Microbiota is made up of trillions of microorganisms such as bacteria, viruses, fungi, archaea, etc. It lives in our digestive tract, our skin, our mouth, our nose and our lungs. These organisms play a crucial role in our wellbeing by helping digestion, stimulating our immune system, and protecting us from infectious diseases. But beyond these functions, microbiota also influences our mood, our metabolism and even our longevity. An imbalance of microbiota, often caused by factors such as diet, lifestyle or medication, could lead to major health problems, from digestive disorders to cardiovascular problems and depression. Maintaining a healthy microbiota throughout our bodies is therefore essentialfor our general health and well-being.

This large survey was conducted by Ipsos among 7,500 people in 11 countries (the USA, Brazil, Mexico, France, Germany, Italy, Portugal, Poland, Finland, China and Vietnam). Within each country, a representative sample of the population aged 18 y.o. and over was interviewed. Representativeness was ensured by the quota method applied to the respondent’s gender, age, region and occupation. The survey was conducted online, from January 21 to February 28, 2025.

The results were presented on June 27, 2025, on the occasion of World Microbiome Day.

About the Biocodex Microbiota Institute

The Biocodex Microbiota Institute is an international hub of knowledge dedicated to microbiota. The Institute educates the lay public and healthcare professionals on the importance of microbiota in healthcare and well-being.

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Is sleep connected to microbiota?

Could the microbiota play a role in sleep-related problems? 

Is there a link between microbiota, sleeping habits, and energy levels?

Sleep, mood and the gut-brain axis

In some cases, sleepless nights and episodes of insomnia could be related to psychiatric disorders. To learn more about how microbiota could influence brain health and mood, check the links below.

For years, forensic investigations in sexual assault crime cases have leaned heavily on the analysis of human male DNA, often from sperm, found on the victim. But this isn't always straightforward. Getting enough viable sperm can be tricky, especially if sampling occurs more than 48 hours after an assault. This is where the microbiome – the vast community of microbes living in and on us – steps onto the forensic stage, offering a potential new avenue for detection and identifying perpetrators in sexual crime investigations. 

This new study ¹ builds on previous work showing that microbial communities differ between body sites and individuals. If these unique microbial signatures transfer during sexual intercourse, could they leave a trace that traditional DNA methods might miss? That's the core question here, specifically focusing on the "sexome (sidenote: Sexome The collection of microbial signatures exchanged specifically during sexual intercourse. ) " – the microbial exchange during sexual intercourse.

Sex and your unique bacterial signature

The researcher recruited 12 consensual male/female couples participating in this science-driven study. Participants collected samples from their genital areas before and after penetrative sexual intercourse. The "before" samples were taken after a period of abstinence (at least 2-4 days). The "after" samples were collected 3 to 12 hours post-intercourse, mimicking a forensic sampling scenario. They then used full-length 16S rRNA gene sequencing (sidenote: 16S rRNA sequencing A method that reads a bacterial “barcode” gene to identify and differentiate species. ) to analyse each sample. Think of the 16S gene as a bacterial barcode allowing for species-level resolution, which is absolutely critical for forensic applications.

As expected, male penis skin samples were generally more diverse than female vaginal samples. Couples showed different levels of microbial similarity after sex depending on their baseline profiles. So being in a couple has a significant impact on the overall composition of bacteria found.

They also saw a clear disruption to the microbial communities in both male and female samples after intercourse. Bacterial types transferred between partners.

Bacteria typically found on male skin (like Corynebacterium, Staphylococcus, Finegoldia) increased in female samples, while key vaginal bacteria (Lactobacillus species) increased in male samples.

Surprising findings with forensic impact

What was surprising, even with condoms, bacteria still transfer, mostly woman to man, leaving microbial evidence behind them. Unique female-only bacteria stayed on a male partner for five days despite hygiene, extending forensic detection beyond sperm DNA. Plus, novel germs from gut or skin can appear in the genitals after sex, potentially offering fresh contact clues. This could add new dimensions to sexual assault cases.

If you are reading this piece, you probably know that the microbiome is foundational to health across so many systems, right from metabolism to immunity and even cognition. But defining what a truly "healthy" gut looks like – one that's not just present but resilient and linked to wellness – has been a massive challenge given its incredible variability across people and places.

A new study published in Cell Reports ¹ brings a fresh view with the Health-Associated Core Keystone (HACK) index. This isn't just another list of microbes; it's a single, robust ranking of 201 key gut bacterial species based on their consistent association with crucial aspects of host and microbiome health.

Not all core members are equal

The study revealed several surprising insights that challenge common assumptions in microbiome research.

Perhaps most striking is the finding that some taxa consistently identified as core-associated – meaning prevalent and tightly linked to the community in non-diseased guts – were also previously linked to multiple diseases. Table-based analysis revealed that Collinsella aerofaciens is one such example. This highlights that simply being a common resident doesn't guarantee a health benefit and reinforces the importance of combining community association with abundance stability and disease association – as the HACK index (sidenote: HACK Index A composite ranking of 201 gut bacterial species based on prevalence/community association, stability, and disease associations. ) does.

From diet to therapeutics

So, what does this mean for clinical practice? The HACK index provides a powerful new tool.

The study showed that a simple score derived from the mean ranked abundance of the top 17 HACK taxa (HACK-top-17-score) performed comparably or better than existing microbiota/microbiome health indices in distinguishing between diseased and non-diseased states, as well as stable and unstable microbiomes. 

In addition, analysis showed a significant positive correlation was observed between a taxon's HACK index and its association with a positive response to immune checkpoint inhibitor (ICT) therapy. This suggests the HACK index could potentially help identify gut microbes most likely to support therapeutic success in oncology and beyond.

Moreover, the index also links microbial patterns to diet. Higher HACK scores correlated with microbes more responsive to Mediterranean-style food interventions, indicating diet-based therapeutic potential.

Diet is not only a modifiable factor, but also a diagnostic lens for understanding the microbiome’s response to specific food patterns.

This article sheds new light on the intricate interplay between human microbiota and health. The HACK index marks a significant step toward a functional, clinically applicable definition of a healthy gut. And while more work is needed, especially in strain-level analysis, this robust and reproducible analysis framework already opens new paths for diagnostic tools and therapeutic targets – especially when integrated with human dietary patterns and response to medical interventions.

Analysis of such tools and indexes through large-scale microbiome data and clinical application tables is now essential in advancing personalized medicine. As gut research evolves, tools like the HACK index could guide interventions grounded not just in microbial presence, but in functional stability – from food-based strategies to immune-based treatments.

How do the hormonal changes associated with menopause alter oral, gut, and urogenital microbiota composition? To answer this question, a team of Spanish researchers analyzed more than 100 studies on the subject. 

Published in the journal npj Women Health ¹, their analysis shows that the decline in sex hormones (estrogen and progesterone) significantly alters mucous membranes, with multiple impacts on the body’s various bacterial communities. Unsurprisingly, this has an impact on women’s health.

Oral microbiota

Changes related to declining estrogen levels are particularly noticeable in the oral cavity. In addition to changes in the mucous membrane that disrupt microbial communities, there is a decrease in the quantity and quality of saliva, which becomes more acidic. 

These two alterations can promote inflammation and colonization of the oral flora by pathogenic bacteria. This disrupted microbiota is less balanced, increasing the risk of lesions and diseases such as candidiasis (proliferation of Candida albicans), gingivostomatitis (inflammation of the gums), and angular cheilitis (inflammation of the corners of the mouth).

Vaginal microbiota

The decline in estrogen reduces the glycogen content of the cells in the vaginal wall, glycogen being the preferred food source for lactobacilli. These bacteria usually dominate the vaginal microbiota, secreting lactic acid which acidifies the vagina and prevents the proliferation of pathogens. 

When lactobacilli become less abundant, the vagina becomes less acidic and bacterial diversity increases. This is known as the “menopause paradox.” This imbalance in the vaginal flora opens the door to disorders such as inflammation, or recurrent infections such as bacterial vaginosis, and may contribute to endometrial cancer. It may also lead to persistent dryness. 

Gut microbiota

Studies to date do not tell us whether the decline in estrogen affects the balance of the gut microbiota. However, we do know that postmenopausal women have lower levels of bacteria from the Ruminococcus family, some of which produce beneficial short-chain fatty acids (SCFAs (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. ) ). They also have a greater abundance of Prevotella and Sutterella, two bacteria associated with obesity.

This imbalance in the gut flora may contribute to certain metabolic, digestive, and immune disorders. A balanced gut flora appears to play an essential role in overall health, including hormone regulation.

Take care of your microbiota

While further studies are needed before specific treatments targeting microorganisms in the gut, vagina, and mouth can be recommended for postmenopausal women (e.g. probiotics tailored to each flora, dietary changes, etc.), limiting damage by taking care of your microbiota seems a good place to start. 

A varied diet rich in fiber and fermented foods, daily physical activity, if possible in a natural environment, giving up smoking and alcohol, and using antibiotics as sparingly as possible: all have proven beneficial effects on the microbiota.

A healthy, balanced lifestyle is thus a sure way to support the balance of the microbial flora during menopause.

A narrative review by Spanish researchers has found that the drop in estrogen associated with the menopause significantly disrupts microbiota, with significant repercussions on women’s health. ¹ In particular, it leads to significant changes in the oral epithelium (thinning, drying out, etc.), which can affect oral health and the microbial ecosystem living on the mouth’s surface.

This alteration of the oral microbiome is frequently accompanied by a variety of oral symptoms in post-menopausal women.

Oral cavity sees significant change

Saliva becomes less abundant and more acidic, which not only increases the risk of caries and periodontal disease but also disrupts the oral microbiota. 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 microbiota has also been observed, which is likely to promote colonization by pathogenic bacteria and the onset of mucosal lesions such as angular cheilitis, an inflammation of the corners of the mouth.

Since the cells of the salivary glands and gums carry estrogen receptors involved in immunity, fluctuating hormone levels can cause inflammation of the mucous membranes. This can affect the balance of microorganisms and promote diseases such as candidiasis, which is linked to the proliferation of Candida albicans, or gingivostomatitis, the simultaneous inflammation of the gums and oral mucosa.

Taking these changes in the flora into account could enrich oral health prevention strategies for older women.

Greater bacterial diversity in the vaginal microbiota

In the vagina, the menopause is accompanied by a decrease in the dominance of lactobacilli, which normally acidify the vagina, thereby preventing the proliferation of pathogens or an increase in bacterial diversity. This is the famous “menopause paradox (sidenote: Menopause paradox The menopause paradox, characterized by a decrease in microbial dominance but an increase in richness observed in the vaginal niche, may apply to other body sites within the microbiome community. ) .” 

These changes increase susceptibility to bacterial vaginosis and may contribute to diseases such as endometrial cancer. Post-menopausal women with severe symptoms of vaginal dryness, dyspareunia (sidenote: Dyspareunia Recurrent or persistent genital pain during sexual intercourse. ) (pain during intercourse), and vaginal pain, often present greater bacterial diversity than women who do not suffer from these symptoms.

Estrogen and microbiota: a dynamic two-way relationship

Certain bacteria in the microbiota are thought to be able to “deconjugate” estrogen bound to proteins in the blood, thereby rendering these hormones biologically active. They are known as the “estrobolome.” The estrobolome can modify the availability of estrogen and thus influence the physiological processes associated with it. But that’s not all...

While certain bacteria in the gingival and gut microbiota can modulate the effect of estrogens by breaking them down, hormones can in turn directly modulate the activity of bacteria: bacteriostatic or bactericidal effects, stimulation of growth or proteolytic activity, modulation of biofilm formation, etc.

They also pave the way for targeted interventions, such as the use of probiotics to restore protective flora.
All of these bidirectional dynamics between sex hormones and bacteria can be completely disrupted during the menopause, with significant repercussions on women’s health. 

These interactions underline the importance of a systemic approach to understanding microbiota.

Towards better care for post-menopausal women

According to the researchers, there are still many unknowns about the interactions between sex hormones and the oral, gut, and urogenital microbiomes. However, with advances in science, new studies should soon give rise to previously unexplored therapeutic avenues (dietary changes, probiotics, personalized interventions, etc.).

The ultimate aim is to alleviate the symptoms of menopause and improve women’s overall health. Stay tuned!

You may not be aware that all organs which come into contact with the outside world, including the bladder (no, urine is not sterile) and the vagina (dominated by lactobacilli), host a resident microbiota that contributes to the organ’s proper functioning or, in the event of dysbiosis, to disease, including the sensation of pain.

To find out more, researchers examined 30 women suffering from chronic pelvic pain (sidenote: Chronic pelvic pain Persistent, noncyclic pain perceived to be in structures related to the pelvis and lasting more than six months. Often no specific etiology can be identified, and it can be conceptualized as a chronic regional pain syndrome or functional somatic pain syndrome. It is typically associated with other functional somatic pain syndromes (e.g., irritable bowel syndrome, nonspecific chronic fatigue syndrome) and mental health disorders (e.g., posttraumatic stress disorder, depression). Explore Speer LM, Mushkbar S, Erbele T. Chronic Pelvic Pain in Women. Am Fam Physician… ) (CPP), half of whom were hypersensitive (sidenote: Pelvic hypersensitivity Decreased cortical nociceptive thresholds leading to discomfort or pain from stimuli that are not usually painful, such as bladder filling; exaggerated perception of digestive system function; vulvar burning on contact; and abnormally intense pain from stimuli that are usually painful. Explore CHU Dijon ) , where pain could be triggered by the mere rubbing of underwear or a full bladder. ¹

Unhealthy microbiota

Women suffering from CPP with hypersensitivity have very low pain thresholds: even the slightest pressure on the bladder, for example, is enough to trigger pain. Moreover, the pain experienced is not only more intense but also more prolonged. In other words, their suffering is twofold.

These women have altered gut, urinary (bladder), and vaginal microbiota, with a general decline in beneficial lactobacilli: less Lactobacillus in the gut; a more diverse vaginal microbiota (not a good sign), enriched in Streptococcus and Prevotella, and depleted of other bacterial groups; and a more diverse urinary microbiota (again, not good), with Clostridium sensu stricto 1 predominant.

Specific bacteria that are the signature of pain

Even more troubling: some of these bacteria that are over- or underrepresented in hypersensitive women are directly associated with clinical symptoms. For example, less Akkermansia or Faecalibacterium in the gut means more rectal pain. Less L. jensenii in the vagina means more painful periods and a smaller bladder capacity. Less Lactobacillus in the bladder means impaired functioning.

Rebalance the microbiota to reduce pain?

Ultimately, the researchers managed to establish bacterial signatures of sensitivity based on bacteria from the gut, vaginal, and urinary flora. But are they the cause or consequence of the pain?

At this stage, it is not possible to say. But these findings open up promising avenues for research: probiotics could in the future be a therapeutic solution for these women, as could prebiotics, synbiotics, and nutritional approaches. By acting on the microbiota, it may be possible to relieve certain forms of pain.

Could rebalancing these microbiomes with probiotics not only alleviate pain but also address the root causes of the disease?

We know the gut microbiota contributes to visceral hypersensitivity through the production of bacterial metabolites. But what about other organs and microbiota? Do urinary or vaginal microbiota contribute to bladder or vaginal pain sensitivity? To find out more, researchers studied 30 patients suffering from chronic pelvic pain (sidenote: Chronic pelvic pain Persistent, noncyclic pain perceived to be in structures related to the pelvis and lasting more than six months. Often no specific etiology can be identified, and it can be conceptualized as a chronic regional pain syndrome or functional somatic pain syndrome. It is typically associated with other functional somatic pain syndromes (e.g., irritable bowel syndrome, nonspecific chronic fatigue syndrome) and mental health disorders (e.g., posttraumatic stress disorder, depression). Explore Speer LM, Mushkbar S, Erbele T. Chronic Pelvic Pain in Women. Am Fam Physician… ) (CPP), half of whom also suffered from hypersensitivity (sidenote: Pelvic hypersensitivity Decreased cortical nociceptive thresholds leading to discomfort or pain from stimuli that are not usually painful, such as bladder filling; exaggerated perception of digestive system function; vulvar burning on contact; and abnormally intense pain from stimuli that are usually painful. Explore CHU Dijon ) in a pelvic organ.

Impaired microbiota in cases of hypersensitivity

Pain pressure thresholds were found to be much lower in women with CPP and hypersensitivity in the vagina, rectum, bladder, and perineum than in women suffering from CPP with no associated hypersensitivity. After stimulation, these women experience not only more intense pain but also longer-lasting pain in the perineal muscles and bladder.
 

In terms of microbiota, hypersensitive women show signs of dysbiosis, including a decline in beneficial lactobacilli. The digestive microbiota is depleted in Lactobacillus; the vaginal microbiota is more diverse (whereas optimal vaginal flora is typically not very diverse), considerably enriched in Streptococcus and Prevotella, and depleted in Lactobacillus jensenii and Gardnerella vaginalis; while the urinary microbiota is also more diverse and enriched in Clostridium sensu stricto 1.

Dysbiosis linked to clinical characteristics

Above all, the relative abundance of certain bacteria in hypersensitive individuals is associated with clinical characteristics and increased organ sensitivity:

• A low intestinal abundance of Akkermansia, Desulfovibrio, Faecalibacterium, and CAG-352 is associated with increased rectal pain intensity;
• in the vagina, a lack of Lactobacillus jensenii is associated with more dysmenorrhea and a loss of bladder capacity, while an increased abundance of two Prevotella species is associated with the occurrence of dysmenorrhea;
• in the urinary microbiota, a lower abundance of Lactobacillus is correlated with reduced bladder capacity and poorer quality of life.

A signature of sensitivity

Lastly, the researchers identified gut, vaginal, and urinary bacterial signatures that serve as biomarkers for pelvic hypersensitivity in women suffering from chronic pelvic pain.

Are these bacteria the cause of the disease? Preclinical animal models will be required to validate any causal relationship. Nevertheless, this work paves the way for nutritional and therapeutic approaches where prebiotics, probiotics, and synbiotics targeting various urogenital microbiota have the potential to improve sensitization in women with CPP.

A lifelong gluten (sidenote: Gluten Gluten (from Latin glue): a viscous nitrogenous substance formed when flour is hydrated. It originates from specific proteins – glutenins and gliadins – found in cereals, primarily wheat. ) -free diet is mandatory after a diagnosis of coeliac disease (sidenote: Celiac disease A disease caused by a malfunction of the immune system, which mistakenly attacks normal components of the body – in this case, the small intestine. It is triggered by the ingestion of gluten in genetically predisposed individuals. ) . Yet its effects on intestinal function and gut microbiota remain poorly understood. Hence the relevance of this observational study, which assesses the intestinal function and microbiota of 36 celiac patients before and after one year on a gluten-free diet, compared with 36 healthy controls following a standard diet.

Before gluten elimination

Newly diagnosed patients not having started a gluten-free diet differed from healthy volunteers in that they showed higher levels of somatization, depression, anxiety, gastrointestinal symptoms and a 5% decrease in stool water content. The researchers also observed:

• a significantly higher water content in the small intestine (+57%), potentially due to a combination of impaired absorption (villus atrophy), increased secretion (crypt hyperplasia) and disrupted intestinal motility;
• slower intestinal transit (+83%), possibly linked to mucosal lesions, inflammation affecting motility, malabsorption and imbalances in gut hormones.

Although the team did not identify a specific gut microbiota signature for celiac disease, it did find differences in certain bacterial taxa – some of which may relate to altered intestinal function. For example, the reduced abundance of Blautia could be linked to slower transit and larger volumes of material in the colon.

A diet that influences the microbiota

After 12 months of gluten elimination, patients reported improved well-being (less somatization, reduced anxiety, slight improvement in transit, milder symptoms, etc.), but not to levels comparable with those of healthy controls. This suggests that while gluten avoidance is essential, it is not sufficient on its own.

One year on a gluten-free diet that eliminates wheat and its fibers (resistant starch and arabinoxylan) had a mostly negative impact on the microbiota and metabolic pathways: reduced abundance of Bifidobacteria and therefore the enzymes involved in breaking down starch and arabinoxylans; and increased presence of E. coli, Enterobacter and Peptostreptococcus, leading to an increase in the associated proteolytic activity.

Persistent symptoms

Most notably, 1 in 3 patients reported persistent or even worsened gastrointestinal symptoms while on the gluten-free diet. 

Branched-chain fatty acids (sidenote: Branched-chain fatty acids Appeared to correlate with symptoms, and the persistence of symptoms was associated with microbiota composition (particularly with respect to the Bifidobacterium, Alistipes and Ruminococcus genera).
Although the gluten-free diet remains the only current treatment for celiac disease, it disrupts the microbiota and does not fully resolve symptoms. As a result, the authors suggest combining the diet with targeted prebiotics and/or synbiotics to counteract these negative effects. ) appeared to correlate with symptoms, and the persistence of symptoms was associated with microbiota composition (particularly with respect to the Bifidobacterium, Alistipes and Ruminococcus genera).

Although the gluten-free diet remains the only current treatment for celiac disease, it disrupts the microbiota and does not fully resolve symptoms. As a result, the authors suggest combining the diet with targeted prebiotics and/or synbiotics to counteract these negative effects.

When you have celiac disease (sidenote: Celiac disease A disease caused by a malfunction of the immune system, which mistakenly attacks normal components of the body – in this case, the small intestine. It is triggered by the ingestion of gluten in genetically predisposed individuals. ) , there is no debate: gluten (sidenote: Gluten Gluten (from Latin glue): a viscous nitrogenous substance formed when flour is hydrated. It originates from specific proteins – glutenins and gliadins – found in cereals, primarily wheat. ) has to go. But what really happens inside the gut after a year on this diet? What are the effects on the gut microbiota? Do symptoms persist? A recent UK study ¹ took a closer look at these questions.

Before going gluten-free, both gut and patient suffer

Before starting their gluten-free diet, patients with celiac disease already show significant differences: low mood, digestive symptoms and less hydrated stools – despite water content in the small intestine being unusually high. In particular, intestinal transit is much slower. The likely culprits? Mucosal lesions in the intestinal wall, which affect water absorption and secretion, and probably also chronic inflammation and some hormonal imbalances in the digestive system.

One year gluten-free: better, but far from perfect

Good news first! After one year on a gluten-free diet, patients generally feel better. Anxiety is reduced and gut transit accelerates slightly. But it’s not a cure-all; their well-being still lags behind that of people without celiac disease, and some continue to experience celiac-related symptoms.

The diet also takes a toll on the microbiota, in other words the community of bacteria living in our intestines. Removing wheat and its by-products (bread, pasta, biscuits, etc.) cuts out not only gluten, but also the fibers derived from this cereal and consequently the beneficial bacteria like Bifidobacteria that feed on these fibers. Instead, this diet seems to stimulate the bacteria associated with protein breakdown, such as E. coli and Peptostreptococcus, which we’d rather not encourage.

Celiac disease, wheat allergy, hypersensitivity to gluten: know the difference! ^6,7

Gluten is not “toxic” for the general population; it is well tolerated by most people. However, it’s involved in two very different conditions:

• Celiac disease: an autoimmune disorder (the immune system attacks its own body) that occurs weeks to years after gluten exposure. It causes lesions in the small intestine lining. It is diagnosed by the presence of autoantibodies (sidenote: Antibodies Antibodies are described in the study as key biological markers for diagnosing and monitoring celiac disease. ) in the blood;
• Wheat allergy: a classic allergic reaction that occurs within minutes or hours after contact with gluten or other wheat proteins. It triggers an immune response on the part of the body along with the release of histamine. Prevalence varies from 0.5% to 9% in children and 0.4% to 1% in adults, depending on the study.

What if the diet isn’t enough?

Another striking finding: 1 in 3 patients report persistent or even worsening gastrointestinal symptoms despite strict gluten avoidance. Specific fatty acids and the presence of certain bacteria in the gut microbiota may explain the persistence of these symptoms.