Micronutrient Biosynthesis Potential of Spontaneous Grain Fermentation Microbiomes

Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics and the purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analysis conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipeline with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were significant differences in the relative abundances of bacteria involved in the spontaneous fermentation of millet namely, Lactobacillaceae, Leuconostocaceae, and Clostridiaceae in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristic of fermented millet. The datasets were collected with fermentations mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as vitamins suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.