Bioinformatic approaches for studying the microbiome of fermented food

Abstract

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.

Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security

“…The shotgun metagenomics technique entails sequencing every genetic molecule found in an environmental sample without first amplifying or focusing on any particular genes [ 87 ]. It enables the identification of microbial taxa that are both known and unknown [ 88 ]. Shotgun sequencing in microbiome studies can simultaneously identify and profile bacteria, fungi, viruses, and other types of microorganisms [ 81 ].…”

Should the microbiota of raw milk cheeses play a role in the definition of geographical indications and quality schemes within the European Union?

“…assuming that the analysis of the metagenome of a product at the time of consumption can characterize the microbiota and its evolution during ripening is wrong ( 2 )…”

Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation

“…As popular interest in global fermentation techniques has exploded, scientific attention to fermented foods has also grown, as part of a larger research focus on the human microbiome and health, and facilitated by the decreasing cost of Next Generation DNA Sequencing (NGS) technologies (Jahn et al ., 2023; Lorimer, 2016, 2020; Mardis, 2017; Yong, 2016). While studies on the microbial ecology of many fermented foods are becoming more common (Landis et al ., 2022; Pasolli et al ., 2020; Walsh et al ., 2022; Yap et al ., 2022), there still exists very little English-language literature on miso ecology. A few older reports exist that use only culture-dependent methods (Hesseltine, 1983), but the few taxa identified ‘do not exclude certain other halophilic yeasts and bacteria from growing in or on the fermenting paste’ (Hesseltine, 1983: 589), as microbial isolation-based taxonomy is biased toward culturable species.…”