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 insectmicrobiome research beyond simple descriptions ofmicrobial
communities.