Let's experiment: exploring my microbiota

As Chris pointed out in a previous mutualism of the month post, you’re eating for 100 trillion. That’s right, bacterial cells outnumber your own humans cells ten to one! And believe it or not, is a good thing. These bacteria are not freeloaders; accounting for 3% of our body mass, these ‘good’ bacteria may block bad microbes from colonizing our bodies, positively affect how our immune system functions and even influence the way we think. Considering our microbiota as its own organ has also led to some unconventional methods for treating disease when we get sick. Yes, eating poop may not be all that bad.

However, I am a ‘I’ll believe it when I see it’ kind of person (and yes, I do see the irony in that as a microbiologist). I want to get to know my microbiota, discover what kind of bacterial species live inside me and put them to the test. Without eating poop.

How can you get to know your microbiota?

Much of our understanding of the vast microbial diversity present in our bodies has come from the use of next-generation sequencing technologies.  These technologies allow researchers, like myself, to extract the genetic material or genomes of the microbes present in diverse microbial populations. Combined, this collection of genomes, referred to as the microbiome, acts as a microbial census to tell us who is there and in what proportions.

Thanks to advances in sequencing technology, costs continue to decline further each year. As a result, several companies have started offering sequencing services to the public.

An example of a DIY (kinda) sequencing kit! This is one of many that I have already tried out.

For example, 23andMe is a private personal genomics company using saliva-based sequencing methods to get you acquainted to the 23 chromosomes that make up your human genome and track your ancestry.  Likewise, companies also exist that specialize in sequencing your microbiome. I chose to get my microbiome sequenced at uBiome, a citizen science startup company from San Francisco  

The plan: learn as much as I can.

As a microbiologist, I was not going to be satisfied just to see what kinds of bacteria live inside me. I wanted to see how much I could change what’s there.

My plan is to sequence my microbiome at three different time points: beginning, middle and end. This strategy will allow for two distinct phases accompanied with some sort of drastic lifestyle change that will last about a month or so.

  • Phase 1: vegan diet – no animal products whatsoever.
  • Phase 2: exercise and probiotics.

How do you take the sample? The kit provides a sterile swab you use to scrap up a tiny amount of our poop onto after you wipe. Luckily, they give you a spare tube in the event of catastrophe. Photo credit: Kenny Flynn

What can we expect to happen?

Not sure but we will find out! That is the exciting part and why I am hoping this post can commemorate the start of a new series: Let’s experiment!

I do some expectations, however. Concerning phase 1, diet plays an important role in our relationship with the microbes inside of us as Chris already discussed. Going from my rather unhealthy, graduate student diet to an extremely radical vegan diet is likely to mix things up a bit.

For example, studies examining the microbiota of obese and skinny mice see large differences. Furthermore, transplanting the microbiota of an obese mouse into sterile, lean mouse leads to rapid weight gain!

Concerning phase 2, organisms that are believed to improve health or probiotics are advertised to modulate your microbiota but does it really work? After scouring the Internet for reviews and opinions, I found many testaments recommending a wide variety of products. In most cases, people said they could feel a difference. Although probiotics certainly work differently for different people, I am looking forward to attaching some actual quantification to my observations.

The probiotic I chose to try. My criteria included good reviews and something I did not need to refrigerate to keep alive.  http://drohhiraprobiotics.com/

The probiotic I chose to try. My criteria included good reviews and something I did not need to refrigerate to keep alive. http://drohhiraprobiotics.com/

Probiotics suffer from something I affectionately refer to as the ‘drop in a bucket’ syndrome. If we have 100 trillion bacteria in our bodies, will adding less than 1% of that make a difference? Hopefully, time will tell but I am optimistic.

Comments, questions or suggestions you would like to see with this and future Let’s Experiment installments? I would love to hear them.

Stay hungry!