Until the 1990s, C. difficile colitis was a relatively rare infection which was not considered a health hazard: an antibiotic treatment was enough to get rid of it. But in a 20-year period, the frequency of this disease more than doubled, while the efficacy of the antibiotics therapy dropped to a 20-30% success rate^8,9. The bacterium is becoming increasingly resistant to antibiotics. It was not until the start of the 2000s and the sequencing of C. difficile genome when a particularly virulent strain was identified. It is resistant to antibiotics and able to produce 10 times the amount of toxins usually secreted by this bacterium.

Beware of relapse with repeated antibiotic courses!

Infection generally occurs after the destruction of the gut microbiota by repeated courses of antibiotics. C. difficile, which is present as resting spores in the colon, proliferates and changes to produce toxins that cause inflammation and diarrhea. Paradoxically, this infection is treated with antibiotics, which progressively exacerbate the gut microbiota disruption at each additional treatment course³ thus leading to a 35% rate of relapse².

FMT should be preferred to antibiotics for recurrent cases

In 1958, the surgeon Ben Eiseman published 4 cases of pseudomembranous colitis that were cured with FMT and sparked interest in this method. Several articles described its efficacy to treat the recurrent form of this disease. But the true turning point came in 2013 with the publication of the first clinical trial in humans. This trial was designed with a robust methodology and demonstrated the therapeutic superiority of FMT over antibiotic therapy to treat recurrent and drugresistant forms of C. difficile infections.

Is fecal microbiota a drug?

The answer depends on the country. In France and in the US, fecal microbiota is considered as a drug. It is not the case in the UK, Denmark or the Netherlands. In France, the National Agency for the Safety of Medicine and Health Products (ANSM) published in March 2014 and updated in 2016 a document regulating FMT which describes the procedure, especially the donor selection process.

Specific procedure

In France, FMT must be prepared under the responsibility of the in-house pharmacy of a health facility³. The collected stools are diluted, mixed, filtered and then filled into syringes before being administered. They can also be frozen, which provides the opportunity to create stool banks that are available at any moment⁵. The ANSM adds that “freezing could also limit the risk of transmission of infectious agents and bypass the pre-screening step (the screening could then be carried out on the transplant itself”.

The gut microbiota (or gut flora) is an organ in its own right, made of billions of microorganisms (bacteria, fungi, viruses...) constantly interacting with each other as well as with the organism they are colonizing (host). In the colon, microorganisms fiercely compete for available space and food, but they also work closely together to digest large molecules. As a treatment for Clostridium difficile infection, FMT is based on four mechanisms of action³:

We now know that a lesser microorganism diversity in the gut microbiota is associated to disorders such as diabetes mellitus, colorectal cancer, and complex gastrointestinal disorders such as chronic inflammatory bowel diseases (IBD). But in order to use this diversity as a biomarker, a proper picture of this diversity is required: fecal metabolites are an indicator of the microbiota composition, but what about blood metabolites?

40 predictive metabolites were identified

To find out, a team tried to predict the gut microbiota diversity based on 1,000 blood analytes in a cohort composed by 399 healthy American adults enrolled in a wellness program. The results show that 40 metabolites found in the host’s blood, of which 13 are of microbial origin, explain 45% of the gut microbiota diversity, and could thus predict it. The predictive capability of metabolites was confirmed in a different validation cohort including 540 people, who were more or less healthy.

Neither too much, nor too little diversity

Moreover, results suggest that instead of maximum diversity, optimal diversity should be prioritized to stay healthy. On the one hand, an association between polyphenol microbial metabolites and gut microbiota diversity has been observed, which could reflect a diet with a high content of fruits, vegetables and cereals (which in turn have a high content of polyphenols); and on the other hand, some microbial metabolites that predict diversity are related to cardiovascular or renal disorders. As a result, not only a lack of diversity but also an excess of it could turn out to be harmful, to the point where the authors mentioned the idea of an ideal range, characterized by “neither too much nor too little” diversity depending on the body mass index (BMI) value. Finally, the authors highlighted that associations between blood metabolites and gut microbiota diversity were not the same along the continuum of BMI, which suggests that limiting the analysis to “normal” and “obese” categories is too restrictive.

Towards clinical tests?

As a whole, these results attest to the close relationship between the host’s physiology and the gut microbiota, and suggest that the host’s blood metabolome is a major interface between the gut ecosystem and human health. Eventually, the ability of plasma markers to predict the gut microbiota diversity could open the way to the development of clinical tests to monitor the gut microbial health, through a simple blood sample, easy to handle.

Non-alcoholic hepatic steatosis is characterized by excess fat in the liver, not related to excessive alcohol consumption. When left untreated, the liver becomes inflamed and progressively deteriorates: this disorder is then referred to as non-alcoholic hepatic steatosis (NASH) and may progress to fibrosis, cirrhosis, and finally liver cancer. It is frequently associated to metabolic diseases such as obesity, and to disruptions of the gut microbiota. However, we do not know the precise mechanisms responsible for the onset of this disease.

Alcohol-producing bacteria

While studying the case of a patient with NASH and auto-brewery syndrome (sidenote: Auto-brewery syndrome–or gut fermentation syndrome–is characterized by a state of intoxication following a high-sugar meal, while no alcohol was consumed. ) , Chinese researchers discovered that bacteria could be the cause of this syndrome, which had been attributed to yeast until then. Stool analysis revealed the presence of Klebsiella pneumoniae bacteria that are able to produce large quantities of alcohol, at levels up to 900 times higher than normal. Their study was broadened to include 43 patients with non-alcoholic hepatic steatosis and showed that 60% of them hosted these bacterial types in their gut microbiota, vs. only 6% of healthy individuals. To go further, researchers had healthy mice absorb these bacteria: after 4 weeks, mice also developed fatty liver disease. Liver damage was as important as that induced by excessive alcohol consumption in mice. Finally, they observed that the administration of glucose to sick mice hosting this bacterium could be a way of detecting alcohol in the blood. Indeed, bacteria need sugar to produce alcohol: it is the very principle of alcoholic fermentation!

Sugar-based test?

These findings could lead to the development of a simple and effective sugar-based diagnostic test. The researchers believe that detecting alcohol in the blood after glucose absorption could indicate the presence of excess amounts of this bacterium and could lead to the development of an antibiotic treatment targeting K. pneumoniae.

Immune checkpoint inhibitor (ICI) therapy is a form of immunotherapy that provides a new therapeutic option against some tumors, such as melanoma and non-small-cell lung cancer (NSCLC). Despite its efficacy, only a small number of patients can benefit from it. That is why it is important to better anticipate the response to treatment and improve routine prescription guidelines. To this end, a team of researchers investigated if the time of administration of broad-spectrum antibiotics (ATB) which are mainly used to treat respiratory infections–either prior or concomitantly to ICI– could have an impact on the treatment efficacy through gut microbiota modulation.

Patient survival decreased from 26 to 2 months

This prospective cohort study, conducted at 2 teaching hospitals, included 196 patients (137 male and 59 female, average age: 68 years) with cancer (119 NSCLC, 38 melanoma and 39 other types of cancer) who received ICI therapy for more than three years. The results indicate that antibiotic therapy given in the 30 days prior to ICI therapy (pATB, i.e prior antibiotics) clearly decreases overall patient survival, regardless of the type of cancer (2 months for patients who received pATB vs. 26 months for those who did not receive any prior antibiotic treatment). The percentage of tumors refractory to therapy is also considerably higher in patients who received pATB (81% vs. 44%). In conclusion, the time of administration of antibiotics seems crucial: while it does not have any negative impact if given concomitantly to ICI therapy, it worsens the prognosis when it is administered previously.

Understanding the role of the gut microbiota

The authors are aware that their results are limited by the small cohort size and by the lack of correlation analysis between antibiotic therapy and composition of the patients’ microbiota. But they are in line with results from previous studies indicating that gut dysbiosis is associated to a poor response to ICI therapy against cancer. One possible explanation is that the use of antibiotics could lead to long-lasting disruptions in the gut ecosystem which would then jeopardize the efficacy of T cells against cancer. However, this is still an imprecise hypothesis, and mechanistic studies should be carried out as soon as possible in order to understand how gut microbiota alterations induced by prior antibiotic use negatively impact the efficacy of ICI therapy.

As the impact of the gut microbiota on our health is increasingly better documented, strategies able to favorably affect it are being developed, particularly through diet. Some researchers thus focus on foods specifically aimed at acting on the microbiota, or MDF (microbiota-directed foods), in this case, polysaccharides (plant fibers).

34 “fibers” were analyzed

A murine model led to a better understanding of how human gut bacteria interact with dietary polysaccharides, as well as with each other: germ-free mice colonized by beneficial gut bacterial strains (Bacteroides spp. from a slim adult male, that distinguish him from his obese twin) were fed different combination of 34 dietary fibers, in addition to a fiber low diet (representative of the typical American diet). By combining several cutting-edge technologies, the researchers identified the fiber bioactive compounds that promote the development of some Bacteroides species. Twenty-one out of 34 tested polysaccharides significantly improved the growth of some species, such as citrus pectin and pea fiber with Bacteroides thetaiotaomicron. These results could eventually allow us to increase the content of these active compounds in our diet.

Inter-species competitions

To understand the mechanisms at play and identify the fibers that are ingested or not, additional experiments were carried out using biosensors, i.e. magnetic beads coated with polysaccharides and easily recovered in the stools. They confirmed that 2 different bacterial species (for instance Bacteroides cellulosilyticus and Bacteroides vulgatus) are able to degrade the same polysaccharide, as long as they are equipped with the necessary genes. As a result, different strains compete for nutritional resources.

Towards personalized nutritional medicine?

By analyzing how gut microorganisms adapt to their environment (by counterbalancing the absence of a specific species or by competing with each other), the scientists observed that some bacteria were more flexible than others, as regards the use of the substrate. This is the case for Bacteroides ovatus, which is able to adapt to the presence of B. cellulosilyticus, its competitor for arabinoxylan (a major component of plant cell walls in cereals and peas), while B. vulgatus does not have this ability. Identifying which organisms are the most flexible helps us understand how some strains can coexist with the other “inhabitants” of the gut community. Based on these results, the team already foresees the development of personalized dietary guidelines based on microbiological and physiological data from the host obtained with biosensors.

A healthy vaginal microbiota is characterized by very low bacterial diversity and predominance of one or few lactobacilli species. On the contrary, high diversity and reduced levels of lactobacilli unbalance the flora, as is the case in bacterial vaginosis. It is a benign infection but it predisposes to sexually transmitted infections, urinary tract infections, and increases the risk of premature delivery. Although effective in the short term, antibiotics do not prevent relapses, which reach a 70% rate within 3 months. Could vaginal microbiota transplant be the solution?

Carefully screened donors

An American team had 20 female volunteers fill out a standard questionnaire with additional health and sex related questions (vaginal infections, number of partners, use of condoms, method of contraception...). After completing clinical and biological exams to determine their infectious status, the investigators analyzed the composition of their vaginal microbiota. This very careful donor selection protocol allowed them to determine the ideal graft: vaginal secretions with high content of lactobacilli leading to acidic pH and ensuring a better protection against infectious germs.

Strict inclusion criteria

The authors suggested to extend the screening process to many other infections in addition to those usually planned in standard transplants and also recommended several exclusion criteria: previous exposure to herpes virus, history of recurrent urinary tract infections, presence of “foreign” bacteria in the vaginal microbiota... Donors must also abstain from sexual intercourse within at least 30 days before sampling and they cannot receive any hormonal treatment. The proportion of eligible women was thus reduced to 35%, a number that should be even lower under real conditions. Moreover, potential recipients should not be exempted from STI screening, not as an exclusion criterium, but to make sure they receive the safest possible post-transplant follow-up.

How can we fight against the transmission of pathogens highly resistant to antibiotics such as vancomycin-resistant Enterococcus faecium (VRE)in healthcare facilities? A promising approach is based on the reinforcement of the gut resistance to colonization through the administration of protective gut bacteria. In mice, bacterial transplant seems to restore the resistance to colonization and reduce the gut density of VRE. This was achieved via the combination called “CBBP_SCSK” of 4 bacterial strains, including Blautia producta (BP_SCSK; where SCSK designates the Blautia strain). However, the underlying mechanisms at play still had to be elucidated. This was partially accomplished by the works recently published in Nature by American researchers.

A lantibiotic similar to E234 preservative

Based on experimental results, BP_SCSK could help reduce the growth of VRE by secreting a lantibiotic (sidenote: Lantibiotic  Low molecular weight bacterial peptide with antimicrobial activity produced by a large number of Gram-positive bacteria ) , similar to nisin A, which is produced by Lactococcus lactis and largely used in the food industry as preservative (E234). Similar...but way more effective and selective.

More effective and selective in vivo

Although VRE growth is inhibited both by BP_SCSK and L. lactis in vitro, things are very different in vivo: only BP_SCSK is detected in the colon (where it represents about 25% of bacteria present 5 days after the administration of CBBP_SCSK); it reduces the density of VRE and inhibits Gram+ pathogens while preserving other gut commensal bacteria. On the contrary, L. lactis is not able to colonize the gastrointestinal tract and has a wider spectrum of action, at the expense of some beneficial bacteria.

A potential probiotic agent

The results also emphasize that genes encoding for the synthesis of lantibiotics are naturally present in human microbiomes from healthy individuals; and that lantibiotic-producing species inhibit VRE. Moreover, in 22 patients with a high risk of contracting VRE infection (because they were undergoing a hematopoietic cell transplant), a high abundance of lantibiotic-coding genes was associated to a reduced density of E. faecium. Similarly, in germ-free mice transplanted with fecal preparations from these patients, the resistance to colonization by VRE is correlated to the abundance of the lantibiotic gene. This supports the idea that lantibiotic-producing gut bacteria reduce the colonization by VRE and are potential probiotic agents that could restore resistance towards this pathogen.