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