IBD, Crohn's disease, and the microbiome

There have been several large scale studies that show a definite association between the microbiome and inflammatory bowel diseases like Crohn’s and colitis.  While it is becoming clear that the microbiome plays a pivotal role in these diseases, the exact mechanisms of pathogenesis are not known.  One of the reasons it has been so hard to uncover this link is because of a lack of robust studies, that usually contain small sample sizes.  In response, a team of leading scientists in the field, including multiple scientists from our own scientific advisory board, assembled a brand new cohort, the largest of its kind, to study the disease.  The cohort consisted of 447 children with newly diagnosed, still untreated, Crohn’s disease and 221 healthy children.   They then combined this data with two other cohorts that included adult patients to bring the total number of samples to 1,742.  The first results of this study were published in Cell Host and Microbe, and shed many insights into IBD and its relationship to the microbiome.

In the study the researchers sampled and sequenced the microbiome of the gut mucosa and stool.  From this data, they identified specific bacteria that had higher abundances in diseased patients, like Enterobacteriaceae and Veillonellaceae, and others that had lower than normal abundances, such as Clostridiales and Bacteroidales.  According to the samples, these relative abundances were more pronounced in the mucosal samples, rather than the stool samples, meaning that the mucosa may play a more important role in Crohn’s pathogenesis and diagnosis.  Moreover, children under age 10 did not have large populations of the ‘bad’ bacteria, which were negatively correlated with age.

Another important finding from the study is that antibiotic treatment of the Chrohn’s disease further exacerbated the microbial imbalances (dysbiosis), and caused the bad bacteria to proliferate and the good bacteria to die off.  The researchers are quick to dismiss antibiotics as the cause of the disease, rather hypothesizing that the antibiotics allow for opportunistic bacteria to grow which may cause dysbiosis.  They also encourage further research on the subject and question whether antibiotics should be prescribed to IBD patients.

The researchers used this knowledge of the dysbiosis to create a potential diagnostic for IBD.  They were able to calculate a microbiome diversity index by sampling the mucous for the existence of certain bacteria and for overall microbiome diversity.  The index shows remarkable ability to not only accurately predict the existence of IBD, but also the severity of it.  Also, the researchers showed their microbiome dysbiosis index could be combined with clinical data to better predict the future outcome of the disease.

A final conclusion of the paper is that the gut mucous is a more accurate signal for IBD.  They conclude that stool samples are composed of higher levels of aerobic, oxygen using, bacteria than those in gut, and that stool is not representative of the overall microbiome.

This study is the first to rigorously tackle IBD, specifically, Crohn's disease, and the microbiome.  We now know what bacteria are most highly associated (both positively and negatively) with IBDs, and how this this information can be incorporated into early diagnostic screens.

Current challenges in microbiome research

Scanning electron micrograph of E. Coli bacterium.

Curtis Huttenhower, Rob Knight, Owen White, Jacques Ravel (all members of our SAB), and others recently published a commentary titled "Advancing the Microbiome Research Community" in Cell.  The paper was a 'State of the Microbiome' address and outlined the current challenges and the future outlooks of the microbiome field.

Among the many challenges they outlined include how to design causality studies, and how to attribute causality of phenotypes to specific bacteria, proteins, or metabolites.  The paper also discussed the bioinformatics bottleneck that is occurring in the field, as the necessary expertise required to properly analyze sequencing data is severely lacking.  There also lacks a proper centralized online repository for all sequencing data that is generated.  This sequencing data needs to include metadata that would describe how the data was generated.  Furthermore, the authors describe the need for guidance on how to properly define and comprehensively describe phenotypes, such as inflammatory bowel disease (IBD), in microbiome studies.  Without this standardization, proper comparison between studies can not take place.  Finally, institutional review boards (IRBs) need guidance on how to properly regulate human microbiome studies in order for scientists to properly prepare and carry out their projects.

While the above areas are only a few of the challenges facing the field, each of them reinforces the mission and programs of the AMI.  The MBQC is standardizing techniques and creating rigorously tested analytical protocols by investigating the sources of variation in microbiome testing.  In addition, the AMI is focusing on future data repository efforts.  These are just a few of the areas we hope to serve the field in the coming years.  We believe a nonprofit, specifically the AMI, can help fill these voids and address many of the issues outlined in this paper.

Caesarean sections, breast feeding, and the microbiome

There is a growing amount of literature on the subject of babies' microbiomes because it is clear that the first few years of life are crucial to the development of the immune system, and poor development can have lasting, life-long consequences.  As we have learned, a healthy microbiome is absolutely critical to a healthy immune system.  Evidence for this connection is vast, but starkly manifests itself in germ-free mice which can not survive long due to autoimmune disease.  So, as the thinking goes, a healthier microbiome as a baby leads to a healthier life.

In any case, a commentary was recently written by AMI Scientific Advisory Board members Maria Gloria Dominguez-Bello, Rob Knight, and a colleague that discusses how delivery mode and infant feeding affect babies' microbiomes.  As it turns out, epidemiological studies on large human populations have correlated Caesarean Section (C-section) delivery to obesity, asthma, celiac disease and type 1 diabetes, which are all autoimmune diseases.  Breast feeding, on the other hand, leads to decreased risk for some of these same diseases.

Research has shown that both C-section and breast feeding have a direct and significant influence on an infant's microbiome.  During vaginal delivery the child's gut is inoculated with the vaginal microbiome, whereas in a C-section the child's gut is associated more with the skin microbiome.  In addtion, breast feeding contains prebiotics that encourage certain bacteria to grow, which selects for a specific infant gut microbiome.  

Interestingly, the authors mention a study that showed the microbiota from the breast milk may actually be different depending on the mode of delivery.  They also comment on a study that showed certain gut bacteria are found in the vaginal microbiomes of pregnant women, as if prepared to inoculate the child.  This is in agreement with another study from Jacques Ravel which I have already blogged about.

It is very important to consider the microbiome when a woman is giving birth and feeding.  If a C-section is required it may be possible to inoculate the child's gut manually, and studies are currently investigating this.  The results of these studies will be the topic of a future blog. 

The microbiome and autism

I want to discuss a really important paper from December 2013 published in Cell by the Mazmanian lab at Cal Tech that links the microbiome to autism spectrum disorders (ASD).  We already know that there is link that is becoming well-established between the gut and behavior.  It has also been shown by other researchers that humans with autism also have high levels of IBD and other intestinal disorders.  This suggests microbiome dysbiosis may be linked to autism, and was the motivation for this research.

In the paper the researchers induced ASD symptoms in mice by using a known method in which  a mother is infected with a virus-like molecule, and the offspring of that mouse have a high likelihood of having ASD symptoms.  After doing this procedure they directly demonstrated that those mice with ASD symptoms had reduced GI tract integrity, and had elevated levels of some metabolites in their blood when compared to offspring mice from the same mothers without ASD symptoms.  Furthermore, some of the metabolites that were elevated are thought to be biomarkers for autism in humans (they are also elevated in humans with autism).  Finally, when the offspring mice with ASD symptoms were given a probiotic, their symptoms were reduced, and those same metabolites were also reduced.  

This research is especially exciting given that the probiotics were therapeutic for mice already displaying ASD symptoms, suggesting a possible cure for autism, but obviously let's not get ahead of ourselves. 

A nice round-up of the article, which was co-authored by our friend Rob Knight, has a great summary of research, and I suggest anyone with further interest to read it.

The great fecal microbiota transplant debate

An article was published today in the Atlantic that does a really nice job of describing the controversy surrounding fecal microbiota transplants (FMTs).  Basically, FMTs have been highly effective (>90% effective) in treating C. Difficile infections, and this efficacy has been even used as proof of the causal role of dysbiosis in C. Diff infection.  

The problem though, is that FMTs are currently unregulated, and the real question is how does the FDA regulate this new treatment, especially with how little is known about the microbiome.  The first question the FDA has to answer is whether or not fecal microbiota is a drug or a tissue.  Currently it is considered a drug but many common definitions would call it a tissue.

In addition, no one knows any long term consequences with FMTs, or what diseases to look for in donors, or how to screen FMTs at all.  Fecal microbiota is obtained just as you would imagine, through stool samples, and everything in that stool is transferred, the entire microbiota, including viruses.  It is a really complex issue that comes down to ethics, the responsibility of government, and the science of the microbiome.  Without guidance though, many have resorted to DIY FMTs which is not a good idea!

At the AMI we are aligned with the editorial written by a consortium of microbiome scientists, including our very own Marty Blaser and Rob Knight.  They support the FDA's cautious approach and note that past transplant procedures, like with blood, have resulted in unexpected disease transfer.  They also do see the benefit of FMTs and want to move forward with research to develop proper protocols, registries, and databases, as well as thorough clinical trials.  

A fellow non-profit here in Cambridge, Open Biome, based out of Eric Alm's lab at MIT, has created the first stool bank.  Organizations such as this will be essential to centralizing data and clinical outcomes, and we support their efforts.

Finally, drugs are being developed for C. Diff infection that are working.  Seres Health is a start-up in Cambridge, that has had great success in an oral treatment to C. Diff.  This may very well be the treatment for C. Diff in the future, but with so many diseases being linked to the microbiome, FMTs will again be at the forefront of therapeutics, even if they have not been successful for more complex diseases such as IBS and ulcerative colitis.