The emergence of omics technologies (amplicon sequencing, metagenomics, metatranscriptomics, metaproteomics and metabolomics) has enabled the present-day researchers in adopting these technologies to redefine the food-based ecosystem. The recent development in omics approaches and affordability of the technologies has enabled a paradigm shift in the food science. Integration of complementary technologies and resources under the aegis of ‘meta-omics’ approaches towards producing essential knowledge such as metabolic typing and pathway-based functional analysis is getting increasingly evident from the published reports.

The high cost of experiments, lack of multidisciplinary approach and data analysis pipelines are still a limitation in the application of meta-omics study in food science as evident by limited research reports till date. Despite this, the ‘meta-omics’ approaches have proven extremely powerful in deciphering spatio-temporal complexities of fermenting microbial communities, functionality of the relevant metabolic pathways, and dynamic physiological processes responsible for aroma, flavor and texture development. Undoubtedly, omics studies have the potentials in systematically decoding the role of fermented foods on human metabolic pathways as well as gut microbial community structure. In the post-genomic era, the R&D sector associated with the food fermentation science has to take the onus of generating evidence-based scientific information for claiming the health benefits as well as safety of the fermented foods.

Meta-omics approaches can expedite technology commercialization of fermented food items through process development and validation, standardized inoculum preparation, quality control of raw and end products, detection of allergens and contaminants, strategy development for pathogenic microorganism containment etc. A myriad of ongoing fermentation-related omics studies have generated a pool of raw-data which is gradually becoming accessible to a wider range of users and analysis platforms. These data provide suitable opportunity to retrieve pivotal information on factors for human nutrition (folate, riboflavin, short-chain fatty acid), taste markers (factors for flavor, odor generation), and biomarkers for monitoring (biogenic amine, volatile organic compounds) in fermentation processes.

The available broad metabolic databases often assign suboptimal functional annotations leading to false-positive outcomes. The lack of databases for specific microbial (e.g. lactic acid bacteria) metabolic pathways is also a hindrance in the systematic study of microbial species, genes, metabolic pathways, metabolites and activities associated with fermented food products. These limitations warrant greater application of the meta-omics technologies to dissipate the boundaries of omics technologies in food fermentation. Such development and breakthroughs in sensitive and specific computational interpretation, genomic technologies and metabolic pathway biomarkers will accelerate the product development process for various fermented foods around the globe.

For this Research Topic, we invite papers relevant to applications of meta-omics technologies in the development of fermented food products. Researchers, academicians and professionals are encouraged to contribute full length, original research articles, reviews, letters to editor, and short communications.

Relevant topics include but are not limited to:

(i) Meta-omics technologies for understanding the microbiome of spontaneous fermentation
(ii) Computational tools and platforms integral to ‘meta-omics’ approaches in food fermentations
(iii) Meta-omics in fermented food quality & safety
(iv) Meta-omics in shelf-life study of fermented foods
(v) Meta-omics in sensory quality assessment of fermented foods

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Frontiers in Microbiology

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