The microbiome affects celiac severity in mice

In non-celiac people, gluten is broken down into its constituent proteins and does not elicit any immune response.  In celiac disease, however, the gluten proteins cause inflammation, which can result in a number of GI issues.  The microbiome has long been thought to play a role in this disease, because of its importance to immune mediation, and its role in gluten breakdown.  An international group of scientists recently tested the role of various different characteristic microbiome communities on the immune reaction in mice with celiac disease.  They published their results last week in the American Journal of Pathology.

The scientists used a mouse model for celiac disease that involved genetically modified mice that had an immune response to gluten.  They split the mice into three groups, one group had a typical healthy microbiome, the next had a healthy microbiome but without proteobacteria, and the final group was germ free (i.e. completely lacking a microbiome).  When the germ free mice were challenged with gluten they had the highest inflammatory response.  This included increases in immune cells, and breakdown of the intestinal villi.  Unsurprisingly, when the germ free mice were colonized with normal microbiota, their inflammatory response was attenuated.   The scientists then discovered an important relationship between celiac’s and Proteobacteria.  The mice that harbored this phylum had more severe responses to gluten, suggesting that these bacteria somehow worsen the inflammatory response to gluten.  Antibiotic treatment that increased the amounts Proteobacteria, and the relative abundances of Escherichia, Helicobacter, Pasteurella, and Lactobacillus, also increased the inflammatory response.

The exact mechanisms by which the microbiome are mediating the immune response are unclear.  Bacteria are known to induce various immune cells and also break down gluten, and these mechanisms may be involved.  In either case gluten sensitivity and celiac disease are clearly affected by the microbiome.

Gut microbiome depletion promotes healthier brown fat and reduces obesity in mice

The white and brown turkey meat from a Thanksgiving dinner

An interesting article from Switzerland was published last week in Nature Medicine.  The scientists reported on a new connection between the gut microbiome and metabolic syndrome (i.e. insulin sensitivity, obesity, etc.)  Whereas most papers observe microbiome disruption and depletion is associated with obesity, this paper describes a different phenomenon: that mice with depleted microbiomes are metabolically healthier than their untouched microbiome counterparts.  As part of the basis for the paper it is important to understand that mammals have two types of fat, brown fat and white fat.  Brown fat is associated with exercise, insulin sensitivity, and health, and white fat is associated with insulin resistance and diabetes.  Brown fat can actually repopulate white fat in a process called browning, and this transition is healthy.  

In the study, the scientists started with either normal mice, germ free mice, or mice that had antibiotics administered to them. They challenged each group of mice with glucose, and noted that antibiotic administration led to improved insulin sensitivity.  When they investigated where the glucose was going, they discovered that it was uptaken by white adipose tissue under the skin.  Then, they compared the normal mice and antibiotic mice, and observed that the antibiotic mice actually had smaller volumes of fat after the glucose uptake.  Interestingly, the fat cells in the germ free and antibiotic mice were smaller and more dense, whereas the normal mice had fewer, larger cells.  The researchers then confirmed that browning of fat was occurring in the germ free and antibiotic mice.  Finally, when the scientists transplanted the microbiome of normal mice into the germ free mice a reversal of many the above described characteristics occurred.  In these mice the fat stopped browning, insulin resistance decreased, and the mice gained weight.

The scientists were able to attribute some of the above phenomena to the release of specific cytokines (molecules that regulate the immune system).  This paper, then, adds to the wealth of research that describes the complex but critical interaction between the gut microbiome, the immune system, and metabolic syndrome.  Although the relationships between these things is yet to be fully understood, this paper may at least change the way you think about the dark and white meat during Thanksgiving dinner this Thursday.

Gastric bypass surgery alters microbiome which possible contributes to weight loss

Schematic of Roux-en-Y anastomosis.

Roux-en-Y gastric bypass surgery and vertical banded gastroplasty are two types of bariatric weight loss surgeries that are highly effective in promoting weight loss.  The mechanisms for their efficacy are complex and not completely known, but both surgeries are shown to reduce caloric intake, suppress hunger and increase gastric emptying.  Little is known about how the microbiome changes during these surgeries, and how this change may effect subsequent weight loss.  A team of Swedish scientists investigated this topic and showed the gut microbiota undergo important changes.  They published their results in the journal Cell Metabolism.

The researchers compared the microbiomes of women that were obese and hadn’t had surgery with those who were of similar BMI presurgery, but had undergone surgery at least nine years earlier.  They observed some major differences in the women’s microbiomes, with the post-operative women had much higher levels of Gammaproteobacteria and lower levels of Firmicutes.  When the scientists looked at actual genetic variations they found many differences.  Some notable differences were a decrease in short chain fatty acid (SCFA) and in increase in trimethylamine N-oxide (TMAO) creation in women who had surgery.  As we have written about in this blog before, SCFAs are often associated with health, while TMAO is a risk factor for some cardiovascular diseases.  Interestingly, when they took the microbiomes from both groups of women and transferred them into germ-free mice, the mice receiving microbiomes of women that had undergone surgery gained less weight than the mice that received microbiomes of obese women.

Gastric bypass surgery is often a last resort for folks that have severe obesity.  While not normally considered, the microbiome is drastically affected by this procedure. The microbiome is certainly altered by the procedure, and it appears that it may even be helping keep the weight off.  However, there may be some negative microbiome-mediated consequences as well, derived from alterations to micrbiome metabolism, such as an increased level of TMAO.  Like all surgeries, folks undergoing this one need to balance the risks and rewards of the procedure, and hopefully after this study, the microbiome will be considered.

Episode 7 of The Microbiome Podcast: Gut bacteria and circadian clocks with Drs. Eugene Chang and Vanessa Leone

On the seventh episode of The Microbiome Podcast we had a great conversation with Drs. Eugene Chang and Vanessa Leone from the University of Chicago. Drs. Chang and Leone found that bacteria in the gut influence the circadian clock in mice.  They discovered that altering the diet of the mouse by introducing a high-fat diet caused conventionally raised mice to have a disrupted circadian clock and became obese. They looked at what genes were expressed in the liver and found that the genes expressed varied widely from mice that were germ-free and those that were normal and conventionally raised.  We talked with them about this work and what influence this could have on humans and on our eating and sleeping patterns.

Listen to the podcast here on our website, here on iTunes, and here on Stitcher.

Below are more detailed show notes:

• Two scientific talks that David saw in New York City. First (0:37), a talk by AMI Scientific Advisory Board member Marty Blaser about antibiotics and obesity. We then (1:23) discussed a talk by Chris Mason about the microbiome and his study on the microbes in the NYC transit system. Dr. Mason published his slides on twitter so if you’re interested in seeing his slides, you can see them here.
• (2:26) Dr. Tim Spector from Kings College London had his son eat only McDonalds for 10 days straight. His son lost approximately 40% of the bacterial diversity in his gut. Read more about it here.
• (3:40) The British Gut Project that Dr. Tim Spector leads, a partner of The American Gut Project. Check out the British Gut Project.
• (5:37) A company called Biomecite Diagnostics that licensed technology from The University of Maryland School of Medicine to develop molecular diagnostics to detect inflammatory bowel diseases like Crohn's disease and ulcerative colitis. Read more here. 
• (6:10) We gave an overview of diurnal changes, circadian clock, and the microbiome.
• (9:21) We began the interview with Drs. Chang and Vanessa Leone and discussed their paper that found that cirdcadian clocks were influenced by gut microbes. Read the paper in Cell Host and Microbe. Read our blog post about this work.     
• (11:47) Dr. Leone discussed a few seminal papers from 2014 about diurnal changes. Read this paper about jet-lag and the microbiome. 
• (34:15) After the interview with Drs. Chang and Leone we talked about our own sleep patterns.
• (37:18) We gave our own opinions on Deflategate and Bill goes on a little rant about the Patriots, Tom Brady, and deflated footballs.

When you eat and what you eat may lead to obesity

Our bodies’ internal circadian clock may be profoundly important to our health, especially as it pertains to our metabolism.  Research has shown that people who have altered sleep cycles, like those who work the night shift, are at an increased risk for diabetes, obesity, and metabolic syndrome.  Researchers from the University of Chicago recently investigated how the microbiome may be involved in the complex relationship between disruptions to circadian rhythms and obesity.  They published their results in the journal Cell Host & Microbe.

The human circadian clock is regulated by a few organs in our bodies, including the brain, the liver, and is now evident from this study, the microbiome.  The researchers first measured gene regulation by the liver in germ free mice and normal mice.  They discovered that many of the genes that had daily rhythmic variations had their rhythms greatly affected by the presence and absence of bacteria in the gut.  They then subjected these mice to high fat and low fat diets and learned that, unsurprisingly, the high fat diet led to obesity in normal mice.  Surprisingly though, the high fat diet did not lead to obesity in germ-free mice.  Interestingly, many of the liver genes that were expressed rhythmically by the gut also had their rhythms affected by diet, with different genes having their expression altered depending on the diet.

The researchers then discovered that the populations of bacteria that comprise the microbiome also exhibited rhythmic variations throughout the day.  These variations did not necessarily relate to time of feeding either, as mice that were fed constantly throughout the day still experienced these variations.  Moreover, they realized that specific metabolic functions also changed rhythmically throughout the day, such as utilization of specific carbohydrates, and that a high fat diet would quell these rhythms.

The scientists then measured certain metabolites produced by the microbiome, such as short chained fatty acids (SCFAs), and saw these were also produced rhythmically throughout the day, which may be, but is not entirely, related to the differences in microbiome populations.  Metabolites rhythms were also affected by diet.  For example the high fat diet decreased SCFA rhythms.  The scientists then determined that these metabolites have a direct impact on the cycling of liver circadian genes.  This means that the microbiome metabolites and the human liver combine to contribute to our circadian clock.

The researchers go on to hypothesize that consuming a high fat diet disrupts our natural circadian rhythms, which leads to a lower metabolic state and results in obesity.  This hypothesis extends to the germ free mice which did not become obese regardless of diet; that is, they did not have a disrupted microbiome to alter their rhythms.  Ultimately, the healthiest and strongest circadian rhythms belonged to the normal mice eating normal food. 

We have written before about how jet lag can lead to microbiome changes that cause obesity.  This paper, in addition to the one described above show how our natural clock and the microbiome’s natural clock work in conjunction to regulate our metabolism.  Our circadian rhythms are not something which many people associate with the microbiome, but over time complex systems like this evolve.  While this paper may not make someone change his or her behavior, it may make him or her think twice before pulling an all-nighter or having that midnight snack. 

Gut bacteria help regulate serotonin levels

Ball-and-stick model of serotonin molecule

Editor’s Note:  In this blog we write about the most recent findings from Elaine Hsiao’s lab at Cal Tech.  You may remember Professor Hsiao’s previous work, which we wrote about last year.  She published the now seminal article that linked autism spectrum symptoms in mice with their gut microbiomes.  Diane will be joining us on the Microbiome Podcast, to be released on May 4.  If you have any questions about this study on serotonin, or on her work with autism and the microbiome, please call this number 518-945-8583 and leave a voicemail.  If possible we will ask her your question during the show.

Serotonin is a crucial multi-purpose hormone in our body that affects our mood, happiness, appetite, and gastrointestinal movement, among other functions.  It is produced in a few places around the body, but mostly in the epithelial cells that line the gut.  It should come as no surprise then, that Professor Diane Hsiao’s group, out of Cal Tech, recently uncovered a critical role that the gut microbiome has in stimulating the production of this molecule.  She published her results in the journal Cell.

The researchers first discovered that germ-free mice produced substantially less serotonin than normal mice in their colons, but not in the small intestines, suggesting the importance of the colon microbiome in serotonin production.  The scientists then investigated the levels of each enzyme responsible for serotonin production and pinpointed one called TPH1 that was produced at much lower levels in the germ free mice colons.  When the germ-free mice were given TPH1 their serotonin levels returned to normal, and when regular mice were given antibiotics their serotonin levels dropped.  Taken together, this suggests that the colon microbiome somehow increase TPH1 levels in the gut.   

The researchers then investigated the effects that specific bacteria had on increasing serotonin levels in germ free mice and discovered that spore forming bacteria, especially those belonging to Clostridia, were able to increase the levels of serotonin in the mice.  After, they tried to determine specific metabolites that may be produced by Clostridia that increase TPH1 production.  They found that deoxycholate, a-tocopherol, p-aminobenzoate, and tyramine all increased serotonin to normal levels when given to germ free mice.

Finally, the scientists colonized germ-free mice with spore producing bacteria and measured the effects on certain traits known to be associated with serotonin.  For example, germ free mice colonized with spore producing bacteria had longer food transit times and more frequent bowel movements.  In addition, blood platelets function better in mice colonized with spore forming bacteria than in germ-free mice.

Overall this work shows an important connection between serotonin production and the microbiome.  Serotonin has been implicated with many critical bodily functions, like bone development, appetite control, heart function, and mental well-being.  The fact that a dysbiosis in the microbiome may be responsible for lowering its levels may turn out to be crucial in developing next generation therapeutics.