Increasing investigations into host-microbiota interactions have revealed that the intestinal microbiota is a critical mediator in maintaining health (Holmes et al., 2011).

Generally the “gut microbiota” is the diverse microbial community (bacteria, fungi, archaea, viruses and protozoa) that colonize the gastrointestinal tract of their host (Shukla et al., 2017).

The composition of the gut microbiome is similar at the phylum level (mainly Bacteroidetes and Firmicutes), but the diversity and species richness tends to vary between individuals (Tremaroli and Backhed, 2012).

Increasing investigations into host-microbiota interactions have revealed that the gut microbiota is a critical mediator in maintaining health (Holmes et al., 2011).
Generally the “gut microbiota” is the diverse microbial community (bacteria, fungi, archaea, viruses and protozoa) that colonize the gastrointestinal tract of their host (Shukla et al., 2017).
The composition of the gut microbiome is similar at the phylum level (mainly Bacteroidetes and Firmicutes), but the diversity and species richness tends to vary between individuals (Tremaroli and Backhed, 2012).

The factors that determine the structure of the microbiota are: host genetics, environmental factors, diet, stress, diseases (Shukla et al., 2017). While it is precisely the microbiota that determines the health and diseases of the host through genes, proteins or metabolites (Shukla et al., 2017).

Physiological energy homeostasis is regulated by the microbiota. For example, Donohoe et al. (2011) reported that butyrate produced by the microbiota provides energy to colonocytes and thus prevents autophagy in the colon. Furthermore, physiological homeostasis can be disrupted by the microbiota but this leads to: disruption of host metabolism, immune dysregulation, neurological and cognitive dysfunction and more (Roy and Trinchieri, 2017).
This altered state would cause a number of disorders, including obesity, diabetes, autoimmunity, allergy, inflammatory bowel disease (IBD), and cancer (Holmes et al., 2011; Buret, 2016). Emerging data on the gut microbiota reveal that it is involved in several diseases via the gut-brain axis (Baruch and Schwartz, 2016), the gut-lung axis (Budden et al., 2017; Shukla et al., 2017), the gut-liver axis (Nicolas et al., 2017; Xue et al., 2017), the gut-bone axis (Ohlssone Sjogren, 2015; Yan et al., 2016; Ridler, 2017; Villa et al., 2017), the intestinal-vascular axis (Zhu et al., 2016; Li et al., 2017) and other axes.

Microbiota-host communication in pathologies

Since the gut microbiota is in the gastrointestinal tract, it is evident that it too can contribute to intestinal pathologies (Holmes et al., 2011). However, emerging evidence shows that the microbiota is also implicated in extra-intestinal organs, based on different bacterial compositions. The alteration in composition could be attributed to diet or environment (cold, antibiotics, use of probiotics and onset of infections) and dominate the physiological state of the host.
More fundamentally, the communication pathways between the intestine and other organs are mediated by direct neuronal contact, enteroendocrine cells, immune cells and microbial metabolites (Schroeder and Backhed, 2016).

This role of the microbiota as a balance between health and disease is due to the different control functions it performs:

In practice, the microbiota operates as a control unit, and is also able to carry out physiological functions such as: