Hello,
I am using MetaboAnalyst 6.0 to analyze untargeted HRMS metabolomics data from an in vitro plant-microbial fermentation matrix with a Lactobacillus sp. My input files consist strictly of lists of significantly upregulated polyphenolic compounds.
I need guidance on correct library selection and biological interpretation:
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Since my specific plant is missing, is it methodologically sound to use Arabidopsis thaliana as a reference? If a plant “Biosynthesis” pathway (e.g., Flavonoid Biosynthesis) is enriched from a list of upregulated molecules in a fermentation system, does this mathematically point to microbial degradation/liberation of complex matrices rather than active gene expression?
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In Vitro vs. Gut Microbiota Library: In the Enrichment Analysis module, I tested the Human Gut Bacteria (KEGG) reference library, which successfully matched my list to specific phenolic degradation pathways. Given that my setup is exclusively an in vitro flask system with a lactic acid bacterium, is this library biologically valid to map the metabolic toolkit of a single plant-associated microbe?
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Modeling Fungal-Bacterial Cascades: Since the Enrichment module lacks a fungal/mushroom reference option, which organism or reference database should I use to do the enrichment analysis for a fungal fermentation setup?
Thank you for your guidance!