Eating fiber alters our microbiome

Pig getting its daily dose of fiber!

Pig getting its daily dose of fiber!

Editor’s Note: Our latest podcast discussing diet and the microbiome, with Erica and Justin Sonnenburg, will be released tomorrow to coincide with the release of their new book.  In the spirit of discussing how diet affects the microbiome, today’s blog will be on that topic.  Enjoy.

Doctors always say to eat your fiber, and that it will make you healthy.  Why though?  Fiber, which broadly describes the complex polysaccharides derived from plant matter, are indigestible by a human’s normal metabolic processes.  Instead, the fiber traverses the digestive tract and is broken down by bacteria along the way.  It can be broken down into important metabolites like short chained fatty acids (SCFAs), which are thought to positively influence our health, among other metabolites.  Therefore, as Erica Sonnenburg says on our podcast to be released tomorrow, it is important to feed your microbiome with every meal.  By this, she means to include foods that are not meant to be digested by our native enzymes, but rather ones that are destined to provide nutrition for the bacteria that live inside us.

On that note, a paper out of Norway, Denmark, and the Netherlands was published last week in the Journal Microbiome that discussed how different fibers modulated the microbiomes of pigs that ate them.  Six pigs were split into two groups.  One of the groups ate a control diet, consisting of limited fiber, and the second group ate a diet that included indigestible tapioca starch.  The groups were fed these diets for 12 weeks and had their feces collected and sampled periodically during this time.

The researchers discovered that the pigs’ microbiomes did in fact change over time dependent on their diets.  The pigs that ate the tapioca starch showed a large change in their gut flora, but surprisingly it decreased its diversity relative controls.  There was also a notable increase in the abundance of Ruminococcus and Prevotella in these fiber-fed pigs compared to controls, while bacteria from other genera, like Blautia and Clostridia had decreased abundances.  The scientists then measured the differences in expressed metabolic pathways between the microbiomes of the groups, and noted that there was some evidence that the starch-fed pigs shifted their microbiomes to become more efficient at degrading starch.

We still do not know in great details how specific foods alter the microbiome, and this study is one of the first in many that are attempting to answer that question.  As you can hear in the podcast tomorrow, Justin and Erica Sonnenburg have devoted their lab at Stanford to answer this question.  They hope to someday controllably modulate the microbiome using dietary fiber in order to improve health and treat disease.    If you are interested in this topic and want to learn more about how diet can affect the microbiome, subscribe to the podcast on Itunes or wherever you get your podcasts and check back in tomorrow.

Please email for any comments, news, or ideas for new blog posts.

The views expressed in the blog are solely those of the author of the blog and not necessarily the American Microbiome Institute or any of our scientists, sponsors, donors, or affiliates.

The infant microbiome changes before the onset of type 1 diabetes


Type 1 diabetes (T1D) is a disease in which your immune system attacks and destroys your insulin-producing cells.  There is a known genetic risk factor in developing T1D, but there are also significant non-genetic components to getting the disease.  Previous research in mice has established the microbiome's connection with the development of diabetes, but the link in humans has not been studied as closely.  Researchers from various institutions in the U.S. and Finland recently assembled a cohort of infants genetically at-risk for diabetes, and tracked the changes in their microbiomes.  They discovered that the microbiomes of those individuals that were eventually diagnosed with diabetes underwent characteristic shifts leading up to diagnosis, and that these changes were not observed in healthy infants.  They published the results of their study in Cell Host and Microbe.  

The researchers sampled the stools of 33 infants in Finland and Estonia that were genetically at-risk for diabetes.  Their first major discovery was that even though the bacterial composition of the microbiome grew, changed, and became more diverse with age, the types and number of genetic pathways that were expressed by the microbiome, as well as the metabolites produced by the microbiome remained stable.  They also found many similar bacterial species between infants, however these infants usually had different strains of said bacterial species.  In most of these cases, once a particular strain established itself in the gut it remained stable and would not be displaced.

The scientists tracked the microbiome changes that occurred with diet as well.  During breast feeding Bifidobacterium and lactobacillus predominated, and Lachnospiraceae decreased.  After cessation of breast feeding the addition of eggs barley and soy seemed to have a direct influence on the microbiome.  One of the biggest factors in the developing microbiome was actually geography, as the Estonian infants had significantly higher levels of Bacteroides and Streptococcus species.

The researchers then compared the microbiome samples between those infants that were eventually diagnosed with diabetes and those that were not.  They discovered that a few bacterial species were much more abundant in those infants that got diabetes: Blautia, the Rikenellaceae, and the Ruminococcus and Streptococcus genera, including Ruminococcus gnavus and Streptococcus infantarius.  Interestingly, each of these bacteria are ‘pathobionts’, or bacteria which exist in many healthy peoples’ microbiomes but have the potential to become pathogenic.  Also, certain bacteria such as Coprococcus eutactus and Dialister invisus were non-existent in the diabetics' guts.  In addition, the researchers discovered that the expression of specific genes, like those associated with sugar transport and the biosynthesis of amino acids, underwent shifts prior to the onset of diabetes.  Finally, many of these bacteria that were associated with T1D appeared right before the onset of the disease, and these bacteria were linked to the presence and absence of certain metabolites in the stool.

These results provide exhaustive evidence for an association between the microbiome and diabetes.  It links specific bacteria in the microbiome and the expression of certain genes by the microbiome to the disease.  The next step is to study the mechanisms by which the microbiome induces diabetes, and then therapeutics can be developed.


Please email for any comments, news, or ideas for new blog posts.

The views expressed in the blog are solely those of the author of the blog and not necessarily the American Microbiome Institute or any of our scientists, sponsors, donors, or affiliates.