Abstract
Vanillin is a phenolic food additive commonly used for flavor, antimicrobial, and antioxidant properties. Though it is one of the widely used food additives, strategies of the human gut microbes to evade its antimicrobial activity await extensive elucidation. The current study explores the human gut microbiome with a multi-omics approach to elucidate its composition and metabolic machinery to counter vanillin bioactivity. A combination of SSU rRNA gene diversity, metagenomic RNA features diversity, phylogenetic affiliation of metagenome encoded proteins, uniformly (R = 0.99) indicates the abundance of Bacteroidetes followed by Firmicutes and Proteobacteria. Manual curation of metagenomic dataset identified gene clusters specific for the vanillin metabolism (ligV, ligK, and vanK) and intermediary metabolic pathways (pca and cat operon). Metagenomic dataset comparison identified the omnipresence of vanillin catabolic features across diverse populations. The metabolomic analysis brings forth the functionality of the vanillin catabolic pathway through the Protocatechuate branch of the beta-ketoadipate pathway. These results highlight the human gut microbial features and metabolic bioprocess involved in vanillin catabolism to overcome its antimicrobial activity. The current study advances our understanding of the human gut microbiome adaption toward changing dietary habits.
Highlights
The human gut microbiome is a stratified, metabolically active, and resilient biotic component of the human body (Yadav et al, 2018)
The human microbiome is a specialized dynamic organ that plays a vital role in the maintenance of host physiology
The human gut microbiome complements with host machinery to metabolize a wide range of ingested foods (Yadav et al, 2018)
Summary
The human gut microbiome is a stratified, metabolically active, and resilient biotic component of the human body (Yadav et al, 2018). Vanillin is known to improve the gut microbiome composition (Guo et al, 2018), as well as protect the host from the onset of various human disorders (Yan et al, 2017) It indicates the possible presence of efficient vanillin catabolic machinery among the human gut microbes; an effort to explore these metabolic pathways is warranted. We have explored the human gut microbiome composition, its genetic content, and metabolic efficiency to catabolize vanillin using a culture-independent multi-omics approach. The metagenome sequence dataset was quality filtered (Denoising and normalization with DynamicTrim, removal of host DNA sequences with Bowtie2) and processed for the identification of rRNA gene features (by rRNA genecalling) and protein features (with genecalling using cutoff similarity% > 70%). Lowest Common Ancestor (LCA) abundance profile, and Data source abundance profile were used to predict taxonomic and functional affiliation of the predicated protein features (Milanese et al, 2019)
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