Unpacking the Proteome and Metaproteome of the Black Soldier Fly Larvae: Efficacy and Complementarity of Multiple Protein Extraction Protocols

Abstract

The larvae of the black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), have demonstrated the ability to efficiently bioconvert organic waste into a sustainable source of food and feed, but fundamental biology remains to be discovered to exploit their full biodegradative potential. Herein, LC−MS/MS was used to assess the efficiency of eight differing extraction protocols to build foundational knowledge regarding the proteome landscape of both the BSF larvae body and gut. Each protocol yielded complementary information to improve BSF proteome coverage. Protocol 8 (liquid nitrogen, defatting, and urea/thiourea/ chaps) was better than all other protocols for the protein extraction from larvae gut samples, and the exclusion of defatting steps yielded the highest number of proteins for the larval body samples. Protocol-specific functional annotation using protein level information has shown that the selection of extraction buffer can affect protein detection and their associated functional classes within the measured BSF larval gut proteome. A targeted LC-MRM-MS experiment was performed on the selected enzyme subclasses to assess the influence of protocol composition using peptide abundance measurements. Metaproteome analysis of the BSF larvae gut has uncovered the prevalence of two bacterial phyla: actinobacteria and proteobacteria. We envisage that using complementary extraction protocols and investigating the proteome from the BSF body and gut separately will expand the fundamental knowledge of the BSF proteome and thereby provide translational opportunities for future research to enhance their efficiency for waste degradation and contribution to the circular economy.

Evaluation of protein extraction methods to improve meta‐proteomics analysis of treated wastewater biofilms

“…For example, the number of proteins identified varies widely among treated wastewater effluents produced by different wastewater treatment plants (WWTPs), with generally less than a thousand identified by metaproteomics compared to the actual number of proteins which is estimated to be in the range of hundreds of thousands up to millions [9,10]. Moreover, different protein extraction methods lead to variations in protein recovery and introduce bias when analyzing the microbial communities, therefore, new protocols for metaproteomics are proposed to improve the yield of extraction, to facilitate the entire workflow from sample processing to data analytics, and to enhance the resolution of metaproteome analysis [11][12][13][14][15]. In particular, protein extraction and sample processing is a subject of improvement by the scientific community in the Metaproteomics Initiative [4,16].…”