Obstructive sleep apnea, which can present in early childhood as well as in elderly subjects, is based on a complex etiology (tonsillar hypertrophy in children, reduction of pulmonary volume, obesity, etc.).

Gut microbiota has also been highlighted by several studies suggesting the existence of dysbioses, but its causal role is still unproven. That is exactly what a Chinese team set out to do using Mendelian randomization, which allowed them to set aside many confounding factors and biases and to show that the microbiota and its metabolites are the cause, and not the consequence, of sleep apnea.

The protective effect of the Ruminococcaceae family

In practice, the researchers conducted the study using pre-existing databases: for sleep apnea, the genetic data of the Finnish project FinnGen ², which includes 33,423 patients with sleep apnea and 307,648 controls; for microbiota, the data of the MiBioGen ³ consortium, which has collected and analyzed the genotypes and data for fecal microbiota 16S from 18,340 people.

The Mendelian randomization focused on 196 gut microbial taxa, 83 types of microbial metabolites, and the risk of sleep apnea. It showed that some bacteria increased the risk of sleep apnea (the genus Ruminococcaceae UCG009 and the genus Subdoligranulum) while others (the Ruminococcaceae family, the genus Coprococcus2, the genus Eggerthella, and the genus Eubacterium) decreased it.

The protective effect of the Ruminococcaceae bacterial family could be due to the ability of these bacteria to produce short-chain fatty acids (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. ) , which reduce inflammation, reinforce the intestinal barrier, and limit the proliferation of pathogenic bacteria, but also due to their implication in the metabolism of bile acids, known for their role in sleep and regulating sleep cycles.

Microbial metabolites incriminated

The study also highlights the role of other microbial metabolites: leucine and 3-dehydrocarnitine are associated with an increased risk of sleep apnea, while gamma-glutamylvaline and betaine show protective effects. Some of these molecules have already been incriminated in previous studies: elevated leucine levels were observed in children with sleep apnea; on the other hand, among patients who had been prescribed a mask to treat sleep apnea, leucine levels fell rapidly. 

Behind the term sleep apnea lies a pathology characterized by abnormally frequent respiratory pauses during sleep. Even if this disease is often found in children and adults, it is not without risk, in the short term (fatigue) and long term (cognitive impairments, cardiovascular diseases, etc.).

It has multiple causes: tonsillar hypertrophy in children, obesity in adults… The gut microbiota have also been mentioned, but their causal role is yet to be proven. However, a study published in 2023 went a step further in demonstrating their causal role. How? Via a technique called Mendelian randomization, which makes it possible to set aside many confounding factors and biases.

Deleterious bacteria, and beneficial ones

The study tracked suspects (bacteria increasing the risk of sleep apnea) but also the superheroes who protect us from these nocturnal respiratory pauses: for example, the Ruminococcaceae bacterial family is thought to promote nights free of respiratory issues.

How can such power over our health be explained? Without a doubt by the ability of these bacteria to produce beneficial molecules, called short-chain fatty acids (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. ) , beneficial for our health in that they reduce inflammation, reinforce our intestinal barrier, and limit the proliferation of pathogenic bacteria; but also because these bacteria are implicated in the metabolism of bile acids, known for their role in sleep and regulating sleep cycles.

Molecules produced by bacteria implicated

The study also tracked various other molecules produced by the bacteria of our digestive tract to identify those with a role in nocturnal respiratory pauses. Bingo: some of them, such as leucine (or others that are more of a mouthful, such as epiandrosterone sulfate) effectively increased the risk of sleep apnea. These molecules often turn out to be unfavorably known: for example, elevated leucine levels were observed in children with sleep apnea; on the other hand, among patients who had been prescribed a mask to reduce sleep apnea, leucine levels fell rapidly. 

A team of Finnish researchers has for the first time identified the presence in the amniotic fluid of extracellular vesicles produced by bacteria from the gut microbiota in healthy pregnant women. ¹ 

These vesicles are made up of various bacterial molecules (proteins, lipids, nucleic acids, etc.) which may play a key role in the maturation of the fetal intestine and in baby’s immunity.

This discovery may be the missing link that explains the presence of bacterial DNA in the placenta, amniotic fluid, and meconium, as found in several recent studies.

Puzzling similarities

This finding came to light when scientists from the University of Oulu looked for extracellular vesicles in the amniotic fluid and feces of 25 pregnant Finnish women undergoing cesarean section delivery. 

The results confirmed the presence of large numbers of extracellular vesicles of relatively diverse sizes in all the fecal and amniotic samples.

An analysis of their content (proteins and 16S rRNA) showed that the vesicles in the fecal and amniotic samples shared a subgroup of proteins with the same functional characteristics and produced by the same bacterial phyla (Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria). These similarities in composition and bacterial origin suggest that the extracellular vesicles are formed in the microbiota, and that the microbiota communicates with the fetus via these vesicles.

By injecting maternal extracellular vesicles of human fecal origin into the blood of pregnant mice, the researchers then demonstrated the presence of vesicles in the amniotic fluid, thus proving that they can cross the placental barrier and accumulate in the fetus.

Preparing the fetal intestine to host its future microbiota

The authors’ hypothesis is that the extracellular vesicles present in the amniotic fluid are ingested by the fetus and then guide the fetal immune system towards the immune tolerance required for early colonization of the gut at birth. Extracellular vesicles are therefore part of the fetus’ natural environment, including during a normal pregnancy.

A team of Finnish researchers has recently made this surprising discovery. 

The microorganisms in the gut microbiota of pregnant women produce tiny extracellular vesicles (EVs) made up of bacterial material that are capable of crossing the placental barrier and reaching the amniotic fluid in which the fetus is immersed. ¹ They may contribute to the proper development of the child’s immune system after birth. 

Fetal microbiota: the end of a controversy?

This discovery should put an end to a long-running debate in the scientific community: do fetuses have microbiota?

A number of studies had reported the presence of bacterial DNA in amniotic fluid, meconium (sidenote: Meconium Earliest “stool” of the newborn, containing the amniotic liquid absorbed in utero. The meconium helps identify microorganisms lining the gastrointestinal tract of the fetus.
  ) , and the placenta. However, the origin of this DNA remained unclear, and many researchers were skeptical about the presence of whole living bacteria in the vicinity of the fetus. 

It now appears that this DNA comes from EVs produced by the maternal microbiota. 

First coming to light around a decade ago, EVs comprise a membrane containing various bacterial molecules: proteins, lipids, DNA, RNA, etc. They are capable of passing into the bloodstream, entering cells or tissue, and modulating functions. They, therefore, constitute a unique means of communication between the microbiota and the host organism.

Communication via vesicles

Until now, no one had investigated the role of EVs in gestation, let alone proved their presence in the fetal environment.

Anne Kaisanlahti and her colleagues at the University of Oulu in Finland took stool samples from 25 pregnant women. 

All then gave birth by cesarean section, which enabled the scientists to collect amniotic fluid in optimal conditions of sterility. The scientists then looked for EVs in all the samples.

They found that vesicles were indeed present, both in the feces and the amniotic fluid, and that they shared a number of features, indicating a common origin.

It should be noted that the authors are hypothesizing. Most vesicles identified in the amniotic fluid are probably cellular debris from the mother or the fetus.

The environment – diet, hygiene, place of residence, lifestyle, pollutants, drugs, etc. – shapes the evolution and composition of the gut microbiota. But so do genetics.

Changes in the microbiota are associated with certain diseases, such as obesity and allergies. Since lifestyle contributes to microbiota changes that influence disease, a team of researchers set out to determine the impact of urbanization on the gut microbiota, while overcoming genetic factors.

Senegalese Fulani people as a study model

They recruited 60 young Senegalese Fulani women and their newborn infants, most of whom were delivered vaginally. All the women belonged to the same ethnic group and were, therefore, genetically unified. However, they lived in radically different environments:

• Half lived in a “traditional” (rural) environment with little or no access to amenities (electricity, health centers, running water, etc.) and a diet that was not very diversified;
• The other half lived in Dakar (urban), with electricity, running water, healthcare, and a much more diversified diet.

The “urban” mothers had a higher body mass index (BMI) (sidenote: Body Mass Index (BMI) Body Mass Index (BMI) assesses the corpulence of an individual by estimating the body fat mass calculated by a ratio between weight ((kg) and height squared (m2). https://www.nhlbi.nih.gov/health/educational/lose_wt/BMI/bmicalc.htm https://www.euro.who.int/en/health-topics/disease-prevention/nutrition/a-healthy-lifestyle/body-mass-index-bmi ) than the “rural” mothers.

The scientists took stool samples from the mothers and babies at two points in time: within six months of delivery (T1), then one year later (T2).

Better living conditions, but adverse effects on gut microbiota

The researchers observed a “delayed maturation” of the gut microbiota in urban infants, characterized by lower microbial diversity. This deficit was not observed in rural infants. This may indicate that urban sanitary conditions, pollution, or diet influence the evolution of their microbiota.

On the other hand, differences in microbiota composition between urban and rural babies were less significant than those between urban and rural women. According to the authors of the study, this may be due to the fact that the babies had been exposed to certain urbanization factors, such as diet, for a shorter time than their mothers, with dietary diversification generally not occurring until the sixth month. 

However, according to the authors, these differences may also be explained by the exposure of urban mothers to a greater number of factors – urbanization, as well as a higher prevalence of parasitism and excess weight – than rural mothers.

Mounting evidence reveals that the gut microbiome influences how well immune checkpoint inhibitors (ICIs) like PD-1 inhibitors work against cancer. But whether antibiotics given shortly before immunotherapy impact outcomes remained unclear, especially in advanced gastric cancer—until now.

In a groundbreaking study published in Cell Reports Medicine ¹, an international research team provides compelling data from 329 patients that taking antibiotics within one month of starting PD-1 blockade unleashes negative consequences.

Analytics illuminate survival gap

The multi-center analysis discovered that 44-46% of advanced gastric cancer patients had taken antibiotics within 28 days pre-immunotherapy. This prior antibiotic (pATB) group experienced markedly lower response rates (1.5% vs 11.8%) and shorter survival time compared to the non-pATB group when given anti-PD-1 (sidenote: Anti-PD-1 immunotherapy based on immune checkpoint inhibitors that target the PD-1 checkpoint, reversing the deactivation by the tumor of the recognition system associated with the PD-1 protein present on the surface of T lymphocytes. The immune system’s effectiveness against tumor cells is thus restored. ) medications (pembrolizumab or nivolumab).

Strikingly, no survival difference occurred with pre-chemo antibiotics group (N=101 patients that received irinotecan as chemotherapy), pointing to an immunotherapy-specific mechanisms.

Microbiome and immune system disruption

To unravel these mechanisms, the team performed microbiome gene sequencing on bacterial genomic DNA extracted from stool samples from 24 PD-1-treated patients. This quantified bacteria species and abundance changes due to antibiotics.

Additionally, they sequenced blood immune cells at the single cell level, enabling intricate comparison of cell subset frequencies and properties.

The researchers uncovered two major interconnected effects of pATB exposure that can foil PD-1 inhibitor efficacy:

• Reduced overall diversity of intestinal bacteria, including fewer “good bacteria” like Lactobacillus gasseri.
• Rise in exhausted CD8+ T cells overloaded with PD-1 and other inhibitory immune checkpoints rather than more robust effector T cells.

Further computational analyses demonstrated that the microbiome and immune metrics statistically associated with patient outcomes: For example, higher Lactobacillus gasseri abundance was linked to longer progression-free and overall survival. Conversely, disproportional enrichment of circulating exhaustiveCD8+ T cell frequency predicted worse prognosis.

You might not know it, but the mouth is more than just a simple chewing machine. It offers room and board for a multitude of micro-organisms—the “oral microbiome”—which plays a significant beneficial role in our health.

The bacteria of the oral microbiome do not like cigarettes

The problem: a study conducted in 2016 on Americans showed that smokers have a severely altered oral microbiome ¹, and this would not be without consequences for their health. Multiple studies have in fact shown that in cases of dysbiosis (sidenote: Dysbiosis Generally defined as an alteration in the composition and function of the microbiota caused by a combination of environmental and individual-specific factors. Levy M, Kolodziejczyk AA, Thaiss CA, et al. Dysbiosis and the immune system. Nat Rev Immunol. 2017;17(4):219-232.   )  of the oral microbiome, the risk of cardiovascular problems and gum disease (inflammation and receding gums) increases.

Is the same public health problem found among Europeans? A team of researchers decided to explore the question and, for the first time, to determine whether quitting smoking would make it possible to fix the situation. ²

They analyzed the salivary microbiomes of 1,601 Italians aged an average of 45 years, of whom 45% were smokers or former smokers. In particular, the scientists tried to determine whether the activity of bacteria transforming nitrates from food into nitrites, compounds beneficial for the blood vessels, was affected by smoking.

Return to equilibrium after quitting smoking

What did the results show? First of all, that Italian smokers had an oral microbiome that was much more altered than that of non-smokers. However—good news! —among ex-smokers, the more significant the number of years since quitting, the more the oral microbiome approached that of non-smokers.

Among those who had quit smoking at least 5 years ago, populations of bacteria in the mouth presented nearly the same profile as those of non-smokers. The oral microbiome thus shows good resilience when it comes to smoking.

In addition, smokers were found to have decreased bacteria able to transform nitrates from food into nitrites. Why is this information of interest? Because nitrites are necessary for the production of nitric oxide (NO).

Implication in cardiovascular risk

In cases of lowered NO, increased blood flow is observed in the gums, which leads to inflammation and receding gums. We also know that NO deficiency is a risk factor for developing cardiovascular disease. The oral microbiome would thus be implicated in the increased cardiovascular risk observed in smokers.

If previous studies ¹ are to be believed, there may be just one step from gut microbiota to skeletal health: certain gut microorganisms are thought to increase the production of T cells, which in turn stimulate the production of immune mediators and inflammatory cytokines, promoting osteoclastogenesis and bone loss in mice. Other studies point to mechanistic links involving the production of microbial short-chain fatty acids (SCFAs) and the metabolism of dietary components involved in bone metabolism (vitamins K, D, and complex polysaccharides). This research field even has a specific name: osteomicrobiology. The field has seen very few clinical studies, but an American team recently published one.

Two separate cohorts, one suspect in common

This research was based on the cohorts from two observational studies: 831 elderly men (mean age 84.2) from the Osteoporosis in Men Study (MrOS) ² and 1,227 younger men and women (mean age 55.2) from the Framingham Heart Study (FHS) ³. An analysis of the data identified 37 microbial genera that appear to be involved in the FHS study (DTU089, Marvinbryantia, Blautia, and Akkermansia were negatively associated with bone density, while Turicibacterand Victivallis were positively associated) and 4 genera in the MrOS study (negative associations with Methanobrevibacter and DTU089 and positive associations with Lachnospiraceae NK4A136).

Thus, despite the difference between the two cohorts in terms of height, sex, and age, a common bacterium was associated with lower bone density in both cohorts: DTU089. DTU089 is known to be more abundant in those with low levels of physical activity and very limited protein intake, two factors unfavorable to bone health.

Meta-analysis

The researchers pooled the two cohorts to perform a meta-analysis. The results: a higher abundance of Akkermansia and DTU089 was associated with a less dense radius and tibia; conversely, a higher abundance of the Lachnospiraceae NK4A136 group and Faecalibacterium was associated with higher bone density.

The researchers also identified eight metabolic pathways associated with bone measurements, the most important of which involved the histidine, purine, and pyrimidine biosynthesis pathway. Previous experiments in mice had suggested a disturbance in purine metabolism in osteoporosis.

These results remain preliminary and require further studies to better understand the mechanisms by which certain bacteria can modify skeletal integrity, but they do support initial preclinical findings. Above all, they give greater hope that we may one day be able to modulate the gut microbiota and better protect bone health.

Do you think that analyses of stool samples may be soon added to tests designed to identify individuals with early Alzheimer’s disease in order to orientate them to appropriate treatments more rapidly?

After reading this article the first question which logically comes to mind is to ask oneself if the analysis of the microbiota could be proposed to identify those individuals with early stage or preclinical AD. From a neurologist’s point of view, the response is rather negative. This is because current data, both for symptomatic AD and for preclinical AD, have failed to identify a specific “standard” microbiota, which may distinguish these cases from a control population using routine stool analysis. Moreover, there are now markers of AD, reliable even at a preclinical stage, easily utilisable in a clinical context. Leaving aside PET imaging which is not available in all centres and analysis of the cerebrospinal fluid which involves a lumbar puncture which can be considered invasive, it is now possible to detect modifications in the expression and/or phosphorylation of certain proteins implicated in the neurodegenerative process in the plasma, i.e. in a simple blood sample, for cases of symptomatic AD as well as at the preclinical stage [3].

Would you consider sharing this publication with your patients to explain the relationship between the gut microbiota and the brain, in order to reinforce the key role played by the gut microbiota in human health?

To end on a more positive note, there is, however, no doubt that this article, by showing for the first time a modification to the composition of the microbiota in preclinical AD, provides new evidence that the microbiota may be involved in the development of AD, and moreover, at an early stage. In this context, its summary and a simplified version may be proposed to the general public or to some patients to emphasise the important role of the microbiota in health. Nevertheless, independent confirmation of these results by other teams will be necessary in the future.