	L-rhamnose	-	builds acid from	62345
68371	L-sorbose	-	builds acid from	17266
68371	D-mannose	-	builds acid from	16024
68371	D-fructose	-	builds acid from	15824
68371	D-glucose	-	builds acid from	17634
68371	D-galactose	-	builds acid from	12936
68371	methyl beta-D-xylopyranoside	-	builds acid from	74863
68371	ribitol	-	builds acid from	15963
68371	L-xylose	-	builds acid from	65328
68371	D-xylose	-	builds acid from	65327
68371	D-ribose	-	builds acid from	16988
68371	L-arabinose	-	builds acid from	30849
68371	D-arabinose	-	builds acid from	17108
68371	erythritol	-	builds acid from	17113
68371	glycerol	-	builds acid from	17754
120151	hippurate	-	hydrolysis	606565

antibiotic resistance

@ref: 120151
metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
is antibiotic: yes
is sensitive: no
is resistant: yes

enzymes

@ref	value	activity	ec
120151	oxidase	-
120151	beta-galactosidase	-	3.2.1.23
120151	gelatinase	-
120151	catalase	-	1.11.1.6
120151	gamma-glutamyltransferase	-	2.3.2.2

API 50CHac

@ref	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
120151	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

isolation

@ref	sample type	country	origin.country	continent	geographic location	isolation date
4493	tea fungus beverage (Komucha)	Switzerland	CHE	Europe
67770	Liquid phase of a tea fungus beverage (Kombucha)
120151	Swiss Kombucha beverage	Switzerland	CHE	Europe	Zurich	1996

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_79.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_64;97_67;98_72;99_79&stattab=map
Last taxonomy: Komagataeibacter
16S sequence: Y14694
Sequence Identity:
Total samples: 4067
soil counts: 662
aquatic counts: 523
animal counts: 2327
plant counts: 555

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
4493	1	Risk group (German classification)
120151	1	Risk group (French classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Gluconacetobacter intermedius gene for 16S rRNA, partial sequence, strain: JCM 16936	AB645730	1411	ena	66229
20218	Gluconacetobacter intermedius strain LMG 18909 16S ribosomal RNA gene, partial sequence	JF793990	1351	ena	66229
20218	Gluconacetobacter intermedius strain DSM 11804 16S ribosomal RNA gene, partial sequence	JF793991	1352	ena	66229
20218	Gluconacetobacter intermedius strain LMG 18909T 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	KC478452	747	ena	66229
20218	Gluconacetobacter intermedius strain DSM 11804T 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	KC478454	749	ena	66229
4493	Acetobacter intermedius 16S rRNA gene	Y14694	1481	ena	66229

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Komagataeibacter intermedius TF2	1231353.3	wgs	patric	1231353
67770	Komagataeibacter intermedius TF2	GCA_000964425	scaffold	ncbi	1231353

GC content

@ref: 67770
GC-content: 61.6
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	no	85.279	no
gram-positive	no	96.266	no
anaerobic	no	97.954	no
aerobic	yes	79.266	no
halophile	no	91.23	no
spore-forming	no	95.362	no
thermophile	no	97.746	yes
glucose-util	yes	90.019	no
flagellated	no	97.498	no
glucose-ferment	no	86.141	no

External links

@ref: 4493

culture collection no.: DSM 11804, BCC 36457, JCM 16936, LMG 18909, BCC 36447, BCRC 17055, CIP 105780, ZIM B073

straininfo link

@ref: 69775
straininfo: 12785

literature

topic: Phylogeny
Pubmed-ID: 13678040
title: Acetobacter intermedius, sp. nov.
authors: Boesch C, Trcek J, Sievers M, Teuber M
journal: Syst Appl Microbiol
DOI: 10.1016/S0723-2020(98)80026-X
year: 1998
mesh: Acetobacter/*classification/isolation & purification/metabolism, Culture Media, DNA Probes, DNA, Bacterial/metabolism, DNA, Ribosomal/metabolism, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial/metabolism, RNA, Ribosomal, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/metabolism
topic2: Metabolism

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
4493	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11804)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-11804
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
39826	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/17837
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
68371				Automatically annotated from API 50CH acid
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69775	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID12785.1	StrainInfo: A central database for resolving microbial strain identifiers
120151	Curators of the CIP	Collection of Institut Pasteur (CIP 105780)	https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105780

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

metabolite utilization

antibiotic resistance

enzymes

API 50CHac

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference