Animal board invited review: The need for, and the path towards, a functional understanding of the farmed insect microbiome

Abstract

The rapid growth of research on industrially produced insect species over the past two decades has coincided with breakthroughs in the speed and affordability of DNA sequencing. This has allowed researchers to rapidly generate data on the microbial communities associated with farmed insects, especially the gut-residing bacteria of the two cornerstone production species: black soldier fly (BSF, Hermetia illucens) and yellow mealworm (Tenebrio molitor). A picture of the most prevalent and abundant microbes associated with these species has rapidly come into focus. Specific microbial functions have been suggested under extreme or challenging rearing settings, but less is known about the contributions of the microbiome to insect rearing under realistic production conditions. There is limited understanding of how microbial communities of farmed insects arise, are maintained, and change in response to stimuli. Likewise for seemingly basic questions: what functions do insect-associated microbes perform for the host? Which (if any) taxa are essential for healthy insects? This is not intended as a criticism of existing research; indeed, these questions turn out not to be simple. Answering them requires targeted research approaches testing specific hypotheses about farmed insect microbiome function. This review aims to recalibrate the state of knowledge by critically assessing common and emerging strategies to study these microbiomes and existing knowledge gaps about the functional role of the microbiome for BSF and mealworm. Overall, it is clear that microbes are an intrinsic part of the ecology of these two farmed insects. Reciprocal interactions between microbes and insects are extensive, though microbiome community composition depends to a large extent on environmental conditions. To date, it remains unclear how taxonomical shifts correspond to functional shifts and to what extent such changes impact insect physiology. For example, when mealworms are fed plastics, their microbiomes undergo significant changes in microbial composition. These changes are presumed to increase the ability of mealworms and their microbiota to degrade plastic, but this change in function is hard to conclusively demonstrate with current tools. Furthermore, analysis of the literature shows that taxonomically disparate microbial communities may provide similar functional benefits, e.g. lignocellulose breakdown in BSF larvae. This review therefore aims to critically assess the state of the art with regard to functional analysis of the farmed insect microbiome and how available experimental methods can be best applied to identify links between microbial functions and insect physiology and improve the efficiency and sustainability of the farmed insect industry.