The microorganisms inhabiting the human gut are abundant (10(14) cells) and 
diverse (approximately 500 species per individual). It is now acknowledged that 
the microbiota has coevolved with its host to achieve a symbiotic relationship, 
leading to physiological homeostasis. The gut microbiota ensures vital 
functions, such as food digestibility, maturation of the host immune system, and 
protection against pathogens. Over the last few decades, the gut microbiota has 
also been associated with numerous diseases, such as inflammatory bowel disease, 
irritable bowel syndrome, obesity, and metabolic diseases. In most of these 
pathologies, a microbial dysbiosis has been found, indicating shifts in the 
taxonomic composition of the gut microbiota and changes in its functionality. 
Our understanding of the influence of the gut microbiota on human health is 
still growing. Working with microorganisms residing in the gut is challenging 
since most of them are anaerobic and a vast majority (approximately 75%) are 
uncultivable to date. Recently, a wide range of new approaches (meta-omics) has 
been developed to bypass the uncultivability and reveal the intricate mechanisms 
that sustain gut microbial homeostasis. After a brief description of these 
approaches (metagenomics, metatranscriptomics, metaproteomics, and 
metabolomics), this review will discuss the importance of considering the gut 
microbiome as a structured ecosystem and the use of meta-omics to decipher 
dysfunctions of the gut microbiome in diseases.