What’s in your Guts? The Importance of the Microbiome

Hello all!

We’ve been talking in the Biobase lately about food science and specifically how it is important to keep sterile conditions where you’re cooking.  I’m sure all of my readers know the negative effects of microorganisms: nausea, diarrhea, fever, or worse.  The next topic that we are discussing, and one that I want to discuss here, is something that people don’t often realize: the importance of good microorganisms!  You may have heard very recently that the White House announced a new Microbiome Initiative:  https://www.whitehouse.gov/blog/2016/05/13/announcing-national-microbiome-initiative .  You may wonder: Why should we care about what’s in our guts?  It’s only recently that we as scientists have come to realize that it’s much more important than we all thought.

Whats in your guts


The Microbiome consists of all of the microorganisms: bacteria, fungi, protozoa and even viruses inside of your intestines.  I’ve mentioned before how your gut contains millions of different cells and, in some respects, makes up more of your body than your actual cells! Microorganisms, such as lactobacillus are used in the production of foods such as yogurts, cheeses, and breads.  When we consume these food the microorganisms and also the probiotics end up in our gut and help them to become part of our microbiome.  Scientists have linked a healthy or unhealthy microbiome to disease such as diabetes(1), cancer(2), and some have even gone so far as to call it your “Second Brain” due to all of the effects it can have on your body.  The microbiome does so much more than just helping to break down your food.  It can help send signals throughout your body to respond to diseases and other negative conditions.

All of these revelations about the gut microbiome have caused a paradigm shift in the way in which we treat microorganism based infections.  I talked before about how our lab studies the development of antifungal resistance in fungi.  Not only can antimicrobial drugs cause the selection of resistant organisms, they can also destroy the positive ones in your gut.  This brings me back to our discussion about “molecular yoga”.  Remember we want to create molecules that are flexible enough to perform multiple tasks but also with high specificity.  Many of the antibiotics that exist currently, for instance, are specific towards bacteria but not necessarily towards toxic bacteria only.  I’m thinking of various ways in which we can use the microbiome as a counter screen in high throughput assays to address this problem.  I hope I can share these ideas with you sometime in the near future!


Thanks for reading again. Please send me any thoughts you might have!






  1. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009085
  2. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0070803

Cancer and the Nature of the Beast

Good Afternoon everyone,

This week I just wanted to make a short opinion piece regarding my take on the outlook for cancer treatment and therapies.  Many times we talk about a “cure” for a disease without fully understanding that disease and what a “cure” would look like.  I tried to stress this point in the class I taught last year, “Finding the Cure: Methods in Drug Discovery”.  For cancer the problem is our own body, not some kind of outside invader, which makes treating and “curing it” very difficult.  I’ll make this bold statement here:


I don’t think we can “cure” cancer.


Cancers arise because information in our genes is not transferred from one step to the other correctly.  Oncogenes are activated and cell growth overtakes the normal cell cycle.  In order to fully “cure” this disease we would have to develop a system that is 100% accurate in translating information from DNA to RNA.  Our RNA/DNA polymerases are pretty good but even if they are 99.9999999% accurate this still means that, relative to the vast number of cells in our body, there is a good chance that one or two will become metastatic.  The reason these mutations can occur stems from our evolutionary heritage.  We developed as organisms that could evolve based on random mutations and sexual reproduction rather than directly sharing genetic information with each other.  Even if we could, theoretically, make all of *our* cells perfect replicators remember the fact that there are thousands if not millions of different types of bacteria and microorganisms in our body.  Is it possible to stop all of these cells from feeding us potential oncogenes?

Will we all die of cancer then?  I believe eventually the answer is yes.  If we somehow created a way to extend life beyond the 100-120 years that humanity seems capped at we will all likely develop cancer.  Prevention, cures, these are not possible for our human bodies.  What we can do, however, is *treat* cancer.  The best options, in my opinion, lie in Cancer Immunotherapies, training our bodies to recognize cancer cells and dispose of them quickly.  People who would like to say, we need “cures” for cancer and not “treatments” don’t understand the issue or they are willfully ignoring it for their own gain.  No drug company has a “cure” for cancer that they are holding back because “treatments” make more money.


Treatments are all we have!


I invite any discussion on this topic about cures versus treatments for cancer.  Perhaps the new wave of gene editing technology can allow us to engineer complex human bodies that can resist cancer.  I think it’s an inherent part of how we evolved but I would love to hear an opposing view point.

That’s all for this week.  Thanks for reading!