Name: Bombella intestini R-52487
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130136

Type strain:

Species: Bombella intestini

Strain Designation: R-52487

Culture col. no.: DSM 28636, LMG 28161

Strain history: <- P. Vandamme, Univ. Ghent, Belgium; R-52487 <- L. Li

NCBI tax ID(s): 1539051 (species)

SI-ID 404319

DSM 28636

Section

Bombella intestini R-52487 is a mesophilic, Gram-negative bacterium that was isolated from crop of a bumblebee Bombus lapidarius.

Gram-negative
mesophilic
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	*Bombella*
	Species	**Bombella intestini**
	Full Scientific Name (LPSN)	Bombella intestini Li et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.999

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22131]

Culture medium

GY-MEDIUM (DSMZ Medium 1543)

[Ref.: #22131]

Culture medium growth

[Ref.: #22131]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22131]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22131]			growth	28 °C

[Ref.: #22131]

Temperature range

mesophilic

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 %99.998

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

[Ref.: #22131]	Sample type/isolated from	crop of a bumblebee Bombus lapidarius
[Ref.: #22131]	Host species	Bombus lapidarius
[Ref.: #22131]	Geographic location (country and/or sea, region)	Ghent
[Ref.: #22131]	Country	Belgium
[Ref.: #22131]	Country ISO 3 Code	BEL
[Ref.: #22131]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host

#Arthropoda

#Insecta

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KJ584313 (>99% sequence identity) for Acetobacteraceae from Microbeatlas

Aquatic Samples	372
Soil Samples	705
Animal Samples	1381
Plant Samples	105
Total Samples	2563

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

[Ref.: #22131]

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.: #22131]	Bombella intestini strain R-52487 16S ribosomal RNA gene, partial sequence	KJ584313	1450	ENA	1539051 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bombella intestini R-52487	GCA_002003665	contig	GenBank	1539051 tax ID	*
[Ref.: #66792]	Bombella intestini strain R-52487	1539051.3	wgs	PATRIC	1539051 tax ID	*
[Ref.: #66792]	Bombella intestini R-52487	2791354941	draft	JGI IMG/M	1539051 tax ID	*

[Ref.: #22131]

GC-content

54.9 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: Bombella intestini strain R-52487 PATRIC: 1539051.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bombella intestini strain R-52487 PATRIC: 1539051.3
[Ref.: #69480]	motile	yes	68.17	no
[Ref.: #69480]	gram-positive	no	98.431	no
[Ref.: #69480]	anaerobic	no	98.577	no
[Ref.: #69480]	aerobic	yes	52.141	no
[Ref.: #69480]	halophile	no	81.112	no
[Ref.: #69480]	spore-forming	no	96.303	no
[Ref.: #69480]	thermophile	no	90.569	yes
[Ref.: #69480]	glucose-util	yes	71.943	no
[Ref.: #69480]	flagellated	no	84.174	no
[Ref.: #69480]	glucose-ferment	no	80.7	no

Availability in culture collections External links

[Ref.: #22131]

Culture collection no.

DSM 28636, LMG 28161

[Ref.: #88690]

SI-ID 404319

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.	Li L, Praet J, Borremans W, Nunes OC, Manaia CM, Cleenwerck I, Meeus I, Smagghe G, De Vuyst L, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.068049-0	2014	*
Phylogeny	Bombella apis sp. nov., an acetic acid bacterium isolated from the midgut of a honey bee.	Yun JH, Lee JY, Hyun DW, Jung MJ, Bae JW	Int J Syst Evol Microbiol	10.1099/ijsem.0.001921	2017	*
Metabolism	Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius.	Li L, Illeghems K, Van Kerrebroeck S, Borremans W, Cleenwerck I, Smagghe G, De Vuyst L, Vandamme P	PLoS One	10.1371/journal.pone.0165611	2016	*

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 )

#22131

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28636

#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) .

#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 )

#88690

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-ID404319.1 )

* These data were automatically processed and therefore are not curated

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Bombella intestini strain R-52487

Bombella intestini strain R-52487

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