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Abstract

The human body hosts a myriad of complex and diversified microbial assemblages on various barrier organs. The symbiotic microbial communities impact several aspects of the host’s biology in health and disease. Nowadays, microbiota research has become a central area of investigation involving diverse fields such as immunology, nutrition, and genetics. Consequently, methods for microbiota studies, comprising study design and laboratory techniques, are central in addressing general and specific research questions and especially in providing clear and reliable insights. Fortunately, approaches that investigate different aspects of microbial communities have greatly improved and expanded allowing unprecedented levels of characterization of host-microbiota interactions.

Through this chapter, we aim to describe the diverse techniques available for researchers to examine bacterial communities associated with numerous human body sites. We describe various culture-based and sequencing methods, additional techniques that characterize several aspects of the entire bacterial community, as well as approaches that define the status of single cells. Moreover, we describe the advantageous strategy of combining distinct approaches in a microbiota study to collect different and complementary insights on the community and/or to confirm each different method’s outcome. Additionally, we thoroughly discuss the crucial steps of study design, sampling strategies, and sample collection and processing which influence the interpretation and conclusions of microbiota study. Overall, this chapter clarifies the critical steps and available investigation tools in a microbiota study and thus assists researchers in defining the experimental design and laboratory methods to conduct a microbiota study.