Hey there,
I am attempting to analyze microbiome results. I mainly do fecal metabolomics, but my advisor sent off some samples for microbiome analysis. The company that analyzed the samples investigated- 1) Sequence curation and metrics, 2) Taxonomic composition, 3) Alpha diversity, 4) Beta diversity similarity among microbiomes, and 5) Differential abundance testing. There are observable differences between groups, but I am interested in what those differences actually mean. I am attempting to use the taxon set analysis to do an enrichment analysis. The company provided phylum and genus. The names provided are not recognized by microbiomeAnalyst in the enrichment analysis.
I would appreciate any help. I have no background in microbiomes.