Popular with patients, alternative treatments to antibiotics aim to prevent recurrence and antibiotic resistance. They are in line with the recommendations of health authorities, including the Haute Autorité de Santé (HAS) in France, which works to “encourage the appropriate use of antibiotics in order to reduce bacterial resistance that can lead to therapeutic deadlock”.¹⁵ Cranberries, in the form of a 36 mg/day dose of proanthocyanidin, can be used to prevent the recurrence of UTIs linked to E. coli.¹⁶

The depletion of the urinary microbiota in women susceptible to UTIs has raised the question of whether an intake of microorganisms via probiotics can reduce UTI rates. An ideal probiotic should have the ability to adhere to cells, prevent and reduce the adhesion of pathogens, secrete acids (e.g. lactic acid), hydrogen peroxide and bactericides capable of reducing the growth of pathogens, be free of adverse side-effects (they should not be invasive, carcinogenic or pathogenic) and be capable of forming clumps to produce normal, balanced flora.¹⁷

According to the literature, probiotics have proven effective in the treatment and prevention of urogenital infections.¹⁷ Certain lactobacilli (L. rhamnosus, L. fermentum and L. reuteri) have been shown to have a beneficial effect in treating urinary tract infections.¹⁸ An inhibitory effect on E. coli has been demonstrated in vitro, with certain strains of lactobacilli (L. rhamnosus and L. plantarum) possessing antimicrobial properties against this bacterium.¹⁹

Therefore, the data increasingly suggests that probiotics may be used as a first step in the regulation of urinary microbiota in order to reduce the risk of, or treat, certain urinary infections, particularly since they are safe, better tolerated than antibiotics and frequently requested by patients.¹⁷ However, further clinical trials involving large numbers of patients will be required to obtain clear evidence on the preventive and curative role of probiotics in urinary tract infections.¹⁷

A HEALTHY VAGINAL MICROBIOTA: LOW DIVERSITY AND DOMINATED BY LACTOBACILLI

The vaginal microbiota consists mainly of lactobacilli with a protective role. Despite considerable variability among women, in general, five types of community have been categorized, depending on whether they are dominated by L. crispatus, L. gasseri, L. iners or L. jensenii, or have few or no lactobacilli and a significant quantity of strict anaerobic bacteria (Megasphera, Prevotel- la, Gardnerella and Sneathia) known to be characteristic of bacterial vaginosis.⁸

Therefore, while a high number of microbial communities is usually an indicator of health for several microbiotas (digestive microbiota, etc.), the vaginal microbiota is balanced when it has low diversity and is dominated by one or a few species of lactobacilli. In women of childbearing age, hormones promote the proliferation of lactobacilli. Estrogen levels induce the deposition of large amounts of glycogen, the main source of energy for lactobacilli, on the vaginal walls.⁸ From adolescence to the menopause, high estrogen levels promote colonization of the vagina by lactobacilli which metabolize glycogen, produce lactic acid and maintain intravaginal health by lowering the pH level.

BACTERIAL VAGINOSIS: WHEN G. VAGINALIS DRIVES OUT LACTOBACILLI

Despite more than sixty years of re- search, the etiology of BV remains unknown. Nevertheless, research seems to point more and more to the dysbiosis theory according to which dominant lactobacilli are replaced by polymicrobial flora derived from numerous bacterial genera (Gardnerella, Ato- pobium, Prevotella, etc.). G. vaginalis is in effect present in 90% of symptomatic subjects and 45% of normal subjects, whereas Lactobacillus sp. is found in 70% of apparently healthy subjects and 40% of symptomatic subjects.⁹ Consequently, G. vaginalis has been suspected of being the main pathogen in BV. However, there is long-standing disagreement in this regard, since this virulent bacterium has also been found in virgin girls and in sexually active wo- men with normal vaginal microbiota; in other words, colonization by G. vaginalis does not always lead to BV.¹⁰

An explanation recently put forward may settle the debate: there is not one, but at least thirteen, different species of the genus Gardnerella, some of which may not be pathogenic. A mechanism for the development of the dysbiosis has even been suggested:¹⁰ G. vaginalis, transmitted sexually, spreads itself among healthy vaginal lactobacilli, such as L. crispatus, initiating the formation of a biofilm, a structure that further protects the pathogen from the hydrogen peroxide and lactic acid secreted by the lactobacilli. By reducing the redox potential of the vaginal microbiota, G. vaginalis gradually reduces the lactobacilli population in favor of strict anaerobic bacteria such as P. bivia and A. vaginae. G. vaginalis and P. bivia seem to facilitate each other’s development, the former providing amino acids to the latter and the latter ammonia to the former. Lastly, both pathogens produce an enzyme that destroys the mucus in the vaginal epithelium, facilitating the adhesion of different bacteria associated with BV, such as A. vaginae, and potentially causing a polymicrobial infection.

VULVOVAGINAL CANDIDIASIS: A PROLIFERATION OF CANDIDA

Vulvovaginal candidiasis could be linked to an imbalance of the vaginal microbiota together with a proliferation of the fungus Candida, including C. albicans in 80%-92% of cases,¹¹ and to a lesser extent C. glabrata, C. tropi- calis, C. parapsilosis and C. krusei.¹² Exposure to antibiotics, whether local or systemic, is thought to be one of the main factors leading to vulvovaginal candidiasis.¹³ The reduction of certain bacterial species, lactobacilli or not, that control the replication and virulence of Candida yeasts apparently allows the Chlamydia tractomatis fungi already present in the vagina to multiply and induce infection. Future studies involving new sequencing technologies are needed to characterize in further details the interaction between vaginal microbiota, these yeasts and the occurrence and recurrence of vulvovaginal candidiasis.

HEALTHY VAGINAL MICROBIOTA: A SAFEGUARD AGAINST STIS

The vaginal microbiota also plays an important role in maintaining vaginal health and protecting the host against the acquisition and transmission of sexually transmitted infections. Vaginal microbiota with a small number of bacterial communities and dominated by lactobacilli (in particular Lactobacillus crispatus) are those most associated with vaginal health, whereas increased diversity seems to be associated with lower resilience to imbalances and higher susceptibility to STIs such as herpes (BV increases the risk of herpes and vice versa), papillomavirus (increased prevalence and likelihood of contracting HPV, delayed elimination, increased severity of cervical intraepithelial dysplasia), HIV (increased risk of acquisition and transmission), and other infections (gonorrhea, chlamydia and trichomoniasis).¹⁴

URINE IS NOT STERILE

Historically, urine was considered sterile but recent scientific discoveries have shown that this is not the case: 562 bacterial species have been identified in the human urinary microbiota.⁶ Of these, 352 species (62.6%) have been linked to at least one report of infection among humans, including 225 (40.0%) described as the causal agent of urinary tract infections. The eight bacteria most commonly implicated in UTIs are Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Chlamydia trachomatis, Neisseria gonorrhoeae, Klebsiella pneumoniae, Proteus mirabilis and Enterococcus faecalis.⁶ Conversely, bacteria that secrete lactic acid, namely Lactobacillus and Streptococcus, are believed to play a protective role against pathogens⁷: lactic acid lowers the pH of urine (≈ 4.5), resulting in a microenvironment that is unfavorable to most pathogenic bacteria, while lactobacilli produce antibacterial metabolites (hydrogen peroxide and bacteriocins).

GLOBAL, GUT AND URINARY MICROBIOTAS

WHEN DYSBIOSIS OPENS THE DOOR TO PATHOGENS

Studies published to date have demonstrated the clear role played by the urinary microbiota in urinary tract infections and responses to treatment.⁷ Several mechanisms have been put forward, for example, commensal bacteria acting as a barrier against uropathogens (secretion of inhibitory or bactericidal molecules), with a loss of diversity in the urinary microbiota leading to a urinary tract infection.⁶ Therefore, while most microorganisms colonize the human body without causing infection, they may be- come pathogenic under certain conditions (immunosuppression, antibiotic resistance, etc.). A urinary tract infection may therefore develop due to the action of commensal bacteria when a dysbiosis exists. Other potential factors include disorders of a traumatic (catheter), bio- chemical (acidity, etc.), hormonal (pregnancy), mechanical (constipation), or alimentary (food pathogen that reaches the urinary tract from the digestive system) nature.⁶ On the other hand, certain eating habits (consumption of fermented dairy products containing probiotic bacteria or of cranberry juice) may help reduce the risk of recurrent urinary tract infections by regulating the microbiota.^6,7

BACTERIAL VAGINOSIS

Bacterial vaginosis (BV) is the most frequently reported microbiological syndrome amongst women of reproductive age. The Amsel criteria, although controversial, remains the standard method for diagnosing bacterial vaginosis and is based on the presence of at least three of the following clinical criteria:³

1. thin, homogeneous vaginal discharge;
2. vaginal pH > 4.5;
3. amine (fishy) odor on adding potassium hydroxide to a vaginal smear;
4. presence of clue cells (cells of the vaginal epithelium to which a large number of bacteria adhere) on microscopy of vaginal secretions.

The Nugent score, a microscopic examination of a Gram stain of vaginal secretions, is also used in many countries and classifies the bacterial flora into three groups: healthy if the score is between 0 and 3, intermediate if the score is between 4 and 6, and indicative of bacterial vaginosis if the score is greater than 6. Some authors believe that BV may actually be a set of common clinical signs and symptoms caused by a wide range of pro-inflammatory bacteria, coupled with a host-dependent immune response. As a result, some experts prefer to refer to it as polymicrobial vaginosis.³

VULVOVAGINAL CANDIDIASIS

Vulvovaginal candidiasis (VVC), so called because it is linked to the spread of fungi (more specifically, yeasts) of the Candida genus, is considered the second most common vaginal infection after BV: 70%-75% of women are thought to have been affected at least once in their lifetime, 50% twice, and 5%-10% suffer from recurrent cases.

The symptoms and signs of vulvovaginal candidiasis are not clear, especially since colonization by the fungus is not a good indicator, with some women remaining asymptomatic despite colonization.⁴ The most common clinical signs are vulvar pruritus, a burning sensation accompanied by vaginal pain or irritation that may lead to dyspareunia or dysuria, and sometimes vulvar or vaginal erythema, edema, or lesions.⁴

Risk factors include pregnancy (and other situations where estrogen levels increase), diabetes mellitus, immunosuppression and the use of systemic antibiotics. Incidence increases with the commencement of sexual activity, but the links with different types of contraceptive remain unclear.⁵

Lastly, many Candida yeasts alternate between a unicellular phase and a much more virulent filamentous phase. The filamentous forms offer greater mechanical resistance, which assists the colonization and invasion of host tis- sues and confers increased resistance to phagocytosis.⁴

SEVEN OUT OF TEN WOMEN

With 150 million new cases each year, urinary tract infections (UTIs) are a global health problem. A gender imbalance is evident in the case of UTIs, with women twice as susceptible as men in the same age group. One in three women is diagnosed before the age of 24, one in two before the age of 35, and up to seven out of ten once in their lifetime (30% on a recurrent basis).¹

The frequency of UTIs increases with age and following two key events, the commencement of sexual activity and the menopause.² Distinguishing complicated UTIs from uncomplicated cases is clinically important, since this will determine the duration and type of treatment. In general, uncomplicated UTIs are found in patients with no anatomical or functional abnormalities of the urinary tract, whereas complicated UTIs are more common alongside factors such as urinary tract obstructions, pregnancy, immunosuppression, fever, catheterization, renal failure, or diabetes mellitus. Prolonged symptoms (> 1 week), non-response to treatment and bacteria that persist despite treatment are also characteristic of complicated UTIs.¹

COLONIZATION BY DIGESTIVE SYSTEM PATHOGENS

Urinary tract infections are rarely the result of an underlying structural abnormality and are instead usually caused by a colonization of the vagina and periurethral area by uropathogens from the digestive tract which travel up the urinary tract. The virulence of pathogens, particularly E. coli, is mainly due to their adhesion capacity, which enables them to colonize the urinary system up to the point where biofilms form inside the urothelial barrier, protecting the pathogens from the host’s immune system.¹

The progression from chronic kidney disease (CKD) to end-stage kidney disease (ESKD) and its complications appears to be linked to the accumulation of toxins in the blood, many of which are thought to originate in the gut microbiota. However, the microbial origins of these metabolites–which include uremic toxins–and the mechanisms underlying them remain unclear. A large international study (223 ESKD patients and 69 control subjects) was carried out to characterize the relationship between microbial composition, uremic toxins and ESKD symptoms.

Fecal and serum metabolites mirror clinical status

Serum and fecal metabolites of the ESKD patients differed from those of the control subjects and were highly correlated with each other. The feces of the ESKD patients contained more secondary bile acids (SBAs)–precursors to uremic toxins–and fewer short chain fatty acids. Serum metabolites in the patient group were characterized by an increased level of nine uremic toxins and bile acid imbalance, with these characteristics closely related to patients’ clinical status. Therefore, intestinal metabolic alterations in ESKD patients are thought to contribute significantly to the accumulation of uremic toxins in the serum. This hypothesis was validated in a study on an independent second cohort (12 ESKD patients and 12 control subjects).

Gut dysbiosis

A shotgun metagenomic analysis identified an intestinal dysbiosis in the ESKD patients, with an increase in certain bacterial species. These bacteria included genes that code for the synthesis of uremic toxins and the biosynthesis of SBAs. Indeed, microbial composition was correlated not only to clinical variables in the patients, but also to the production of uremic toxins and SBAs. The authors believe that the intestinal microbiota speeds up the production of toxins, thereby contributing to the aggravation of the disease.

Involvement of the microbiota confirmed in rodents

When the feces of ESKD patients were transplanted into germ-free mice, the mice displayed an increase in serum levels of uremic toxins, an aggravation of renal fibrosis and oxidative stress. Intestinal dysbioses are therefore partly responsible for kidney disease via the production of uremic toxins. Two species that produce precursors to these toxins, Eggerthella lenta and Fusobacterium nucleatum, seem to be responsible. Lastly, the administration of a probiotic (a strain of Bifidobacterium animalis) reduced both toxin levels and the severity of the disease in rats. In sum, intestinal dysbioses in CKD patients generate harmful metabolites that aggravate the disease. This suggests that targeting the gut microbiota could reduce uremic toxicity in these patients.

Numerous studies have shown that, in addition to its other benefits, regular moderate physical exercise increases diversity among the bacteria in the intestine, favoring beneficial species. However, this is only the case for regular exercise, since ceasing all activity may lead to an imbalance in the intestinal microbiota (dysbiosis).

Avoid excessive exercise

The opposite situation also has its dangers. Whether you are an amateur or a professional, training too intensely or disproportionately to your level may lead to a dysbiosis, which can be all the more sudden and acute the more intense the activity. Such dysbioses may result in increased intestinal permeability, which, by allowing bacteria and their components to pass into the bloodstream, can lead to inflammation in the body. They may also be the cause of abdominal pain, nausea and diarrhea that certain people experience during extreme exertion.

A gut-muscle axis?

The most likely hypothesis is that the muscles and intestinal bacteria communicate via a gut-muscle axis. This communication is thought to work both ways: the gut microbiota influences muscular health and physical exercise modulates the composition of the microbiota. In humans, although supported by the link between intestinal dysbioses and various muscle-related metabolic alterations (protein synthesis, release of molecules promoting muscle development, etc.), this hypothesis remains tentative.

The immune system: at the crossroads of the gut-muscle axis?

Shaped by the intestinal bacteria, the immune system may also play a key role in muscular health. By helping to build a strong immune system, a “healthy” gut microbiota may influence the gut-muscle axis and the health of our muscles, especially among people having an active lifestyle. Conversely, a dysbiosis caused by a negative interaction with the immune system may promote muscular disorders. This is one more hypothesis that needs to be verified if we are to finally understand the relationship between exercise, the immune system, the gut microbiota and muscular health.

Sjӧgren syndrome (SS) is an autoimmune epithelitis characterized by dry mouth and dry eyes. The epithelial cells in the salivary glands act both as agents and targets by transforming into cells capable of activating the immune system (T cells, dendritic cells, then B cells) and synthesizing chemokines that cause lymphocytic infiltration. The inflammation of the salivary glands associated with these infiltrates is one of the diagnostic criteria for SS. However, it is not yet known what causes the disease. Among the suspects is a dysbiosis of the oral microbiota, already implicated in several autoimmune diseases (systemic lupus, Crohn’s disease, rheumatoid arthritis). The study described below sought to characterize the oral microbiota of patients with SS and to identify whether it had any role in the onset of the disease.

Dysbiosis of the oral microbiota

Oral bacterial communities were sampled via full mouth washing in 25 patients with a primary form of SS (17 with dry mouth and 8 without) and in 25 control subjects (11 with dry mouth and 14 without). These subgroups were selected in order to characterize the changes in the oral microbiota associated with SS, while controlling for the effects of dry mouth. Compared to that of control subjects, the oral microbiota of the SS patients had a higher bacterial load and, in correlation, was more diverse, with bacterial diversity even more pronounced in those not suffering from dry mouth.

The role of Prevotella melaninogenica

In order to assess whether bacterial species associated with the syndrome act as pathogens, the researchers tested in vitro three of the oral bacteria species that signal dysbiosis in SS patients, selecting those that express porins (proteins that allow membrane exchanges). Of these species, P. melaninogenica is able to induce functional (secretion of interferon λ by tumor cells, causing inflammation) and phenotypic (presentation of antigens) changes in the epithelial cells of the salivary glands. The question remained as to whether this bacterium could reach the salivary glands, and this was confirmed by a series of biopsies revealing its presence in salivary ductal cells and infiltration areas. This is thought to result from a rupture of the epithelial barrier due to inflammation and/or fibrosis. In this first scenario, the bacterial infection aggravates the inflammation and the deregulation already underway within the epithelial cells of the salivary glands. However, since the bacterium is also present in non-inflamed areas, another scenario is also possible, in which bacterial infection precedes lymphocyte infiltration. In short, a dysbiosis of the oral microbiota may initiate deregulation of the epithelial cells in the salivary glands. This would lead to a bacterial invasion of the ductal cells able to fuel the inflammation by itself.

Against the current pandemic backdrop, everyone would want a stronger immune system and develop better resistance to infections. Numerous articles have highlighted the key role played by nutrition in immunity, but what can we really expect from nutrition in this regard? In fact, no study to date has shown that an improved diet can help fight viruses^1,2, while protective measures and social distancing remain the most effective means of doing so. However, a well-chosen diet can optimize our immune defenses.

Two levers of action

Our food provides essential nutrients that contribute to the proper functioning of the immune system³, particularly zinc⁴, vitamin D^5,6, vitamin A⁷ and antioxidants such as vitamin C⁵. Moreover, food affects the immune system by shaping the intestinal microbiota^8,9. The billions of bacteria living in the gut are in constant dialogue with immune cells³ and play an important role in the immune response triggered by infections^{10 12}. A well-balanced microbiota also helps regulate the immune system, preventing it from “overreacting”^10,11 (i.e. maintaining a state of alert harmful to the body when it should return to standby once its mission is accomplished). For this reason, the aim is to “strengthen” rather than “boost” the immune system.

Which foods to choose?

In practice, which foods should be consumed? Fruit and vegetables–which are a source of antioxidant vitamins–, and vitamin D-rich oily fish (supplemented if possible by exposure to the sun, which favors vitamin D synthesis by the skin) provide the immune system with all its basic requirements¹. In addition, a varied diet rich in fiber and probiotics such as yogurt or cheese strengthens the microbiota, promoting health and immunity^14,15. Conversely, a diet too rich in calories, fats and processed foods containing additives depletes the microbiota^1,8,14.

Childhood asthma affects 8% of young Americans and Canadians. Its prevalence doubled in the second half of the 20^th century, but the trend seems to be reversing. Is this decline linked to a reduction in antibiotic prescription and to the resulting beneficial effects on the intestinal microbial community? To test this hypothesis, the authors analyzed government data on asthma diagnoses and antibiotic prescriptions in British Columbia (sidenote: Data from the BC PharmaNet government database, which collects data from all health centers in the province (database population: 4.7 million) )  (Canada), as well as the intestinal microbiota of 2,644 children participating in the Canadian CHILD Cohort Study (sidenote: Canadian CHILD Cohort Study Canadian Healthy Infant Longitudinal Development study, a prospective study of children recruited before birth between 2008 and 2012 ) .

Fewer antibiotics means less asthma

At population level, between 2000 and 2014, the incidence of asthma among one- to four-year-old children fell by 7.1% in absolute terms, from 27.3% to 20.2%, based on Canadian government data. In the same period, the prescription of antibiotics to children under the age of one decreased significantly (from 1,253.8‰ to 489.1‰). In 2014, one in three children (34.8%) was prescribed antibiotics at least once before the age of one, compared to two in three children (66.9%) in 2000. Statistical analysis shows a link between antibiotic prescription and asthma: the incidence of asthma increases by 24% with each 10% increase in antibiotic prescription. This trend observed at population level was also found at individual level in the CHILD cohort. After excluding children who had received antibiotics for respiratory problems, the diagnosis of asthma at five years of age was more frequent among children prescribed antibiotics before the age of one. Furthermore, the incidence of asthma increased with the number of prescriptions: 5.2% for no prescription, 8.1% for one, 10.2% for two and 17.6% for three or more.

Role of the microbiota

According to the authors, a dysbiosis of the intestinal microbiota in infants could explain the link between antibiotic exposure and childhood asthma. Children with asthma at five years of age showed less diversity in their gut microbiota at the age of one. This diversity decreased with the number of antibiotic treatments and the earlier the age of prescription (with a sharp reduction if taken before three months). The lower diversity was associated to a decrease in five key bacterial groups, particularly two species involved in the production of immunomodulating short-chain fatty acids. Therefore, the reduction of certain bacterial species may influence the development of children’s immune systems, making them susceptible to allergies. Hence the potential value of strategies aimed at maintaining the diversity of the microbiota after antibiotic use and the need for prudent use of antibiotics before the age of one.