I Got My Gut Sequenced For Science

The packet arrives in the mail. Two little cotton-tips in a test tube. You don’t want to know what I had to do with them.

Such is the price progress demands. I’m about to join an experiment on the bleeding edge of science, one that could reveal potentially huge new insights about our health and wellbeing.

I’m about to find out what’s growing inside me.

The science of the microbiome is red hot right now. Researchers have always known that our stomachs – our whole bodies – are filled with microbes. Only now do we have the technology to find out what those creatures are doing.

“The research in this area has just exploded in the last five or 10 years. What we’re finding is there are an incredible number of links between the microbes on our body and disease states,” says Dr Alena Rinke​, spokeswoman for Microba, the company that received my cotton-tips.

Those links are tentative, but incredibly diverse: diabetes, colon cancer, inflammatory bowel disease, melanoma, rheumatoid arthritis – maybe even anxiety disorders and depression. The microorganisms in our gut appear to play a big part.

As the technology gets better, it’s also getting radically cheaper. That’s allowing a new group of companies to start offering personal microbiome sequencing. Microba is among the first in Australia to bring the test to market (although it’s still in beta).

“Five years ago if you wanted to do this type of analysis it would have cost you a half-million dollars,” Dr Rinke says.

“Do your bacteria have genes that code for neurotransmitters, or essential vitamins or amino acids? Now we can tell you what this bacteria can do, because we have access to all the genes that make up this bacteria.”

Before I get too excited, I speak to Associate Professor Andrew Holmes, one of the country’s foremost microba experts from the University of Sydney.

“The era of including microbiome analyses in personalised medicine is very rapidly approaching – but not quite here yet for most conditions,” he tells me.

Professor Holmes says lots of people ask him for advice about getting their own microbiome sequenced – so many he has a cut-and-paste advice email.

“[These places] deliver a reliable result, but in my opinion are more profit-making enterprises than diagnostic services since the probability of the results informing a change in how one might manage one’s health is very limited.

“It’s kind of cool to be able to say ‘this is my microbiome’ but a good parallel would be to ask yourself ‘Would I get a bunch of liver function tests done just so I could say this is how my liver works?’”

Six weeks later, my results arrive.

So what’s inside of me? A lot. Ruminococcus, Blautia, Prevotella copri. My own personal zoo, all feeding and breeding and fighting and dying inside me. Living out their tiny lives.

Microba’s test attempts to crunch the sequence data into usable insights.

I ask Associate Professor Holmes to have a quick look over my results. The first key measure is the number of Proteobacteria present, he says.

“Typically a healthy person has a low proportion of so-called ‘inflammophilic’ bacteria. You would be looking for numbers of Proteobacteria to be less than 5 per cent, and ideally less than 2 per cent.”

My number is below 1 per cent – less than a quarter of the average. Doing well.

My microbiome is slightly more diverse than average – that’s good. It means I’m healthy and eating a broad diet. I have above-average levels of plant-digesting bacteria, and below-average levels of protein and animal-fat digesting species.

Overall Microba’s test tells me my gut flora suggests I have “excellent” fitness and a BMI of 20.7. Based on my microbiome, the test predicts I’m aged 28 – pretty close (I’m 26, with a BMI of 21.9).

More depressing is the presence of a little critter called Dialister in above-average quantities. Dialister is a good predictor for gingivitis. Time to book in a visit to the dentist.

Perhaps the most interesting – and troubling – result comes last. Microba’s test looks for bugs that code for GABA, a neurotransmitter that in mice studies has been linked to reducing anxiety and depression.

My number of GABA-producing bugs is 13 per cent below average. Worrying.

But how worried should I be? Both Associate Professor Holmes and Microba tell me there’s a huge range of healthy microbiome states – and mine looks perfectly normal. I’m different to other people, but what does that mean for my health?

That’s the key flaw in all this – it’s impossible to know. The science remains on the cutting edge.

As Professor Holmes cautions, there is a lot of interesting data – but not a lot of usable insights. Microba says that will radically improve as the service comes out of beta, but for now the service is full of unrealised potential.

The list of bugs inside me is fascinating – I spend an afternoon Googling them all – but it does not tell me that much.

Each sample Microba receives allows it to improve its algorithm. And as new research is done that will be added into the beta results, meaning the service should improve quickly. The service will launch to the public early next year.

Worth it?

While Associate Professor Holmes said there was “not much insight into your health that you would not already know”, I nonetheless found it fascinating.

This article originally appeared in Digital Life, The Sydney Morning Herald’s home for everything technology. Follow Digital Life on Facebook and Twitter.