Manganese (Mn) contamination poses a significant environmental threat, yet the mechanisms underlying its toxicity remain poorly characterised. Here, we used an integrative multi‐omics approach to elucidate how dietary Mn disrupts the gut‐microbiome axis in the silkworm, Bombyx mori . High‐dose Mn exposure triggered severe, dose‐dependent growth retardation, reducing larval weight by 55.1%. This was concurrent with profound gut...