Our micro-roommates

Some of you may have heard of the gut microbiome, which refers to the bacteria and other microorganisms that inhabit our intestines and help us distribute nutrients throughout our bodies. They influence our behavior and our emotions, but they can also be the cause of illnesses if they are dysfunctional. In order to better understand all of this in an upcoming Molecular and Cellular Biology article, it's important to understand what the microbiome is and what it represents.

We find in the word "microbiome", different from microbiota, the term biome. A biome, for scientists, represents an ecosystem made up of flora and fauna. As for "micro", it indicates that it is invisible to the naked eye for a human being. In the broad sense, we find viruses, bacteria, fungi: each has a role in the stability of the environment. All living things, plants, animals or ourselves, have our own unique microbiome, like the environment, land and water (ocean, rivers, lakes ...).

Hot spring where green sulfurous bacteria thrive in Yellowstone National Park in the United States (Reference: https://www.futura-sciences.com/sciences/actualites/physique-photosynthese-artificielle-nanotubes-imitant-bacteries-sulfureuses-40011/)

When we talk about the microbiome, we are talking about microorganisms, their genes and environmental conditions. Not all are beneficial or commensal (living in an organism without harming it). Some species of bacteria are beneficial and perform vital functions.

Hot spring where sulfurous bacteria thrive in Yellowstone National Park in the United States (Reference : https://www.deviantart.com/miss-tbones/art/Bacteria-Color-and-Steam-Yellowstone-6-828215613)

Humans have different main areas of the microbiome with their specificity: the skin, the mouth, the vagina, and the digestive system, which is the most colonized. We harbor more than 100 billion microorganisms from more than 1000 different species, weighing 1 to 5 kilograms only in the intestine.

Photograph made with an electron microscope and color reconstruction by Dennis Kunkel (Refrence : https://www.sciencemag.org/news/2019/01/bacteria-your-gut-may-reveal-your-true-age)

There are differences between the microbiomes of each person, even if they are healthy. These differences are the result of complex combinations of genetic factors of the individual, but also of the environment where the bacteria are found and the lifestyle of the individual concerned. The most subtle differences can have serious consequences such as the development of diseases such as diabetes. Even if there is no such thing as a "healthy" microbiome, there are plenty of possibilities for our way of life to interfere with the bacteria that make it up. The diversity of our microbiome is important. Its multiplicity allows us to overcome various health problems such as allergies.

The skin microbiome is acquired at birth, when the baby passes through the cervix. The recourse to cesarean section can therefore cause in the newborn a lack of bacteria for the constitution of its own microbiome. Over time, the microbiome will change and adapt to the environment and living conditions. The major microbial change in the skin occurs during puberty, which often leads to acne-like skin problems. Microorganisms on our skin perform several functions: they protect us from attack by other microorganisms that do not belong to us, infections of all kinds and UV radiation that can come from the sun.

The study of the human microbiome is not only interested in the skin area. Researchers are also interested in the lungs with a type of disease, including asthma. Today, the data obtained tend to show, whether there is predisposition or not, that the more diverse the type of bacteria in the environment (microbiota), the lower the risk of developing asthma. The other much studied lung disease related to the microbiome is cystic fibrosis. It is a potentially serious genetic disease and one of the most common in France and Western countries. It affects digestive and respiratory functions. With this disease, life expectancy is greatly reduced.

As mentioned above, the most populous microbiome in our body is the digestive system. It is also called our second brain (this topic will be developed shortly). The gut microbiome plays a role in human health and influences the development of diseases such as intestinal disorders or cancer. Eating habits as well as external factors have a strong impact on our health. Many pharmaceutical compounds can be metabolized by the gut microbiome due to the high absorption of molecules in this area. Studies in this area could thus make it possible to develop personalized treatments in order to limit side effects in patients. For this, a study of the interaction of bacteria with each other, but also of bacteria cells and the expression of their genes, is essential.

3D illustration of the intestinal microbiome (Reference: https://www.genengnews.com/topics/omics/microbiome-link-with-colorectal-cancer-drug-toxicity-points-to-predictive-tests-and-prevention/)

It is thanks to the increase in platform analyzes of DNA, RNA and proteins (see the article The protein, that unknown star) that the study of the genes of microorganisms has gained momentum. Thanks to these technologies, it is possible to describe their structure, their functions but also their entire communities. With the cost of sequencing coming down, scientists have been able to study organisms other than those they previously cultivated in laboratories. It is now possible to collect and directly sequence genes. We can therefore quickly identify bacterial strains and variations in their genes. For this type of manipulation, however, it is important to note that it is better to sequence RNA rather than DNA. This method makes it possible to better observe changes in gene expression which may reveal genetic variation within the species of bacteria studied.

"A beautiful microbe can do things that are not healthy"

However, everything does not turn to this analytical technique of sequencing. Other teams are using metabolic techniques from the microbiome. This is a chemical analysis allowing the study of the communication of bacteria between themselves or between cells directly.

A project launched in 2010, The Earth Microbiome Project, aimed to compile a global catalog of the uncultivated microbial diversity on the planet. It is now the largest database available on the subject.

This type of study therefore allows us to better understand how our internal ecosystem thrives, but also the one around us. Concerning us, it is essential to take care of our microbiome whatever it is, and in particular that of our digestive tract by nourishing it in a healthy and balanced way, otherwise it could make us pay for it ...

Reference :

1.   Eisenstein, M. The hunt for a healthy microbiome. Nature 577, S6–S8 (2020).

2.   Gilbert, J. A., Jansson, J. K. & Knight, R. The Earth Microbiome project: successes and aspirations. BMC Biol. 12, 69 (2014).

3.   Jobin, C. Microbiome - Un nouveau facteur de risque de cancer colorectal ? Med Sci (Paris) 29, 582–585 (2013).

4.   Kho, Z. Y. & Lal, S. K. The Human Gut Microbiome - A Potential Controller of Wellness and Disease. Frontiers in Microbiology 9, 1835 (2018).

5.   Wang, B., Yao, M., Lv, L., Ling, Z. & Li, L. The Human Microbiota in Health and Disease. Engineering 3, 71–82 (2017).

6.   Weissenbach, J. & Sghir, A. Microbiotes et métagénomique. Med Sci (Paris) 32, 937–943 (2016).

7.   (PDF) The vocabulary of microbiome research: A proposal. ResearchGate https://www.researchgate.net/publication/280667622_The_vocabulary_of_microbiome_research_A_proposal doi:10.1186/s40168-015-0094-5.

8.   Gut Microbiome: Profound Implications for Diet and Disease. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6682904/.

9.   Le microbiome pulmonaire en 2015 - Une fenêtre ouverte sur les pathologies pulmonaires chroniques | médecine/sciences. https://www.medecinesciences.org/en/articles/medsci/full_html/2015/12/medsci20153111p971/medsci20153111p971.html.

10.Xénobiotiques et microbiome intestinal actif - Des effets insoupçonnés | médecine/sciences. https://www.medecinesciences.org/en/articles/medsci/full_html/2013/10/medsci20132910p846/medsci20132910p846.html.

11.https://atlasbiomed.com/blog/whats-the-difference-between-microbiome-and-microbiota/

12.https://www.bioalternatives.com/en/microbiota-vs-microbiome/

13.https://lejournal.cnrs.fr/articles/microbiote-des-bacteries-qui-nous-veulent-du-bien#:~:text=Il%20pèse%20entre%20un%20et,microbiote%20est%20votre%20indispensable%20allié.