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

Leilei Li; Koen Illeghems; Simon Van Kerrebroeck; Wim Borremans; Ilse Cleenwerck; Guy Smagghe; Luc De Vuyst; Peter Vandamme

doi:10.1371/journal.pone.0165611

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

PLoS One. 2016 Nov 16;11(11):e0165611. doi: 10.1371/journal.pone.0165611. eCollection 2016.

Authors

Leilei Li¹, Koen Illeghems², Simon Van Kerrebroeck², Wim Borremans², Ilse Cleenwerck³, Guy Smagghe⁴, Luc De Vuyst², Peter Vandamme¹

Affiliations

¹ Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
² Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
³ BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
⁴ Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium.

Abstract

The whole-genome sequence of Bombella intestini LMG 28161T, an endosymbiotic acetic acid bacterium (AAB) occurring in bumble bees, was determined to investigate the molecular mechanisms underlying its metabolic capabilities. The draft genome sequence of B. intestini LMG 28161T was 2.02 Mb. Metabolic carbohydrate pathways were in agreement with the metabolite analyses of fermentation experiments and revealed its oxidative capacity towards sucrose, D-glucose, D-fructose and D-mannitol, but not ethanol and glycerol. The results of the fermentation experiments also demonstrated that the lack of effective aeration in small-scale carbohydrate consumption experiments may be responsible for the lack of reproducibility of such results in taxonomic studies of AAB. Finally, compared to the genome sequences of its nearest phylogenetic neighbor and of three other insect associated AAB strains, the B. intestini LMG 28161T genome lost 69 orthologs and included 89 unique genes. Although many of the latter were hypothetical they also included several type IV secretion system proteins, amino acid transporter/permeases and membrane proteins which might play a role in the interaction with the bumble bee host.

MeSH terms

Acetic Acid / metabolism*
Animal Structures / microbiology*
Animals
Bacteria / drug effects
Bacteria / genetics*
Bacteria / growth & development
Bacteria / isolation & purification*
Bacterial Proteins / genetics
Bacterial Proteins / metabolism
Bees / microbiology*
Carbohydrate Metabolism
Cell Membrane / metabolism
Electron Transport
Genome, Bacterial*
Glucose / pharmacology
Metabolic Networks and Pathways
Metabolome / drug effects
Open Reading Frames / genetics
Sequence Analysis, DNA / methods*
Symbiosis / genetics

Substances

Bacterial Proteins
Glucose
Acetic Acid

Grants and funding

The BCCM/LMG collection is supported by the Federal Public Planning Service—Science Policy, Belgium (contract no. C4/00/BCCM). The authors acknowledge the financial support of the Research Foundation-Flanders (FWO-Vlaanderen; http://www.fwo.be; grant no. G.0.910.10.N.10), the Research Council of Ghent University and the Vrije Universiteit Brussel (http://www.vub.ac.be/en/research; SRP7, IRP2 and IOF342 projects) and the Hercules Foundation (grant number UABR09004). L.L. acknowledges the Chinese Scholarship Council (http://www.csc.edu.cn; file no. 2011533075) and Ghent University Co-Funding (http://www.ugent.be/nl/onderzoek/financiering/; grant no. 01SC1111).