For scientists, an “association” is where two phenomena occur at the same time, without necessarily having a cause-and-effect relationship. Is the gut dysbiosis (i.e. imbalance of the gut flora’s composition) observed in those infected with human immunodeficiency virus (HIV) a cause or a consequence of the disease? Or is it both? With only a few days to go before World AIDS Day on December 1st, the jury is still out, since the state of the gut microbiota prior to infection is not well known, and many other factors influence the appearance of dysbiosis, including age, diet, antibiotic use, and even sexual behavior, according to some recent data^2,3.  

To get a clearer picture, US researchers brought together gut microbiota samples from about 50 men who have sex with men, collected during different studies. They selected individuals with similar profiles (age, ethnicity, sexual behavior, etc.), half of whom were infected with HIV during the course of the studies, with the other half remaining HIV free. They were thus able to compare the gut microbiota of the infected men before and immediately after infection, and to compare the infected men’s gut microbiota with that of the healthy uninfected pairs.

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Minimal changes in microbiota before/after HIV infection... 

The authors first found that the composition of the infected men’s gut microbiota changed very little during the acute phase of HIV. Only increased Fusobacterium mortiferum was observed. Not normally resident in the gut flora, this bacterial species had already been associated with HIV in other studies.

... but significant pre-infection differences vs. controls

In contrast, the gut microbiota of the men who would go on to be infected with HIV (i.e., their “pre-infection” gut microbiota) differed from that of the controls (who remained HIV free). In particular, they had fewer bacteria from the Bacteroides group, and increased levels of Megasphaera elsdenii, Acidaminococcus fermentans, and Helicobacter cinaedi. This type of dysbiosis has frequently been observed in HIV-infected individuals. However, in this new study, the gut imbalance appears to have been present before infection, potentially influencing susceptibility to HIV, according to the authors.

Gut microbiota, a new tool for preventing HIV?

So, does gut microbiota composition play a role in susceptibility to HIV infection? Encouraged by similar conclusions from another US team⁵, the researchers propose that this avenue be followed up by studies on larger samples. They hope that this will identify a “gut microbiota signature” associated with greater susceptibility to HIV infection, thus allowing more targeted prevention via treatment of the gut microbiota of people at risk.⁶  

The researchers make it clear that this finding does not contradict the idea that HIV can itself cause dysbiosis. The short duration of the study meant it was not possible to observe the changes in gut microbiota composition that occur during chronic HIV. In addition, these results were obtained in a small group with a specific profile and thus generalizability beyond this population is limited.

With only a few days to go before World AIDS Day on December 1st, let’s take a look at the links between HIV and the microbiota. Numerous studies have associated changes in the gut microbiome with HIV infection. However, many of these studies have been cross-sectional and methodologically heterogeneous, and therefore subject to various confounding factors. HIV infection is known to be accompanied by gut dysbiosis and bacterial translocation linked to systemic inflammation, but the time course involved is not fully understood. Furthermore, recent studies have shown that, in addition to age, diet, and antibiotic use, sexual behavior also influences the gut microbiota, regardless of HIV status^2,3, further confounding the evidence.

Longitudinal study with bias controlled

 To measure changes in the gut microbiota and markers of inflammation during HIV infection, the researchers selected fecal and blood samples from four different longitudinal studies (USA, Peru) conducted over periods of 4 months to 2 years among men who have sex with men. Of these men, 27 were infected with HIV. The samples from the infected men were paired with those of 28 controls with similar demographic and behavioral characteristics.

Changes in the gut microbiota and inflammatory markers precede seroconversion 

The researchers noted few changes in the gut microbiota of subjects during the acute phase of HIV. In a subgroup from a US study, only an increase in Fusobacterium mortiferum was observed shortly after seroconversion, together with a decrease in Prevotella intermedia. The most significant differences were between pre-HIV infection subjects and controls. The gut microbiota of pre-HIV infection subjects showed reduced levels of several Bacteroides species and a higher level of Megasphaera elsdenii. They also had higher plasma levels of inflammatory cytokines (B cell activating factor, IL-8, TNF-α).

Gut microbiota, a targeted prevention option?

According to the authors, the study suggests that the changes to the gut microbiota existed before HIV infection. Together with similar results from another US team⁴, this shows that gut dysbiosis is a contributing factor to HIV rather than a consequence of it, even if dysbiosis is subsequently observed in chronic HIV. The observation period of the study was too short for the researchers to identify subsequent changes. In addition, the small sample size and the specific characteristics of the participants (sex, age, drug use, sexual behavior, etc.) may also limit generalizability. However, the researchers believe that the discovery of a gut signature for HIV susceptibility and/or inflammatory markers may provide a new tool for targeted prevention.

Recommended by our community

This new format is dedicated to irritable bowel syndrome (IBS). It’s estimated that 10% of people suffer from IBS, but 75% of those affected by the disease remain undiagnosed. This is because the disease cannot be explained by any detectable physical anomaly.

The first episodes in our series have been produced with the support of the French Association of Irritable Bowel Syndrome Patients (APSSII).

Jennifer is 32 years old and works as a product manager in the fashion industry. She was diagnosed with irritable bowel syndrome at the age of 29, after 21 years of wandering between health professionals.

Following a period of acute appendicitis, Mihai, 25, developed irritable bowel syndrome. He tells us how his daily life has been turned upside down since diagnosis, and discusses the constraints he now faces.

Aline, 50, has suffered from Irritable Bowel Syndrome since childhood. Despite the difficulties in her daily life, she has now learned to live with the disease to lead the most normal life possible.

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The gut microbiota interacts with the central nervous system and is involved in numerous diseases, including mental illnesses. It determines the way the body adapts and responds to its environment, which may include our responses to alcohol consumption. Some people seem to enjoy and/or tolerate alcohol more than others, while others are more prone to abuse and addiction. Spanish researchers have explored the links between the gut microbiota and behavior towards alcohol in humans and animals.

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Gut microbiota and transit modified in heaviest drinkers

The researchers used a questionnaire to assess the weekly alcohol consumption in grams of 507 students (83.3% female, mean age 19.8 years), taking into account the type and amount of alcohol consumed, the time elapsed between 2 drinking episodes, and the subject’s weight. The appearance of the participants’ feces was classified according to the Bristol scale. While nearly 55% had type 3 stool, the heaviest drinkers tended to have type 1, with a linear relationship between stool type 1 and alcohol consumption. This result was unexpected, since alcohol abuse is usually associated with diarrhea. To study the effect of alcohol consumption on the composition of the gut microbiota, the researchers analyzed fecal samples from the 17 non-drinkers in the cohort and from the 17 heaviest drinkers. Alpha diversity (sidenote: α diversity A measure indicating the diversity of a single sample, i.e. the number of different species present in an individual. Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 2010;4:17-27. https://www.nature.com/articles/ismej200997 ) did not differ significantly between the two groups, but beta diversity (sidenote: β diversity A measure indicating the species diversity between samples, it allows to assess the variability of microbiota diversity between subjects. Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 2010;4:17-27. https://www.nature.com/articles/ismej20099 ) showed a greater abundance of Actinobacteria in the heavy drinkers.

Rats receiving a transplant develop a taste for alcohol

The researchers then induced alcohol dependence in 8 rats via intragastric administration of alcohol for ten days, until signs of withdrawal appeared. Fecal samples were taken from these animals and transplanted into recipient rats. Two weeks later, the voluntary alcohol consumption among the latter was 27.4% higher than among controls. This time-lapse suggests that the new microbiota is the cause, rather than a consequence, of increased alcohol consumption. A gut microbiota analysis in the alcoholic donor and recipient rats suggests that the genus Porphyromonas, which was significantly less abundant in these animals than in controls, may be associated with the urge to consume alcohol. The researchers did not find any bacterial genus with increased content, but noted that in other studies, Actinobacteria were more abundant in alcoholic mice, just like they are in humans.

They believe the implanted microbiota to be a predisposing factor: when alcohol is added, this new microbiota somehow favors the abundance of bacteria that benefit the most from alcohol consumption. Moreover, given the observed reduction in locomotor activity in the recipient rats, the implanted microbiota may also modify their behavior towards alcohol by influencing cerebral dopaminergic neurotransmission and the brain’s reward system.

Managing alcohol use disorders via the microbiota

To conclude, the authors believe that this study supports a link between the gut microbiota and alcohol consumption. Furthermore, treating the gut microbiota with probiotics and/or prebiotics may help manage alcohol use disorders. The relevant genera and species have yet to be determined.

Studies show that alcohol influences the composition of our gut microbiota, which in turn influences our behavior. But does the gut microbiota influence our behavior towards alcohol? Spanish researchers have explored this hypothesis by comparing the weekly alcohol consumption and gut microbiota composition of 507 students. They first noted that the “heavier drinkers” had harder stools typical of constipation. This came as a surprise since alcohol was thought to cause diarrhea. They then found that the main difference in gut flora composition between the students who drank the most alcohol and those who did not drink was that the former had significantly higher levels of Actinobacteria (sidenote: Actinobacteria Actinobacteria are one of the gut microbiota’s four major bacterial groups (phyla), together with Bacteroidetes, Firmicutes, and Proteobacteria. Notable among Actinobacteria are Bifidobacteria, the most common Actinobacteria in the gut flora. Binda C, Lopetuso LR, Rizzatti G, et al. Actinobacteria: a relevant minority for the maintenance of gut homeostasis. Digestive and Liver Disease. 2018 May 1;50(5):421-8. ) .

Rats receiving the microbiota of alcoholic conspecifics develop a taste for alcohol

The scientists continued their research on rats by making them dependent on alcohol and transplanting their fecal microbiota into “sober” rats. Two weeks after the procedure, when given a choice between water containing alcohol and pure water, the formerly sober rats were more likely to prefer the water containing alcohol than “control” rats. According to the researchers, the time-lapse suggests that the new gut microbiota composition is the cause, rather than a consequence, of increased alcohol consumption. In the recipient rats, the gut microbiota of the alcoholic rats is a predisposing factor in an increased desire to consume alcohol, which in turn favors the abundance of certain “alcohol-loving” bacteria. Through the “gut-brain axis“, the gut microbiota may also affect the so-called “reward” neuronal circuits, which are involved in the development of addictions.

The scientists thus believe that the gut microbiota modifies our behavior towards alcohol. A recent study, this time on humans, seems to confirm this, but with a more positive outcome: alcoholics saw their cravings for alcohol strongly reduced after a fecal microbiota transplant from non-alcoholics.

Probiotics, a solution to alcoholism? 

A gut microbiota analysis in the alcoholic donor and recipient rats suggests that the bacterial genus Porphyromonas, which was less abundant in these animals than in controls, may be associated with the increased urge to consume alcohol. The researchers did not find any bacterial genus with increased content, but noted that in other studies, Actinobacteria were more abundant in alcoholic mice, just like they are in humans. However, they believe that treating the human gut microbiota with, for example, probiotics and/or prebiotics, may help manage alcohol use disorder. The relevant genera and species have yet to be determined.

Discover content to keep your microbiota healthy during the festive season. We wish you a merry Christmas and a happy microbiota!

Good resolutions to take care of your intestinal flora

No need to feel guilty, the holidays are good for our gut microbiota!

It’s a well-known dietary trick: avoid weight gain by replacing sugar in our diet with non-nutritive sweeteners (NNS). Although usually considered risk-free, previous studies in mice have found that these ingredients could disrupt the intestinal microbiota and glycemic response. The same team this time explored the effects of NNS in humans using a randomized controlled trial of 120 healthy adults divided into six groups. Four groups were administered sachets containing, respectively, sucralose, saccharine, aspartame, or stevia, all at doses lower than the acceptable daily intake (sidenote: The acceptable daily intake, or ADI, is the estimated quantity of a substance in food or drinking water that can be ingested daily over a lifetime with no appreciable health risk. ) for these substances. Because the sweeteners contained glucose (vehicle ingredient), a fifth group was given sachets of glucose (glucose control) and a sixth received no supplement at all (no supplement).

Sweeteners modify the microbiota and its functions...

Sequencing (shotgun) found that the four sweeteners caused specific changes (i.e., specific to each NNS) in the composition and/or metabolic function of the intestinal microbiota and oral microbiota. The most marked effect on intestinal microbiota was observed in the sucralose group. However, only sucralose and saccharine had a significant effect on glucose tolerance, with an increase in glycemia in both groups.

...with possible repercussions for the glycemic response

The changes seen in the intestinal microbiota, its functions, and the circulating metabolites mediated by the various NNS were correlated with the participants’ glycemic response. To determine whether these changes were the cause of the glycemic disruption, the researchers transplanted into axenic mice (sidenote: Germ-free mice mice that have no microbes at all, raised in sterile conditions. ) the intestinal microbiota of selected individuals from the four test groups: those whose glycemic response was most affected (top responders) and least affected (bottom responders) by the NNS. The glycemic responses observed in the mice reflected the observations in the respective human donors, thus corroborating the causal hypothesis.

A person-specific, microbiota-dependent response to NNS

Finally, the researchers showed that the intestinal microbiota of the top vs. bottom responders evolved differently during exposure to the various NNS, possibly due to differences in baseline status. This led the researchers to compare the microbiota to a center of reactivity or adaptation that conditions physiological response to sweeteners, with effects only in certain individuals with a specific microbiota.

Guilt-free pleasure, the sweet taste of sugar without either the calories or the health problems (obesity, diabetes etc.) likely to rear their ugly heads if we eat too much: such is the promise of sweeteners, these sugar substitutes that we add to drinks, “diet” fizzy drinks and even “diet” cookies, which are increasingly popular among consumers. Could they be too good to be true? That is what an Israeli study of 120 adults asked to use one of four sweeteners for two weeks (sucralose, saccharine, aspartame or stevia) suggests.

A varying impact on blood sugar, depending on the individual

Ironically, some of the groups taking the sugar substitutes (sucralose and saccharine) soon recorded an abnormal rise in their blood levels of...sugar (glycemia). However, within a single group, there was a wide range in glycemic response between individuals. Given this variability, the researchers turned their attention to the gut microbiota gut microbiota, which is specific to each person and already known to play a direct role in digestion. They found that the four sweeteners, affected the composition of the intestinal (and oral) microbiota and/or its functions, each in its own way. These changes were correlated to the effects on blood sugar levels, suggesting a causal link.

The gut microbiota, a “hangout” for sweeteners

Wanting to be sure of their findings, the researchers transferred the gut microbiota of the participants into axenic (sidenote: Germ-free mice mice that have no microbes at all, raised in sterile conditions. ) mice. In confirmation of their hypothesis, this sole step was enough to reproduce in the recipient mice the same glycemic responses observed in their respective donors. In other words, the mice had a higher blood sugar level if they had received microbiota from participants whose blood sugar level was also affected. This led the researchers to compare the microbiota to a center of reactivity, producing a greater or lesser reaction to sweeteners depending on its make-up.

Although some individuals seem better protected by their microbiota against sweeteners than others, these results cast serious doubt onto the supposed inertia of these substances. Pending further studies to clarify the health recommendations, your next can of soda, whether sugar-full or sugar-free, may leave a bitter taste in your mouth.

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To mark World Antimicrobial Awareness Week (18-24 November), the Microbiota Institute is handing the floor to two antibiotic resistance’s experts: Dr. Windi Muziasari (sidenote: Dr. Windi Muziasari has gained years of experience and the know-how to monitor antibiotic resistance in the environment using a high-throughput gene profiling during her PhD and PostDoc at the University of Helsinki, Finland. She wanted other researchers to gain easy access to this technology and that was why she moved from academia to entrepreneurship by founding Resistomap in 2018. Headquartered in Helsinki, Resistomap's mission is to mitigate the spread of antibiotic resistance by providing robust tools for monitoring. Resistomap combines molecular genetics methods and data science to provide a service to detect and quantify antibiotic resistance genes from environmental samples such as wastewater and soils. Since fully operating in January 2019, Resistomap has served over 250 projects and analysed over 7000 environmental samples across 40 countries. ) , PhD, CEO of Resistomap, and Pr. Christian G. Giske (sidenote: Christian G. Giske is the head physician of bacteriology, mycobacteriology and mycology at Karolinska University Hospital, Solna, Sweden. He is also the head of the Division of Clinical Microbiology and the Division of Clinical Immunology at the Department of Laboratory Medicine at Karolinska Institute, where he also leads a research group. The most important research activities in Giske’s research group pertain to deep-characterization of molecular mechanisms of resistance, virulence, and molecular epidemiology of extensively drug-resistant enteric bacilli. Giske’s research is strongly translational, involving extensive collaboration with infectious diseases (including mycobacteriology), hematology, and intensive care. Giske also has extensive international collaboration, serving in the advisory board of ECDC’s European resistance surveillance, and as the chair of the European Committee on Antimicrobial Susceptibility Testing. ) from Karolinska Institute in Sweden.

Why is antibiotic resistance a major public health problem?

Antibiotic resistance is indeed a global health threat that causes more than 1,2M deaths annually¹. Antibiotic resistance is the condition when antibiotics are no longer efficient to treat bacterial infections. This can lead us back to the era before antibiotics were first discovered by Alexander Flemming in 1928. Bacterial infection diseases such as tuberculosis, pneumonia, and simply urinary tract infection could kill us again and in a worst-case scenario, performing any surgery and delivering a baby could have high mortality rates. Antibiotics are heavily used in both human and animal medicines which accelerate the increase of antibiotic resistance levels in bacteria.

Antibiotic resistance is in fact a web of several problems. It varies a lot between geographical settings whether the problem is confined to hospital-acquired infections or also widespread in the community. The results of antibiotic resistance are well documented – it leads to increased mortality, longer hospital stays, increased costs for healthcare, and more side effects related to the treatment. In many cases some hospital-acquired infections can be extremely difficult-to-treat. Antibiotic resistance will also lead to fear of complications to complicated surgery and/or immunosuppressive treatment – infections with highly drug resistant strains that will severely compromise results of other treatments. Hospital-acquired infections will usually not affect so many individuals, but still represent a public health problem due to the fear that resistant infections cannot be managed. On an individual patient level, the consequences can be dire, but also for patients in the same unit in the hospital to which resistant strains can be transmitted. Community acquired infections will affect more individuals and will also lead to increased hospitalization and thus affect the capacity in health care. There is not one single solution to the antibiotic resistance problem – rather a complex combination of several mitigation approaches is needed.

You’re monitoring antibiotic-resistant genes at hospitals by collecting wastewater samples. Can you explain why, and why are you not collecting samples directly from patients to quantify these genes?

W. Muziasari: There are two important limitations to how antibiotic resistance is currently monitored in hospitals. First, current monitoring focuses mainly on a limited number of pathogenic bacteria. Second, it is often based on passive surveillance of bacteria isolated from patients. This leads to delayed detection of outbreaks, non-comparable data, and the inability to capture other pathogenic bacteria and antibiotic resistance profiles which are often carried by commensal bacteria. 

Wastewater-based monitoring will be a potentially valuable addition to current options for antibiotic resistance monitoring in hospitals. Though not a substitute for existing monitoring methods, wastewater monitoring can provide data that is otherwise hard to obtain and become the easiest means for obtaining comprehensive information on the prevalence of resistance in hospitals. As waste from all patients are released into wastewater, wastewater monitoring can cover a wider range of antibiotic resistance profiles compared to the partial data from a few selected pathogenic bacteria. In addition, analyzing wastewater samples does not require informed consent, thus limiting ethical concerns. The practical and logistical barriers for sampling wastewater are also limited. Wastewater-based monitoring can therefore be used to better understand the development and spread of antibiotic resistant bacteria in hospitals and serve as an early warning system for future outbreaks.

How does your research & technology help physicians to prevent antibiotic resistance?

W. Muziasari: Through wastewater-based monitoring physicians will have in-depth information on the levels of antibiotic resistance from their hospitals over time.

What is the connection between antibiotic resistance and microbiota?

C. G.Giske: Many resistant strains are first acquired as colonizers in the human microbiome – either intestinal or respiratory. Once the strains are acquired in the microbiome, they can establish there as long-term carriage and will sometimes cause infections in the host, or potentially spread to other individuals who may be more susceptible to bacterial infections. Thus, carriage of resistant strains remains a significant risk for resistant infections in either the host or in other people in the proximity of the original host. While in the microbiome, strains can also easily exchange genetic material and thus transmit resistance to other bacterial strains – sometimes strains that are more adapted to the gut of that individual and can therefore remain in the microbiome for very long. Monitoring carriage of resistant strains in the microbiome remains an important part of infection control, as it can inform decisions on patients who need to be hospitalized in single rooms by dedicated staff for instance – to avoid transmission events.

Could microbiota help researchers to tackle antibiotic resistance?

C. G.Giske: The microbiome is complex and contains a variety of microorganisms – among them also viruses. Some of the viruses, the so called bacteriophages, can infect selectively bacterial strains and kill them. Such bacteriophages can be isolated from the microbiome and could be used therapeutically to treat infections in patients. Numerous studies highlight the in vitro and in vivo potential of their therapeutic uses and while a number of clinical trials have taken place over the last decade, the biggest challenge remain to produce additional data presenting a robust regulatory case for their clinical use². Moreover, monitoring resistance in the microbiome can be highly informative for understanding the pool of resistance genes available in a population and can be very useful to design strategies for counteracting antibiotic resistance.

We now know that a diet rich in sugar and fat contributes to increased gut inflammation, and that the gut’s immune system plays a key role in metabolic homeostasis. We also know that the gut microbiota is an important modulator of gut immunity and that it influences metabolic functions as well. Lastly, we know that cells such as type 3 innate lymphoid cells (ILC3) and T helper 17 cells (Th17) may be involved, depending on the context, in protecting against metabolic syndrome. However, the series of molecular mechanisms linking the high-fat diet (HFD) to its metabolic effects remains poorly understood.

To shed some light on the matter, researchers fed mice on an HFD diet or a normal diet for four weeks. Unlike the second group, the HFD group developed a typical metabolic syndrome, involving weight gain, insulin resistance, and glucose intolerance. Analyses of the gut mucosa and feces of the HFD mice revealed that the HFD diet induced a rapid loss of segmented filamentous bacteria (SFB) in the gut microbiota, which in turn led to the loss of Th17, and ultimately the onset of metabolic syndrome.

Probiotics restore protection against metabolic syndrome

Investigations on the involvement of other immune cells such as ILC3 or CD4 T cells allowed the researchers to affirm that the gut microbiota needs Th17 cells to protect against metabolic syndrome. These additional investigations also showed that the loss of Th17 cell homeostasis via the elimination of SFBs was indeed involved in the adverse effects of the HFD diet. 

Next, the mice were fed SFBs by oral gavage for four weeks, which resulted in: 

• Significant recovery in Th17 cells and their expression in the gut 
• Decrease in gut inflammation
• Weight loss
• Protection against insulin resistance 

A microbial diet that stimulates Th17 cells may therefore improve metabolic syndrome and diabetic obesity by recalibrating gut immunity homeostasis.

Is sugar the main culprit in the Western diet’s harmful effects?

However, knowing that in addition to fat, the Western diet is also rich in sugar, the researchers compared the effects on mice of the HFD diet (25% sugar, including sucrose and maltodextrin, common in candy and soda) with the effects of another diet very low in sugar (3%-6%). They found that sugar indirectly reduced Th17 cells by increasing gut microbiota levels of bacteria such as Faecalibaculum rodentium at the expense of SFBs that promote Th17.

A diet that treats metabolic syndrome? Not so fast...

While sugar has been shown to be enough to cause the concomitant loss of SFBs and Th17 cells, the elimination of dietary sugar only has a therapeutic benefit where the appropriate immune cells are present in the gut. A simple change of diet may not be sufficient in some people. The researchers believe their work shows that metabolic syndrome, obesity, and type 2 diabetes mellitus are regulated by a complex network of interactions between diet, the gut microbiota, and immune cells. The management of these diseases cannot therefore be identical for each patient. Accordingly, in the future, precision therapeutic approaches should take into account differences between individuals in terms of the gut microbiota’s immunomodulatory system.