Eating more vegetables appears to improve microbiome-mediated health indicators

There are many diets that have been rigorously shown to decrease metabolic syndrome (obesity, diabetes, etc.) and are generally associated with a healthy lifestyle, such as vegetarian, vegan, and Mediterranean diets.  The one thing they share in common is a high consumption of plant material, and a low consumption of meat.  There are mechanistic reasons for why high veggie - low fat diets should improve health, and many researchers now believe this is partly due to the gut microbiome that these diets create.  In order to help demonstrate the microbiome-mediated health benefits of a high vegetable – low meat diet, a team of researchers from Italy recently measured the microbiome and specific metabolites produced by the microbiome in 153 individuals.  They then compared these results with the diet that the individual had consumed prior to the measurements, and confirmed that these ‘healthy’ diets were creating ‘healthy’ microbiomes.  They published their results in the journal Gut.

The scientists asked 51 vegans, 51 vegetarians, and 51 ominivores individuals to self-declare their eating habits over the past seven days, and then sampled their stool and urine for bacteria and metabolites.  They learned that amongst the different types of diet the individuals’ overall microbiome diversities were relatively similar.  However, they did show that Bacteroidetes were more prevalent in vegetarians and vegans than in ominvores, and that a higher Firmicutes to Bacteroidetes ratio existed in the guts of ominvores than in vegans and vegetarians.  In addition, the abundance of Prevotella, which is normally associated with health, was positively correlated with overall vegetable intake, and on the contrary Ruminococcus was negatively associated with a high vegetable diet.

The scientists also measured specific metabolites in the individuals.  They discovered that short chained fatty acids (SCFAs), which are normally implicated with health, were associated with the consumption of fruits, vegetables, and legumes.  In addition, there were positive associations between SCFAs and specific populations of bacteria, such as Prevotella.  On the other hand, the metabolite trimethylamine oxide (TMAO), which is a microbiome metabolite whose concentration is directly related to atherosclerosis and other diseases, was significantly lower in vegetarian and vegan diets compared to omnivore diets. It was also directly associated with the abundance of the aforementioned Ruminococcus. 

These relationships between SCFAs and veggies are unsurprising, because SCFAs are the byproducts of bacteria breaking down the complex glycans found in fiber.  In addition, the TMAO is produced by gut bacteria from carnitine and choline, two molecules that exist in red meat and eggs, among other things.  Regardless though, this study should remind us that our diet can shape our microbiome and have lasting health effects.  This study only reinforces that a diet high in veggies that feeds the microbiome is probably a healthy choice.

Can hookworms fight against celiac disease?

Helminths, or gut worms, are native inhabitants of our microbiome that are known to have substantial immunosuppressive effects.  Some scientists believe they are a keystone species in the microbiome and that their absence in people following a Western lifestyle may be contributing to the rise in autoimmune diseases, such as celiac disease.  In fact, scientists have recently shown that hookworm infection leads to higher gluten tolerance in individuals with celiac disease.  The cause of hookworm’s broad immunosuppression is unknown, but those same scientists investigated the possibility that it may be caused by the worms’ ability to modulate the bacteria in the gut.  The researchers recently tested this hypothesis and published their results in Nature Scientific Reports.

First, the researchers measured the fecal microbiota of eight human subjects with celiac disease, all of whom had followed a gluten free diet for at least five years prior to the trial.  Compared to a control group that hadn’t followed a gluten free diet, the trial subjects had a greater abundance of Bacteroidetes, while the control group showed greater abundance of Firmicutes.  Next, the subjects were successfully infected with hookworm and gluten was slowly reintroduced into their diets over a period of 44 weeks. The scientists measured the subjects gut microbiota at different time points and discovered that the hookworms, in conjunction with the gluten introduction, restored levels of Firmicutes in the celiac disease patients.  By the end of the study all of the remaining participants had rich abundances of both Bacteroidetes and Firmicutes.

It should be noted, and the authors admit, that the study is limited by its small sample size.  Still though, the results lead one to believe that helminths are modulating the microbiome, and that this may contribute to the overall immunosuppressive effects of these worms.  People have been known to practice helminth therapy to achieve immunosuppression in the gut, however this is dangerous for a number of reasons.  Instead researchers, such as the ones that performed this study, are in search of the mechanism for this immunosuppression.  There is certainly some very interesting biology that occurs during a helminth infection, and hopefully sometime soon scientists can turn these helminths into therapies.

Helminths may provide therapeutic benefit to treat brain disorder

We’ve recently talked about a few articles that have studied helminth infection with respect to the microbiome, and how these infections could possibly confer some therapeutic benefits.  Another recent study conducted by researchers at Duke University reinforces these findings.  Autoimmune and inflammatory disorders appear to be more common in developed societies, and many have suggested that the microbiome is a major driver of these changes to our immunity.  These investigators wanted to assess whether or not helminths – which have a lot of influence on the immune system – had any effect in modulating the brain immune system in the context of living conditions and early-life infection, as this has been shown to result in neurodevelopment disorders. 

In this study, male and female rats were infected with a H. diminuta cystercircoid rat tapeworm a few weeks prior to breeding.  The rats were segregated by living conditions, housed in either dirty colonies (or “farm-like” environments), where no water or air filtration was provided) or standard clean pathogen-free laboratory conditions.  The offspring in both environments were delivered helminths, and the males were infected with E. coli early in life. 

Later in adulthood, the immune systems of the progeny animals were challenged by lipopolysaccharide (LPS) inductions in learning tests, and brains were collected shortly after to examine changes in molecular immune responses.  Exaggerated immune responses were observed in rats that were infected with E.coli early in life in the standard clean lab conditions.  Alternatively, the cohort that lived in the farm-like conditions did not experience an increase.  Both groups were infected with helminths.

To narrow down further, the researchers examined the impact of helminths alone in rats housed under clean pathogen-free laboratory conditions.  Indeed, cytokine responses in rats infected with E.coli were reduced in the animals whose mothers were infected with helminths before giving birth.  In addition to immunologic modulation, helminth infections in adult rats where shown to reduce memory deficits that are common following E. coli infection, suggesting helminth infection played a role in modulating developmental disorders due to bacterial infection. 

The helminths also had an effect on the microbiomes of the rodents.  16s rRNA sequencing revealed an average 25% shift in microbiome composition of animals infected with helminths (with a predominant shift of Bacilli to Clostridia).  Rats that were infected with E. coli early in life experienced a microbiome composition shift in adulthood, as more harmful Bacteroidetes species were found in adults.  Interestingly, this observation was not found in those who were E.coli infected but also infected with helminths, suggesting helminths prevented this composition shift. 

Overall, these findings suggest that helminths could provide therapeutic benefit, especially after infection early in life.  It will be interesting to see how this research can translate to human models, especially by narrowing down bacterial infections that could harm or benefit development.  Understanding what drives these developmental complications could have immense health benefits for the public. 

Microbiome composition of children infected with helminths

Schistosoma parasite worm, otherwise known as a blood fluke.

While much has been explored regarding the microbiome’s role in nutrition and immunology, more research is needed in uncovering interactions between the host microbiome and infection as this represents a high unmet medical need.  A few weeks ago we talked about a study that describes an interesting relationship between helminth infection and sensitivity to insulin in Indonesia.  Helminth infections are also prevalent in sub-Saharan Africa, where many children become exposed to Schistosoma haematobium, causing schistosomes and dramatically affecting childhood health and development.  Researchers from Africa sought to investigate whether there were significant differences in microbiome composition between children who were infected with S. haematobium and those who were not.  Furthermore, investigators explored whether praziquantel (PZQ) – an effective agent that kills schistosome worms – has any influence on the human microbiome composition of infected patients. 

Stool samples were collected from 139 pediatric patients from six months to 13 years old, and groups were segregated following proper diagnosis of S. haematobium infection.  DNA was extracted from the samples and microbiota were characterized using 16S rRNA sequencing.  Overall microbiota compositions were similar across sex and all age groups, and Bacteroidetes phyla were found to be most abundant.  However, there was a significant difference in operational taxonomic unit (OUT) microbiota clusters (a measurement that categorizes bacteria colonies) between infected and non-infected groups.

In the next experiment, researchers investigated the microbiomes in the 62 patients who took the PZQ therapy, comparing microbiota after 12 weeks of treatment to their baseline compositions (i.e., prior to PZQ administration).  Interestingly, there was no statistical difference in microbiota composition in patients between pre and post administration time points. 

Though this study did not necessarily present breakthrough findings, the researchers presented more data that will assist doctors and clinicians to better understand helminth infection with respect to the microbiome.  Learning more about the exact differences in microbiota composition between infected and non-infected children will advance our understanding of interactions that could potentially lead to a novel and much-needed therapy.  

What happens to dietary fiber after we eat it?

Complex carbohydrates from dietary fiber, such as from fruits and vegetables, are, with some exceptions, largely indigestible to normal human metabolism.  These polysaccharides though, form the basis for much of the gut microbiome’s nutrition because they pass into the colon largely unaffected.  For this reason, many scientists are considering complex carbs as prebiotics, or foods that can manipulate the microbiome to improve health.  At this point in time, the fate of many prebiotics in the gut, and the mechanisms by which they are broken down and shared by the microbiome bacteria, are still largely unknown.  Last week a paper in Nature Communications investigated this question, and measured the breakdown of complex xylose molecules in the gut.

The researchers discovered that Bacteroidetes have many different enzymes to break down complex xylans, and regulate and induce different ones based on the type of xylan, e.g. whether or not it has many long chains stemming from its backbone.  They then discovered that these enzymes work in conjunction with one another to break down highly complex structures into smaller oligosaccharides.  These breakdown products are often released into the lumen of the gut where other bacteria can feed on them.  As it turns out, the initial xylan is most important to determining which smaller xylans are produced by Bacteroidetes, and therefore which other bacteria will benefit from the xylan metabolites.  Taken together, this study illustrates the complex ecology of the gut, with some bacteria breaking down large carbohydrates into smaller pieces, and other breaking those down into even smaller pieces, until finally a xylose monosaccharide is broken down into a short chained fatty acid.

Overall, this study lends itself to the value of prebiotics.  Clearly, the food we eat affects the composition of the microbiome.  We are now learning the mechanisms by which this happens, through a hierarchical food chain in the gut.  Once these are completely understood scientists should be able to produce foods that will controllably alter the populations of the gut, which could lead to methods to combat a variety of diseases.

Asthma could be brought on by maternal diet and lack of bacterial metabolites

Asthma has become increasingly prevalent in Western societies, and while many theories have been explored as to the reason for this rise in prevalence, many are beginning to explore connections between dietary intake and associations with the microbiome as a manifestation for this malady.  High fat, low fiber diets – which are common in the West – are associated with high rates of asthma.  Investigators in Australia sought to explore this relationship further by understanding the cellular underpinnings of these associations.  Specifically, they explored whether or not high fiber diets in mice could suppress the onset of Allergenic airway disease (ADD -i.e. asthma).  Furthermore, maternal fiber intake was also examined to see what affects would result for the progeny when challenged with asthma inducing conditions.  They published the results in Nature Communications.

Using 16S sequencing the researchers first confirmed that the high fiber diet shaped gut microbiome composition in mice.  Specifically, a significant difference was observed between control diet and no fiber diet.  Bacteroidetes were highly abundant in mice that were fed the high fiber diet, including high acetate producing Bacteroides acidifaciens strain, while Proteobacteria were found abundant in the no fiber diet.  High fiber diet mice also displayed higher levels of short-chain fatty acids, metabolic products of the gut microbiota that provide overall positive health benefits. 

Turning next to the pathology, experimenters were first able to validate that HDM did indeed induce AAD, as confirmed by inflammatory cells and signal markers found in the bronchoalveolar fluid of mice.  Indeed, mice that were on the high fiber diet did not develop AAD symptoms.  Interestingly, this was also shown in control animals who were administered HDM but were provided acetate (a short-chain fatty acid) in their drinking water. 

Mice were then bred and split into three dietary groups based on diet, a control group, high fiber group, and no fiber group.  Allergenic airway disease (AAD) was induced using a house-dust mite (HDM) model which replicates certain aspects of human asthma.  Diets were provided three weeks prior to sensitizing the animals to HDM, and AAD was evaluated after 16 days following 15-day HDM exposure.

Pregnant mice were also subjected to the three different diet regiments in the previous experiment.  The offspring were born and given a control diet, but after 6 weeks they were administered AAD.  The mice that were born from mothers on the high fiber diet did not develop AAD into adulthood, demonstrating that maternal diet can suppress AAD in adult offspring.  Interestingly, these findings were correlated with human data that demonstrated that high fiber diets in mothers’ in late-stage pregnancy was correlated to high acetate in serum samples.  Maternal acetate levels above median levels of samples taken was associated with significantly less visits to the general practitioner for wheezing complaints and/or asthmatic incidences in their children.    

Increasing numbers of studies are showing similar patterns that behaviors of the mother can affect microbiome transfer to progeny, consequently affecting the health and development of the offspring.  One of these important factors as we have seen is the diet of the mother.  As further evidence is uncovered as to the importance of high fat diets and specifically the diet of the mother, it will be important to have conversations on the best way to educate the public about this evidence as well as implement recommendations for dietary habits during pregnancy.