Initiated by MetaGenoPolis-INRAE and supported by INRAE with public institutions (APHP, Inserm…) and private partners, Le French Gut is the French part of an international project called the "Million Microbiomes from Humans Project" (MMHP). The objective is to build the world's largest database on microbiota with 1 million microbial samples from the intestine, mouth, skin, reproductive tract and other organs. Le French Gut will be contributed with its national collect.

Biocodex Microbiota Institute’s involvement

The Biocodex Microbiota Institute plays an active role in this initiative, producing and sharing exclusive news and informations on the Institute’s website and social networks (Facebook, Twitter, LinkedIn…) in order to favor the recruitment of volunteers.

With your help, we can make great strides in microbiota research to improve the quality of life of as many people as possible reaching our ambition to become the leader in microbiota care. By participating, you will help the research to explore innovative and personalized therapies for chronic diseases (diabetes, obesity, cancer...), neurodevelopmental disorders (autism...) and neurological diseases (Parkinson, Alzheimer...). We need your donation! If you are an adult, living in metropolitan France, follow the guide

Statins reduce the risk of atherosclerotic cardiovascular disease by inhibiting the activity of the 3-hydroxy-3-methylglutarate-coenzyme-A (HMG-CoA) reductase enzyme involved in the hepatic synthesis of low-density lipoprotein (LDL). Unfortunately, their effectiveness on LDL levels varies considerably among patients and adverse effects can occur, particularly insulin resistance, which increases the risk of type 2 diabetes mellitus. For physicians, determining the “maximum tolerated dose” for each patient based on the guidelines¹ is often down to trial and error. However, this approach wastes time and can undermine patient compliance.

A blood marker to measure response to statins

Recent studies have already shown links between the gut microbiota and atherosclerotic cardiovascular risk, but also between the microbiota and statin use. Now US researchers² have studied the gut flora’s role in responses to statins. By metabolizing statins, bacteria in the gut microbiota may modulate their bioavailability and potency to the host, or even contribute to their adverse effects. In a US cohort of 1,848 adults, 244 of whom were statin users, the researchers first validated a marker of statin response, plasma levels of the HMG-CoA reductase substrate, or HMG. HMG levels were found to be significantly higher in statin users than in non-users, and were negatively correlated with blood LDL levels in statin users only. The level of HMG reflected both the intensity of statin therapy and the presence of genetic variants in patients affecting their response to therapy.

Microbiota profile influences treatment efficacy and metabolic risk

The researchers then studied the association between statin efficacy as measured by HMG levels, the effect of statins on glucose control as measured by the Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) score, and the composition of the gut microbiota, analyzed via 16S rRNA sequencing. They found that a more Bacteroides-enriched and diversity-depleted gut microbiome was associated with more intense statin responses, both in terms of efficacy and adverse effects on glucose control. However, a flora richer in Ruminococcaceae seemed to protect against the metabolic risk. These results were confirmed in a European cohort of 991 subjects whose gut microbiota was sequenced using a different method.

Towards precision statin therapies? 

This work not only explains variability in statin response, but also holds out the prospect of clinical tools to manage this variability. Indeed, plasma levels of HMG may supplement LDL levels as a source of information on treatment efficacy. Identifying the gut microbiota profile of patients may also allow us to predict responses to statins, to improve such responses using probiotics where necessary, and lastly, to propose to patients a more personalized treatment strategy for cardiovascular diseases.

It has the color and texture of milk – but it’s not milk. Horchata de chufa is a beverage made from tiger nuts (chufa, in Spanish) originally from Valencia, Spain. Not only refreshing, this drink also promotes the proliferation of gut bacteria beneficial to health.

So concluded researchers from the Spanish National Research Council (CSIC) after asking 31 healthy adults to drink a glass of horchata (300 ml) with their breakfast every morning for three days. The researchers collected stool samples from the volunteers before and after the experiment. Their aim was to analyze the effects of horchata on the bacteria of the gut microbiota.

Effects similar to those of a high-fiber diet

The results showed that the gut microbiota of all volunteers was positively modified by horchata². 

In general, the new bacterial profiles were similar to those of people following the Mediterranean diet (sidenote: Mediterranean diet Rich in fruit, vegetables, cereals, oilseeds (nuts) and fish, and low in red meat, saturated fats and dairy products. Lăcătușu CM, Grigorescu ED, Floria M, et al. The Mediterranean Diet: From an Environment-Driven Food Culture to an Emerging Medical Prescription. Int J Environ Res Public Health. 2019 Mar 15;16(6):942. ) or a diet rich in plants. In the volunteers’ gut microbiota, the researchers noted an abundance of bacteria that produce butyrate, a short-chain fatty acid (sidenote: Short chain fatty acids (SCFA) Short chain fatty acids (SCFA) are a source of energy (fuel) for an individual’s cells. They interact with the immune system and are involved in communication between the intestine and the brain. Silva YP, Bernardi A, Frozza RL. The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication. Front Endocrinol (Lausanne). 2020;11:25. ) (SCFA) known for its numerous health benefits.

The changes observed also appear to have been dependent on the initial bacterial profile. Effectively, two main groups of microbiota could be distinguished after consumption of horchata, one enriched in Akkermansia, Christenellaceae, and Clostridiales, and the other with a remarkable presence of Faecalibacterium, Bifidobacterium, and Lachnospira. Some of these bacteria were already known for their beneficial effects on health, such as:

• better weight control,
• a reduced risk of diabetes mellitus,
• and improved immune responses,
• among others...

High in resistant starch and polyphenols: viva la chufa!

What explains these changes?

Tiger nuts (Cyperus esculentus), from which horchata is made, have a relatively high content of resistant starch. According to the researchers, this compound may “feed’ certain beneficial bacteria, such as Akkermansia, Lactobacillus, and Bifidobacterium, thus promoting their development.

Tiger nuts also contain numerous polyphenols which, thanks to their antimicrobial action, help slow down the proliferation of other bacterial species.

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The French Gut is part of a vast international project, the "Million Microbiome of Humans Project" (MMHP), which brings together several research institutes around the world. The MMHP's ambition is to create the world's largest database on human microbiota, by collecting one million microbial samples from the intestines, mouth, skin and reproductive tract of volunteer subjects. The French Gut, led by INRAE in partnership with public and private players involved in the microbiota field, will make a significant contribution to the development of this international database by collecting 100,000 French intestinal metagenomes.

The French Gut can count on the strong support of the Biocodex Microbiota Institute. The objectives of this project are to recruit 100,000 participants, and to raise awareness among the general public, including healthcare professionals, of the fascinating powers of the intestinal microbiota, particularly its role in the onset of a number of pathologies.

A shared objective: to highlight the importance of the effects of the intestinal microbiota on our health

The Biocodex Microbiota Institute shares the same ambition as Le French Gut: to raise awareness among the general public and train healthcare professionals in the major importance of the microbiota, particularly the impact of dysbiosis on our health. Since 2017, the Biocodex Microbiota Institute:

BMI 22.46

Bile acids are currently a hot topic in research: in addition to helping the absorption of nutrients, they may play an important role in interactions between gut microbiota and host. Following their synthesis in the liver, bile acids are released into the gut and transformed by bacteria whose activity influences the composition of the gut microbiota. Reabsorbed by the colon, these “secondary” bile acids may then act as signaling molecules in various metabolic and immune processes.²

Sequencing, metabolomics, and statistics

Chinese researchers have put forward the idea that the gut microbiota and bile acids are involved in the still poorly understood relationship between chronic insomnia and cardiometabolic disease. Several recent discoveries have led them down this path. For example, the gut microbiota has its own circadian rhythms, different from that of the host and sensitive to insomnia. In mice, repeated sleep interruptions modify gut microbiota composition and the metabolism of bile acids. Lastly, gut microbiota dysbiosis and the dysregulation of bile acid metabolism both impair metabolic health.

To test their hypothesis, the researchers used two cohorts, a “discovery cohort” (sidenote: Discovery cohort The “discovery cohort” included 1,809 subjects from the prospective Guangzhou Nutrition and Health Study (GNHS) ) and a “validation cohort” (sidenote: Validation cohort The “validation cohort” included 6,122 participants from the cross-sectional Guangdong Gut Microbiome Project (GGMP), whose gut microbiota was sequenced by the researchers. ) . They collected detailed information on the subjects’ sleep and cardiometabolic parameters over a six-year period prior to the collection of the stool samples. Lastly, they analyzed the fecal bile acid metabolome of 954 subjects from the Guangzhou Nutrition and Health Study (GNHS) cohort.

Two bacterial genera and specific bile acids stand out

The researchers showed that chronic insomnia and cardiometabolic disorders were correlated with lower levels of two bacteria from the Ruminococcaceae family in both cohorts studied. By further analyzing the GNHS cohort, they also found that:

• Certain bile acids, such as isolithocholic acid (IsoLCA), murocholic acid (MCA), and norcholic acid (NorCA) mediated these associations. 
• Tea consumption (green, black, oolong, etc.) was associated with higher levels of Ruminococcaceae and lower levels of NorCA, as well as a decreased risk of insomnia.

Tea time to reduce the cardiometabolic risk of chronic insomnia?

The researchers believe that the gut microbiota-bile acid axis may be a potential intervention target for reducing the impact of chronic insomnia on cardiometabolic health. However, they remain cautious regarding tea: more research is needed to confirm that tea consumption has a beneficial effect on the bacteria in the microbiota linked to cardiometabolic health.

Contrary to popular belief, drinking water isn’t sterile: it contains 10-100 million microorganisms (sidenote: Microorganisms Living organisms that are too small to be seen with the naked eye. They include bacteria, viruses, fungi, archaea and protozoa, and are commonly referred to as “microbes”. What is microbiology? Microbiology Society. ) per liter! But not to worry, as previously shown by an Anglo-American study, these bacteria seem to feed our gut microbiota. Now Italian scientists have taken water samples from public fountains and domestic taps in the city of Parma with the aim of exploring microbial biodiversity in their city’s water and its effects on the gut microbiota of residents.

Water, a vehicle for significant bacterial diversity

Examining the samples, the researchers found that five bacterial species had a greater relative abundance, although with significant variability from one sample to another. For example, in one fountain, Acidovorax delafieldii represented more than half of the bacteria present, while in another the dominant bacterium was Sphingomonas ursincola, which made up a quarter of the bacteria found. Moreover, this variability was just as great in tap water. The five dominant species were no surprise, since they are known to be frequently found in drinking water. More surprising was the fact that a large proportion of the bacteria present in drinking water, whether from fountains or the tap, were unknown, a sort of microbial “dark matter” that scientists must now explore.

From a glass of water to the gut microbiota

Given that we drink about two liters of water per day, do these bacteria have an impact on our gut microbiota? Yes, say the researchers, who detected the bacteria in the stool of regular tap water drinkers, with presence profiles that reflect the composition of the water consumed. In other words, day in, day out, tap water helps shape our gut microbiota. The researchers even showed that some bacteria appear to settle permanently (and remain even when we drink bottled water), while the presence of others seems closely linked to regular consumption (they disappear when we drink bottled water for several days).

These preliminary findings are somewhat incomplete but they open two fields of research still only superficially explored. Firstly, what bacteria are present in drinking water? Secondly, what influence does the water we drink have on our gut microbiota and our health? Water still has secrets hiding below the surface...

Excessive alcohol use is responsible for three million deaths each year and is a causal factor in more than 200 diseases.¹ On the other hand, when consumed in moderation (sidenote: Moderation Adults of legal drinking age can choose not to drink or to drink in moderation by limiting intake to 2 drinks or less in a day for men and 1 drink or less in a day for women, when alcohol is consumed. Drinking less is better for health than drinking more. https://www.niaaa.nih.gov/alcohol-health/overview-alcohol-consumption/moderate-binge-drinking ) , beer is thought to have beneficial effects on health, particularly in the prevention of cardiovascular disease. These beneficial effects have long been known for both beer and wine, but it is not yet clear whether they are due to moderate consumption or to the compounds contained in these beverages, such as the polyphenols (sidenote: Polyphenol An organic molecule present in plant matter. https://www.medicalnewstoday.com/articles/319728 ) found in large quantities in beer.

Beneficial effect... with or without alcohol?

To shed some light on the matter, a team of Portuguese researchers² carried out a study comparing the effects of alcoholic and non-alcoholic beer on the gut microbiota and on markers of cardiometabolic health (weight, fat mass, cholesterol levels, insulin resistance, etc.).

^Sources

Without changing their diet, 10 men drank 33 cl of lager (alcohol content 5.2%) each day with their dinner for four weeks, while another 9 men consumed a non-alcoholic beer.

A more diverse gut microbiota

Good (and surprising) news for beer lovers: no weight gain and no increase in liver enzymes were noted.  There were also no major changes in cardiometabolic health markers. Stool analyzes revealed greater microbial diversity in the gut microbiota (a sign of good health), but also a tendency towards greater fecal alkaline phosphatase activity – a marker of the gut barrier function – regardless of the type of beer consumed. Therefore, the compounds present in beer seem to outweigh the harmful effects of alcohol on the gut flora.

Benefits linked to polyphenols

The researchers attribute these benefits to polyphenols and isoxanthohumol, an antioxidant substance abundant in beer which reduces the risk of chronic disease. These compounds are found in greater quantities in unfiltered beers, which may have an even greater impact on the health of our gut flora, according to the researchers.

Further work is needed to confirm these results. In the meantime, drink in moderation.

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Over the decades, urbanization and modern infrastructure have reduced our exposure to environmental microorganisms. Improvements in hygiene have protected us from many infectious diseases.

However, a lack of contact with natural bacterial ecosystems in plants, soil, water, etc. is detrimental to our microbiota. What’s more, this absence of nature has consequences for our health: according to scientists, the urban lifestyle (commute-work-sleep routine) favors allergies and diseases with an auto-immune component. Our skin isn’t spared, with urbanization modifying its microbial balance.

However, a touch of nature can help rebalance it. Our skin microbiota is enriched when we walk in urban green spaces, while our children’s microbiota becomes more diversified if they attend green daycare centers. But how can we benefit from plants if we’re locked up in the office eight hours a day?

Green walls for a re-seeded skin microbiota...

A team of Finnish researchers¹ installed air-circulating green walls in university offices. The idea: indoor air is circulated through green plants (philodendrons, Dracaena, ferns, and other plants) using fans. The team compared skin and blood samples from staff working in these green wall offices with those of employees not working between green walls.

The results? Lactobacilli abundance and the diversity of skin proteobacteria, known to help balance the skin microbiota and protect it against harmful microorganisms, rapidly increased in the staff working in green wall offices. In the blood of these employees, the scientists also found a decrease in the level of a pro-inflammatory cytokine (sidenote: Cytokine A small protein involved in communication between cells, especially in the immune system.  Cytokines: Introduction_British Society for Immunology ) and an increase in the level of a cytokine involved in immune response regulation.

...and better quality of life at work

According to the authors of the study, air-circulating green walls balance the moisture in the air and release plant spores or bacteria (including proteobacteria) that settle on the skin. The ability of plants to filter air pollutants may also have a positive effect on the skin microbiota. Either way, green walls are pleasant to look at and potentially beneficial for our health. So while we wait for the results of new studies, should we bring our favorite potted plants to the workplace?

To be continued...

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We already know that taking antibiotics can disrupt gut bacteria. It seems that they are not alone. While most studies focus on the impact of antibiotics on bacteria, few assess the effect on other microorganisms, such as fungi, whose role should not be underestimated. Fungal microbiota or mycobiota dysbiosis has been associated with various disorders and diseases (IBD, celiac disease and colorectal cancer). However, this mycobiota develops progressively in the first few years of life in the same way as bacterial colonization, depending on the mode of delivery, diet or even possible antibiotic treatments.

A study on 37 antibiotic-naive infants

To learn more, researchers followed 37 children for 9.5 months with an average age of 2 months who had never received antibiotics. These infants were hospitalized with respiratory syncytial virus (RSV) infections. Stool samples were taken before, during and after one to four antibiotic treatments (amoxicillin, macrolides) that were prescribed to 21 of them due to complications (otitis media, etc.). The remaining 16 untreated children made up the control group.

At the time of hospitalization (i.e. before treatment), the mycobiome of the 37 children was overwhelmingly dominated by Saccharomyces and to a much lesser extent Malassezia, Candida and Cladosporium.
 

More Candida, diversity and abundance

One to two days after the start of the antibiotic treatment, the abundance of Candida greatly increased in infants on amoxicillin, at the expense of Saccharomyces. An overabundance of Candida continued to be observed more than 6 weeks after the start of treatment.

In addition, antibiotics, which are known to induce a collapse in the diversity and abundance of bacterial microbiota, were associated with an increase in the abundance and diversity of the mycobiota. This appeared within 3 to 5 days of the start of treatment and persisted well beyond that time (> 6 weeks) with the difference most marked in the macrolide group.
 

Are there bacteria that play a regulatory role?

These results strongly suggest that gut bacteria regulate mycobiota on an ongoing basis.  This regulation takes the form of competition for nutrient sources through the production of antifungal compounds by bacteria and, conversely, antibacterial compounds by fungi. As soon as bacteria are affected by an antibiotic, their regulatory role is altered and certain fungi, particularly Candida, are given free rein to develop. As such, gut mycobiota dysbiosis after a single antibiotic treatment could, together with an alteration of gut bacteria, induce the long-term effects of antibiotics on human health.

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