Gut Sequencing Q and A
Dr. Ghannoum has been continuously funded by the National Institutes of Health since 1993 with over $25 million in scientific grant funding. He’s dedicated his entire career to studying medically important fungus and it’s role in health and wellness. He is a Fellow of the American Academy of Microbiology.
Dr. Ghannoum is also the scientist credited with naming the mycobiome (the body’s fungal communities), and was the researcher that discovered digestive plaque being created by fungus and bacteria working together.
It was in part this research that lead led his team to create the BIOHM Gut Report, the most sophisticated microbiome sequencing service available to consumers.
In this Q&A, Dr. Ghannoum explains what gut microbiome sequencing entails, and how it can play a role in our health and wellness.
So what exactly is gut microbiome sequencing?
When you talk about “gut microbiome sequencing,” what we’re really talking about is pretty straightforward. Through sequencing the DNA of organisms in someone’s digestive tract, we are able to not only identify the specific bacteria and fungi present in that person’s gut, but the levels of each organism as well.
That is a very important point to keep in mind. Having “bad” fungus or bacteria in the gut is actually normal. But what’s more important, is to understand exactly how much of that organism is present in the gut.
I like to use the analogy of sharks. Of course we’re afraid of sharks, but if sharks suddenly became extinct, the marine life that sharks control would flourish out of control, upsetting the homeostasis of the ocean.
So that’s why it’s important that we’re not only considering what organisms we find in the gut, but how high the levels of each are, because if a few are at too high or low a level, there can be a ripple effect that causes the gut to go out of balance.
So why is it important to actually know what microorganisms are in our guts?
For almost the entire history that we’ve been aware of microorganisms in the body, the view in the scientific and medical community was that they were pathogenic, or harmful, to our health and wellness.
Well as the science has developed over the last decade, what we’ve come to realize is that in fact, microorganisms play an incredibly important positive role in not just our digestive health, but in our overall health and wellness.
What we’ve also come to learn is that health issues can start to arise when the balance of good and bad microorganisms in our body is disturbed.
I’ll give you a specific example. Many people have heard of Candida, and in fact, it actually generally has a bad reputation. But when Candida is present at the appropriate levels in our system, it actually aids our body’s ability to absorb nutrients and properly digest food. However, if Candida is allowed to grow out of control, it can actually start to break down the gut’s tissue lining, which can cause very serious issues.
So by being able to know exactly what organisms a person has in their gut’s microbiome, and at what levels, we have actionable information to inform decisions regarding our health and wellness.
So that makes sense for people with pressing digestive health issues, but what about perfectly healthy people, why is it important for them to understand the makeup of their gut’s microbiome?
That is a great question! The simplest way I can explain it is that “being healthy” is not a singular state of being. It’s an ongoing process, where we can continuously work to optimize our current health, and tweak our lifestyle to optimize our wellbeing.
Take myself. Every morning, no matter what, I get up and I get on the elliptical. I don’t eat red meat, and in fact, other than fish I basically eat a vegetarian diet. I take a few minutes every day to also do some basic meditation (which admittedly is very hard for me and I am working on). Put simply, I really try to take care of myself.
But even with all of that work, I still have physicals at least once a year to monitor my various levels, ranging from my cholesterol to of course my microbiome. Invariably, there will be something that comes up that will indicate I should probably make an adjustment. So for example, my blood pressure has gone up a little the last few years, so I have started to reduce the sodium in my diet.
So with your gut’s microbiome, even if you are healthy and don’t have any apparent digestive or wellness issues, it can be extremely informative to understand the state of your microbiome. This can allow you to not only further optimize your well-being, but to be able to get ahead of any potential issues if certain unexpected organisms are found, or levels seem to be disproportionately high or low.
Now that we know just how important a role our microbiome plays in our health and wellness, monitoring our microbiome periodically is a phenomenal tool for supporting our health and wellness.
How have you used microbiome sequencing in your own research? Can you share a specific example or two?
I’ve been fortunate enough to have lead some fascinating studies that have taken advantage of our ability to sequence the microbiome in various parts of the body.
I’ll give you two specific examples:
Through the support of the National Institutes of Health, in 2010, I was the first scientist to identify the fungal community that lives in the oral cavities of healthy people (HERE is a link to that study). In fact, this was how I came up with the term, the “Mycobiome” to describe the fungi that lives in our bodies. I was able to identify the species of fungi using microbiome sequencing.
Having established a baseline of what the fungal community looks like in our mouths when we are healthy, I turned my attention to identifying the fungi that exists when disease comes into play.
Specifically, I have identified the mycobiomes present in people infected with HIV, and in people who have Crohn’s Disease.
These are just a few of the studies I have done where I’ve utilized microbiome sequencing.
In fact, it is from my years of experience doing microbiome sequencing in my own scientific research, that lead me to develop the BIOHM Gut Report Kit that would allow everyone to have access to the same type of microbiome analysis themselves.
So how does gut microbiome sequencing work? Walk me through the process from start to finish.
No problem. So let’s say someone wants to get their gut microbiome sequenced with our BIOHM Gut Report Kit. When the kit arrives, it contains a double-swab, a swab self-contained tube, a bag for the tube, and a self-addressed stamped return envelope.
They simply take the swabs, brush them against fecal matter from their used toilet paper, and put the swabs in the container.
[Side discussion between interviewer and Dr. Ghannoum “Do you mind if I just call it poop? It’s poop! Fecal matter sounds so clinical and I don’t want people to think of it as something so foreign. It’s their poop!”]
So they take the container, put it in the plastic bag, and place the plastic bag in the return envelope and drop it in the mail. That’s it.
Once it reaches my microbiome sequencing labs at Case Western Reserve University School of Medicine, their sample is first logged into the system. Next DNA from the microorganisms are extracted from their sample, and processed to ensure that the DNA is from their gut’s microorganisms and not from human cells.
Once this is done, the extracted DNA goes though a process that produces nucleic acid data which allows us to identify the specific microbes in the gut, and their levels.
Once the analysis is completed, we create their BIOHM Gut Report. Now when we first get the data, it looks like an endless sea of words and numbers on excel sheets.
Unless you know what you’re looking at, it’s basically useless in that form. We spend a tremendous amount of time creating a report format that people would find very easy to understand.
We did this through creating heat maps that shows the specific organisms in their gut, and the levels of each of them. It makes it very easy to quickly see how your gut microbiome looks.
Now, additionally, the BIOHM Gut Report includes a second heat map, which shows people what the average healthy gut microbiome looks like, which is based on data we retrieve from the National Institutes of Health’s Human Microbiome Project. This gives people some perspective of how their gut looks compared to the average healthy gut.
Tell me about the NIH Human Microbiome Project?
The NIH Human Microbiome Project is absolutely fascinating and incredibly important. Here’s the easiest way I can put it in perspective. For every one human cell, there are ten microbial cells. But yet, we have barely scratched the surface, when it comes to studying how microbial cells impact our health and wellness.
As a result, the NIH launched the Human Microbiome Project with the singular goal of identifying the entirety of our body’s microbiome, and the role it plays in health and wellness.
Over the last ten years, the NIH has sequenced tens of thousands of microbiome samples, creating a tremendous resource for scientists like myself to understand the role of the microbiome in our health and wellness.
Other companies do gut microbiome analysis. Why is the BIOHM Gut Report Kit different?
I appreciate you asking this, because I think it’s one of the biggest strengths we have as a company.
There are a few things that differentiates us from other companies that conduct similar testing. First, we are the only company that that we are aware of that analyzes both the bacterial and fungal communities in the gut.
This is of critical importance because our gut contains not just bacteria, but fungi as well. More importantly, in an NIH study we conducted, we recently discovered that bacteria and fungi in the gut work very closely together, potentially effecting our digestive health.
So it is critical that we not only look at the bacteria in the gut, but our fungus as well.
Another important differentiator is that not only have we been doing microbiome sequencing in some of the most important NIH-backed research in recent years, we literally have the largest collection of fungal strains of any medical research institution in the United States.
That gives us unrivaled expertise in creating the most sophisticated gut microbiome sequencing service available to consumers.
Nowadays, people are very concerned with their personal data, especially their health data. How do you ensure that people’s personal information is secure?
This is perhaps the most important question you have asked!
First, from the time the envelope leaves their hands, through the time it is processed, absolutely no one in our laboratory knows who that person is. We do that by assigning each person an anonymous personalized code. The code is literally a number, and contains absolutely no way to personally connect it to a person.
We include that code on the container, the plastic bag and the return envelope.
So from the time they drop the envelope in the mailbox, through the entire time it is processed in our labs, absolutely no one knows who a sample belongs to other than being able to tie it to the personalized code. When a report is completed, it is sent to our headquarters with the identifying anonymous code linked to it.
From there, only a single designated person in our headquarters has access to tie an anonymous report to a specific person, in order to email their report to them.
I think this is very important and the ethical way to handle such sensitive information that we have been entrusted with.
People should feel comfortable that their personal information is protected, and I personally take that very serious as the scientist behind the BIOHM Gut Report Kit.
Do you do anything with people’s microbiome data? For example, are you creating a database of people’s collective microbiomes?
Now, I want to make sure you note this, and I would caution every person to ask this question before they use any microbiome sequencing:
What is the company doing with your data other than providing it back to you?
There are companies who are trying to build giant businesses based off being able to create giant databases of people’s microbiome data, which they turn around and sell to pharmaceutical companies and others who may be interested in the data. They often bury the fact that they do this in hard to find language on their website.
I view that as frankly unethical.
Let me put this as plainly as I can. A person’s microbiome data is their business not mine. They have entrusted me and my colleagues with this process, which I take very seriously.
So other than keeping a record of their report, so that if they ever need it again we can send it back to them, we do not collect, re-use, aggregate, analyze, sell or do anything else with their data. Full stop!
They paid us to perform to sequence their microbiome, so once that’s done, we are done looking at their data. End of story.
Where can people find out more about the BIOHM Gut Report Kit?
All they have to do is visit the BIOHM website, where they can learn all about the BIOHM Gut Report Kit, and more about the exciting things we’re working on when it comes to the microbiome!