Escherichia coli is naturally present in our intestinal microbiota but can become a pathogen by using some of its infectious properties such as the ability to adhere to the bladder. It is then referred to as uropathogenic Escherichia coli (UPEC). Urinary tract infections occur when the urogenital area is contaminated by the fecal flora. Bacteria can colonize the urethra exclusively (causing urethritis), spread to the bladder and cause acute cystitis, or reach the kidneys (causing pyelonephritis). This bacterial migration from the anal area to the urogenital system raises two questions: are the responsible strains different from a genetic standpoint or do they need to adapt when they migrate from the intestines to the bladder? For preventive purposes, could it be possible to predict the risk of contracting a UTI using fecal Escherichia coli samples?

No adaptation is required

Several studies^{4, 5} from a Danish team provided us with some answers. The researchers observed that the fecal strains of Escherichia coli in patients with UTI were the same as those found in their own urine samples and also the same as in healthy women. The only differences were a few minor genetic variations. In other words, Escherichia coli is able to migrate from the intestines to the bladder without needing to adapt at all. The evidence thus showed that fecal microbiota composition cannot predict the risk of developing a urinary tract infection. Then, what are the causes of UTIs? UPEC-mediated urinary tract infection probably results from a combination of factors related to the bacteria (ability to adhere to intestine cells, virulence...) and to the host’s immune status, creating an infection-prone environment

Although it affects nearly 20% of women in France¹ and millions of women every year in the world, bacterial vaginosis remains under-diagnosed and poorly treated because of its unclear definition.

Bacterial vaginosis has been described as an infection, an inflammatory disease, a dysbiosis (microbiota imbalance), a syndrome, or even a normal situation. A proper definition has not yet been found and it keeps causing controversy among the scientific community. Canadian microbiologist, Gregor Reid² reminded that while the disease had been discovered in 1954 and defined as an infection caused by Gardnerella vaginalis, the term “bacterial vaginosis” only appeared in 1983. But the fact that the responsible bacterium can also be found in healthy women without causing vaginosis undermines this theory. Six years later, vaginosis was described as “a complex change in vaginal microorganisms associated with malodorous discharge and no visible inflammation”. Some time later, researchers observed an increase in inflammation markers and classified it as an inflammatory disease. However, this definition was invalidated in 2010 due to lack of evidence. More recently, the term “dysbiosis” was added to the list. In conclusion, after nearly 65 years of research, no consensus has been reached yet.

Poorly defined, poorly treated

According to the literature, vaginosis is not a disease as generally understood, that is to say a deterioration of health characterized by specific signs. It presents as a range of symptoms (inflammation, foul vaginal odor, increase in bacterial diversity, etc.) which vary greatly from one woman to another. In some cases, it may cause no symptoms at all. Nevertheless, its diagnosis, prevention and management depend on its definition. To this day, only a pharmacologic approach receives financial support from health authorities, thus excluding alternative avenues aiming at restoring and maintaining the flora, such as probiotics and prebiotics. Gregor Reid believes this to be an aberration and calls for the term “vaginosis” to be abandoned and replaced by a term which better describes the different disorders it encompasses. According to him, “vaginal dysbiosis” or “vaginal inflammation” would help provide a more appropriate treatment.

Rheumatoid arthritis (RA) is a chronic autoimmune disease affecting joints and characterized by synovial membrane inflammation which reaches surrounding bones and cartilages. For some years the gut microbiota has been the focus of increasing interest from the scientific community, who believes it is involved in RA.

Dysbiosis observed as soon as the early stages

While previous works had already reported dysbioses in patients at an advanced stage of the disease, a Korean team focused on the early stages, and exclusively on women, who are more affected by RA. The 29 female patients included in the study were either at a preclinical stage (PC, n=17), or with clinically apparent early-stage RA (ER, n=12), and were DMARD-naive (DMARD = disease-modifying antirheumatic drugs). The bacterial DNA from fecal samples extracted from patients was compared to that of 25 control healthy women. First finding: the microbiota of patients with RA was characterized by a lesser bacterial diversity (without any difference between PC and ER patients). Moreover, differences were observed in the present bacterial species: for instance, bacteria from the Bacteroidetes phylum were over-represented in patients with RA, while those from the Actinobacteria phylum were under-represented, especially those from the Collinsella genus.

Altered genetic functions

These differences in composition were reflected in genetic differences: genes involved in the synthesis of ubiquinone (co-enzyme Q10) and menaquinone (vitamin K2) were more abundant in controls, while genes involved in the transport and absorption of iron were more abundant in patients with RA. This characteristic, which promotes the absorption of iron by bacteria from the microbiota, could explain the anemia often observed in people with RA. Finally, genes coding for the synthesis of lipopolysaccharides–molecules expressed on the surface of gram-negative bacteria which cross the gut barrier and promote systemic inflammation–were especially represented in female patients with clinically apparent RA. This is an astounding result regarding the inflammatory nature of RA. Larger studies based on complementary sequencing studies could specify the role of the gut microbiota in RA and determine whether dysbiosis is a cause or a consequence of the disease.

Young children have always had to adapt to the diversity and abundance of their environmental microbiome. But with urbanization, our homes have lost some of this abundance and diversity, and the frequency of asthma (and allergies) has simultaneously increased. Many scientists assume there is a link between these two phenomena and are trying to document it and understand underlying mechanisms. An international research team recently made progress on this matter.

Mirror of the environment

First step: analysis of the microbiota (population of microorganisms) present in the dust collected in farms on the one hand, and other homes on the other hand, as part of two studies conducted with cohorts of 2-month old Finnish children (for whom asthma was diagnosed in the first 6 years of life). Important composition differences were observed: dust from farm homes had strong bacterial diversity and abundance, as well as small amounts of specific bacteria and species of archaea (sidenote: archaea Archaea are small microorganisms with the same morphology as bacteria but with a different genetic composition )  typically associated to the rumen (sidenote: rumen First compartment of the stomach of ruminants )  of cattle. The indoor microbiota of non-farm homes contained significant proportions of bacteria associated to humans. Finally, the abundance of fungi varied depending on homes, although not significantly..

Protective diversity

These differences in composition were linked to the development of asthma in the first six years of life. Result: in children growing in non-rural environments, the risk of developing asthma decreased as the microbial composition of indoor dust got closer to that of farms. This pattern was later confirmed in German children living in rural areas. Although the “protective farm effect” is still unclear, the pool of data collected confirms the hypothesis that the presence of specific bacteria and archaea in the indoor environment, and especially in the dust, can protect against asthma. This is good news for the development of a new type of preventive strategies.

In the wake of the hygiene hypothesis which consists in believing that excessive hygiene in recent years is partly responsible for the explosion of allergies in the industrialized world, it is now accepted that an immune system less exposed to microorganisms in very early childhood can lead to allergies later in life¹⁴. This problem, which is very acute in industrialized countries, finds a rather worrying echo in Japan where the incidence of allergies in three-year-old children in Tokyo rose from 8.5% in 2004 to 16.7% in 2014¹⁵. Faced with this public health issue, the local scientists are taking action.

In Japan, they know that everything (or almost everything) plays out before the age of one year

Some of their scientists examined the first year of life with the aim of finding a sort of “microbial signature” in infants who developed food allergies before they were two years old¹⁶. In their hypotheses, these researchers paid great attention to the two key moments in the development of the intestinal microbiota: the lactation period (usually up to nine months after birth), during which the flora is dominated by lactic acid bacteria (Bifidobacterium); and the weaning period, during which the microbiota diversifies, becomes more abundant, and becomes closer to that of an adult¹⁷. During these periods, tolerance to food antigens–foodderived macromolecules external to the organism capable of triggering an immune response via the production of antibodies– develops. Any impairment of this process can then create allergies in children¹⁸. For this prospective study in 56 babies, the Japanese team analyzed stools at one month, two months, six months and one year: fourteen developed food allergies before they were two years old–ten of them even before they were one year old. By correlating these results with analyses of the microbiota, the researchers noticed that during the lactation period, and from the age of two months, certain lactic-acid producing bacteria were already present in markedly smaller numbers in children who developed food allergies before the age of two years. This was enough to assign a protective role to certain species, present particularly in the mother’s milk and derived from the mother’s intestinal microbiota, according to some studies¹⁹. The researchers also noted considerable differences in bacteria which assimilate lactate (Veillonella), under-represented in the allergic children.

Lactation and weaning at the heart of the allergic process

During weaning, the intestinal microbiota of children with allergies (food and other allergies) was characterized by a greater abundance of some types of enterobacteria–one of the largest bacterial families–and that of children with food allergies was characterized by two species of Clostridium whose mode of action should be the subject of more detailed research. Moreover, the bacterial diversity of allergic children was significantly lower than that of healthy children. This is interpreted by the researchers as a sign of the imminent onset of the allergy. Finally, these results–showing that very early impairment of the intestinal microbiota during lactation and weaning can cause food allergies–are globally consistent with those of previous studies conducted in other countries. Whether it is the dysbiosis that generates the disease (the allergy) or the other way around, remains to be determined. Thanks to the results of this research, the mother’s intestinal microbiota, a source of protective lactic acid bacteria, represents a means of preventing food allergies in infants.

KEY FIGURES ON FOOD ALLERGIES:

Prevalence of food allergies steadily increases in Western countries. Among possible causes: gut dysbiosis related to new lifestyles (overuse of antibiotics, poor dietary habits, increased rate of cesarean deliveries...). This hypothesis was explored by an American team which focused on anaphylactic reactions in mice colonized by gut microorganisms extracted from children with or without b-lactoglobulin allergy.

Allergenic fecal transplant

Fecal samples from 4 allergic newborns and 4 healthy newborns were administered to groups of axenic mice (germ-free mice), before exposing them to b-lactoglobulin. Result: “allergic” animals presented a sharp body temperature decrease and a significantly higher production of IgE and Ig1 anti-b-lactoglobulin antibodies and murine mast cell protease compared to “healthy” mice. However, mice who received a transplant from non-allergic children had no anaphylactic reaction and few temperature variations, thus suggesting the gut microbiota is involved in the mechanisms at play.

Protective vs. non-protective bacteria

Analyses carried out on the donors and on mice have shown notable variations of 58 OTUs (sidenote: Operational Taxonomic Unit groups of organisms usually not cultivated or not identified, classified on the basis of the similarity of the DNA sequencing of a given gene. Frequently used as an equivalent to the concept of species ) based on sensitivity to b-lactoglobulin allergens. 34 of them, from the Lachnospiraceae family, are qualified as “protective” (more abundant in healthy donors) and 24 as “non protective” (more abundant in allergic donors). Their relative abundance, expressed as a ratio, could be used to distinguish between allergic and non-allergic individuals.

Anaerostipes caccae: the ideal ileal bacteria?

Since tolerance to food allergens begins with absorption in small intestine, the team then characterized local bacterial populations and their potential action on the anaphylactic response. A beneficial species was thus identified in the ileum, where microorganisms of the small intestine are most abundant: Anaerostipes caccae (from the Lachnospiraceae family), whose increased content could be synonym of a better protection. This bacterium uses lactate and acetate and produces butyrate, three metabolites involved in the modulation of immune responses in the gastrointestinal tract. All these results highlight the role of commensal bacteria in food allergic reactions and open the way to the development of preventive and therapeutic strategies based on the modulation of the gut microbiota.

Based on recent works, it seems that marathon runners should not be the only ones to step onto the podium: their gut bacteria are also involved in their athletic performance.

The bacterium that turns mice into champions

A team of researchers observed that the postmarathon gut microbiota of runners was particularly rich in bacteria from the Veillonella genus and they isolated in their stool a specific species called Veillonella atypica. The simple inoculation of this bacterium to mice transforms them into seasoned athletes: the little rodents run longer on treadmills!

Marathon runners feed bacteria...

The underlying mechanisms still had to be elucidated. One specificity of Veillonella bacteria gave the researchers an idea: they feed on lactic acid which is produced by the body during extended physical exercise and which causes muscle soreness on the day following a sporting feat. After several additional experiments, the researchers suggested the following model: when they exercise, marathon runners use the sugar (or glucose) stored in their muscles and it is transformed into lactic acid (leading to muscle cramps). A portion of this lactic acid reaches the liver where it will be transformed back into glucose; the rest crosses the intestinal wall and feeds Veillonella bacteria living in their digestive tube.

... and bacteria boost marathon runners

Veillonella, which are well fed by their long-distance runner hosts, rapidly multiply. And that is why the microbiota of runners is so abundant and diverse at the end of a marathon. But it is not the only reason: during physical exercise, bacteria consume lactic acid and transform it in the colon into propionate, a beneficial substance derived from lactic acid which returns into the muscles of athletes via the blood flow and improves their performance. Moreover, in mice, the injection of propionate in the colon was enough to turn them into the kings of treadmill. This win-win relationship between the bacterium and its host allows the athlete to complete its marathon in a record time... their belly full of Veillonella!

What is the current state of research on the relations between immunity and gut microbiota?

Although the microbiota has been known since the days of Louis Pasteur, it was forgotten for a long time. However, it has been better understood in the past twenty years. Thanks to technical innovations (bacterial culture, metagenomics), bacteria from the gastrointestinal tract, which used to be poorly accessible, have been better characterized. We now have to refine our knowledge regarding their interactions with the body’s defense mechanisms, the way gut and other microbiotas are involved in the development of the immune system, which in turn has an impact on pathogen heterogeneity. The concept of “shaping” (or modulation of gut bacteria by the production of IgA in the gastrointestinal tract) is of foremost importance. This research approach is still poorly understood, but it should be critical in the years to come. Interactions between gut microbiota and immunity is a true shift in paradigm, and their results and study are not yet given their rightful place.

Do we know all the diseases associated with these relations?

There are many. Among those related to the immune system, in no hierarchical order, it is logical to mention autoimmune diseases and allergies, which are characterized by a breakdown of immune tolerance. Cancers are characterized by inflammatory processes and disruptions of the physiological balances between bacterial populations (dysbiosis). Less directly, regarding the role of the immune system, we should also mention obesity and metabolic disorders: bacteria-related inflammatory processes in the fatty tissue have been identified. Neuropsychiatric diseases could also be concerned: the intestinal production of serotonin that is transported to the brain through the vagus nerve should be further explored, but the link with immunity disorders is not obvious. Autism has also been mentioned: although the association with the gut microbiota is not crystal clear, it has already been suggested in several studies. Convincing mechanisms must be identified for the hypothesis to be confirmed.

Modulation of the gut microbiota: could it soon become a standard clinical practice?

One possibility could be to correct dysbioses or improve the gut flora with second-generation probiotics that are more targeted depending on the dysbiosis, compared to those from the first generation. Fecal microbiota transplants remain difficult because of the lack of standardization regarding protocol, sample collection or storage conditions. Modulation of the gut microbiota should rather be seen as an adjuvant: for instance, although the links between some bacterial populations and some types of cancer have been demonstrated, it would be unthinkable to manage without anticancer treatments. Standardized tests should be conducted to determine which populations should be grown and which should be destroyed. In a second phase, the efficacy of induced modifications should be confirmed and a durable colonization should be ensured. Before concluding anything, we should let research the time to progress.

In 2011, 198 students from the Massachusetts campus participated in a randomized, double-blind, placebo-controlled study that assessed the effects of probiotics during 3 weeks in the prevention of morbidity associated with upper respiratory tract infections.¹⁸ These infections are common among young people that are possibly stressed, lacking sleep and living in crowded dorms. On average, volunteers who received a daily dose of a strain of Lactobacillus and Bifidobacterium were ill 2 days less (over a total duration of 6 days on average for infections that occurred in the cohort), and the severity of their symptoms was down by 34%. Probiotics thus improved their quality of life and increased their resistance to environmental respiratory pathogens.

SYNBIOTICS UNDER INVESTIGATION

In 2008, an Italian team explored the impact of synbiotics (combination of prebiotics and probiotics) on the intestinal health (bloating and transit especially) and resistance to respiratory infections.¹⁹ For 90 days, more than 230 participants were divided into groups who received different combinations of probiotics (3 to 5 strains of Lactobacillus and Bifidobacterium), prebiotics (fructooligosaccharides, FOS) and/or lactoferrin and/or galactooligosaccharides (GOS). Beneficial effects were demonstrated on the intestinal functions and the resistance to respiratory infections (decrease of the incidence, duration and severity) in patients who received synbiotics. Lactoferrin did not provide any visible benefit compared to FOS or GOS. However, the combination of the 5 strains of probiotics with FOS or GOS seem to improve symptoms. FOS seem to act in synergy with bacteria by helping them colonize the gut mucosa and roll out their immunomodulating effects. According to researchers, this alternative could be very useful in the long-term prevention of this type of pathology, for which current treatments are associated with adverse effects.