| Summary: | The gut microbiota (GM) is a complex microbial community that exerts a considerable influence on human health, and its accurate characterisation has become essential to understanding its roles and implications in various medical conditions. Recent technological advances have paved the way for analytical methods that can uncover this complex microbial community. For these reasons, this review describes the methods used by research teams to discover and understanding the impact of GM in our environment. This paper explores the first phase of collecting and preserving samples, highlighting the impact of storage methods on sample stability and the reliability microbiological analyses. Then, it examines various methods for analysing GM. This diversity of approaches adapted to the specific objectives of each study, whether to characterise diversity using metagenomics, quantify specific micro-organisms using real-time PCR, or use techniques based on microbial targets. These methodologies promise new perspectives for understanding the physiological impact of the microbiota. Finally, concrete examples from Moroccan studies illustrate the application of these techniques to the characterisation of GM. By providing practical advice, this article guides researchers in the judicious choice of methods adapted to their research objectives and budgetary constraints, thereby contributing to the advancement of knowledge about the GM.
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