The intestinal microbiota
A digestive tract-associated flora has been known to exist for more than a century. The distribution of this flora varies throughout the intestinal tract (see diagram)1.
Its physiological role and its deterioration consequences following the use of antibiotics: diarrhoea and symptoms of immuno-suppression were still considered as simple side effects of antibiotics. Its deterioration was thought to be harmless, as the number of micro-organisms is highly elevated.
The qualitative and quantitative preponderance of this flora could initially be assessed through the development of culture methods and perfecting of specific culture media.
New technologies have progressively given rise to the idea that the flora forms a true diverse and complex ecosystem within the organism hosting it2: the intestinal microbiota.
Diagram of the intestinal tract showing the density of microorganisms (CFU/ml)
From purity to uniqueness
Our life begins in a gentle and nearly-sterile environment: the uterus3.
Our first contact with micro-organisms takes place at birth through the vaginal canal. Our mother’s intimate microbiota inoculates us with the first strains that will cover our skin and mucous membranes4. Expulsion of the meconium then makes it possible for the surrounding micro-organisms to colonise our intestine. Our intestinal microbiota can now begin to develop. Food, breathing and our first physical contact are the main channels of exposure to bacteria such as Lactobacillus and Bifidobacterium, which form our personal microbiotic fingerprint: the blank microbiota.
The microbiota will stabilise after a few weeks under the influence of several factors in relation to each of us or to the environment5.
Environmental factors include:
- the way of delivery,
- the composition of the maternal microbiota influenced by her diet and lifestyle,
- type of infant feeding,
- dietary habits,
- dietary or temperature stress,
- intake of certain drugs, especially antibiotics.
Other person related parameters may involve:
- intestinal pH,
- microbial interactions,
- body temperature,
- biliary acids,
- intestinal secretions,
- immune responses and receptors of epithelial cells.
After colonisation of the digestive tract from birth until about the age of 2 years, the strains identity makes up our personal and unique microbiotic fingerprint (or Core Genome), which will remain stable over time.
From uniqueness to universal
The unique character of each microbiota, by virtue of the existing strains, does not however exclude forms of bacterial dominance common to mankind that can be classified, like the blood groups, into 3 distinct types (or enterotypes):
- Enterotype 1 is dominated by Bacteroides.
- Enterotype 2 is dominated by Prevotella.
- Enterotype 3 is dominated by Ruminococcus.
Unlike the blood groups, which remain unchanging throughout life, the 3 enterotypes of the microbiota can be deteriorated with:
- diet changes,
- problems of the immune system,
- drug poisoning,
- contracted diseases.
However, the resilient character of microbiota tends to naturally restore it to its personal configuration specific to each of us and our Core Genome, made up of permanent colonisers, changes very little.
Role in health and in disease
It is now well established that a healthy intestinal microbiota brings a balanced state to in its host’s health.
The intestinal microbiota plays a specific and essential protective role :
- it maintains the integrity of the natural barrier formed by the mucous membranes,
- it acts against colonisation of the digestive tract by pathogenic micro-organisms,
- it enables the maturation of the immune system 1,2,6.
1 Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut microbiota in health and disease. Physiol Rev. 2010; 90: 859-904.
2 Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486: 207-214.
3 Jiménez E, Marín ML, Martín R, Odriozola JM, Olivares M, Xaus J, Fernández L, Rodríguez JM. Is meconium from healthy newborns actually sterile? Res Microbiol. 2008; 159: 187-193.
4 Collado MC, Cernada M, Baüerl C, Vento M, Pérez-Martínez G. Microbial ecology and host-microbiota interactions during early life stages. Gut Microbes. 2012; 3: 352-365.
5 Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr. 1999; 69: 1035S-1045S.
6 Landman C, Quévrain E. [Gut microbiota: Description, role and pathophysiologic implications]. Rev Med Interne. 2016; 37: 418-423.