Microbial ecology-based methods to characterize the bacterial communities of non-model insects

Abstract

Among the animals of the Kingdom Animalia, insects are unparalleled for their widespread diffusion, diversity and number of occupied ecological niches. In recent years they have raised researcher interest not only because of their importance as human and agricultural pests, disease vectors and as useful breeding species (e.g. honeybee and silkworm), but also because of their suitability as animal models. It is now fully recognized that microorganisms form symbiotic relationships with insects, influencing their survival, fitness, development, mating habits and the immune system and other aspects of the biology and ecology of the insect host. Thus, any research aimed at deepening the knowledge of any given insect species (perhaps species of applied interest or species emerging as novel pests or vectors) must consider the characterization of the associated microbiome. The present review critically examines the microbiology and molecular ecology techniques that can be applied to the taxonomical and functional analysis of the microbiome of non-model insects. Our goal is to provide an overview of current approaches and methods addressing the ecology and functions of microorganisms and microbiomes associated with insects. Our focus is on operational details, aiming to provide a concise guide to currently available advanced techniques, in an effort to extend insect microbiome research beyond simple descriptions of microbial communities.

Hydrolytic Profile of the Culturable Gut Bacterial Community Associated With Hermetia illucens

“…Handling a collection of microbial strains can allow to directly test, by means of in vitro and in vivo assays, hypotheses about their importance for the insect host, an aspect that is not always possible relying solely on DNA-based techniques (Prosdocimi et al, 2015). Beyond the characterization of their function in the FIGURE 2 | Metabolic activities and EPS production ability for the bacterial isolates obtained from the gut of H. illucens larvae.…”

“…Handling a collection of microbial strains can allow to directly test, by means of in vitro and in vivo assays, hypotheses about their importance for the insect host, an aspect that is not always possible relying solely on DNA-based techniques ( Prosdocimi et al, 2015 ). Beyond the characterization of their function in the native host, culturable microorganisms can be directly exploited in different biotechnological applications ( Crotti et al, 2012 ; Valiente Moro et al, 2013 ; Epis et al, 2020 ).…”

“…For instance, larval development on poultry manure has been shown to benefit by supplementation with Bacillus subtilis isolated from BSF both in term of larval weight increase and developmental time reduction (Yu et al, 2011). The strategy to assess the role of specific isolates as beneficial probiotics characterizes their phenotypic properties in vitro to select potentially suitable strains and tests their effectiveness in promoting larval weight, growth rate and adult survival along the insect cycle, upon supplementation in the host diet (Prosdocimi et al, 2015). In this work we implemented such strategy on a large collection of bacterial isolates from the gut of BSF larvae reared on a nutritionally complete diet (standard diet, SD).…”

Bamboo lignocellulose degradation by gut symbiotic microbiota of the bamboo snout beetle Cyrtotrachelus buqueti

“…The symbiotic microbiota of insects includes bacteria, protozoa, fungus and archaea, among which bacteria are the most representative. Symbiotic bacteria exist in Coleoptera, Blattaria, Isoptera, Diptera, Hemiptera, Mallophaga, and Anoplura [35] and the symbiotic bacteria of insects primarily belong to the phyla: Proteobacteria, Bacteroidetes, Firmicutes, Actinomycetes, Spirochetes, and Verrucomicrobia [36].…”

Malaria vector species in Amazonian Peru co-occur in larval habitats but have distinct larval microbial communities

“…DNA was extracted from whole larvae using the DNeasy Blood & Tissue kit following surface sterilization in 100% ethanol. Prior to bead-beating, larvae were suspended in the manufacturer-recommended enzymatic lysis buffer (containing lysozyme) to enhance DNA purification from gram-positive bacteria as suggested in [81]. All extractions and post-extraction manipulation of samples and 16S PCR reactions were performed in a biosafety cabinet with pre-sterilized materials where possible to avoid contamination, and all extractions were performed using the same extraction kit to avoid batch contamination effects [82].…”