Intestinal Microbiota

This article is an extract of the PDF “The Intestinal Microbiota”, available for free download.

The fact that there is a flora associated with the intestinal tract has been known for more than a century. Evaluating the qualitative and quantitative preponderance of this flora has been made possible thanks to the development of anaerobic culture methods, specific media and, nowadays, biomolecular technologies. The physiological role of the flora and its involvement in diarrhoea symptoms are known as a result of the use of antibiotics. Gradually, the idea that the flora forms an ecosystem within the host body has emerged.

Studies have shown that this flora is not distributed homogeneously along the intestinal tract.

bacterial tract

Only digestive, nutrient absorption or vitamin synthesis functions have been described on this diagram. Thus, for a very long time, intestinal flora has, at best, been credited with being a barrier to exogenous pathogens, and its role in immune defences has mainly been demonstrated in animal models. The concept of intestinal micro-ecology has emerged from these results.

The intestinal microbiota

While the study of intestinal flora concerns the genera and species of culturable bacteria populating the digestive tract, the study of the intestinal microbiota primarily concerns the complex colonies of micro-organisms colonising the digestive tract. The development of high-throughput gene sequencing techniques coupled with biocomputing has made it possible to detect viable but non culturable bacteria. In short, to identify the species to which a given sequence belongs, we determine which of the sequences held in the data banks are phylogenically closest. To this end, we first search for all of the most similar sequences. These sequences are then aligned, including the one for which we wish to determine the species, and the phylogenic tree is built.

The intestinal microbiota, colossal figures

  • 100,000 billion bacteria
  • 10 times more than the number of cells in the body
  • 1,000 different species
  • 1 to 2 kg
  • 3.3 million genes (150 times more than the number of genes in the human genome)

The small world inside the intestine


With a density of 1011 cells/g colon, the intestinal microbiota is approximately 10 times greater than eukaryote cells, hence the concept that humans are not 100% human but made up of 90% microbes and 10% human [CANI 2011]. The Human Microbiome Project (HMP) in the United States and The Meta-genomics of the Human Intestinal Tract (MetaHIT) in Europe are the 2 main initiatives aiming to characterise the microbial communities in various sites of the human body (cutaneous, nasal, oral, uro-genital and intestinal flora) and to establish a correlation between changes in flora and the occurrence of certain diseases. Similarly to blood groups, each individual is host to a specific composition of intestinal bacteria called an enterotype.


3 separate enterotypes characterised by a predominant bacterial population have been identified: Bacteroides, Prevotella and Ruminococcus. It appears that these enterotypes are independent of geography, short-term diet or skin colour (black, white or yellow).

  • Enterotype 1 is dominated by Bacteroides which mainly draws its energy from sugar fermentation. This genus is rich in biotin synthesis-coding genes.
  • Enterotype 2 is dominated by Prevotella, rich in thiamin synthesis-coding genes. This genus mainly draws its energy from the biodegradation of mucin glycoproteins.
  • Enterotype 3 is dominated by Ruminococcus, rich in haem-coding genes, unlike those of the Prevotella enterotype. Ruminococcus is also capable of degrading mucins.

Despite close links between the Prevotella and Bacteroides genera, they are mutually exclusive in healthy persons [ARUMUGAM 2011].

Intestinal microbiota evolution

Source: Ottman et al. published in 2012 a study of intestinal microbiota evolution.


There was also a study [RAJILIC-STAJANOVIC 2013] conducted on 5 non-related healthy persons over a very long period. It showed that the microbiota composition:

  • started to vary after 10 to 12 years where Bacteroides are concerned
  • was affected in the short term by antibiotic treatment because samples taken immediately after the administration of antibiotics were dominated by the Firmicutes phylum. The authors considered that when the same probes hybridised with all the samples from the same subject, this indicated the presence of a stable core; in contrast, detecting a single micro-organism in a single sample revealed that its presence in the microbiota was accidental
  • varied according to race and long-term diet

Another study [DRAGO 2012] was conducted to characterise the qualitative and quantitative composition of the intestinal microbiota of healthy centenarians (n=14) and of young adults (n=10). With ageing, the equilibrium of the intestinal flora could be affected by profound physiological changes.


In this article about the intestinal microbiota which hosts billions of bacteria, we have focussed on its composition in fit and healthy individuals. Unlike blood groups, which do not change throughout the course of a lifetime, the three microbiota enterotypes characterised by the Bacteroides, Prevotella and Ruminococcus genera may evolve, although the core made up of permanent colonisers does not evolve much. Microbiota composition is dictated by long-term diet, and a short-term change of diet could only affect the abundance of certain genera or species. Indeed, we are colonised from birth by the maternal flora which provides the “first building blocks” essential to the development of our microbiota. The gradual colonisation of our intestines and the rest of our skin is ensured by skin contact and breast feeding. Once the intestinal microbiota has set in and stabilised at the age of 2-3 years, these bacteria play a crucial role in nutrition and health. Indeed, they play a fundamental role in the synthesis of vitamins and they participate in breaking down non-digestible products for energy production. This partnership between the intestine and its flora is not always a harmonious one, and studies have shown that the intestinal microbiota has an influence on disease. The intestinal microbiota should be considered as an organ in its own right because it contributes to our health, both physical and mental.

This article is an extract of the free ebook “The Intestinal Microbiota”, available for download 

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ARUMUGAM M., RAES J., PELLETIER E. et al. Enterotypes of the human gut microbiome. Nature, 2011, 473 (7346), 174-180. Doi:10.1038/nature09944
CANI P.D. & DELZENNE N.M. The gut microbiome as therapeutic target. Pharmacology & Therapeutics, 2011, 130, 202-212.
DRAGO L., TOSCANO M., RODIGHIERO V., De VECCHI E. & MOGNA G. Cultivable and pyrosequenced microflora in centenarians and young subjects. J. Clin. Gastroenterol., 2012, Oct. 46, Suppl. S81-S84. Doi: 10.1097/MCG.0b013e3182693982
KORECKA A. & ARULAMPALAM V. The gut microbiome: scourge, sentinel or spectator? Journal of oral Microbiology, 2012, 4, 9367-9380. Doi: 10.3402/jom.v4i0.9367
RAJILIC-STAJANOVIC M., HEILIG H.G., TIM S., ZOETENDAL E.G. & De VOS W.M. Long term monitoring of the human intestinal microbiota composition. Environ. Microbiol., 2013, 15 (4), 1146-1159.
OTTMAN N., SMIDT H., DE VOS W. M., BELZER C. (2012). The function of our microbiota: who is out there and what do they do? Front. Cell. Inf. Microbio. 2:104.10.3389/fcimb.2012.00104