Cereal-based fermented foods are major contributors to energy intake in developing countries (DC). Their microbiota is dominated by lactic acid bacteria and has been extensively investigated. Diversity studies have been facilitated by molecular methods enabling genotyping of isolates; the rapid development of ‘omics’ approaches should facilitate more comprehensive studies to describe the relation between microbial diversity, cell physiology and product characteristics. Also, the link between the food microbiota and health benefits, in particular in nutrition, should be investigated. There is a need to encourage researches in the field of DC cereal-based foods in direction of more mechanistic approaches.