Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity

Alicja K Warda; Roland J Siezen; Jos Boekhorst; Marjon H J Wells-Bennik; Anne de Jong; Oscar P Kuipers; Masja N Nierop Groot; Tjakko Abee

doi:10.1371/journal.pone.0156796

Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity

PLoS One. 2016 Jun 7;11(6):e0156796. doi: 10.1371/journal.pone.0156796. eCollection 2016.

Authors

Alicja K Warda^{1

2

3}, Roland J Siezen^{1

4

5}, Jos Boekhorst^{1

4

6}, Marjon H J Wells-Bennik^{1

6}, Anne de Jong^{1

7}, Oscar P Kuipers^{1

7}, Masja N Nierop Groot^{1

3}, Tjakko Abee^{1

2}

Affiliations

¹ TI Food and Nutrition, Wageningen, The Netherlands.
² Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands.
³ Wageningen UR Food & Biobased Research, Wageningen, The Netherlands.
⁴ Center for Molecular and Biomolecular Informatics, RadboudUMC, Nijmegen, The Netherlands.
⁵ Microbial Bioinformatics, Ede, The Netherlands.
⁶ NIZO Food Research B.V., Ede, The Netherlands.
⁷ Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands.

Abstract

We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed.

Publication types

Comparative Study

MeSH terms

Bacillus cereus / genetics
Bacillus cereus / growth & development*
Bacillus cereus / isolation & purification
Biosynthetic Pathways
Carbohydrates / biosynthesis*
Carbohydrates / genetics
Food Microbiology
Genome, Bacterial*
Genotype
Phylogeny
Sequence Analysis, DNA / methods*

Substances

Carbohydrates

Grants and funding

The project is funded by TI Food and Nutrition (TIFN), a public-private partnership on precompetitive research in food and nutrition. The public partners are responsible for the study design, data collection and analysis, decision to publish, and preparation of the manuscript. The private partners have contributed to the project through regular discussion. TIFN provided support in the form of salaries for authors (AKW, RJS, JB, MHJWB, AdJ, OPK, MNNG, TA), but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the “author contributions” section. NIZO food research (http://www.nizo.com) is a contract research organization. NIZO was paid by TIFN to provide input on experimental design, bioinformatics analysis and data interpretation (i.e., the salary of JB and MHJWB was indirectly paid by TIFN). NIZO has no financial interest in any specific outcome of the study. Food & Biobased Research (FBR) is a contract research organization, part of Wageningen University and Research centre. FBR was paid by TIFN to provide input on experimental design, data generation, data interpretation, preparation of the manuscript (salary of MNNG, AKW). FBR has no financial interest in any specific outcome of the study. TIFN financed subcontracting to Microbial Bioinformatics (RJS) for input on experimental design, data interpretation and preparation of the manuscript. Microbial Bioinformatics has no financial interest in any specific outcome of the study.