Human Gut Microbiome: A Connecting Organ Between Nutrition, Metabolism, and Health

Abstract

The gut microbiome plays a vital role in human health, functioning as a metabolic organ that influences nutrient absorption and overall well-being. With growing evidence that dietary interventions can modulate the microbiome and improve health, this review examines whether healthcare systems should prioritize personalized microbiome-targeted therapies, such as probiotics, prebiotics, and microbiota transplants, over traditional pharmaceutical treatments for chronic diseases like obesity, diabetes, cardiovascular risk, and inflammatory conditions. A systematic review using Web of Science and Scopus databases was conducted, followed by a scientometric analysis. Key metabolic pathways, such as dietary fiber fermentation and short-chain fatty acid production, were explored, focusing on their impact on lipid and glucose metabolism. The interactions between microbial metabolites and the immune system were also investigated. Dietary interventions, including increased fiber and probiotic intake, show potential for addressing dysbiosis linked to conditions, such as type 2 diabetes, obesity, and autoimmune diseases. The review emphasizes the need to incorporate microbiome modulation strategies into clinical practice and research, calling for a multidisciplinary approach that integrates nutrition, microbiology, and biochemistry to better understand the gut microbiome's complex role in health.

Keywords: gut microbiome; microbiome biochemistry; microbiome modulation; nutrient assimilation.

Figure 6

Accurate genome relative abundance estimation for closely related species in a metagenomic sample. Adapted from [61].

Figure 1

Systematic and automatized workflow for data processing and document selection.

Figure 2

Scientific production over time.

Figure 3

Scientific collaboration network among countries. (a) Distribution of scientific communities based on a clustering algorithm, identifying five distinct communities of collaborating countries. (b) Evolution of new scientific collaborations over time, where “nodes” represent newly added countries in the network, and “links” indicate newly established collaborations between countries in each year. (c) Network Scientific collaboration between countries, based on author affiliations. The size of each node represents the degree (number of connections), while the color indicates community membership. Link thickness represents the collaboration strength, with thicker links indicating stronger ties between countries.

Figure 4

Citation network among scientific journals. (a) Identification of the main journal communities based on a clustering algorithm, grouping journals into thematic clusters. (b) Evolution of the proportion of new journals and new citation links per year, where “nodes” represent newly added journals, and “links” indicate new citation connections between journals each year. (c) Citation network among scientific journals, where node size represents the journal’s centrality (number of citations received), and link thickness indicates the strength of citation connections. The color of each node represents its community membership.

Figure 5

Total bacterial abundance according to different body sites and autochthonous and allochthonous Members of bacterial taxa distributed in different compartments of the TGI [9,51].

Figure 7

Metabolic pathways employed by the microbiome for SCFAs synthesis, along with absorption routes and their distribution throughout the human body to various organs.