Abstract
Alterations in the human gut microbiota play an important role in disease pathogenesis. Although next-generation sequencing has provided observational evidence linking shifts in gut microbiota composition to alterations in the human host, underlying mechanisms remain elusive. Metabolites generated within complex microbial communities and at the crossroads with host cells may be able to explain the impact of the gut microbiome on human homeostasis. Emerging technologies including novel culturing protocols, microfluidic systems, engineered organoids, and single-cell imaging approaches are providing new perspectives from which the gut microbiome can be studied paving the way to new diagnostic markers and personalized therapeutic interventions.
Highlights
Alterations in the intestinal microbiota, termed dysbiosis, have been associated with a variety of pathological conditions including metabolic disorders, inflammatory chronic diseases, allergies, neurodegeneration, and cancer [1,2,3,4,5,6]
Preclinical and clinical studies have over recent decades been characterizing the changes in the composition and in the metabolic functions of the microbiota during gut dysbiosis in the attempt to expand our knowledge on the role of the gut microbiome in human diseases and to answer questions such as ‘who’s there?’ and ‘what genes are there?’ [7]
It is well established that the microbial composition can only partially explain dysbiosis-related pathologies and that the metabolic functions of the gut microbiota (‘what’s it doing?’) impact homeostatic and pathological conditions
Summary
Alterations in the intestinal microbiota, termed dysbiosis, have been associated with a variety of pathological conditions including metabolic disorders, inflammatory chronic diseases, allergies, neurodegeneration, and cancer [1,2,3,4,5,6]. The large body of data that exists has provided information on the link between dysbiosis and pathophysiological alterations, but not about microbial mechanisms of pathogenesis To bridge this gap, experimental and clinical researchers have been exploiting multidisciplinary approaches that combine traditional microbiology and cell biology to biomedical engineering and microfluidic technology to investigate bacteria-bacteria and bacteria-host interactions. Experimental and clinical researchers have been exploiting multidisciplinary approaches that combine traditional microbiology and cell biology to biomedical engineering and microfluidic technology to investigate bacteria-bacteria and bacteria-host interactions In view of these considerations, the current work set out to briefly review the -omics technologies employed to characterize the gut microbiota dedicating particular attention to their potential and limitations.
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