Bioinformatic approaches for studying the microbiome of fermented food
Citation
Liam H. Walsh, Mairéad Coakley, Aaron M. Walsh, Paul W. O’Toole & Paul D. Cotter (2022) Bioinformatic approaches for studying the microbiome of fermented food, Critical Reviews in Microbiology, DOI: 10.1080/1040841X.2022.2132850Abstract
High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.Funder
European Union; Science Foundation Ireland; Department of Agriculture, Food and the Marine; Enterprise IrelandGrant Number
818368; FI/12/RC/2273_P2; FI/16/RC/3835; C/2018/0025ae974a485f413a2113503eed53cd6c53
https://doi.org/10.1080/1040841X.2022.2132850
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