HRMS is a universal detection technique that presents a very high selectivity and sensitivity offering simultaneous structural and quantitative information. On the other hand, the current state-of-the-art technology in faecal metabolomics is the hyphenation of high-resolution mass spectrometry–based techniques (HRMS) with high-performance chromatography. However, this approach is typically laborious and expensive for application on small batches of samples, as it is common in clinical practice moreover, factors that influence microbial RNA stability can produce a significant variation in the gut microbiome composition. The most frequent approach to study the microbiota composition is to target the bacterial 16S ribosomal RNA (rRNA) extracted from faecal samples.

In these settings, the faecal metabolic profiles complement sequencing-based approaches to provide a functional readout of the gut microbiome and gain insight for improving the diagnosis and prognosis of several diseases. For instance, the faecal microbiome and metabolome are simultaneously found to be disordered in colorectal cancer, systemic lupus erythematosus, metabolic syndrome, asthma and central nervous system disorders. The influence of the GM in regulating metabolic activity is now recognized with increasing evidence. The human GM is characterized by diverse microbial communities of multiple phyla of bacteria, archaea, viruses and microbial eukaryotes, which perform many essential protective, structural and metabolic functions for human health, including food processing, digestion of complex indigestible fibres, pathogen displacement and synthesis of many compounds responsible for regulating the activity of distal organs (e.g. Over the last decade, with the rapid development of microbiome sequencing technologies, an integrated omics analysis of faecal material has gained attention as a non-invasive method for studying the complex interactions between the human gut microbiota (GM) and the host. Human faeces are a very complex biological matrix with a broad biochemical composition that represents a rich source of diverse metabolic compounds derived from the host, the gut microbiota and xenobiotics. More recently, faecal samples have become a valuable choice, since they can be obtained noninvasively.

The most frequently explored specimens for metabolomic analyses in humans are serum, urine and tissues. Metabolomics is a systems biology approach that aims at the qualitative and quantitative analysis of small molecules (below 1.5 kDa) in biological samples.

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