The presence of bacteria in human tumors is no new discovery: we have known about it for over a century. Despite this, due to its low biomass, little is really known about the tumor microbiota. Using a combination of multiple technologies, a team of researchers has studied 1,010 tumor samples and 516 samples of healthy adjacent tissue, with a total of seven tumor types screened: breast, lung, ovarian, pancreatic, melanoma, bone, and brain.

Bacteria in tumors and macrophages

First finding: the frequency of bacterial DNA detection depends on the type of tumor, from 14.3% for melanoma to over 60% for breast, pancreatic and bone cancers. A study of more than 400 additional tumors has confirmed bacterial components (16S rRNA and lipopolysaccharides (sidenote: Lipopolysaccharides Molecules found in the outer membrane of bacteria ) ) to be frequently present in both cancer cells and adjacent immune cells. On the other hand, the detection of spherical or rod-like bacteria was rare, suggesting a possible alteration of the envelope of intra-tumoral bacteria.

A specific microbiota for each cancer

Second finding: breast cancer has a particularly rich and diverse microbiota, with an average of 16.4 bacterial species detected per tumor, compared to less than 9 for other types of cancer. The culture of fresh tumor samples appears to confirm that these bacteria thrive. More importantly, each type of tumor has a distinct bacterial composition. For example, species belonging to the Firmicutes and Bacteroidetes phyla are the most frequent in colorectal tumors, whereas Proteobacteria predominate in pancreatic cancer.

A niche effect

Lastly, metabolic activities of intra-tumoral microbiota are highly dependent on the type of tumor. For example, in lung cancer, there is an increase in the number of bacteria capable of breaking down the chemicals present in cigarette smoke (toluene, acrylonitrile, etc.). According to the researchers, high concentrations of these metabolites may create a niche favorable to bacteria capable of metabolizing them.

Manipulating the tumoral microbiota?

At this stage, the study does not tell us whether bacteria play a causal role in the development of a tumor, or whether the tumor itself is responsible for their presence (the tumor may disorganize the vascular system, allowing bacteria to penetrate its cells). However, just as other studies have shown the gut microbiota to influence response to ICIs (sidenote: Immune checkpoints are used by tumors to protect themselves from immune system attacks and may be blocked by ICI therapy in order to restore the immune system function. ) , the researchers hope that by manipulating the tumoral microbiota it may be possible to alter the tumor’s defenses and, therefore, its response to immunotherapy. Indeed, the microbiota of melanoma varies between patients who respond well or poorly to immunotherapy. This creates hope for new diagnostic tools or even treatment methods.

Nearly a quarter of the world’s population could be affected by intestinal parasites. However, parasites–as well as their interactions with the microbiota–are among the least known microorganisms colonizing the intestinal ecosystem. This is why a team tried to assess the links between presence of parasites and composition of the gut microbiota, its metagenome, and the host’s immune response, by studying 575 Cameroonian adults. The composition of the microbiota was analyzed through 16 S rRNA sequencing and amplification, as well as shotgun metagenomics.

Microbiota, an indicator of parasitism

Besides subsistence strategy (pastoralist, agropastoralist, or hunter-gatherer lifestyles), the presence of parasites–especially strong in hunter-gatherers–was the factor most strongly associated with microbiota composition. A larger number of gut parasites, and especially the (co-)presence of four soil-transmitted helminths–Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis (called “ANTS” parasites)–was correlated to an increased alpha diversity. The composition of the microbiota could predict the presence of helminths in the gut with an accuracy reaching about 80%, and up to 84% for ANTS parasites. Gut colonization with ANTS is associated with higher levels of circulating cytokines (including some proinflammatory), indicating that ANTS could modulate immune mechanisms. The microbiota could be involved in this process: its composition could predict circulating levels of interleukin 5, largely involved in the immune response to helminth infection.

Functional interactions between parasites and microbiota

To explore potential metabolic interactions between microbiota and parasites, the researchers have established a connection between the presence of parasites and different functions in the bacterial metagenome. In ANTS-positive individuals, they observed a larger presence of bacterial genes involved in the metabolism of purine and pyrimidine, two nitrogenous molecules used in the composition of DNA nucleotides that some parasites are not able to synthetize and are forced to extract from their surroundings. The size of the cohort also made it possible to analyze the links between subsistence strategy and gut microbiota. For instance, in the microbiota of some pastoralist ethnic groups, they observed an increased amount of several species that are able to metabolize galactose and dairy lipids, which are different from bifidobacteria found in Europeans. According to the researchers, deepening the knowledge on the interactions between host, parasites, and microbiota, could help develop microbiota-targeting strategies to treat or prevent helminthiasis.

Alcoholism is a major cause of death and has serious consequences for the proper functioning of organs. Collateral damage from alcoholism includes major alterations to the intestinal microbiota, leading to a dysfunction in the dialogue between gut and brain. The intestinal microbiota is thought to play a role in behavioral disorders and addictions, and with this in mind, a team of researchers investigated whether alcohol dependence can be reduced by transferring the gut microbiota of healthy individuals to alcohol-dependent patients. To this end, twenty men aged between 60 and 70 and suffering from chronic alcoholism were divided into two groups, one of which received a fecal microbiota transplant (FMT) from a healthy donor and the other a placebo enema.

Alcohol craving and consumption reduced by FMT

Fifteen days after the FMT, the researchers observed:

– a reduction in craving for alcohol among 90% of the FMT patients, compared with 30% of the placebo patients

– a decrease in the marker molecules for alcohol consumption in the urine of the FMT patients, a sign of reduced consumption

– an improvement in the FMT patients’ cognitive performance and psychosocial wellbeing

Six months after the transplant, the FMT patients continued to report fewer serious alcohol-related problems (hospitalization, admission to emergency rooms).

Gut-brain communication involved?

The beneficial effects of FMT to treat alcohol dependence were accompanied by an increase in both microbial diversity and the abundance of short-chain fatty acids (SCFAs) in the stool and blood. High SCFA levels were associated with the presence of certain bacteria and lower addiction scores. According to the authors, the improvement in patients’ behavior in relation to alcohol may result from the increase in SCFAs following FMT, with SCFAs potentially acting as messengers that enable improved communication between gut and brain. Although preliminary, these results anticipate the introduction of therapies that alleviate alcohol addiction disorders via modulation of the microbiota.

Non-alcoholic steatohepatitis (NASH) is thought to affect 24% of the world’s population and an alteration of the gut microbiota has been implicated in the progression from advanced fibrosis to cirrhosis. The stool microbiota of 163 US subjects was analyzed to determine the diagnostic capacity of this link. The participants included 54 non-NASH control subjects, 27 NASH patients suffering from cirrhosis (the most advanced stage of the disease) and their first-degree relatives. The results were supported by data from two independent Chinese and Italian cohorts.

Two independent signatures

The results showed a loss of bacterial diversity in the NASH-cirrhosis patients. This was found to be correlated with certain clinical parameters, notably LDL levels, coagulation, and blood insulin levels. More importantly, a machine learning (sidenote: Machine Learning Automatic learning whereby artificial intelligence solves a task based on metagenomic and metabolomic data collected, in this case the identification of discriminating bacterial species. Wazid M, Das AK, Chamola V, et al. Uniting cyber security and machine learning: Advantages, challenges and future research. ICT Express, 2022; 8(3), 313-321. ) approach identified a bacterial signature for cirrhosis based on 19 species with a diagnostic accuracy of 0.91. This dysbiosis was associated with a functional signature, notably the biosynthesis of specific amino acids (aromatic and branched), fatty acids and nucleotides. These results, which were confirmed in independent cohorts, suggest that the dysregulation of essential microbial metabolic processes may contribute to the progression of the disease to cirrhosis. Therefore, altered metabolite production may explain how gut dysbiosis can affect the liver. To further support this potential causal link, an independent signature based on 17 metabolites was identified, which provided the same diagnostic accuracy as the microbial signature. Significant correlations were found between the two signatures.

Distinguishing cirrhosis from fibrosis

The researchers subsequently sought to refine this microbial signature. By also considering age and blood albumin levels, they slightly improved the signature’s precision in distinguishing cirrhosis patients from control subjects, and above all validated its effectiveness in the Chinese and Italian cohorts. Lastly, the inclusion of a highly discriminating additional parameter (increased levels of aspartate aminotransferase (AST) in the blood of cirrhosis patients) has made it possible to distinguish cirrhosis from early-stage mild to moderate fibrosis.

A non-invasive diagnostic tool or even a treatment?

The robustness of this intestinal signature across geographically and culturally distinct populations shows its potential as a diagnostic tool for cirrhosis. Some bacterial species in the gut microbiota may become a useful non-invasive and universal diagnostic tool, or even potential targets for new therapeutic approaches.

Introduction

Though a more rational use of antibiotics has long been overdue, we must not lose sight of the fact that over the course of the last 80 years their widespread use has saved many millions of lives. They have served as our principal weapon in the fight against bacterial infections. Alongside vaccinations, they have added around 20 years to the average life.¹

FROM THE ANTIBIOTIC ERA TO THE MICROBIOTA ERA

Unfortunately, antibiotics eliminate not only pathogenic bacteria, but commensal ones too.² The intestinal microbiota is affected, and likewise all the other human microbiota (cutaneous, lung, urogenital...) that protect against pathogen overgrowth. While it remains difficult to define a healthy microbiota with any precision or to provide an adequate description of dysbiosis, science is beginning to understand the ways in which antibiotics affect the functioning of these ecosystems and likewise the consequences of such changes for health over the short and long term³ (See Figure 1).

ANTIMICROBIAL RESISTANCE, A GLOBAL PUBLIC HEALTH PROBLEM

Because of the widespread overuse and misuse of antibiotics in humans and animals, bacteria causing both benign and life-threatening infections are becoming increasingly resistant to them. In 2015, antibiotic-resistant pathogens were estimated to be causing over 50,000 deaths each year in Europe and the United States.³ “Antibiotic resistance is one of the biggest threats to global health, food security and development today” states the WHO.

More and more evidence has come to signal Fusobacterium as an important intestinal bacterial pathogen associated with colorectal cancer. However, prior to a recent retrospective study, the bacterium’s role in locally advanced rectal cancer as well as its fate following chemotherapy and its involvement in tumor progression, all remained unknown. This study measured levels of F. nucleatum in the tumor microenvironment of 143 patients prior to the excision of their tumor: 87 of these patients were treated with neoadjuvant radiochemotherapy prior to excision, while the remaining 56 were control subjects.

Lower abundance of F. nucleatum with pre-operative chemotherapy

Visualization and quantification of F. nucleatum using in situ hybridization showed that the bacterium was mainly found on the luminal surface of the tumor and that radiochemotherapy significantly reduced its frequency. The density of F. nucleatum was significantly higher in untreated tumors than in treated tumors (median score of 7.4 versus 1.6), while 58% of tumors tested positive for F. nucleatum in control patients, compared to only 26% in chemotherapy patients.

Abundance is not harmful, but persistence signals relapse

The effects of treatment were evaluated using paired samples (taken before and after radiochemotherapy) from 71 patients. F. nucleatum abundance was not predictive of response to treatment. However, persistence of the bacterium following radiochemotherapy increased the risk of relapse by a factor of nine. Although no causal relationship has been confirmed, this may be due to a lack of immune cytotoxicity activation: tumors that became F. nucleatum-negative following treatment showed a strong increase in CD8+ T cells, whereas tumors that remained F. nucleatum-positive showed no induction of CD8+ T cells in post-treatment samples.

Persistence of F. nucleatum, a future biomarker?

Therefore, the persistence of F. nucleatum following chemotherapy may be associated with high relapse rates in locally advanced rectal cancer, a finding potentially related to the suppression of immune cytotoxicity. This promising biomarker for predicting the risk of relapse following neoadjuvant radiochemotherapy may lead to a more personalized clinical management of rectal cancer.

Defined as the inability to conceive offspring despite frequent sexual intercourse over at least a year, infertility affects 8% to 12% of couples of childbearing age. While IVF has quickly emerged as the most effective treatment, some women fail to become pregnant due to recurrent implantation failure (RIF). Hormonal, vascular, or immune disorders have recently been blamed, but such disorders cannot explain all embryo implantation failures. Already linked to numerous gynecological diseases and pregnancy-related disorders, might imbalances in the vaginal microbiota be involved in IVF failure as well?

An unbalanced, lactobacilli-depleted microbiota

To test this hypothesis, the vaginal microbiota of 67 women who had previously attempted IVF was analyzed. Of these, 27 had experienced unexplained RIF and 40 had carried their pregnancy to term following a single treatment cycle. The results showed the women who had experienced an RIF to be suffering from vaginal dysbiosis, specifically a more diverse and abundant microbial flora, with more bacteria linked to various genital infections (bacterial vaginosis, vaginitis, urinary tract infections). Conversely, their vaginal microbiota was relatively less rich in lactobacilli. According to the authors, the pregnancy rate exceeded 72% where lactobacilli made up more than 90% of the vaginal microbiota and fell to 34% where this was not the case.

Will the risk of IVF failure soon be predictable?

Lastly, the RIF patients also had different levels of certain substances produced by the vaginal microbiota, in particular significantly fewer of the molecules necessary for the implantation and development of the embryo, with this scarcity directly correlated to the reduced abundance of lactobacilli. The authors believe that the composition of the vaginal microbiota, and particularly lactobacilli depletion, plays a key role in the recurrent embryo implantation failure. They hope these results will pave the way for the development of biomarkers capable of predicting the risk of RIF.

Most people contract a respiratory syncytial virus (RSV) infection before the age of one. While symptoms are limited to a mild upper respiratory tract infection in most infants, 0.5%–2% of them develop a severe infection of the lower respiratory tract, such as bronchiolitis or pneumonia, requiring hospitalization. There is currently no vaccine or other preventive treatment for RSV.

Phylogenetic clusters

With the links between the intestinal microbiota and respiratory health becoming increasingly clear, a research team compared the microbiota of 37 healthy infants to that of 58 hospitalized infants with confirmed moderate or severe RSV infection. A fecal analysis using 16S RNA sequencing showed no significant differences in microbial diversity (alpha) among the three groups. However, the analysis did reveal phylogenetic clusters able to discriminate not only RSV infants from the control subjects, but also the 53 moderate cases from the 5 severe cases. In particular, when compared to the control subjects, infants with severe RSV infection showed an increased abundance of the S24-7 bacterial family in their gut microbiota, whereas bacteria from Moraxellaceae, Tissierella and Soehngenia families were found to be reduced

S24-7: a severity marker?

Within the S24-7 family, OTU (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 )  191 was of particular interest to the researchers, since it was more abundant in the severe cases than in either the control subjects or moderate cases. OUT 191 may therefore be an indicator of the severity of the disease. The hypothetic mechanism of action could be a potential interaction with the immune system. S24-7 bacteria carry genes that code for enzymes that degrade IgA, an immunoglobulin involved in the protection of mucous membranes and the prevention of upper respiratory tract infections. However, available data do not reveal whether S24-7 bacteria are the cause or the result of RSV infection, especially since IgA degradation or a modification of immune responses may be caused by other metabolites in the microbiota that are not associated with S24-7 bacteria. In any case, this study lays the groundwork for identifying microbial clusters associated with RSV infection and its severity. It may help identify infants at risk of developing severe RSV infection and lead to the development of immunoprotective microbial mixes.

Although relatively stable, the composition of the intestinal microbiota can evolve, favorably or unfavorably, due to multiple factors (diet, environment, health status, medication, etc.), with an impact on the metabolism. Studies have already shown the beneficial effects of physical exercise on its composition and diversity. But what about the intensive training of professional athletes? A team of Polish researchers tried to answer this question, comparing the microbiota of 14 marathon runners and 11 cross-country skiers with that of 46 sedentary subjects. Their objective was to determine whether there is any link between training level and bacterial composition.

A richer and more diversified microbiota

The intestinal microbiota of the high-performance athletes was richer and more diversified overall, ensuring better resistance to various diseases. This was all the more so when their diet was high-calorie and rich in nutrients (especially zinc and copper). As heavy consumers of vegetables and starchy foods, the professional athletes harbored more of the bacteria involved in breaking down fiber in their digestive tracts.

An influence on athletic performance?

Their microbiota was also richer in bacteria belonging to the large Firmicutes family and poorer in Bacteroidetes. According to a recent study, a high F/B ratio is associated with high oxygen consumption (VO2 max), which is essential to high-level athletes. Prevotella bacteria were also abundant in the athletes. They are associated with enhanced physical performance and were particularly common in the marathon runners. Another difference was the increased production, in the athletes, of certain molecules thought to improve degradation of sugars and fats and to enhance performance during strenuous exercise. So, does the level of training influence the composition of the microbiota? For the authors, the former shapes the latter, and the latter, in turn, contributes to the level of athletic performance.

From its early days, metagenomic research has sought to understand the links between the gut microbiota and obesity. Since 2012, MetaCardis (sidenote: European project involving over 2,000 participants in good health or at different stages of progression of cardiometabolic diseases (obesity, diabetes mellitus and cardiovascular disease). The participants were recruited in Paris (France), Leipzig (Germany) and Copenhagen (Denmark). www.metacardis.net )  has been studying the potential role of microbiota in the development of cardiometabolic diseases. Its work includes the characterization of the microbiota of 888 obese and non-obese subjects, more than 42% of whom reported taking at least one type of medication. The effects of the most common therapies were assessed, particularly those of statins.

An enterotype marker for inflammation?

Several links were found between obesity markers and gut microbiota in the 782 participants not taking statins. For example, stool softness and inflammation increased with body mass index (BMI), while BMI, body fat percentage and serum triglyceride levels were correlated with changes in the gut microbiota. Most importantly, a link was observed between the prevalence of Bact2 enterotype (high proportion of Bacteroides, low proportion of Faecalibacterium), BMI and inflammation. Thus, while only 3.90% of normal weight and overweight people had this enterotype, this percentage rose to 17.73% in obese individuals. Moreover, the greater the number of Bacteroides, the more acute the inflammation, including among slim people. In addition, the inflammation levels of participants with the Bact2 enterotype were higher than expected based on their obesity status alone, which suggests Bact2 is a potentially dysbiotic enterotype associated with low-grade inflammation.

Effect of statins on microbiota

Conversely, among the 106 participants receiving statins, the prevalence of Bact2 did not increase with BMI: among obese subjects, only 5.88% of those treated with statins had the Bact2 enterotype (vs. 17.73% of obese subjects not treated with statins). This result–confirmed on two separate cohorts–suggests that statins may limit alterations to the intestinal microbiota. Although the study did not establish a causal link between the drug and the lower prevalence of Bact2, two processes, or a combination thereof, may be involved:

• By influencing the growth of certain microorganisms, statins may counteract the role of gut bacteria in patients with inflammatory and metabolic obesity comorbidities

• And/or the anti-inflammatory effects of statins may attenuate the microbiota-host interactions and allow the subsequent development of enterotypes not associated with inflammation

New projects will be launched to verify whether statins have a direct effect on the bacterial flora or whether other factors (such as an improved lifestyle for people with higher awareness of cardiovascular risk) are involved.