openbiome

Episode 4 of The Microbiome Podcast: What's hot in the microbiome field with Kristina Campbell

Last podcast I bet Dave that Duke would go further than Kentucky in the NCAA tournament.  I sacked Dave with my NCAA basketball foresight, so here is Dave being sacked by Jason Pierre-Paul of the New York Giants.  Tonight is the championship game, Duke vs. Wisconsin, and for the record, my money is on Duke.   Image by Julio Cortez of the Associated Press.

Last podcast I bet Dave that Duke would go further than Kentucky in the NCAA tournament.  I sacked Dave with my NCAA basketball foresight, so here is Dave being sacked by Jason Pierre-Paul of the New York Giants.  Tonight is the championship game, Duke vs. Wisconsin, and for the record, my money is on Duke. 

Image by Julio Cortez of the Associated Press.

On this week's podcast, we talked with Kristina Campbell from Gut Microbiota for Health. Kristina had recently traveled to three conferences around the world so we talked with her about what's going on in the field and the most recent breakthroughs in the field.  We also announced that we set up a voicemail for callers to call-in and ask us questions or leave comments for the next episode of the podcast. The number is 518-945-8583 and we hope to hear from you with any questions, simple or complex, that you want us to answer on the podcast. 

Listen here: 

And listen here on iTunes and Stitcher

See below for more detailed show notes: 

The episode begins with a few recent news stories:

  • (2:57) The Obama administration announced a $1.2B plan to fight antibiotic resistant bacteria. Read more
  • (5:00) A group at the University of Nottingham used a 1000 year old recipe to kill MRSA and it was very successful. Read more.
  • (7:13) The Massachusetts Host-Microbiome Center is being created by a $4.8M grant from the Massachusetts Life Sciences Center. Read more

In the conversation with Kristina (@bykriscampbell on twitter and read her personal blog here) we discussed:

(41:35) After the interview with Kristina, we again discussed the NCAA tournament and how our picks before the Round of 32 are faring.

The next podcast will be with Justin and Erica Sonnenburg, scientists at Stanford University School of Medicine. Leave a voicemail for us at if you have a question for Erica and Justin about the impact of diet on the microbiome or anything else microbiome related.

Please email blog@MicrobiomeInstitute.org 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.

Revisiting FMTs, and the patient that was cured of C. diff but became obese

Happy Valentine's Day to all our readers!  We will be back blogging on Tuesday, February 17, after we take off Monday, February 16 for President's Day.

Happy Valentine's Day to all our readers!  We will be back blogging on Tuesday, February 17, after we take off Monday, February 16 for President's Day.

Clostridia difficile infections can be nasty to deal with.  They cause pain and diarrhea, and are sometimes fatal.  They normally occur after a course of antibiotics, which leaves the gut in a state of dysbiosis where the C. diff can thrive.  Doctors normally prescribe antibiotics to cure this infection, but this can sometimes exacerbate the problem, making the gut even more prone to infection.  As we have discussed, fecal microbiome transplants (FMTs) have been successful in curing over 95% of C. diff infections.  Practically speaking, FMTs involve transferring the stool of a donor into the bowels of an infected patient.  While they are highly effective in treating C. diff, this practice is not without controversy.

The microbiome donor is generally a healthy person who is related to the patient and lives in the same household, generally a husband or wife.  The logic behind this is that these people share a similar microbiome, and some evidence supports this.  There are other ways to identify donors including the much publicized OpenBiome which has a stool repository which functions much like a blood or sperm bank.  These transplants come from ‘healthy’ strangers.  In most cases of FMTs, the stool is screened similarly to the way blood is screened, for specific diseases such as AIDS or hepatitis, and a few microbial pathogens (like C. diff).  The problem is, the microbiome is SO much more complex than blood, and as we learn every day on this blog, its impact on health and disease is not fully understood.  In fact, the promise of the microbiome is that it is connected with such far ranging diseases and phenotypes, from depression, to obesity, to arthritis.  We have numerous examples in mice where FMTs are actually able to transfer specific phenotypes, even unexpected ones such as anxiety.  What happens in humans though?  When we transplant feces between humans do phenotypes carry over?

Unfortunately, because the practice is mostly new, mostly unregulated, mostly isolated, and generally not a part of scientific studies, the long term impacts of FMTs are largely unknown.  The people who should and would know most about this, OpenBiome, have not published their findings, or at least are not talking about them.  We know that FMTs are really, really, good at curing C. diff, and may be the best solution to this debilitating disease, but at what cost is unknown, a classic bioethics dilemma.

Enter a healthy, 32 year old 136 pound woman from Rhode Island.  She had taken antibiotics for a vaginal infection and came down with a nasty C. diff infection which progressed over the course of a few months.  After antibiotics failed she opted for an FMT from her 16 year old, healthy daughter.  Fortunately, the FMT cleared the infection.  Unfortunately, over the ensuing year, the patient gained 34 pounds, and now weighs 170 pounds.  These are the kinds of results that make people nervous about FMTs.  We notice the weight gain because it is outward-facing and easy to measure, but what else has changed that we can’t notice, both physically and emotionally?  We need to be thinking about when we consider FMTs, especially when other, less complicated methods for treating C. diff are passing clinical trials.

FMTs exemplify both the promise and repercussions of the microbiome.  If the microbiome is as important and powerful as we think it is, then we need to investigate its clinical uses with deliberateness and care.

Please email blog@MicrobiomeInstitute.org 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.

Altering the microbiome, diet, probiotics, and FMT

I recently had the pleasure of hearing a lecture by Eric Alm, an associate professor at MIT.  During the lecture he described a number of studies his group has performed, and I would like to share some of his conclusions.

In his first study he and his student sampled their own microbiome every day over the course of one year, while cataloging every minute detail of their lives over the same time frame.  They were investigating what activities have real effects on the microbiome, and as they discovered, unsurprisingly, what one eats is the most important.  They found that the amount of fiber in the diet perturbed the microbiome most, in addition to things like orange juice, yogurt, fruits, and soup.  They also discovered that after flossing, a certain bacteria from their mouth, would show up in their stool.  More importantly, they confirmed that the microbiome is robust, and rebounds after drastic changes like vacationing in foreign countries.  In addition, they learned that perturbations occur within 24 hours.  Most of the results of the study can be found here.

In another study, Eric discovered that the microbiome is a hotbed for horizontal gene transfer.  With so many genetically different bacteria living and evolving in close quarters there has been a great amount of genes passed around.  He also discovered that the microbiome of farm animals (which are given antibiotics to gain weight), develop antibiotic resistance, which is then transferred to our own guts' microbiomes through this lateral gene transfer.  The results from this study are published here.  

Another study focused on mice that were fed Lactobacillus in their drinking water versus those control mice that were not.  The mice that were given the probiotic were skinnier than control mice, and had shinier coats and healthier skin.  They then discovered that it was alterations to the immune system, rather than the Lactobacillus themselves, that were causing these changes.  These results are not yet published.

Finally, Eric talked about his stool bank, OpenBiome, which we previously discussed in a separate blog post.  OpenBiome is dristributing fecal material to be used in fecal microbiota transplants (FMTs).  We have talked about FMTs in this blog extensively, and even touched on some studies that showed mice lose weight, or become less stressed, when given the microbiome of a healthy donor.  I asked Eric if any additional phenotypes were being transferred with FMTs in humans.  He mentioned in one case a patient with alopecia suddenly grew hair after the FMT, but eventually lost the hair again.  In another case he mentioned a skinny woman that became obese after treatment with FMT.  We will leave the reader to decide how these things play into the overall ethical controversy surrounding FMTs.

Please email blog@MicrobiomeInstitute.org 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.