The Human microbiome: a burning research field with multiple applications

The microbiome is an ecosystem of microbes such as bacteria, fungi or viruses living in and on the human body. It plays an essential part in the functioning of our metabolism, our immune system and in our mental health. While the definition of a “healthy” microbiome remains to be defined, microbiome disruption is associated with numerous diseases, offering new therapeutic opportunities.

 New York Times, Paul Rogers 

Why do we talk about the microbiome revolution?

We cohabit with our microbiomes. Humans are colonized by trillions of bacteria, viruses, fungi, and parasites. The recent decrease in the cost of DNA sequencing has allowed scientists to generalize their use of powerful technologies, such as metagenomics. Uncharted territories of our bodies were therefore explored with a more precise overview of human microbiome diversity. Bacteria occupy not just the skin, but also many other parts of our bodies. The Human Microbiome Project, launched in 2008, has identified 48 body sites for microbiome sampling: among these, the top four are feces, the buccal mucosa, the vagina, and the rectum [1]. Surprisingly, our blood, our urine, and also our organs harbor their own specific bacterial communities [2, 3, 4].

As highlighted in Figure 1, the prevalence of each group of bacteria is largely dependent on the body site of interest. Moreover, there is no current definition of a “healthy” microbiome, as the distribution of bacteria across healthy individuals fluctuates largely (depending on life habit, genetics, medications…).

 Fig 1: Prevalence of various taxa of bacteria on different selected sites (www.genome.gov)

While it is increasingly admitted that a diversified microbiome is often correlated with a healthy gut, a growing number of articles on the subject also emphasizes that changes in the composition of microbiomes are associated with numerous diseases [5].

Likely because of a long co-evolution, most of these microbes live in symbiosis and some of them are even essential to maintain our bodies healthy, such as those producing vitamin B12. Nonetheless, the exact role of most of these organisms is yet to be understood. While bacteria account for just 1 to 3 percents of the body mass (~1.5 kg for an adult), the total number of genes is 10 to 100 times the number of human genes, thus increasing the complexity of their functional analysis.

To conclude, thanks to metagenomics development, the characterization and understanding of the human microbiome has opened the door for multiple applications. They are already spreading from nutrition to diverse therapeutic areas, such as gastrointestinal and metabolic diseases, infections, neurologic diseases, and oncology.

While some associations have been found between microbiome dysbiosis and certain pathologies, causality and underlying mechanisms still represent an important scientific challenge. Moreover, considering the interpersonal variability, stratification of persons based on microbiome analysis and life habits should be explored towards personalized nutrition and medicine.

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Athors:

Marc-Olivier Bévierre (Cepton Strategies), Etienne Casal (Biofortis – Mérieux NutriSciences), Murielle Cazaubiel (Biofortis – Mérieux NutriSciences), Françoise Le Vacon (Biofortis – Mérieux NutriSciences), Charles Savoie (Cepton Strategies), Alessandra De Martino (Biofortis – Mérieux NutriSciences). 

References:

1 - Human Microbiome Project website

2 - Païssé S, Valle C, Servant F, Courtney M, Burcelin R, Amar J, Lelouvier B. (2016) Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing. Transfusion. 56:1138-47. doi: 10.1111/trf.13477.

3 - Aragón IM, Herrera-Imbroda B, Queipo-Ortuño MI, Castillo E, Del Moral JS, Gómez-Millán J, Yucel G, Lara MF. (2016) The Urinary Tract Microbiome in Health and Disease. Eur Urol Focus. pii: S2405- 4569(16)30159-6. doi: 10.1016/j.euf.2016.11.001.

4 - Nguyen LD, Viscogliosi E, Delhaes L (2015) The lung mycobiome: an emerging field of the human respiratory microbiome. Front Microbiol. 13;6:89. doi: 10.3389/fmicb.2015.00089.

5 - Kumar A, Chordia N (2017) Role of Microbes in Human Health. Appli Microbiol Open Access 3:131. doi:10.4172/2471-9315.1000131