Abstract

Native gut microbiota enhanced proteolytic enzyme activity and protein use in BSFL. • Core taxa enhance host protein and amino acid metabolism. • Engineered SynCom optimizes protein degradation and synthesis via gut pH gradient. • Host ALDH links microbial signals to TOR pathway to regulate protein anabolism. • SynCom-BSFL boosts protein degradation in wastes and larval protein accumulation. Black soldier fly larvae (BSFL) are efficient bioconverters of diverse organic wastes into sustainable alternative protein resources. However, the interactive mechanisms between the core gut microbiota and its host that govern efficient protein degradation and synthesis remain elusive. This study employed multi-omics and synthetic microbial communities (SynCom) in germ-free models to examine microbiota-associated protein conversion under controlled conditions. We identified the bacteria Bacillus and Lactobacillus and the yeast Issatchenkia functionally relevant taxa associated with improved host protein conversion and amino-acid metabolic responses under the tested gnotobiotic conditions. Bacillus showed direct proteolytic activity, whereas Lactobacillus and Issatchenkia were associated with improved protein conversion performance in the tested SynCom. Among the tested inoculation schemes, a tripartite SynCom comprising these taxa showed the highest protein conversion performance and was associated with distinct spatiotemporal distribution patterns along the gut pH gradient, increasing final larval protein content by 63%. The host aldehyde dehydrogenase (ALDH) was identified as a candidate host node, associated with microbiota-responsive branched-chain amino acids, tryptophan metabolism and the host’s Target of Rapamycin (TOR) related signaling. Thus, function-guided SynCom recapitulates selected functional features associated with the native microbiota in a tractable gnotobiotic system. Furthermore, when applied to chicken manure and kitchen waste, the SynCom-BSFL