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Microbiota, the intestinal revolution. © INRA

Microbiota, the intestinal revolution

Symbiotic man (2)


Updated on 04/25/2017
Published on 02/16/2017

Metagenomic tools to better understand human intestinal microbiota and how it affects health.. © INRA
Metagenomic tools to better understand human intestinal microbiota and how it affects health. © INRA


Magnificent metagenomics

By taking a stool sample of an individual and analysing it in a DNA sequencing platform, scientists are able to see the genes and bacteria that make up said individual’s microbiota. If they analyse 100 stool samples from healthy people, and 100 samples from people who suffer from disease, they can make statistical comparisons and find the answers to burning questions: Is the microbiota of one individual as diverse as that of the next? Are some bacteria that are found in healthy people missing from the microbiota of the ill? Or are there, inversely, bacteria that are specific to ill people? Studies based on these questions, all concerning a field known as metagenomics*, have led to extraordinary discoveries over the past few years. Researchers have found, for instance, that people who suffer from diabetes, cirrhosis or obesity have microbiota that differ from that of healthy people. Metagenomics is opening up new avenues for studying the effect of bacterial populations on health, and for identifying the “good” bacteria that serve to protect us.


Viruses: striking a balance

Bacteriophages, viruses that infect and kill bacteria, play a key role in the microbiota. They keep bacterial populations that would otherwise proliferate in check. However, the presence of bacteriophages is not indispensable in controlling bacterial populations.

Most bacteria harbour viruses in a dormant state in their genome. These viruses can awake at any moment, killing their host and infecting neighbouring bacteria. INRA researchers have modelled the behaviour of bacteriophages in the digestive tract of mice. They found that their activity is 50 times greater than previously thought. In another surprise result, they found that in one infection out of five, the virus enters the genome of the bacteria and stays there in a dormant state, rather than killing its host.

An iron fist

Iron is essential for the human body, but it must be closely regulated: too much or too little can cause health problems. A team of INRA and Inserm researchers has shown that the microbiota plays an active role in maintaining the metabolism of iron. Indeed, the intestinal cells of mice devoid of a microbiota have trouble storing iron. The findings prove that the microbiota is a key player in absorbing and distributing iron, and are boosting science’s understanding of certain iron-related disorders.

A closer look: microbiota of the lungs

The presence of bacteria in the lungs has long been associated with disease. In fact, lungs were considered a sterile organ in healthy humans. It is now known, however, that a newborn’s lungs are home to a thriving microbial population. From the start, INRA researchers have taken an interest in how the lung microbiota impacts the respiratory epithelium, the immune system, and the severity of asthma - questions that are pushing the boundaries of science. Working in tandem with a Belgian team, the researchers discovered that some bacteria present in the lungs can have beneficial or deleterious effects on asthma. The researchers are moving forward in their work, notably to try and find out if these lung bacteria play a role in respiratory disorders in newborns. 

 © Shutterstock

Old mcdonald had a…microbiota?

Cows, pigs, chickens… since the beginning of time, man has reared these farm animals to obtain ever-more productive and robust breeds. Over the past few decades, animal rearing has intensified and become more streamlined. In a new and exciting development, INRA researchers are now exploring how the microbiota impacts the health and growth of these animals. Indeed, high throughput sequencing technologies now allow scientists to associate slight variations in the make-up of microbiota with individual variations that could be of interest to breeders. For instance, certain characteristics of some microbiota can now be associated with chickens that can digest certain foods, pigs that display more robust growth, and cows that emit less methane. It goes without saying that this holds tremendous potential in economic as well as environmental terms.


The incredible bacterial richness of pigs

Extra! Extra! The first ever catalogue of pig intestinal microbiota genes is now a reality, thanks to an international consortium that INRA participated in. No less than 7.7 million genes, most of them bacterial, have been identified, to the delight of biomedical researchers and scientists who are trying to improve pig breeding. The catalogue lays out all the rich diversity of pig microbiota. Among the biological functions identified in the human microbiota, 96% of them are also found in pigs. But pig microbiota have also been found to be responsible for 800 functions that humans do not share. Another highlight of this study, published in 2016, is the quantification of genes resistant to antibiotics in pig intestinal bacteria. These genes, found in all pigs that were analysed, were much more prevalent in pigs bred in China, where antibiotics are administered non-stop. This goes to show that reducing the use of antibiotics lowers the risk of resistance significantly.


More robust poultry thanks to microbiota

What is the relationship between the innate immunity of chickens, their capacity to digest, and the composition of their microbiota? That is the question INRA researchers working on the Galmide project (for Gallus Microbiota, Immunity and Digestive Efficiency), are asking. The goal of the project is to gain a better understanding of the bacteria that play a part in the digestive system of poultry, and thereby make the farm animals more robust. Findings have already shown that the intestinal microbiota of chickens selected for their very good or very poor digestion varies according to the animals’ ability to digest. Scientists have also identified certain regions of the chicken genome that harbour genes that can modify the make-up of microbiota. It has been suggested that some of these genes may also play a role in the innate immunity of the birds.