Colonization of the gut microbiota begins at birth through contact with the microorganisms in the mother’s vaginal flora (in the case of vaginal delivery) or microbes on the mother’s skin and in the environment (in the case of caesarean section). According to various studies, it then evolves steadily towards a stable adult-like composition 2-3 years after birth. But has the gut microbiota really reached maturity at this stage? A team of Swedish researchers studied the dynamics of the gut microbiota’s development during the first 5 years of life in a birth cohort of 471 infants (302 born vaginally, 169 via C-section). The infants’ gut microbiota was profiled via the 16S rRNA gene sequencing of fecal samples collected during their first week of life, at 4 and 12 months, and at 3 and 5 years. It was then compared to that of the infants’ mothers and that of healthy adults. The main finding was that the alpha diversity (of species) in the children’s stool, which indicates the richness of their gut microbiota, was still lower than that of adults at 5 years of age.

Maturation in stages throughout childhood

By measuring the prevalence and proportion of the main taxa at each age studied, the authors were able to observe that the gut microbiota developed at different speeds in different children but along relatively similar trajectories. Gut microbiota composition changes the most between 4 and 12 months, at the time of food diversification. There is major colonization by Ruminococcus gnavus, whose relative abundance decreases progressively from 12 months. Archaea such as Methanobrevibacter and bacteria belonging to the Christensenellaceae family, typical of the adult gut microbiome, appear first at 12 months and continue to increase in abundance between the ages of 3 and 5. This dynamic seems essential to the maturation of the gut microbiota: the more diversified the child’s gut microbiota, the more abundant these late colonizers and the lower the proportion of R. gnavus. Both low gut microbiota richness and high proportions of R. gnavus have been repeatedly linked by studies to illnesses such as metabolic syndrome, cardiovascular disease, and inflammatory bowel disease, while an increased abundance of Methanobrevibacter and Christensenella, among others, has been linked to metabolic health and a lower body mass index.

A balance to be protected from disturbances

This study was widely reported in the press and although the authors have not made any recommendations at this stage, they emphasize that the gut microbiota is likely to be extremely sensitive to disturbances during its development, with such disturbances having profound effects on health. However, some of their findings on the impact of early factors on the development of the gut microbiota are surprising. For example, antibiotic use during pregnancy or in the infant’s first year of life does not affect gut microbiota diversity over time. Moreover, mode of birth seems to play a limited role: gut microbiota diversity in children born by C-section is certainly lower at 4 months than in children born vaginally, but this normalizes by the age of 3. Therefore, we should ensure optimal development of the gut microbiota at very least beyond the age of 5 to give children every chance of a healthy future.

It is an undisputed scientific fact that babies in the womb have no gut microbiota: their digestive system is sterile. The microbiota begins to develop from birth through contact with the microorganisms present in the mother’s body during delivery and through contact with the environment. The microbiota gradually becomes stronger and richer in “friendly” bacteria and comes to resemble that of an adult by the time the child is 2 or 3 years old–or so, scientists thought until now. Recently, some research teams have shown that this process may take longer, a finding now supported by a Swedish study which followed more than 470 children from birth to 5 years of age.

Gut microbiota “adult” at age 5? Not quite!

The researchers analyzed the microorganisms present in children’s stool at different ages (at birth, at 4 and 12 months, and at 3 and 5 years) and compared them to samples taken from their mothers and other adults. They began by looking at diversity in the samples. Their first finding was that only a very small minority (3.5%) of the 5 year olds had a gut microbiota as mature as that of the adults.

They subsequently observed how these microorganisms colonized the gut. Roughly speaking, from birth to 4 months, the gut microbiota contains mainly lactic acid bacteria and Bifidobacterium. From 4 months to 1 year, dietary diversification results in a great upheaval: many new microorganisms arrive and settle in, with some microbes multiplying and others becoming less abundant. Between the ages of 1 and 3, this small community develops towards a more “adult” gut microbiota. However, some microorganisms known to be essential for health do not appear until 1 year of age and continue to increase in abundance beyond 3 years of age. Even at 5 years, these microorganisms are still short of adult levels.

For better health, protect the microbiota’s development

The authors of the study stress that the gut microbiota is sensitive to disturbances throughout its development. It is now also known that a gut microbiota imbalance (dysbiosis) in infancy (e.g. due to antibiotic use) can have health repercussions later in life: digestive disorders, excess weight, allergies^2,3,4, etc. We also know that a healthy diet during food diversification helps build a healthy gut microbiota.⁵ Therefore, we should ensure optimal development of the gut microbiota at very least beyond the age of 5 in order to give children every chance of a healthy future.

When it comes to painful periods, we’re not all in the same boat. There is significant variability between women when it comes to the intensity of menstrual pain, the number of painful areas or associated gastrointestinal symptoms. The biological causes of this variability remain poorly understood but researchers are now focusing their attention on the vaginal microbiota. Indeed, the symptoms/pain intensity of dysmenorrhea (sidenote: Dysmenorrhea  Medical term for menstrual pain or cramps. )  may be exacerbated by inflammation that results from changes to this microbiota. Although the vaginal microbiota has already been studied in relation to several gynecological conditions (vaginosis, miscarriage and endometriosis), this study is the first to focus on the link between the composition of the vaginal microbiota during menstruation and the intensity of period pain.

Heterogeneous vaginal microbiota

In a pilot study, 20 women filled out questionnaires and were classified into three groups according to the pain they experienced during their period: “mild localized pain”, “severe localized pain”, or “severe multiple pain and gastrointestinal symptoms”. The vaginal microbiota was analyzed both during menstruation and outside of menstruation. The results showed that the vaginal microbiota composition significantly varied between women as well as over the course of the menstrual cycle, but the composition during menstruation varied even more depending on intensity of pain. In particular, during menstruation, women with more severe dysmenorrhea had a lower abundance of lactobacilli and a higher abundance of potentially pro-inflammatory bacteria.

Hope for women in pain

Although limited in terms of size, age groups studied and ethnic diversity, this pilot study is a first step towards larger studies on associations between the intensity of pain during menstruation and the composition of the vaginal microbiota. The researchers hypothesize that during menstruation endometrial tissue is broken down, releasing compounds (prostaglandins) that may cause uterine muscle contractions and increased sensitivity, thus contributing to menstrual pain. Certain bacteria in the vaginal microbiota may promote the release of these compounds and of pro-inflammatory cytokines that exacerbate the symptoms of dysmenorrhea. If these hypotheses are confirmed, the pilot study would underline the importance of taking into account inter-individual differences and the dynamics of the vaginal microbiota during the menstrual cycle. These findings may contribute to the development of personalized dysmenorrhea treatments and/or biomarkers, ultimately improving women’s quality of life.

Gut dysbiosis and gastrointestinal disorders are frequently observed in children with ASD. There is also growing evidence that the gut microbiota plays a role in modulating brain signaling, an association commonly known as the gut-brain axis. Despite this, research on the relationship between gut microbiome composition and ASD has produced inconsistent results, highlighting the complexity of the disorder and the need for more sophisticated experimental designs. With this goal in mind, a US research team:

• compared the gut microbiota composition of young ASD patients to that of controls in Arizona and Colorado in order to understand whether geographic location can influence the gut microbiome.
• conducted a longitudinal study (sidenote: Subjects in Arizona were not included in the longitudinal study )  to evaluate the relationship between gut microbiota composition, ASD behavioral severity, diet, and gastrointestinal symptoms of the disorder.

Impact of geographical location on the microbiota

The researchers showed that gut microbiota composition differed between the individuals in Arizona and those in Colorado, with the Arizona children showing greater microbial diversity than the Colorado children. This came as a surprise to the researchers, who used the same stool collection and DNA extraction and sequencing methods at both locations. A further cross-analysis of a subset of DNA samples taken in both Colorado and Arizona confirmed that the DNA extraction site had no influence on microbial diversity. The researchers also showed that ASD patients had more gastrointestinal symptoms than controls in Arizona, but not in Colorado. For the researchers, this confirms the impact of the study site on the gut microbiota composition and suggests that these variations in ASD-related gastrointestinal symptoms between sites may contribute to inconsistent results in the literature.

Correlation between deteriorated speech and microbiota diversity

The longitudinal analysis revealed an association between increased severity of ASD behavioral symptoms and changes in the gut microbiota. In particular, a decrease in gut microbial diversity over time was linked to increased severity of ASD behavioral symptoms such as deteriorated speech, lethargy, or social withdrawal. On the other hand, the authors did not find any significant relationships between ASD-associated behavioral disorders and gastrointestinal symptoms or diet. For the authors, additional multicenter and longitudinal studies with more participants are required to characterize the relationship between ASD and the gut microbiota.

The tightly regulated interplay between gut microbiota and host influences many physiological functions including immune homeostasis. A body of preclinical and clinical evidence shows that gut microbiota composition is transiently altered in the context of acute viral respiratory infections. In the case of Covid-19, studying the gut microbiota during infection is particularly important, given that SARS-CoV-2 can bind to ACE2 receptors in the gut, the virus is found in the intestine in up to 25% of patients, and the gut microbiota alterations associated with pulmonary and intestinal complications are likely to influence disease severity. This preclinical study is the first to investigate the role of SARS-CoV-2 infection in dynamic changes in the gut microbiota of monkeys.

The monkey: a good model for SARS-CoV-2 infection

The human data currently available on Covid-19 are abundant but do not allow the disease to be followed throughout its course, from pre-infection to post-resolution. The researchers used two species of monkeys (cynomolgus monkey and rhesus monkey) to fill in certain missing pieces of the infection puzzle. These non-human primates are a suitable model for the study of Covid-19, since SARS-CoV-2 infection led to virus replication in their upper and lower respiratory tracts, resulting in lung pathology and respiratory disease with no overt clinical symptoms. Two monkeys from each species were infected intranasally and intratracheally. Blood (to measure cytokine levels) and stool samples were collected 9 days prior to infection and at 0, 3, 5, 7, 10, 13, 20, and 26 days post-infection (dpi). Two of the monkeys had transient diarrhea at 4 dpi.

Covid-19: persistent dysbiosis even after resolution...

16S rRNA gene sequencing revealed significant changes in the composition of the monkeys’ gut microbiota, with a peak at 10-13 dpi. Some alterations in the microbiota persisted after SARS-CoV-2 was eliminated from the upper respiratory tract (virus undetectable in the nasopharynx and trachea at 20 dpi, but still detectable in the stool of two monkeys) and even at 26 dpi. A significant number of changes in the abundance of bacterial taxa were observed during infection, particularly at 13 dpi. In particular, the relative abundance of Acinetobacter and some genera of the Ruminococcaceae family was positively correlated with the presence of SARS-CoV-2 in the upper respiratory tract.

...and a gut microbiota with altered functional activity

A metabolomic approach was used to evaluate the functional consequences of the changes in the gut microbiota associated with the infection. The aim here was to quantify three of the most important categories of microbiota-derived metabolites: short-chain fatty acids (SCFAs), bile acids, and tryptophan metabolites. SCFA levels changed over the course of the infection, particularly between 2 and 13 dpi. Changes in several bile acids and tryptophan metabolites were also identified in infected animals. The relative abundance of several taxa known to be SCFA producers (mostly from the Ruminococcaceae family) was negatively correlated with certain systemic inflammatory markers, while the genus Streptococcus was strongly and positively correlated with the same markers. This study shows that experimental infection with SARS-CoV-2 in monkeys is associated with a disruption of the gut microbiota’s composition and functional activity. The persistence of dysbiosis after resolution of the infection may play a role in the long Covid-19 symptoms currently being reported in humans.

What do you brush away only for it to return immediately? Why dandruff, of course! Dandruff is a skin condition characterized by excessive flaking of the scalp, with or without itching, and involves a number of factors, including genetic susceptibility, the composition of the sebum and the scalp microbiota. A fungus called Malassezia is known to accelerate the development of dandruff and inflammation. Although effective against Malassezia, antifungals do not prevent the reappearance of dandruff after treatment is stopped. In Asian countries such as India, coconut oil is used to maintain scalp health, moisturize the skin and strengthen the skin’s barrier function. The researchers in this study compared the impact of coconut oil and a neutral shampoo on the scalp bacterial and fungal microbiota of 140 women with and without dandruff.

Dandruff: a specific fungus on the scalp?

The scalps of the women with dandruff had a much higher abundance of uncharacterized Malassezia species. Conversely, the fungus species M. globosa, was found in abundance on the scalps of the women with no dandruff or itching. Treatment with coconut oil brought the ratio of M. globosa to other groups of Malassezia in line with that of healthy scalps.

Coconut oil for the scalp’s engine?

Although no significant differences were observed between the bacterial microbiota of the healthy group and that of the dandruff group, both groups saw an increase in bacteria involved in the metabolism of biotin following coconut oil treatment. Biotin, a B vitamin, is essential for the maintenance of healthy skin and a healthy scalp, and is also known to reduce inflammation. Further studies are required to understand the underlying mechanisms, but for the researchers, the positive effect of coconut oil on the composition and function of the scalp microbiota is the first step towards the longer-term restoration of scalp health.

What is bacterial vaginosis?

Bacterial vaginosis is the most common vaginal infection in women of reproductive age. It results from an imbalance in the vaginal microbiota, a delicate ecosystem normally dominated by protective lactobacilli.

This infographic explains what bacterial vaginosis is, how it differs from vulvovaginal candidiasis, its main risk factors and potential consequences, and how symptoms can be relieved. Understanding the role of the vaginal microbiota is key to better prevention and care.

Women’s microbiota: the missing piece in intimate health

This infographic explores the intimate microbiota — an essential yet often overlooked component of women’s health.
It highlights the distinct microbial ecosystems of the vulva, vagina, bladder, and perianal area, and explains how their balance protects against infections and supports overall well-being.

Discover the main factors that influence this delicate microbiota, common signs of imbalance, and practical tips to help patients maintain intimate health through proper hygiene.

Does gut microbiota influence satiety?

This infographic helps healthcare professionals explain to their patients how the gut microbiota influences satiety.

Discover how a balanced microbiota supports appetite regulation and overall health, and why maintaining its balance is essential for well-being.

From sampling to results: the microbiota analysis journey

Your patients often ask you about the purpose of microbiota analysis?

This infographic can be a first step in answering them. It outlines the key steps of microbiota analysis, from sample collection to final insights. Simplify complex processes and explore how microbiota data can impact health and personalized care.

Is healthy aging connected to the gut microbiota?

This infographic explores the link between gut microbiota and aging, highlighting how diet and lifestyle impact digestive health, immunity, and overall well-being in seniors.

Discover key factors influencing microbiota balance and strategies to promote healthy aging.

Gut-lung axis: how does gut microbiota protect against respiratory infections?

This infographic illustrates the gut-lung axis, detailing how gut microbiota modulates immune responses to safeguard against respiratory infections. It highlights the bidirectional communication between the gut and lungs.

Discover the mechanisms through which gut bacteria influence lung immunity and learn strategies to support this vital connection.

Gut-brain axis: gut microbiota as a mediator of stress response

This infographic explores the connection between gut microbiota and stress, highlighting how the gut-brain axis influences both mental and physical well-being.

It explains how stress impacts gut microbiota, the body's response mechanisms, and strategies to restore balance through lifestyle, diet, and psychobiotics.

Does vaginal microbiota play a role in infertility?

The vaginal microbiota plays a key role in reproductive health, yet its impact on fertility is often overlooked. An imbalance in vaginal flora can reduce pregnancy chances and affect assisted reproduction outcomes.

This infographic highlights the link between microbiota and fertility, emphasizing the importance of maintaining a balanced ecosystem through proper hygiene and patient education.

Gut brain axis: how your microbiota talks to your brain?

Your gut and brain are in constant communication, primarily through the gut microbiota. This connection plays a crucial role not only in digestion but also in various diseases, including neurological, psychiatric, and metabolic disorders.

Understanding this link could pave the way for new approaches to maintain our health.

The importance of the first 1000 days of life

This infographic highlights the critical importance of the first 1,000 days of an infant’s life, from conception to toddlerhood, in the development of gut microbiota and intestinal immunity. It explains how early factors, such as diet and environment, influence long-term health.

Learn how these foundational stages shape immune function and disease risk.

What is the Irritable Bowel Syndrome (IBS)?

This infographic explains Irritable Bowel Syndrome (IBS), a common functional bowel disorder characterized by recurrent abdominal pain and transit issues.

It explores how an imbalanced gut microbiota may contribute to IBS symptoms and highlights the role of diet, lifestyle, and psychological factors in managing the condition.

Discover strategies for improving quality of life and relieving IBS symptoms through microbiota management.

Do you know that an unbalanced microbiota is called a dysbiosis?

This infographic examines dysbiosis and how it disrupts thevarious microbiota of the human body, contributing to conditions like digestive, metabolic, and skin disorders, among others.

It outlines the causes of dysbiosis and offers strategies to restore balance through diet, lifestyle, and medical treatments.

5 things to know about the gut microbiota 

This infographic highlights 5 key facts about the gut microbiota, its essential role in digestion, immunity, and overall health. It explains how a balanced microbiota supports gut function and defends against pathogens, while imbalances can be linked to digestive, metabolic, and even neurodegenerative diseases.

Learn how lifestyle choices can influence microbiota health and reduce the risk of disease.

5 things to know about the vaginal microbiota

This infographic outlines 5 important things to know about the vaginal microbiota, including how it protects against infections and how hormonal changes affect its composition.

It also covers the consequences of dysbiosis and offers tips for maintaining a healthy balance through hygiene and lifestyle choices.

What you should know about antibiotics

This infographic covers key facts about antibiotics, explaining how they help fight infections while also affecting the balance of beneficial bacteria in the microbiota.

Overuse or misuse of antibiotics can lead to complications like antibiotic-associated diarrhea and contribute to the rise of antibiotic resistance.

What you need to know about the 6 microbiota of the human body

This infographic introduces the six microbiota of the human body, highlighting the unique functions and characteristics of each one, from the gut to the skin.

It explores how these microbiota are shaped by factors such as hormones, lifestyle, and delivery method, and how they contribute to overall health by protecting against infections and supporting immune function.

What are probiotics?

This infographic explains what are probiotics and how they help maintain a balanced microbiota, supporting overall health. It explores the types of beneficial microorganisms and the rigorous processes behind their production to ensure their effectiveness in promoting well-being.

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