How do antibiotics unbalance the gut flora?

While antibiotics eradicate the pathogens (sidenote: Pathogen A pathogen is a microorganism that causes, or may cause, disease. Pirofski LA, Casadevall A. Q and A: What is a pathogen? A question that begs the point. BMC Biol. 2012 Jan 31;10:6. ) responsible for infection, they can also destroy some of the beneficial bacteria in your microbiota, systematically causing an imbalance of varying degrees in this ecosystem. This imbalance (known as 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.   ) ) causes AAD, as the gut microbiota is less able to perform its protective functions. AAD can affect up to 35% of patients^1-3 and up to 80% of children receiving antibiotic treatment.¹

Furthermore, while the gut microbiota shows a certain degree of resilience (i.e. it reverts to a composition similar to that existing before the antibiotic-induced imbalance), it does not always fully recover.^4,5 Recent research has shown that antibiotics can alter the diversity and abundance of bacteria, and that this imbalance can be prolonged (usually 8-12 weeks after the end of treatment).^1,6

In most cases, diarrhea without further symptoms 

The main short-term consequence of antibiotic treatment is the altered bowel movements experienced by some patients, most often resulting in diarrhea. AAD is defined as three or more very loose or liquid stools within 24 hours of the beginning of antibiotic treatment or up to 2 months after its cessation.^7-9 Its incidence depends on several factors, including age, context and the type of antibiotic. The diarrhea is usually mild to moderate in intensity and in the vast majority of cases is functional, i.e. associated with a gut microbiota imbalance.¹ Antibiotics with the broadest spectrum of antimicrobial activity (i.e. that act on a very wide range of bacteria) are associated with higher rates of diarrhea.³

However, in 10%-20% of cases the diarrhea results from an infection by Clostridioides difficile (C. difficile), a bacterium that can become pathogenic due to certain factors, such as antibiotic use, being older than 65 or being affected by certain associated conditions.³ The colonization of the gut microbiota by this bacterium triggers an inflammatory reaction, with clinical consequences ranging from moderate diarrhea to much more serious symptoms, including death.³

Is ending antibiotic use the most effective treatment?

The management of AAD depends on the symptoms and the pathogen (e.g. C. difficile).¹⁰ For mild to moderate diarrhea, treatment involves ending antibiotic use (or replacing the antibiotic with one less likely to cause diarrhea) to allow the microbiota to recover and the patient to rehydrate.¹⁰

Numerous studies have shown that probiotics may help reconstitute the gut microbiota, while some probiotics have proven effective in preventing and treating AAD.^6,11,12 When taken during antibiotic treatment, other probiotics have been shown to reduce the risk of primary and secondary infection with C. difficile.^13-15 Lastly, fecal microbiota transplantation (naturally transferring a healthy microbiota into a sick individual in order to restore his or her microbial ecosystem) is currently only used for the most serious infections, i.e. relapses of infections with C. difficile.^16,17

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What is infantile colic?

Infantile colic is characterized by excessive crying for unknown reasons in otherwise healthy infants. Gastrointestinal disorders (e.g. immaturity of the gastrointestinal tract, an allergy or intolerance to cow’s milk, stomach reflux)² are mainly to blame,³ but other causes unrelated to the gastrointestinal system,³ such as parental stress,⁴ or maternal smoking, have also been studied.²

Colic is common in babies, but its symptoms, such as persistent crying, can cause distress in parents.

What are the symptoms of infantile colic?

The baby cries a lot, is inconsolable, grimaces and may have a red face. It keeps its fists clenched and may have gas.⁵ Pediatricians have long used the “rule of three” to diagnose infantile colic.⁶ Introduced in 1954, these criteria have since been adapted by an international organization to give a new definition with the following criteria: recurrent and prolonged periods of restlessness, crying or irritability without obvious cause such as stunted growth, fever or ill health, and which cannot be prevented or resolved by the caregivers.⁷

What is the gut microbiota’s role?

A link between infantile colic and the gut microbiota – also known as the gut flora – has recently been established.⁸ Studies have shown that the gut microbiota of infants affected by colic differs from that of other babies:⁹

• Their microbiota is less rich in beneficial bacteria, particularly bifidobacteria (sidenote: Bifidobacterium A genus of Y-shaped bacteria, most species of which are beneficial to humans. They are found in the gut of humans, and in some yogurts.
  
  They:
  - Protect the gut barrier 
  - Participate in the development of the immune system and help fight inflammation 
  - Promote digestion and improve symptoms of gastrointestinal disorders Sung V, D'Amico F, Cabana MD, et al. Lactobacillus reuteri to Treat Infant Colic: A Meta-analysis. Pediatrics. 2018 Jan;141(1):e20171811.  O'Callaghan A, van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Front Microbiol. 2016 Jun 15;7:925. Ruiz L, Delgado S, Ruas-Madiedo P, et al. Bifidobacteria and Their Molecular Communication with the Immune System. Front Microbiol. 2017 Dec 4;8:2345. ) and lactobacilli (sidenote: Lactobacilli Rod-shaped bacteria whose main characteristic is the production of lactic acid, from where they get the name “lactic acid bacteria”.  Lactobacilli are present in the oral, vaginal and gut microbiota of humans, but also in plants and animals. They are found in fermented foods, such as dairy products (e.g. certain cheeses and yoghurts), pickles, sauerkraut, etc. Lactobacilli are also found in probiotics, with certain species recognized for their beneficial properties.   W. H. Holzapfel et B. J. Wood, The Genera of Lactic Acid Bacteria, 2, Springer-Verlag, 1st ed. 1995 (2012), 411 p. « The genus Lactobacillus par W. P. Hammes, R. F. Vogel Tannock GW. A special fondness for lactobacilli. Appl Environ Microbiol. 2004 Jun;70(6):3189-94. Smith TJ, Rigassio-Radler D, Denmark R, et al. Effect of Lactobacillus rhamnosus LGG® and Bifidobacterium animalis ssp. lactis BB-12® on health-related quality of life in college students affected by upper respiratory infections. Br J Nutr. 2013 Jun;109(11):1999-2007. ) ,⁸ which can modulate immune responses to protect against colic.⁵
• Instead, their microbiota appears to be colonized by Escherichia coli,⁵ Klebsiella or other potentially pathogenic species.⁵

This gut microbiota imbalance, known as a “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.   ) ”, appears to be strongly linked to colic: according to one hypothesis, an altered gut microbiota composition modifies intestinal motility (the way in which food moves through the digestive system), resulting in excessive production of gas.⁵

How to help babies... and parents?

The family doctor is still the first port of call to diagnose infant colic and reassure parents. There is no cure¹⁰ for colic, but a few simple daily practices can help relieve the symptoms. These include breastfeeding, carrying your baby and balancing your child’s gut microbiota, particularly using probiotics.⁵ Probiotics appear to be a promising avenue, since the intake of “good” bacteria for a few months may reduce gut inflammation⁶ and help shorten the daily duration of crying.¹¹ Since they help maintain a good intestinal balance, probiotics can also be used as a preventative measure.⁵

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What is a vaginal yeast infection?

A vaginal yeast infection is an infection of the vulva and the vagina caused by a yeast-like fungus, in most cases Candida albicans³. After bacterial vaginosis, it is the second most common infectious vaginal disease.¹ It is important to consult a doctor to confirm diagnosis, since its symptoms are not very specific. The most common clinical symptoms are abnormal vaginal discharge (leukorrhea), genital itching, and a burning sensation accompanied by vaginal pain or irritation that can lead to dyspareunia (sidenote: Dyspareunia Recurrent or persistent genital pain during sexual intercourse. ) or dysuria (sidenote: Dysuria Painful urination, often described by the patient as a burning, tingling or itching sensation. ) .¹

Is the vaginal microbiota involved?

Every woman’s vaginal microbiota is unique and, unlike other microbiota, the vaginal microbiota is well-balanced when its diversity is low⁴ Species of the genus Lactobacillus (sidenote: Lactobacilli Rod-shaped bacteria whose main characteristic is the production of lactic acid, from where they get the name “lactic acid bacteria”.  Lactobacilli are present in the oral, vaginal and gut microbiota of humans, but also in plants and animals. They are found in fermented foods, such as dairy products (e.g. certain cheeses and yoghurts), pickles, sauerkraut, etc. Lactobacilli are also found in probiotics, with certain species recognized for their beneficial properties.   W. H. Holzapfel et B. J. Wood, The Genera of Lactic Acid Bacteria, 2, Springer-Verlag, 1st ed. 1995 (2012), 411 p. « The genus Lactobacillus par W. P. Hammes, R. F. Vogel Tannock GW. A special fondness for lactobacilli. Appl Environ Microbiol. 2004 Jun;70(6):3189-94. Smith TJ, Rigassio-Radler D, Denmark R, et al. Effect of Lactobacillus rhamnosus LGG® and Bifidobacterium animalis ssp. lactis BB-12® on health-related quality of life in college students affected by upper respiratory infections. Br J Nutr. 2013 Jun;109(11):1999-2007. ) dominate the vaginal microbiota,⁴ but yeasts such as Candida albicans are also found in smaller quantities.⁵

The vaginal ecosystem evolves over the course of a woman’s life.⁶ This change is normal and is influenced by the menstrual cycle, puberty and the menopause, sexual activity, contraception, intimate hygiene, and pregnancy.^7,8,9

A 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.   ) is when the vaginal ecosystem is unbalanced (due to antibiotic treatment, douching, stress, smoking, etc.)^2,6: species of Lactobacillus no longer predominate and instead certain opportunistic (sidenote: Opportunistic infection An infection caused by a microorganism that is normally non-pathogenic, but which becomes so when the host microbiota loses its balance (through factors such as a weakened immune system, disease, age, certain medication, etc.). ) species may proliferate. This is what happens with vaginal candidiasis: Candida – yeasts normally present in the vagina and the gut⁵ – proliferate abnormally and become pathogenic under specific conditions. It is estimated that 10%-30% of women contract yeast infections following antibiotic treatment.¹⁰

Other factors that can increase the risk of infection¹ include corticosteroid use, pregnancy, immunosuppressive diseases, poorly controlled diabetes, oral contraception, and IUD. Many factors have been identified but the mechanisms are not yet fully understood.¹¹

Antifungals and probiotics

The classic treatment for vaginal yeast infections is antifungal medication administered orally or topically.¹¹ However, relapses can occur and new therapeutic approaches are currently being evaluated.¹¹ Recent work suggests that oral or topical probiotics (capsules or vaginal suppositories) may rebalance the vaginal microbiota and reduce the frequency of relapse.^12,13

To reduce the risk of infection, certain intimate hygiene practices are recommended¹⁴ – daily habits to help care for your vaginal microbiota.  

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What is bacterial vaginosis?

Bacterial vaginosis is a harmful and hard to detect disorder. 50% of women are asymptomatic, while others suffer from local irritation or foul-smelling discharge.³

In practice, doctors use the Amsel score⁴ to diagnose bacterial vaginosis. Diagnosis is based on the presence of at least three of the following criteria:

• Thin, homogeneous vaginal discharge 
• A vaginal pH above 4.5 
• An amine smell (similar to a fishy smell) after a specific test is performed on a vaginal smear
• Presence of vaginal tissue cells coated with bacteria when discharge is examined microscopically

Many risk factors are associated with the disease, including age, menstrual cycle, pregnancy, and sexual history, but also vaginal douching and smoking.³ A vaginal dysbiosis induced by antibiotic treatment may also participate in the development of bacterial vaginosis, creating a vicious circle, since antibiotics can be used to treat the infection.³

Lastly, women with bacterial vaginosis are more likely to contract sexually transmitted infections (STIs), including herpes, HPV, AIDS and bacterial infections.^5,6

Is there a link with the vaginal microbiota?

Bacterial vaginosis is associated with an imbalance (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 vaginal microbiota.² The vaginal microbiota is dominated by different species of the bacterial genus Lactobacillus (sidenote: Lactobacilli Rod-shaped bacteria whose main characteristic is the production of lactic acid, from where they get the name “lactic acid bacteria”.  Lactobacilli are present in the oral, vaginal and gut microbiota of humans, but also in plants and animals. They are found in fermented foods, such as dairy products (e.g. certain cheeses and yoghurts), pickles, sauerkraut, etc. Lactobacilli are also found in probiotics, with certain species recognized for their beneficial properties.   W. H. Holzapfel et B. J. Wood, The Genera of Lactic Acid Bacteria, 2, Springer-Verlag, 1st ed. 1995 (2012), 411 p. « The genus Lactobacillus par W. P. Hammes, R. F. Vogel Tannock GW. A special fondness for lactobacilli. Appl Environ Microbiol. 2004 Jun;70(6):3189-94. Smith TJ, Rigassio-Radler D, Denmark R, et al. Effect of Lactobacillus rhamnosus LGG® and Bifidobacterium animalis ssp. lactis BB-12® on health-related quality of life in college students affected by upper respiratory infections. Br J Nutr. 2013 Jun;109(11):1999-2007. ) . These bacteria help maintain an acidic pH in the vagina and thus prevent the proliferation of pathogenic bacteria.⁷ The vaginal microbiota also contains yeasts such as Candida albicans in smaller quantities.⁸

With bacterial vaginosis, this normal microbial flora is replaced by a polymicrobial flora comprising numerous bacteria (Gardnerella, Atopobium, Prevotella, Mobiluncus, etc.).² This leads to an increase in the pH of the vagina (which is normally very acidic), mainly attributed to the decrease in the predominance of Lactobacillus species.⁹ However, the mere presence of species from this polymicrobial flora does not in itself seem to cause infection, i.e. a woman whose vagina contains Atopobium or Prevotella species will not necessarily report symptoms. In fact, Gardnerella vaginalis is present in 90% of symptomatic subjects and 45% of healthy subjects.⁴ For a long time, this bacterium was considered the main pathogen behind bacterial vaginosis, but new research has shown that Gardnerella vaginalis can colonize the vagina without triggering infection.¹⁰ The causes of the infection are yet to be determined and research in the area continues.³

How to avoid bacterial vaginosis

Treatment is only recommended for women who are symptomatic. Recommended treatment currently involves the prescription of oral or vaginal antibiotics.² While antibiotics may help alleviate symptoms, relapse is unfortunately very common.¹¹

However, there are a number of ways to reduce your chances of getting bacterial vaginosis. Firstly, avoid certain risk factors, such as vaginal douching or smoking.³ Vaginal or oral probiotics,^12,13 that restore the balance of the vaginal microbiota can be used to treat or prevent relapses.

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What is travelers’ diarrhea?

Contrary to popular belief, travelers’ diarrhea is not caused by exotic foods poorly digested by unaccustomed stomachs. It is a real infection most frequently caused by bacteria  (Escherichia coli, Salmonella, Shigella, Campylobacter).² It may also be caused by a parasite (Giardia, Cryptosporidium, etc.)² or a virus (norovirus, rotavirus).² The pathogen responsible for the diarrhea is identified in only 40%-60% of symptomatic travelers.⁴ The main source of the microorganisms involved are contaminated food (especially raw vegetables, undercooked meat or fish, unpeeled fruit, etc.) and contaminated water.⁵ It can also be transmitted through contact with other people when hygiene rules are not respected.⁵

What is the microbiota’s role? 

One of the gut microbiota’s roles is to prevent or limit the invasion of the intestine by pathogens (sidenote: Pathogens A pathogen is a microorganism that causes, or may cause, disease. Pirofski LA, Casadevall A. Q and A: What is a pathogen? A question that begs the point. BMC Biol. 2012 Jan 31;10:6. ) .⁶ Although common, the “tourista” is not without consequences. Regardless of the pathogen, diarrhea disrupts the balance of the gut microbiota at least temporarily, leading to 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.   ) .¹ This imbalance may have long-term consequences, including an increased risk of developing post-infectious⁷ irritable bowel syndrome, which occurs in 3%-17% of patients.² A research team recently showed that gut microbiota diversity was significantly lower in Swedish travelers who contracted a Campylobacter infection than in travelers who remained uninfected.⁸ Another research team found that diarrhea during travel was associated with a higher relative abundance in the gut of a specific bacteria (Prevotella copri) before departure and after return.⁹ Could travelers’ gut microbiota composition be used to predict the risk of developing diarrhea during the trip? Since there are still very few studies in this area, it remains to be confirmed.

What are the symptoms of traveler’s diarrhea?

The symptoms and duration vary depending on the cause⁴ (bacterial, parasitic or viral), but on average symptoms last 4-5 days without treatment.² In addition to frequent loose or watery stools (at least 3 per day),⁵ at least one of the following symptoms must be present: fever, nausea, vomiting, abdominal cramps or an urgent need to go to the bathroom.² The major risk is dehydration resulting from the loss of fluids through watery diarrhea. At-risk individuals (children, the elderly, or those with chronic conditions that weaken the immune system²) are more likely to be hospitalized.

Definition of travelers' diarrhea:

How to prevent and treat travelers’ diarrhea

The prevention of travelers’ diarrhea mainly involves hygiene measures such as frequent hand washing and food precautions.⁵ Ask your doctor or pharmacist for advice before traveling. Rehydration is key to treating travelers’ diarrhea:⁵ clean water (bottled water, etc.) or herbal teas drunk often and in small quantities. Any lightly sweetened and/or salted food is recommended (solid foods are not contraindicated).⁴ Antidiarrheal drugs help reduce the risk of dehydration and may be recommended in some cases.¹⁰ Antibiotics may also be necessary. However, antibiotics can lead to a reduction in the diversity of the gut microbiota, which thus loses its ability to act as a barrier against pathogens (sidenote: Pathogen A pathogen is a microorganism that causes, or may cause, disease. Pirofski LA, Casadevall A. Q and A: What is a pathogen? A question that begs the point. BMC Biol. 2012 Jan 31;10:6. ) . Moreover, antibiotic use can lead to the selection of antibiotic-resistant bacteria.¹¹ For this reason, they are only recommended for severe diarrhea, and in some cases for moderate diarrhea,¹⁰ under the supervision of a doctor. Probiotics may be useful as a preventive measure¹², and to limit the intensity and duration of symptoms.^13,14

BMI 21.20

What exactly is the skin microbiota?

Let’s start by focusing on the skin, the largest organ in the human body and its first line of defense. The skin acts as a triple protective barrier:^1,2

• a physical barrier that protects the internal organs from the external environment³
• a chemical barrier: dry and rich in salt and acidic compounds, the skin is a hostile environment for many microorganisms⁴
• an immune barrier, thanks to defense cells in the skin that prevent colonization and infection by pathogenic microbes²

Despite this, the skin is home to its own distinctive microbiota which includes bacteria (Cutibacterium acnes, Staphylococcus epidermidis, etc.), fungi (e.g. Malassezia), viruses (e.g. papillomavirus) and parasites (including mites such as Demodex). These microorganisms live in perfect harmony and together form the skin microbiota.^1,5

As you may have noticed, your skin changes from one part of the body to another: 

• drier on the forearm and the palms of the hand.^1,5
• oilier on the face, chest and back.^1,5
• and more humid in the armpits, the elbow fold, the nostrils, on the back of the knee and on the groin.^1,5

Each of these skin sites is home to a distinct microbiota adapted to its specific environment¹. Some researchers also distinguish a fourth site in the foot (nails, heel and space between toes).¹
In addition to these variations across the skin’s surface, there are also variations according to depth or skin layer: the deeper you go into the dermis, the fewer the microorganisms (sidenote: Microorganisms Living organisms too small to see with the naked eye. This includes bacteria, viruses, fungi, archaea, protozoa, etc., collectively known as ’microbes’. Source: What is microbiology? Microbiology Society. ) and the more similar these microorganisms are from one person to next.⁶

How does the skin microbiota change throughout life?

The skin microbiota is relatively stable over time^1,5 and only changes at the major stages of life. 

At birth, children born vaginally are passed on vaginal bacteria (Lactobacillus, C. albicans), while those born by caesarean section receive skin microbes (Staphylococcus, Streptococcus). At puberty, the rate of secretion of growth hormones explodes. The skin becomes oilier and selects more well-adapted microorganisms that live on through adulthood. The skin gradually changes as it ages, with a weakened immune system, reduced cell renewal, less sweat, and altered sebum production.^7,8

These physiological changes modify the skin environment and alter the microbial balance⁷, which becomes more diverse and sees a change in dominance in bacterial groups.⁸

Why is the skin microbiota a key factor in skin health?

The skin microbiota knows how to thank its host for giving it food and shelter. It protects the host from pathogens (sidenote: Pathogens A pathogen is a microorganism that causes, or may cause, disease. Pirofski LA, Casadevall A. Q and A: What is a pathogen? A question that begs the point. BMC Biol. 2012 Jan 31;10:6. ) through its physical presence on the skin and by secreting antibacterial molecules and acids.² But that’s not all. The skin microbiota also plays a key role in immunity: it stimulates the immune defense mechanisms of the epidermis and the body as a whole and calms inflammation where necessary.⁴

What diseases are associated with an unbalanced skin microbiota?

The composition of the skin microbiota is mostly influenced by host characteristics (age, sex, genes, immune status, diet, stress levels) and the environment (lifestyle, domestic and personal hygiene, living arrangements, geographical location, sun exposure, etc.).² At times, factors such as stress, a lifestyle change or the use of medication (e.g. antibiotics) or personal hygiene products disrupt the balance of the microbiota: bacteria previously beneficial to the host take the upper hand and become pathogenic.¹ Many common skin diseases are associated with changes in the microbiota. This situation is known as a 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.   ) .¹

Dysbiosis is often associated with pathological skin conditions such as acne,⁹ atopic dermatitis,¹⁰ psoriasis,¹¹ seborrheic dermatitis,¹² rosacea¹³ or skin cancer.¹⁴ Changes in the skin microbiota can also be observed in non-pathological skin conditions such as sensitive skin, sensations of discomfort or irritation, or diaper rash. The skin is constantly exposed to various external factors linked to lifestyle (cold, heat, sun, UV, hygiene products, etc.) or the individual (genes, sensitivity, allergies, etc.) that can affect the physical, mechanical or microbial properties of the skin barrier.¹⁵ The microbiota is also involved in wound healing¹⁶ and body odor.¹⁷

How can you take care of your skin microbiota? 

You now know the importance of the skin microbiota for the health of your skin, and that the gut microbiota also plays a role in skin health. So how can you take care of the various microbiota so that your skin stays healthy? Many researchers have looked into this question. Unfortunately, the answer isn’t as straightforward as using beneficial bacteria or yeast to replenish or enrich the existing microbiota or replace a microbiota that’s not up to the job. Instead, the idea is to modify the microbiota so that it functions correctly, thus improving host health. How? There are several ways to improve the balance and diversity of the gut microbiota, each with its own characteristics:

Oral preparation: 

The existence of a gut-skin axis raises hope that we may be able improve the health of the skin by modulating the gut microbiota by taking probiotic, prebiotic and symbiotic supplement or through a better diet:

• Probiotics are living microorganisms that confer a health benefit on the host when applied in appropriate quantities^19,20. For certain inflammatory skin diseases, the use of specific probiotics appears to be effective.¹⁴
• Prebiotics are specific non-digestible dietary fibers that confer a health benefit. They are selectively used by beneficial microorganisms in the host microbiota.^21,22 Symbiotics²³ mixture containing both prebiotic and probiotic have shown promising results in atopic dermatitis.²⁴
• Diet, the diversity and quality of what we eat contributes to the balance of our gut microbiota.^25,26 A poorly balanced diet can affect the composition of the gut and give rise to certain conditions.²⁷ To keep our gut in shape we should know what foods have a beneficial or adverse effect on it.²⁸

Topical preparations

While few studies existed, products applied to the skin that contain certain probiotics, prebiotics or both, have shown positive resulted in improving the skin's health of patient with skin condition.^14,24

However, clinical trials are still required to optimize their formulation. Hence the importance of following our latest news on the skin microbiota.

BMI-21.13

The term ENT includes three parts of the body: Ears, Nose, and Throat (which also includes the mouth).

• The oral microbiota brings together more than 700 bacterial species, which contribute to oral health (teeth, gums, tongue, etc.) and, more generally, to overall health. A disruption in this equilibrium (dysbiosis), resulting from poor oral hygiene, a drop in immunity, or a genetic origin may lead to local infections (cavities, periodontitis, etc.) that are likely to migrate or cause more serious diseases, such as cardiovascular diseases. Hygiene and dental care remain the most effective method of prevention.
• In the ear canal, the composition of the auricular microbiota is closely related to that of the skin. Recent work has shown the harmless presence of Alloiococcus otitis and Corynebacterium otitidis, two bacterial species that until now have only been associated with middle ear infections. This discovery suggests that the ear canal serves as an infectious reservoir for the middle ear.
• Although close to the oral microbiota, the nasopharyngeal microbiota, which covers the nasal airways and the pharynx, is composed of very different germs.

Analyzing the realm of ENT and its microbiota may enable early diagnosis for various diseases that appear because of dysbiosis (sidenote: Dysbiosis Generally defined as an alteration in the composition and function of the microbiota caused by a combination of environmental and individual-specific factors. Levy M, Kolodziejczyk AA, Thaiss CA, et al. Dysbiosis and the immune system. Nat Rev Immunol. 2017;17(4):219-232.   ) and may also contribute to the development of personalized medicine based on probiotics.

The Biocodex Microbiota Institute is dedicated to education about human Microbiota for General Public and Healthcare Professionals, it doesn't give any medical advice.
We recommend you to consult a healthcare professional to answer your questions and demands.

What is the lung microbiota?

In contrast to its big brother, gut microbiota, it is only very recently that lung microbiota has been investigated. This delay can be partly explained by the difficulty of collecting samples and accessing the lungs themselves, both of which often require the use of an invasive method.³ In addition, the risk of bacterial infection of the upper airways is a real issue.⁴ Lung flora was first identified in 2010;⁵ there have since been very few studies devoted to elucidating the role of the communities of micro-organisms that live there.³  

Nonetheless, our understanding of the composition of the lung microbiota can be summed up in three points:

• Low density of bacteria⁵
• High level of biodiversity. In healthy individuals, bacteria from the Prevotella, Veillonella, Streptococcus, Neisseria, Fusobacterium and Haemophilus⁵ genera are predominant in the lungs. Maintaining the balance of this bacteria relies on the rhythm of inhalation and exhalation⁶
• A tremendous abundance of “anaerobic” bacteria, which develop in the absence of oxygen. These are species of bacteria belonging to the Fusobacterium, Porphyromonas, Prevotella and Veillonella⁷ genera

Nor are bacteria the only micro-organisms (sidenote: Microorganisms Living organisms that are too small to be seen with the naked eye. They include bacteria, viruses, fungi, archaea and protozoa, and are commonly referred to as “microbes”. What is microbiology? Microbiology Society. ) that develop in the lung microbiota of healthy individuals! Fungi (species belonging to the Eremothecium, Systenostrema and Malassezia genera and to the Davidiellaceae family) and viruses (member species of the Anelloviridae family, along with a large number of bacteriophages (sidenote: Bacteriophage Virus that specifically targets and infects bacteria Scitable by Nature education_2014. Bacteriophage definition ) ) are also found to live there.² Recent discoveries have also identified the presence of archaea (sidenote: Archaea Type of micro-organism (different from bacteria) found in all environments, including extreme environments Archaea. Microbiology Society )  in the lungs.⁸ Lastly, while these micro-organisms form an integral part of the lung microbiota, the data currently available are limited. 

Why does the lung microbiota play a major role in our health?

The lung microbiota plays a key role in maintaining the balance of lung function. It acts in four major ways:

• As a barrier to pathogens and an aid to resistance against respiratory infections,⁹ in exactly the same way as the gut microbiota
• It plays a defensive role by actively helping to stimulate innate and adaptive immunity (sidenote: Innate and adaptive immunity  The human body protects itself using two kinds of defense mechanisms: innate immunity and adaptive immunity. Innate immunity is the first line of defense against disease agents and is an immediate response, while adaptive immunity is delayed but provides lasting protection Janeway CA Jr, Travers P, Walport M, et al. Immunobiology: The Immune System in Health and Disease. 5th edition. New York: Garland Science; 2001. Principles of innate and adaptive immunity. ) in case of infections^10,11
• It is involved in the maturation of the pulmonary immune system, enabling, inter alia, tolerance to allergens¹²
• It affects the morphology of the lungs and more specifically, the number of pulmonary alveoli, according to studies in mice¹³

Diseases linked to an imbalance in lung microbiota

When there is an imbalance in the composition of the lung microbiota, a 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.   ) ¹⁴ emerges, which may be linked to various diseases. Scientific studies to date have not always been able to determine whether the dysbiosis causes or results from such diseases, though.

Let’s take a closer look at the disorders linked to pulmonary dysbiosis:

• winter respiratory infections such as colds and flu (most often viral), where there is an imbalance in lung immunity, along with dysbiosis¹⁵ in the lungs and gut
• asthma:¹⁶ a chronic disease of the respiratory system affecting more than 260 million people worldwide.¹⁷ This condition is associated with an imbalance in the lung microbiota,¹⁶ as well as in gut¹⁸ and nasal¹⁹ microbiota
• cystic fibrosis, a rare genetic disease that mainly affects the airways and the digestive system²⁰
• chronic obstructive pulmonary disease (COPD), which is characterised by progressive narrowing and permanent obstruction of the airways and lungs, causing difficulty breathing¹⁶

Looking after your lung microbiota

You now know about the important role played by the lung microbiota and the gut-lung axis in your health. Researchers have grasped this fully and are currently investigating strategies to prevent or cure lung infections.^23,24

When it comes to preventing winter respiratory infections, there have been some encouraging results when combining probiotics with prebiotics.²⁵ In infants, certain probiotics may well prevent winter infections as early as the first few months of life.²⁶ Lastly, some studies in students have demonstrated the value of using probiotic treatment to achieve a significant reduction in symptom duration.^27,28
 

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What is exactly the human urinary microbiota?

You have probably heard less about the urinary microbiota than its more well-known neighbors, the gut microbiota and the vaginal microbiota. This is no surprise, since it is a less rich and diverse environment³ whose role requires further research.¹

However, recent studies have shown that the urinary tract is home to a unique urinary microbiota.^4,5 Urine analyses based on culture-dependent methods have traditionally identified pathogens (sidenote: Pathogens A pathogen is a microorganism that causes, or may cause, disease. Pirofski LA, Casadevall A. Q and A: What is a pathogen? A question that begs the point. BMC Biol. 2012 Jan 31;10:6. ) responsible for urinary tract infections (UTIs), such as Escherichia coli.

Advances in detection technologies have led to the discovery of additional bacteria in the urinary microbiota. The genus Lactobacillus is frequently identified, while Gardnerella, Streptococcus, and Corynebacterium also tend to be present, although to a lesser degree.³ In addition, communities of fungi have also been observed.⁶ 

Why is the urinary microbiota a key player in our health?

Microorganisms (sidenote: Microorganisms Living organisms that are too small to be seen with the naked eye. They include bacteria, viruses, fungi, archaea and protozoa, and are commonly referred to as “microbes”. What is microbiology? Microbiology Society. ) inhabiting the urinary microbiota can play a protective role in our health.¹ However, under certain conditions, they can also influence urinary tract infections.²

Several mechanisms have been described: for example, the bacterial genera Lactobacillus and Streptococcus secrete lactic acid, which is believed to play a protective role against pathogens.⁸ Lactic acid lowers the pH of urine (≈ 4.5), creating a microenvironment that is hostile to most pathogenic bacteria.

Furthermore, Lactobacillus (sidenote: Lactobacilli Rod-shaped bacteria whose main characteristic is the production of lactic acid, from where they get the name “lactic acid bacteria”.  Lactobacilli are present in the oral, vaginal and gut microbiota of humans, but also in plants and animals. They are found in fermented foods, such as dairy products (e.g. certain cheeses and yoghurts), pickles, sauerkraut, etc. Lactobacilli are also found in probiotics, with certain species recognized for their beneficial properties.   W. H. Holzapfel et B. J. Wood, The Genera of Lactic Acid Bacteria, 2, Springer-Verlag, 1st ed. 1995 (2012), 411 p. « The genus Lactobacillus par W. P. Hammes, R. F. Vogel Tannock GW. A special fondness for lactobacilli. Appl Environ Microbiol. 2004 Jun;70(6):3189-94. Smith TJ, Rigassio-Radler D, Denmark R, et al. Effect of Lactobacillus rhamnosus LGG® and Bifidobacterium animalis ssp. lactis BB-12® on health-related quality of life in college students affected by upper respiratory infections. Br J Nutr. 2013 Jun;109(11):1999-2007. ) produces additional substances, antibacterial metabolites such as hydrogen peroxide, which also protect against pathogens.⁹ As with the gut microbiota, the urinary microbiota acts as a barrier against pathogens.¹

What diseases are associated with an unbalanced urinary microbiota?

As with all microbiota (gut microbiota, lung microbiota, etc.), when the composition of the urinary microbiota is disrupted, an imbalance, or “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.   ) ”,⁹ results. Studies comparing the urinary microbiota of healthy subjects to that of patients suffering from various urinary diseases have identified a link between these diseases and the composition of the urinary microbiota.

In fact, studies published to date have demonstrated a clear role for the urinary microbiota in urinary tract infections (UTIs).^8,10 For example, decreased diversity in the urinary microbiota may be a risk factor for urinary tract infections.¹¹

Furthermore, disorders such as urgency urinary incontinence,¹² interstitial cystitis,¹³ and sexually transmitted infections¹⁴ have also been associated with an altered urinary microbiota.

How can we take care of our microbiota? We can have a direct influence on it.

• Diet: it is common knowledge that dietary factors can influence the risk of urinary tract infections. Certain food and dietary products (such as cranberry juice or fermented dairy products containing probiotics) may help reduce the risk of recurrent infection by regulating the microbiota.⁸

• Probiotics: oral and vaginal probiotic have been successful in decreasing recurrence rates for UTIs.¹⁵

• Water: drinking plenty of water is important, but researchers have not yet confirmed that it can cure UTIs.¹

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What is exactly the human gut microbiota?

You probably have already heard about the “gut flora”, well, scientifically, it is called “the intestinal microbiota” or to put it more simply “the gut microbiota”. What is the definition of gut microbiota ? It consists of trillions¹ of microorganisms (sidenote: Microorganisms Living organisms that are too small to be seen with the naked eye. They include bacteria, viruses, fungi, archaea and protozoa, and are commonly referred to as “microbes”. What is microbiology? Microbiology Society. ) that populate your intestines like bacteria, viruses, fungi (including yeasts), and even parasites.

By the way, microbiota and microbiome are two words often used as one to the other but they have two different meanings while microbiota is used to talk about the microorganism and answer the question “who is there?” basically the “individuals”, the microbiome talks about their genome “what is inside of them”² to answer the question “what are they doing” meaning their function.

Each one of us has a unique microbiota, like a fingerprint.¹ When you’re born, fecal and vaginal microorganisms transmitted by your mother during vaginal delivery, or environmental microorganisms for cesarean delivery,³ induce the start of your gut microbiota colonization⁴. It takes around three years for the gut microbiota to build up, diversify and stabilize.⁵ During adulthood,⁶ the composition is relatively stable until old age when it undergoes profound changes again to become slightly impoverished.⁷

Why is gut microbiota important for your health?

The gut microbiota can be considered a functional organ of the human body. Why should we take care of our microbiota ? It works closely with your intestines and have 4 important roles:

What affects your gut microbiota ?

The composition of the gut microbiota is characterized by its high diversity (number of different species present in an individual) and its abundance (total number of microorganisms present). When the composition is disrupted, the balance is broken, and a 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.   ) emerges,¹³ which can be associated with several diseases. 

Numerous factors can have an impact on the diversity and composition of the gut microbiota. Among these factors, these are the following:

Factors linked to the individual themselves, such as:

• The age⁶
• Genetics¹³ 
• Certain illnesses and injuries¹³ 

Others factors are linked to the individual's environment:

• Medication use: antibiotics, anti-inflammatories, etc.⁸ 
• Infections (viral gastroenteritis…)¹³
• Lifestyle: unbalanced diet (high-fat diet for example), or changes in diet, stress, smoking, alcoohol excess, etc. ¹³

What are the diseases that could be linked to gut microbiota ?

Dysbiosis, cause or consequence of these diseases? The question has not yet been answered with certainty by scientific studies.

But the role of the human gut microbiota doesn’t stop at the gut: recent studies have identified that the gut microbiota may play a role beyond the gastrointestinal tract. In fact, gut microbiota has been associated with several extra-intestinal diseases: for example, acne²³ , allergies²⁴ , obesity,²⁵ anxiety disorders,²⁶ autism-spectrum disorders²⁶…And that’s not all of it. It seems that gut microbiota can also be associated with neurodegenerative diseases like Alzheimer’s,²⁷ Parkinson’s.²⁸ In fact, there is bidirectional communication between the gut and the brain, named “gut- brain- axis”, and gut microbiota could influence these interactions. That is why your gut is sometimes called your second brain.

How to take care of your microbiota?

You know by now the central role of the gut microbiota in human health. So how should you take care of your own microbiota? How to improve your gut microbiota ? Many scientific studies raised the question of how to avoid any disruption in its composition and keep it as balanced as possible.²⁹ The answer is not as simple as bring in good bacteria or yeast to fill or enrich the existing microbiota or replace the bad ones. In fact, the idea is to influence the microbiota to help it to function smoothly thereby improving host health.³⁰

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