Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation
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Abstract
Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators’ sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of S. epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.
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. By exploring these questions further, future studies would promote the development and enjoyment of miso and other fermented plant-based foods, facilitating product quality, sustainability, and food diversity, while deepening our knowledge of the microbiology of food fermentation, both traditional and novel.
This is a really cool study. It's awesome you are pursuing a deeper understanding of misos and other fermented foods. I agree they have so much potential for helping us move towards a sustainable food system.
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Hypothesising horizontal gene transfer (HGT), we investigated where the MS strain had acquired these genes from
From the MAG of the MS S. epidermidis strain, is there anything about the surrounding genomic region of these carotenoid genes that suggests HGT/that they may be on a mobile element? Are these genes co-localized in a biosynthetic cluster? Since carotenoid biosynthesis is pretty well-studied, can you comment on where these genes are in the pathway and what carotenoid they may produce?
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To overcome this limitation by further characterising the microbiota independently of the set references, we applied an analysis using two marker genes—ychF and leuS—from the assembled metagenomes.
Aside from using metaphlan or marker genes, can you tell from the assemblies what other fungi were recovered? How many different fungal MAGs did you get (even if not high quality)? Do you think sequencing depth was an issue in recovering fungal MAGs?
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—habanero-barley (HB), maitake-soy (MS), and toasted sesame (TS)—were co-dominated by other species of the Saccharomycetales family, mainly Millerozyma farinosa, Starmella-Candida spp., Debaryomyces hansenii and Candida glabarata.
Can you think of any reason why these misos might favor Saccharomycetes? Any commonalities in pH or other factors that are different from the others?
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The MAGs are available at doi: 10.17632/sjyf9kncs9.1.
I think ENA supports submission of MAGs- is there a reason you didn't deposit those here as well? If you do, you can also request MGnify analysis (https://www.ebi.ac.uk/metagenomics) which is nice and also provides greater visibility of this data for other microbiome researchers
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generating a dataset of at least 16M paired-end reads
is this 16M reads per sample ?
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Chimeras were removed using the removeBimeraDenovo dada2 R function.
Can you add references for cutadapt and dada2 if they are not present ? Same for SILVA and UNITE, metaWRAP
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ecology and supporting the production of both traditional and innovative misos.
This whole introduction was very clearly written and made me excited to keep reading the paper!
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