However, initial studies suggest that the microbiota, as the interface between our body and the outside world, may play a key role. They show that:

• Lifestyle modernization is having as much impact on ecosystems as on our health and the health of our microbiota; 
• An environment rich in diverse microbes plays a protective role;
• At the very beginning of life, there’s a window of opportunity where the nature of exposures can predispose the body to chronic disease or, on the contrary, protect it;
• There are simple ways (low-processed and plant-based food, physical activity, quality sleep, contact with nature, limiting chemicals and drugs, etc.) to move towards an exposome more favorable to our health.

Diet

• Favoring whole, organic, and seasonal foods (fruits, vegetables, legumes, wholegrain cereals, etc.), which are rich in fiber, vitamins, and minerals, and reducing our intake of ultra-processed foods (ready-made meals, processed meats, snacks, industrial cakes, sweets, etc.);
• Give preference to poultry and limit other meats (pork, beef, veal, mutton, lamb, offal) to 500 g per week; alternate with foods that provide more plant proteins, such as pulses or whole or semi-whole cereal products;

• Avoid bottled water, which likely contains microplastics; instead opt for water filtered with an activated carbon cartridge or reverse osmosis system, which at present appear to be the most effective means of eliminating “forever chemicals” (PFAS) ⁴⁰;
• Limit the use of plastic packaging and stretch film, and instead use bulk packaging and bee wrap (cloth coated with beeswax) to cover leftovers and wrap snacks; 
• Use glass or Pyrex (inert) containers instead of plastic containers, especially when heating food in the microwave; 

Hygiene

Use the most simple and unscented products available: vegetable oils, hydrolats, natural soaps, creams based on natural products with a limited number of ingredients, etc. Apps such as Yuka, INCI Beauty, and QuelProduit allow you to scan products and identify those that contain fewer problematic substances. 

Health

• Avoid self-medication, especially with antibiotics;
• Return unused medicines to the pharmacist (avoid throwing them in the garbage or down the sink);

Household

• For the household, use traditional products (Marseille soap, vinegar, soda crystals, clay powder, etc.) and avoid harsh, perfumed detergents and fabric softeners; 
• Avoid going on a germ hunt by banning bleach and all anti-microbial products from your home;
• Avoid scented candles, air fresheners, sprays, etc.;
• Avoid particle board furniture, varnishes, paints, etc. – sources of volatile organic compounds (VOCs) – especially in babies’ and children’s bedrooms; 
• Air rooms for 10 minutes a day.

Leisure, physical activity, stress management

• Spend as much time as possible in contact with nature;
• Let children play in contact with vegetation and animals.

• Limit screen time and instead encourage artistic, creative, and shared leisure activities (games, music, painting, etc.).
• Avoid a sedentary lifestyle by making physical activity part of your daily routine: walk, cycle, or rollerblade instead of using motorized transport; take the stairs instead of the elevator, etc. ;
• Opt for environment-friendly vacations, whether in terms of practices or transport;
• Look after your mental health by practicing stress management techniques (meditation, breathing, cardiac coherence) and learning to slow down, listen to yourself, contemplate, communicate, etc.

Professional activity

• Inform yourself about any occupational exposure to chemical substances (diesel emissions, silicon dioxide, asbestos, etc.), biological agents (bacteria, viruses, or molds likely to cause infection, allergy, or poisoning), physical agents (noise, heat, cold, radiation, etc.), and stress (working hours, work pace, lack of resources, interpersonal tensions, etc.);
• Follow professional preventive advice

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First 1,000 days

We’ve known for some time that the microorganisms in the gut microbiota are essential to the development of our immune system. However, other mechanisms related to early exposure of the fetus and young child to environmental factors may be involved ³³. 

Perinatal period

• Pregnancy: a mother’s  microbiota (gut, skin, lung, and perhaps placental microbiota) appears to have important effects on the maturation of the immune function in her offspring. For example, one study showed that exposing pregnant women to bacteria from barns reduced the risk of their children subsequently developing asthma. The placental  microbiota, which more closely resembles the maternal oral  microbiota than the vaginal or gut  microbiota, may play a role in this maturation.
• Birth: babies born vaginally are colonized by microbes similar to those present in their mother’s vagina. They also have a richer and more diverse gut  microbiota than those born by Cesarean section, which is associated with a lower risk of asthma.
• Breastfeeding

Other factors in the perinatal exposome (antibiotic treatment, breastfeeding, diet, etc.) are also thought to be involved.

Early childhood

Since the middle of the last century, the trend towards more affluent lifestyles and more modern and “hygienic” habitats has altered our exposure to microbes. These alterations may predispose children to chronic inflammatory diseases.

Indeed, there’s strong evidence that early exposure to rich, diverse microbial populations plays a protective role, provided it occurs early in life. This period is known as the “window of opportunity”. 

Various studies have counter-intuitively shown that the presence of pets, rodents, fungi, or bacteria in the living environment of infants and toddlers improves the bacterial diversity of their  microbiota and may protect them from asthma. 

Childhood and adolescence 

The value of the exposomic approach was highlighted by a study of 504 children aged 6 to 9, who were followed for eight years. Researchers measured the impact of different exposures (diet, physical activity, sleep, air pollution, socio-economic status) on blood markers (metabolites).

What’s more, a high exposome score is associated with lower levels of acetate, 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. ) produced by the gut microbiota. Studies suggest that acetate may play a beneficial role in metabolic, cardiovascular, and neuronal health ³⁴ . 

Acne

Another study, this time on teenagers, showed that numerous lifestyle factors (consumption of skimmed milk and whey protein supplements, stress, pollutants, medication, climate factors, etc.) had a clear impact on the progression and severity of acne, and on the efficacy of treatments. 

Skin care products and cosmetics are part of the external exposome. They can activate inflammation and cause acne flare ups by altering the skin barrier and the balance of the skin  microbiota, promoting sebum secretion, modifying microbes, and activating the innate immune system ^₃₅. 

Mental health

We also know that during adolescence, stress – often more intense than at other times of life – and the increased production of androgens (such as testosterone) are likely to modify the  microbiota and, consequently, the gut-brain axis. 

Research suggests that these internal exposome changes may play a role in the emergence of psychiatric illnesses, many of which first appear during adolescence ³⁶. 

Adulthood 

It’s becoming increasingly clear that the gut microbiota is involved in various aspects of physical and mental well-being, and that its structure and function largely depend on lifestyle. 

While the impact of the exposome is crucial early in life, we know that its harmful effects can continue into adulthood. A Western diet (low in fruit, vegetables, and whole grains; high in animal products and ultra-processed foods) can, for example, disrupt the biofilm and gut barrier, making the gut more permeable. 

This can allow pieces of bacteria (endotoxins or lipopolysaccharides) to enter the bloodstream, leading to chronic low-grade inflammation, with potentially harmful metabolic and behavioral consequences. Conversely, a diet rich in fiber and phytochemicals from plants can promote microbial diversity and reduce oxidative stress and inflammatory load. 

An unbalanced diet combined with stress, a lack of contact with nature, a microbe-poor environment, and a lack of outdoor physical activity can also alter the microbial diversity of the gut and skin  microbiota. A lessdiverse  microbiota means immune dysfunction and chronic inflammation, which can affect all organs and pave the way for chronic disease.  

Among seniors

Aging is generally associated with alterations in the gut  microbiota. Over time, the gut microbiota tends to lose its diversity and balance (dysbiosis), contributing to an accentuation of inflammatory processes and increased susceptibility to diseases that make the elderly more fragile. 

On the other hand, maintaining a balanced  microbiota over time promotes a healthy metabolism and immune system, and preserves heart, bone, and cognitive health. 

While the causes of  microbiota alterations with age are still under research, the study of centenarians’  microbiota tells us that certain exposome factors may be involved. 

Eating habits, such as adherence to the Mediterranean diet (rich in fiber and antioxidants), are correlated with gut microbial species linked to longevity ^38,39. Physical activity, not smoking, and satisfactory working conditions may also play a part.

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Psychiatric disorders

A number of studies have shown that exposure of the gut microbiota to environmental factors has consequences for mental health:

• Stress during pregnancy, by disrupting the maternal  microbiota, increases the risk of psychiatric disorders in offspring ²¹;
• Stress associated with a reduction in microbial biodiversity in the environment, by disrupting the gut barrier, is thought to promote systemic inflammation, which is known to play a role in certain psychiatric disorders, particularly depression ;
• 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. ) has been shown to improve cognitive function and ward off depression by increasing anti-inflammatory bacterial metabolites and decreasing those that are pro-inflammatory ^23,24.

Moreover, an imbalance in the microbiota can expose the brain to disturbances via the gut-brain axis. A gut dysbiosis may thus be involved in the initial onset of psychosis. 

Asthma and allergic diseases

The number of people affected by allergic diseases continues to rise worldwide. This surge in allergies may well originate in the exposome.

A growing number of studies suggest that exposure to environmental substances (air pollution, detergents, microplastics, nanoparticles, processed foods, emulsifiers, etc.), as well as the decline in biodiversity and environmental degradation, are responsible for changes that favor these immune disorders:

• disruption of epithelial barriers in the skin, respiratory tract, and gut;
• changes in microbial composition of the  microbiota. 

At gut level, certain exposure factors have been shown to damage epithelial barriers, resulting in dysbiosis and increased permeability. This is thought to be responsible for a loss of the “immunomodulatory” (allergy-protective) effects of bacteria in the  microbiota ²⁵ . 

Cancer and bowel diseases

More and more young people are being diagnosed with cancer, including bowel cancer. Over the past three decades, the incidence of cancer has risen by around 50% among people aged 25 to 49 in the US, Canada, Australia, and several European countries. 

The same is true of chronic inflammatory bowel disease (IBD), the highest incidence of which is found in the most industrialized countries, such as those in north-western Europe and the United States, and whose frequency increases with socio-economic development. 

Although the causes of IBD remain poorly understood, dysbiosis is known to play an important role ²⁹.  

According to a team of French researchers, there’s growing evidence that ultra-processed foods (UPFs), in particular food additives, play a role in IBD, colorectal cancer, and irritable bowel syndrome. In particular, emulsifiers, sweeteners, colorants, microplastics, and nanoparticles are known to affect the gut microbiota, intestinal permeability, and intestinal inflammation, with a potentially significant impact on the risk of intestinal disease ³⁰. 

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The problem is that many features of the external exposome (low-fiber or high-fat diet, emulsifiers, heavy metals, phthalates, microplastics, fine air particles, pesticides, environmental pollutants, stress, etc.) can upset the balance of our microbiota and lead to dysbiosis. 

We know that dysbiosis is linked to numerous chronic diseases, such as obesity, type 2 diabetes, asthma, chronic inflammatory bowel disease, autoimmune diseases, depression, and cerebral development disorders ¹. 

Collapse of biodiversity = microbiota and health at risk

This ticking time bomb has been confirmed by international expert group IPBES : biodiversity is “declining globally at rates unprecedented in human history” ¹³ . This collapse is the result of global warming, over-exploitation of land, and pollution. 

That’s a problem for our microbiota, since fewer animal and plant species means less microbial diversity in ecosystems and therefore more alteration of microbiota-mediated immunomodulatory circuits, as well as more allergies and autoimmune diseases ¹⁴. 

According to the World Allergy Organization, the loss of biodiversity results in reduced interaction between environmental and human microbiota, which can lead to immune dysfunction and impaired tolerance mechanisms ¹⁵. 

On the other hand, we’ve known since 2005 that microbe-rich environments (living on a farm, close to nature, etc.) are associated with protection against immune diseases. 

Fungal exposome: regulating the immune response

The microbiota, whether in the gut, vagina, lungs, or on our skin, comprises not only bacteria, but also viruses, archaea... and fungi. The fungal “mycobiota” is essential to the balance and stability of our microbiota. Numerous studies on infants have shown the microbiota fungal composition to be associated with the risk of developing an allergic disease. 

We now know that the mycobiota largely depends on the fungal exposome. Analyses of fungal taxa have shown that the fungi most frequently found in the gut, mouth, lungs, and on the skin are the same as those found in the environment, whether indoors (walls, furniture, indoor air, etc.) or outdoors (food, water, soil, etc.).  

Fungi present everywhere in the environment may therefore come into sustained contact with our organism, modulating our immune responses.

Drugs, exposome, microbiota: a delicate balance  

As part of our exposome, drugs interact in complex ways with the gut microbiota, influencing both its composition and functions. 

Take, for example, common treatments such as proton pump inhibitors (PPIs), used to treat gastroesophageal reflux disease. PPIs modify the acidic environment of the stomach, allowing oral bacteria to reach the gut. This can influence the microbial ecosystem by favoring the growth of certain strains. These changes are associated with an increased risk of infection, such as those caused by Clostridium difficile, but can be controlled through appropriate use (avoiding long-term treatment where possible) and medical follow-up ²⁰.  

The  microbiota is no mere bystander. It plays an active role in the processing of drugs. 

For example, gut bacteria can improve the efficacy of metformin (an anti-diabetic drug) by stimulating the production of 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. ) (SCFAs) beneficial to health. 

Conversely, in rare cases, the  microbiota can transform active molecules into toxic compounds, as in the case of brivudine, a now-banned antiviral used to treat shingels, which gut microorganisms can convert into liver-toxic bromovinyluracil.

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The food we eat, the water we drink, the air we breathe, not to mention our living and working environment... To what extent do the factors we’re exposed to from cradle to grave play a role in the relentless advance of chronic disease? This question poses a real challenge for the scientific community. 

While scientists have been working for many years to measure the impact on health of each of these factors, we still know very little about the physiological harm they cause when combined and accumulated over the years.

Some act synergistically (cocktail effect), while others offset each other. Furthermore, their impact differs according to the stage of life when one is exposed to them and on the duration of exposure¹. 

Exposome: a global approach to health

Urbanization, stress, climate change, modern diet, toxic products... In 2005, driven by the need to better understand the often complex exposure to these multiple environmental factors, British epidemiologist Christopher P. Wild (current director of the International Agency for Research on Cancer – IARC) proposed the concept of “exposome”. Wild defines the exposome as “the sum of all exposures a person experiences from conception to death.” 

He sees the exposome as“a complex and dynamic representation of the exposures we experience during our lifetime that integrates chemical, microbiological, physical, recreational, medicinal, lifestyle and dietary environments, as well as infections.”²  

Breathing, washing, dressing, eating, working, and sleeping are not so trivial after all. They expose us to sources of micro-particles, chemicals, pollutants, heavy metals, stress, noise, radiation... all potentially harmful to our bodies and microbiota.

A better understanding of the exposome, i.e. the exposures we experience during our lifetime, is therefore crucial to reducing the risk of disease and making good habits part of our daily lives. But what about the microbiota? 

Microbiota and exposome: a dialog at the core of our health 

What if our health depended on the dialogue between our environment and the billions of micro-organisms that inhabit our bodies? Pollutants, food, stress, nature... the exposome constantly interacts with our microbiota and can influence their fragile balance. A little-known but central link, particularly in the prevention of chronic diseases. The impact of nature on our microbiota, and that of urbanization, bear witness to this.

Discover how this silent exchange shapes our health.

Microbiota under pressure: how the exposome promotes chronic disease

Our environment has a profound influence on our health... by affecting our microbiota. Endocrine disruptors, microplastics, drugs, ultra-processed foods: these are all components of the exposome that weaken our intestinal ecosystem and promote chronic disease. Science is now revealing how these disturbances can lead to obesity, depression, IBD and allergies. Examples include the fungal exposome and bacterial resistance.

Explore the links between environment, dysbiosis and modern diseases

From birth to death, an exposome with different consequences on our health

Our sensitivity to the environment evolves with age. From pregnancy onwards, the exposome modulates immunity, shapes the infant's microbiota and influences his or her future risk of asthma or allergy. In adolescence, it impacts mental and skin health. In adulthood, it determines inflammation and overall well-being. In senior citizens, it can preserve or alter longevity, as shown by the study on the microbiota of centenarians.

Discover how each stage of life interacts with the exposome.

Towards a more favorable exposome 

We may not have everything under control, but we can do something about it! A beneficial exposome is possible: a fiber-rich diet, physical activity, living in contact with nature, gentle hygiene, reducing disruptors... all simple levers to protect our microbiota and prevent disease. The Mediterranean diet and a rich microbial environment are living proof of this.

Discover concrete ways to cultivate a healthy environment.

Microbiota are the sentinels of our environment. Living interfaces between our bodies and the outside world, microbiota are a faithful reflection of our environment. Understanding the exposome means identifying the levers we need to live better, age better and prevent the diseases of tomorrow. The exposomic approach sheds new light on our relationship with public health, ecology and everyday behavior.

The vaginal microbiome is crucial to gynecological health. But with one main difference: unlike many other microbiomes, where healthy means diverse, the “gold standard” for a healthy vaginal flora is (at present) an ample predominance of Lactobacilli. 

However, in an opinion article on vaginal health, a group of international experts have pointed out the limitations of the current five CST (sidenote: Five community state types (CST) - CST I dominated by Lactobacillus crispatus, 
- CST II dominated by L. gasseri,
- CST III dominated by L. iners 
- CST V dominated by L. jensenii
- and the more diverse CST IV, which is not dominated by Lactobacillus but by a group of anaerobic bacteria, including Gardnerella, Atopobium, Prevotella, and Finegoldia. 
  ) classification: it does not reflect the full biology and functionality of the vaginal microbiome. The authors cite the Belgian Isala study, where 10.4% of participants displayed a co-dominance of L. crispatus (CST I) and L. iners (CST III), suggesting that CSTs may co-exist in some women. Another limitation is that the role of fungi, eukaryotes, archaea, and viruses remains largely unexplored.

Data mainly from wealthy countries

To illustrate their point, the authors considered bacterial vaginosis. This condition is diagnosed using the Nugent score (sidenote: Nugent score A diagnostic scoring system used to assess bacterial vaginosis based on the presence and proportions of certain bacteria in a Gram-stained vaginal sample. ) or the Amsel criteria (sidenote: Amsel criteria The Amsel criteria might provide a more clinical diagnosis of BV because they are based on the following four signs: vaginal fluid pH above 4.5, positive whiff test (foul odor after adding 10% potassium hydroxide – KOH), presence of clue cells, and abnormal vaginal discharge. At least three of these signs must be present before BV is diagnosed. ) , but these systems suffer from biases, particularly geographical biases.

Is the lower presence of Lactobacilli and higher frequency of vaginosis in black and Latin American women (vs. women of Asian or European origin) in the United States real or simply due to methodological limitations? Could socioeconomic inequalities between populations explain some of the differences? What about different behaviors, such as douching, a noted risk factor for vaginal dysbiosis? What about the many American women classified as African American even though (more than) half of their ancestors were white Europeans?

Ultimately, what do we really know about the make-up of a “healthy” and balanced vaginal microbiota in women with distinct geographical and ethnic origins?

Projects on every continent

The authors highlight the lack of studies in low- and middle-income countries, despite a growing number of initiatives attempting to fill this gap:

• The Vaginal Human Microbiome Project (VaHMP) maps data on the vaginal flora of women from different ethnic backgrounds in the United States;
• The VIRGO database supplements the US data with data from six countries on different continents;
• The Vaginal Microbial Genome Collection (VMGC) contains data from 14 countries; 
• The Vaginal Microbiome Research Consortium has a specific section for Africa and Bangladesh.

Another approach is citizen science (public contribution to vaginal microbiome research around the world using a bottom-up, local approach), such as the authors’ Isala project on vaginal flora. Following its success in Belgium (more than 6,000 applications for 200 women sought), the initiative has been extended to a global network of partners on different continents (the Americas, Africa, Asia, and Europe), promoting collaboration between teams.

The authors consider all these initiatives necessary for a more complete understanding of a “healthy” vaginal microbiome. 

These advances may also help us to better understand the conditions that promote a balanced vaginal microbiota, in particular by further investigating the protective role of certain species, such as Lactobacillus crispatus, and by rigorously evaluating the benefits of probiotics in this equation.

Sodas and other sugary drinks are a major target of public health policies. The harmful effects associated with consuming too many of them include diabetes (sidenote: Diabetes mellitus Chronic disease that occurs either when the pancreas does not produce enough insulin or when the body cannot effectively use the insulin it produces. Over time, diabetes can damage blood vessels in the heart, eyes, kidneys and nerves. ) , more specifically type 2 diabetes. How does this happen? Undoubtedly through weight gain, insulin resistance (sidenote: Insulin-resistance An altered response of cells to the action of insulin (a hormone that helps the body use sugar for energy), insulin resistance results in poor regulation of blood sugar levels. Sources
Inserm. La résistance à l’insuline, une histoire de communication. 2018. 
Centers for disease control and prevention. Diabetes - Resources and Publications -Glossary  ) , inflammation and dyslipidemia. But research carried out on Hispanic and Latino Americans shows that our gut microbiota also plays a role.

More sodas, more bad bacteria

A weakness for sugary drinks (especially if you drink more than 2 glasses a day) has serious consequences for the gut microbiota. In fact, regular consumption of these drinks appears to reduce the number of various bacteria that are considered beneficial because they 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. ) (SCFAs), which are known for their protective effects.

For example, Bacteroides pectinophilus, which feeds on pectin but doesn't know what to do with the sugars found in sodas, declines when soda is consumed. However, this isn’t true of all bacteria: those that like to feed on fructose and glucose (two sugars found in high amounts in sugary drinks) multiply like wildfire.

Diabetes-linked bacterial metabolites 

As a direct consequence of this bacterial disturbance, our microbiota changes, so it no longer produces the same metabolites (sidenote: Metabolites Small molecules produced during cellular or bacterial metabolism. For example, short-chain fatty acids are metabolites produced by intestinal microbiota during fermentation of non-digestible complex carbohydrates (fibers, etc.). 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.  Lamichhane S, Sen P, Dickens AM, et al An overview of metabolomics data analysis: current tools and future perspectives. Comprehensive analytical chemistry. 2018 ; 82: 387-413 ) and it impacts our health differently. With sodas, we're no longer getting the good SCFAs that are so beneficial for our bodies! Instead, the molecules produced by the intestinal flora of people who drink a lot of sugary drinks are linked to blood sugar issues and the risk of diabetes. And the more sodas and sugary drinks you consume, the greater the presence of these harmful molecules in your blood, leading to an increased risk of diabetes.

Note: being overweight could play a role in this phenomenon, as extra pounds seem to be part of the link between sugary drinks, metabolites and diabetes.

It’s time to cut down on sodas

These findings suggest that the gut microbiota and bacterial metabolites may play a role in the link between drinking sugary drinks and an increased risk of diabetes. Of course, further studies on other populations are still needed to better understand this link. But in the meantime, this study should be seen as yet another reason to drink less sodas! Instead, how about a glass of horchata, which boosts good bacteria?

Intratumoral dynamics in colon cancer are complex, with microbiota, fatty acid metabolism (FAM) (sidenote: Fatty Acid Metabolism (FAM) The cellular process involved in breaking down and synthesizing fats, influencing tumor growth and progression. ) , and the tumour microenvironment (TME) (sidenote: Tumor Microenvironment (TME) The surrounding environment of a tumor, including immune cells, blood vessels, and signaling molecules that impact cancer development. ) all playing a role. A recent study ¹ delved into this "unresolved trinity" in colon adenocarcinoma (COAD) (sidenote: Colon Adenocarcinoma (COAD) A type of colon cancer originating in the glandular cells of the colon. ) . By leveraging a substantial cohort of patient data from The Cancer Genome Atlas (TCGA) and employing sophisticated bioinformatic and pathological image analysis techniques, the researchers aimed to uncover novel diagnostic and therapeutic avenues for this aggressive cancer.

Microbial-metabolic connections

The research team initiated their investigation by analysing comprehensive data from 420 patients diagnosed with COAD. A key methodological step involved categorising these patients into two distinct subgroups:

• those exhibiting high fatty acid metabolism (FAM_high)
• and those with low fatty acid metabolism (FAM_low).

This stratification based on the Gene Set Variation Analysis (GSVA) (sidenote: Gene Set Variation Analysis (GSVA) A computational method used to evaluate the activity of specific gene pathways in patient samples, aiding in diagnostic subtyping. ) score calculated for FAM pathway genes.

Surprisingly, despite the overall microbial alpha diversity (a measure of within-sample diversity) appearing similar between the two groups, deeper analysis of the microbial beta diversity (a measure of between-sample diversity) revealed remarkably distinct bacterial compositions strongly linked to these underlying metabolic profiles.

The researchers observed that patients whose tumors exhibited a low FAM signature (FAM_low group) experienced significantly better overall survival (OS) compared to their FAM_high counterparts. The identification of four specific genes (ADIPOR2, HAO2, ALAD, HPGD) whose expression levels were significantly correlated with patient survival, solidifying the critical prognostic role of FAM in COAD.

Metabolic signatures as predictive tools

Beyond diagnosis and prognosis, the study's comprehensive drug sensitivity analysis illuminated substantial and potentially clinically actionable differences in how the two FAM-defined subtypes responded to a broad spectrum of therapeutic agents.

By calculating the IC50 values (the concentration of a drug required to inhibit 50% of cells) for an extensive panel of 195 candidate drugs, the researchers uncovered that the FAM_high and FAM_low groups exhibited significantly different sensitivities to a remarkable 120 of these compounds. For example, the high FAM group showed less sensitivity to drugs like JQ1, suggesting these agents might be less effective in this metabolic context. Such insights could support more personalized cancer treatment strategies.

When it comes to nutrition, fruit and vegetable juices provide a vitamin, mineral, and antioxidant boost. However, according to a clinical trial published in the journal Nutrients, “detox juice cleanses” may not be the best option when it comes to the recommended “five portions of fruit and vegetables a day”. ¹

Students on a diet

The authors put 14 students on three different diets for three days:

• five followed a diet consisting exclusively of cold-pressed fruit and vegetable juices (800 to 900 kcal per day, i.e. about 10 glasses); 
• four followed a “normal” diet accompanied by fruit and vegetable juices; while
• five followed a low-calorie diet rich in “whole” plant foods containing fiber (800 to 900 kcal).

Before starting their respective diets, in order to assess the influence of different foods on microbial composition, all participants followed a three-day “elimination diet” consisting of organic fruit, vegetables, whole grains, and eggs, with very little or no red meat, dairy products, processed foods, gluten, alcohol, coffee, or sugar.

To analyze how the different diets impacted the microorganisms in the volunteers’ gut, oral, and salivary microbiota, the researchers collected samples from their stool, saliva, and from the inside of their cheeks before the experiment, between the two diets, and afterwards.

Increased risk of periodontitis and tooth decay

They found that fruit and vegetable juices, whether consumed alone or with food, significantly alter the oral microbiota by increasing pro-inflammatory bacteria, even if these changes are temporary.

The researchers noted a reduction in Veillonellaceae, a bacterium capable of converting salivary nitrates into nitrites. However, fewer nitrites means less effective inhibition of the bacteria responsible for periodontitis and an increased risk of tooth decay.

For the gut microbiota, the impact of juices was less pronounced, but the researchers noted an increase in bacteria associated with inflammation, intestinal permeability, and cognitive decline.

Too much sugar, too little fiber

According to the authors, juices are higher in sugar and carbohydrates, and lower in fiber than whole fruits and vegetables, which adversely impacts both the oral and gut microbial flora.

The elimination diet had the most positive impact on the gut microbiota: by providing more fiber, it promoted the growth of bacteria that produce highly beneficial 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. ) (SCFAs) such as butyrate. 

While the scope of this study is limited by its small size and short duration, it confirms that the priority for microbiota health should be the consumption of whole fruits and vegetables in order to fully benefit from their fiber.

For decades, the conversation around Chlamydia trachomatis, the most common bacterial sexually transmitted infection globally, has revolved around sexual behavior: number of partners, condom use, prior STI history.

But a groundbreaking new study published in Cell  ¹ invites us to reframe that narrative. Instead of focusing solely on behavior, we’re asked to consider a more intimate and microscopic protagonist: the cervicovaginal microbiome (CVM).

In a longitudinal study, researchers tracked 560 Black and Hispanic adolescent and young adult (AYA) women in New York City, communities disproportionately impacted by Chlamydia infections.

They followed participants before, during, and after an incident Chlamydia infection. But rather than just charting symptoms or behaviors, they analyzed the entire microbial community of the cervicovaginal tract using high-resolution 16S rRNA and ITS1 gene sequencing.

The result? A nuanced and highly predictive microbial fingerprint for Chlamydia risk, reinfection, and even possible complications like pelvic inflammatory disease (PID) and miscarriage.

mBV-A and CST-IV-A: microbial fingerprints of risk

The team used a powerful molecular algorithm (molBV) to quantify bacterial vaginosis (BV)-like states, then categorized microbial communities into “Community State Types” (CSTs).

Among these, CST-IV-A, dominated by Candidatus Lachnocurva vaginae, emerged as the microbial signature most strongly associated with incident Chlamydia infection.

When CST-IV-A overlapped with a high molBV score, a state dubbed mBV-A, the risk of acquiring Chlamydia skyrocketed. Women with this mBV-A profile had more than double the risk of infection compared to those with a Lactobacillus-dominant microbiome (e.g., L. crispatus).

Even more striking? This elevated risk existed months before infection, revealing mBV-A not as a result of Chlamydia, but as a harbinger. This microbial landscape, characterized by high diversity and a drop in protective Lactobacilli, undermines the vaginal environment's natural defenses. It’s not just about pH or lactic acid. 
 

Candidatus Lachnocurva vaginae (sidenote: Candidatus Lachnocurva vaginae A bacterium commonly found in women with bacterial vaginosis and strongly associated with CST-IV-A. It is not yet cultivable in the lab ("Candidatus" denotes this) but has been implicated in increased susceptibility to sexually transmitted infections like Chlamydia. ) , the star of CST-IV-A, may metabolize D-lactate, a compound with antimicrobial properties, potentially weakening the cervicovaginal defense against pathogens like Chlamydia.
And it doesn’t stop there. The researchers identified a network of 10 bacterial genera, including Prevotella, Megasphaera, and Clostridium, tightly linked and predictive of infection. These weren’t isolated villains; they were a microbial clique.

Their collective presence formed a Microbial Risk Score (sidenote: Microbial Risk Score (MRS) A composite score representing the cumulative risk posed by a group of specific microbial taxa associated with disease. In this study, it predicts Chlamydia risk based on the presence and abundance of 10 interrelated bacterial genera. ) (MRS), essentially a microbial polygraph test, that outperformed any single genus in predicting Chlamydia acquisition.

Reinfection, recovery, and the microbial set point

Even after treatment, the microbiome tells a story. Most women treated for Chlamydia saw their microbiome shift back toward its pre-infection state. But among those who carried the mBV-A profile post-treatment, the risk of reinfection tripled.

One in five previously infected women experienced reinfection, compared to just 4% of controls. The CVM, in a sense, carried a microbial “memory” of susceptibility, one that wasn't erased by antibiotics.

This points to a deeper truth: treatment of the pathogen does not equal treatment of the terrain. Even more provocatively, the researchers found that some women developed the high-risk mBV-A profile after antibiotic treatment, raising questions about how treatment regimens may unintentionally reshape the microbiome in ways that increase future vulnerability.

There were also early signs, though limited by small sample size, that this microbial fingerprint may be associated with complications like PID and miscarriage.