Red wine and coffee modulate the microbiome

Prebiotics are foods that alter the microbiome.  They are important to many potential microbiome therapeutics because they could be used to shift the microbiome from a dysbiotic, or unhealthy state, to a normal healthy state.  Most scientists that study prebiotics investigate indigestible fiber, because these are known to survive digestion are broken down by specific microbes, thus predictably selecting for specific organisms’ growth.  Recently though, other prebiotics are being studied.  A major class of these are polyphenolic compounds, which provide the antioxidant characteristics of plant material.  Last week researchers from Spain studied the shift in the microbiome that may be induced by red wine and coffee in particular.  They published their results in the journal Food & Function.

The researchers studied 23 patients that had allergic rhinosinusitis or asthma as well as 22 age-matched controls.  They chose individuals with autoimmune diseases because of the promise of prebiotics affecting their diseases.  They asked all of the individuals to fill out a food survey of what they had eaten in the past year, and how often they ate it.  After, the scientists took samples of their feces and measured the bacteria within it.  The scientists found that the abundance of Clostridium, Lactococcus and Lactobacillus was directly associated with polyphenol intake from coffee, and that Bacteroides was positively associated with red wine consumption.  Unfortunately, they noted that these did not differ between allergic people and healthy ones.

This study was certainly lacking in its scope and rigor.  It did not attempt any interventional studies to controllably reproduce these effects, and it did not identifiy specific polyphenols that are responsible.  Nonetheless, it does begin to define how alternative prebiotics may affect our microbiome.  Polyphenols in particular are linked to all sorts of health benefits, normally attributed to their anti-oxidation, however perhaps they positively impact the microbiome as well. 

Microbiome differences between healthy people and those with IBS

Methane (above) is produced by Methanogens, which are increased in the guts of healthy individuals compared to those with diarrheal IBS.

IBS affects somewhere around 11% of all humans.  It is not known exactly what causes the disease but it is characterized by a low grade inflammation in the colon which can manifest itself as cramping, bloating, diarrhea, constipation, and overall abdominal discomfort.  Many scientists now believe this is a microbiome mediated disease that is caused by some sort of dysbiosis in the gut, unfortunately efforts to characterize exactly what differences occur in IBS individuals have not been successful.  A new article published last week in Nature Scientific Reports describes newly discovered differences in butyrate and methane producing bacteria in the guts of people with IBS.

The scientists sequenced the microbiomes of 66 healthy controls and 113 folks with IBS, at two time points 1 month apart.  They discovered that IBS patients had higher amounts of Bacteroides and lower levels of Firmicutes than healthy individuals, as well as an overall lower microbiome diversity.  In addition, there were no major changes to either group’s microbiomes over the one month measurement window.  Interestingly those people with diarrheal IBS had much lower levels of methanogens than healthy controls, and those people with constipation IBS had higher levels of methanogens than healthy controls.  Methanogens convert hydrogen gas to methane in the gut, and this study revealed a link between methane production and gastrointestinal (GI) transit time.  Finally, the researchers determined that diarrheal IBS patients also had much lower levels of known butyrate producers.  Butyrate, a short chained fatty acid (SCFA), is associated with improved GI permeability and overall GI health.

This study described a few important insights in IBS and the microbiome.  These insights, such as the metabolic differences between bacteria in healthy individuals and those with IBS may be important to future therapeutics to treat this disease.  For example, perhaps folks with IBS could eat a lot of fiber and in the hopes of increasing the amount of butyrate in their guts.  Of course, the observed difference is only an association at this point, but other studies have suggested an increase in fiber can help relieve symptoms of the disease. 

Stool consistency should be considered during microbiome research

Stool sampling remains the most common method of measuring the microbiome of the GI tract.  Researchers are well aware of its limitations, but its ease and convenience for both scientists and donors makes it nearly irreplaceable at the moment.  The most common issue regarding stool samples that is often pointed out is that it is not representative of the GI tract, and that it only samples the lower colon and not the more proximal GI tract.  In addition, it does not account for bugs that are attached to the mucous linings of the intestine rather than those that transiently pass with our feces.  Related to this point, last week Jack Gilbert and John Alverdy, professors from the University of Chicago, published a piece in the journal Gut regarding stool microbiome sampling and stool consistency.

Professors Gilbert and Alverdy argue that stool consistency greatly affects the stool microbiome populations.  The stool consistency is normally a function of intestinal transit time, with the shorter the duration between eating and passing stool being associated with watery stool, while a longer duration is associated with a more solid stool.  They point to studies that that show different bacteria have evolved to either grow rapidly when the stool is quickly moving through the lumen, in order to proliferate with the shorter duration access to nutrients, or to grow slowly and more completely utilize the available nutrients when the stool is accessible for longer periods.  Measurements of stool consistency are hardly ever performed during normal sampling, and these same studies tend to make generalizations about different phyla, like Bacteroides and Ruminococcacea, when in fact these different can be explained by stool consistency. 

In a time where microbiome diagnostics are starting to be considered as helpful indications for varous diseases, this type of quality control needs to be established.  Stool sampling is not perfect, but it is necessary, and for that reason steps should be taken now to improve and control its usefulness, especially in a clinical setting. 

What bacteria live in the gym?

A lot of research goes into understanding the complexity and dynamics of the human microbiome in the GI tract or the mouth, to name a few locations. In an article published by Microbiome, researchers at Northwestern University took a different perspective in that they looked at how the human microbiome affects the environments around us. A very interesting point raised by the article is that Americans spend most of their time in so-called “built environments,” which are indoors. The microbes of these indoor environments are mainly affected by the humans that interact with them, so the scientists at Northwestern University took to studying how the bacterial composition of indoor athletic equipment and facilities are affected. This specific environment was chosen mainly because of the numerous different human encounters it experiences.

For 2 days, the researchers collected swab samples in 3 athletic facilities. Samples were collected every 2 hours from the floor, mats, elliptical handles, free weights, and benches from 8 am to 6 pm, and a total of 356 samples were collected.  After sequencing and analysis, the researchers concluded that, consistent with all three facilities, the bacteria found on the equipment was most likely to be from the human skin, with Pseudomonas and Acinetobacter showing up in the most samples. Besides microbiota from the skin, other bacteria were found to be abundant such as Bacteroides from the human intestinal tract on elliptical handles and Finegoldia, also from the GI tract, on benches.

As for which sampled location had the most stable bacterial community, it was found that the floor and mats showed the least change in structure. This is most likely because elliptical handles, free weights, and benches come in more direct contact with human skin. Across the board, the only genera which were found in all samples from every surface type were Staphylococcus and Pseudomonas. It is important to remember that none of this means athletic facilities are blooming with harmful bacteria, and we should stay far away. In fact, the environment is not very conducive to the thriving of bacteria, because it lacks a lot of resources. What we should take away from this study is that any surface that comes in contact with human skin is likely to reflect the microbiome of that person. 

Elderly people's microbiomes may contribute to their frailty

The ELDERMET program is a microbiome project in Ireland out of the University College Cork that is attempting to define the elderly microbiome and discover any associations between the microbiome and diseases linked with frailty and old age.  The team has published multiple papers from this project, some of which we have already blogged about, and last week they published another one in the ISME Journal.  In this latest paper the researchers described in fine detail just how the microbiota changes with diet within a geriatric population, and how this is actually independent of where the elderly people live.

The researchers studied the fecal microbiota of 384 elderly subjects over the course of one year.  They noticed immediately that the microbiomes clustered dependent upon whether the person was living in a nursing home or living amongst the general community.    The researchers characterized the microbiota in 4 groups based on a certain characteristics: M1, M2, M3, and M9.  M1 is a group of genera that is present in almost all subjects sampled, so it represents a core microbiome and is composed of genera such as Bacteroides, Alistipes, Parabacteroides, Faecalibacterium and Ruminococcus.   M2 is a cluster that is composed of bacteria that are associated with high-fiber diets and health, and is comprised of Coprococcus, Prevotella and Catenibacterium.  M3 is associated with folks who lived long-term residential care facilities, and consists of Anaerotruncus, Desulfovibrio and Coprobacillus genera.  Finally, M9 consists of other bacteria that were often found, like strains of Bacteroides, Parabacteroides and Alistipes.

The scientists then compared these microbiome groups with health indicators.  They discovered that highly diverse microbiomes were associated with health, especially among those living in the general community.  However, even though living in long term care facilities often increased diversity, having an M3 microbiome was overall associated with negative health.  In addition, the researchers noted that while individual foods were not strongly correlated with any health indicators, ‘healthy diets’ characterized by high fiber intake, were associated with better health than ‘unhealthy diets’.  Finally, when looking at how the microbiome changed over time, it was apparent that entering a nursing home increased the likelihood of shifting the subjects’ microbiomes to the M3 state, which is associated with bad health.  The researchers think this is likely due to the lack of fiber in nursing home food, and the high use of antibiotics.

The authors state that older people have many differences in their eating habits as compared to a normal adult population, like number of teeth, amount of chewing, and intestinal transit time, and all of these things may be contributing to the altered microbiome.    Regardless of these exogenous factors, this study reinforces the notion that lack of diet diversity and high use of drugs in nursing homes may be creating dysbioses that contribute to frailty disease.  If you have loved ones in an extended stay facility we recommend considering supplementing their diet with some fresh vegetables, so as to keep their microbiome from turning against them.

Schisandra chinensis fruit modulates microbiome in obese women

Flower from Schisandra chinensis fruit plant

A search for the blog posts on our site about obesity will result in a list of posts discussing correlations between obesity and bacteria in the gut. People have hypothesized that by modulating the microbiome, you may be able to alter obesity levels in humans. Many studies have looked at how probiotics and prebiotics can modulate bacterial structure to control obesity and metabolic diseases, however little has been done to look at how herbs and fruits could modulate bacterial composition.

A recent study from Korea looked at Schisandra chinensis fruit (SCF), a fruit found most commonly in northern China, that has a long history of being used in East Asian culture as a therapeutic for conditions such as diabetes, obesity, cough, and other conditions.  Previous studies of SCF in mice have shown that it modulates the microbiome, however no human trials had been previously conducted. To analyze this in humans, a clinical trial was conducted in Korea to look at the impact that SCF had on gut bacteria, body composition, and blood chemistry.

At the Dongguk University Ilsan Hospital in Korea, scientists recruited women who were obese (BMI over 25) who met other specific medical conditions. 28 women ended up participating in the study, 13 in the SCF treatment group and 15 in the placebo group. The study participants each took either SCF or placebo twice a day for twelve weeks and blood and fecal samples were taken before and after the treatment as well as a physical examination including heart rate, waist circumference, body weight, and blood pressure.

After twelve weeks, both the placebo and experimental group saw a decrease in waist circumference and fat mass, thought the SCF group saw a greater decrease in fat mass, blood glucose and other parameters. An analysis of the fecal samples before and after the twelve weeks saw greater clustering in the SCF group than the placebo group. At the genus level, there was significant differences between the two groups and the SCF group saw a greater abundance of genus levels (both groups saw similar levels of phyla changes). They saw specific clustering between patients in the SCF group despite dissimilar clustering prior to treatment. This showed that SCF had an influence on gut microbiota that was dependent on gut bacteria prior to treatment.

This study found differences between bacterial composition in patients who were given the Schisandra chinensis fruit and those in the placebo group. Many of the bacteria that saw an increase in the SCF group, including Akkaermansia, Roseburia, Prevotella, Bifidobacterium, and Bacteroides, had shown an association with reduced obesity levels in previous studies. While decreased waist circumference, body mass, and other weight loss parameters were seen in the SCF group, the results were not statistically significant. Much research has been done to look at ways of altering the microbiome and this study shows us that we should continue to investigate the effects of herbs and fruits on our microbiome.