Bacterial spores are robust survival vehicles that are highly resistant towards stress conditions including heat and other stresses commonly applied during food production and preservation. Heat treatments are conventionally applied in food processing to reduce the microbial load of food products, however, in compliance with consumer desire for products with higher sensory and nutritional values, the treatment intensity may become milder. Consequently, subpopulations of spores, including those of the toxin-producing food-borne human pathogen Bacillus cereus, may emerge that are sublethally damaged rather than inactivated conceivably causing quality and safety issues after repair and outgrowth. The research described in this thesis has added novel insights in B. cereus capacity to cope with spore damage and provided insights in the distribution and putative functionality of (sub)clusters of GRs and carbohydrate utilisation clusters. Knowledge on spore damage repair, germination and metabolism capacity adds to further understanding of B. cereus ecology and transmission capacity.