Novel methods of microbiome analysis in the food industry

The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies.
The work in our research groups was funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 818368 (MASTER), and the grants RTI2018-095021-J-I00 (funded by (MCIU/AEI/FEDER, UE), AGL2016-78085-P and AGL2016-78311-R (funded by (MINECO/AEI/FEDER, UE). Carlos Sabater acknowledges his Postdoctoral research contract funded by the Instituto de Investigación Sanitaria del Principado de Asturias (ISPA) and Postdoctoral research contract Juan de la Cierva-Formación from Spanish Ministry of Science and Innovation (FJC2019-042125-I).