Photo by http://benvandenbroecke.be/ Copyright, ISAPP 2019.
High-throughput DNA sequencing technologies and advanced computational techniques of the past two decades have allowed significant advancements in knowledge about human-associated microorganisms. Different areas on the human body—the digestive tract (‘gut’), the skin, the vaginal tract, the oral cavity, and others—are home to different communities of microorganisms, called microbiomes. The word microbiome generally refers to the genetic content of all the microorganisms in a defined environment (e.g. the human colon), but some use it to refer to the entire habitat, including the microorganisms, their genomes, and the surrounding environmental conditions. While microbiome and microbiota are sometimes used interchangeably, the microbiota properly refers to the microorganisms themselves: bacteria, archaea, lower and higher eukaryotes, and viruses in a defined environment. It is now clear that human microbiomes play important roles in health and disease.
The gut microbiome
The gut microbiome is the most studied microbiome associated with the human body, with the digestive tract containing the highest density of human-associated microorganisms. Bacteria in the gut are involved in digestion, harvesting energy from food, producing neurotransmitters, enzymes, and vitamins, and they participate in immune and metabolic functions.
To date, researchers have been unable to define a ‘healthy gut microbiome’. For example, a normal community of gut microbes in a healthy person often includes both benign and opportunistic pathogenic strains of E. coli. A few associations have been established so far: for example, individuals from industrialized populations have gut microbiota compositions that are less diverse and are dominated by different species than those from rural, non-industrialized areas. Differences in gut microbiota composition have been demonstrated in people with various chronic diseases, compared to healthy controls, but in most cases causality has not been determined.
Diet and medications are two important factors that account for gut microbiota variability in large cohort studies. Antibiotics are a particularly powerful way to alter the gut microbiota: when someone is on antibiotics, the microbial community is altered drastically throughout the course of the medication but microbes gradually return to their baseline levels (or close to baseline levels) after the treatment ends.
Dietary changes may also modulate the gut microbiota in a matter of days; probiotics, prebiotics, fermented foods, and fiber are considered dietary means of influencing gut microbiota. Indeed, a prebiotic must by definition have a mechanism of action that involves their use by gut microorganisms.