Can testing our microbiome aid in our health

By Mary Beth Albright November 2, 2021 â€" 10.45am

The trillions of microscopic organisms that live inside your digestive tract - your gut microbiome - may hold the key to many health conditions, such as obesity, inflammation and cancers, research suggests. In response, several start-ups have begun to offer test kits to help consumers map that microbiome, with the promise of helping to improve disease symptoms and even lose weight by eating the “right” food for your unique gut bacteria.

Some are also selling vitamins and probiotics that promise to improve your microbiome - and through it your overall health.

Eat the rainbow - but what else will a microbiome test tell you?Credit:iStock

The questions is: Can testing and manipulating our microbiome based on a test actually improve health?

Experts say it’s too soon to know. Testing needs more development for accuracy and scientists still need to figure out what to do with the information once you have it, they say.

“We don’t know what it means,” says Felice Jacka, director of the Food & Mood Centre at Deakin University in Australia and founder and president of the International Society for Nutritional Psychiatry Research. “We thought that there were particular metrics [for testing] that might be useful, but it’s just so much more complex than we first thought.”

For instance, she says, two companies analysing the same sample of gut bacteria could come up with different reports about what microorganisms live inside you. That’s because companies use different methods of testing and have their own different genomic “libraries.” Each library contains fragments of DNA from each type of microorganism (microorganisms have DNA that identify them, similar to humans). The company compares the sample you send in to its library to identify which microorganisms call you their host.

“You might get a completely different set of data by applying one library compared to another library,” Jacka says.

Also, the tests represent only a snapshot in time - a person’s microbiome changes regularly, within days, depending on factors such as diet, sleep, exercise and stress. And some medicines, such as oral antibiotics, wipe out a lot of the bacteria in your gut microbiome, making it hard to even get a snapshot.

Theories about gut bacteria influencing human health go back centuries. But for the past 10 years, researchers have been examining how those microorganisms may affect such issues as depression, Alzheimer’s disease, obesity prevention and even athletic performance.

Many researchers believe gut microorganisms played an important role in our evolution as humans because they help with digestion, immunity and even brain development.

“We need to remember that the microbes were here first. There has never been a time when we existed without microbial signals,” says John Cryan, vice president for research and innovation at University College Cork in Ireland and a neurobiologist researching food and the gut microbiome. Cryan cites breastmilk as an example.

For instance, the sugars in human breastmilk “cannot be broken down by the infant. They can only be broken down by microbes [in the infant’s gut],” he says. “The bacteria take those sugars and turn them into chemicals, like sialic acids, that are good for brain development.”

“All of our systems have evolved with the microbes,” Cryan says. “There are jobs microbes do because they’ve always done them. They’re our friends with benefits.”

Researchers say today’s gut microbiomes are different from the way they were when our hunter-gatherer ancestors subsisted on foraged foods. Some researchers believe that gut microbiomes are dramatically different from even 75 years ago, as the food system now produces more processed food devoid of the fibre and nutrients found in whole foods.

“Food is the major component that, among other lifestyle factors, has changed in the last 75 years,” says neuroscientist Emeran Mayer, professor at the David Geffen School of Medicine at UCLA. “It’s really the diet that sticks out that has this negative influence on the microbiome in Western countries and specifically North America.”

Evidence is mounting, he says, that such changes in what we eat and, therefore, what we feed our microbes are associated with modern health ills such as obesity, Type 2 diabetes, intestinal inflammation, brain disorders, and even depression and anxiety.

“While the science is still emerging, what’s already there is pretty compelling,” Jacka says.

With the caveat that gut microbiome testing may not be ready for prime time, I wanted to see for myself what I was harbouring and whether a test might give me actionable health information. I was recently given an unusual diagnosis of Type 1 diabetes - what used to be known as “juvenile diabetes” - as a 47-year-old adult, and I wanted to know whether a test could give me any indication of why.

So I ordered one.

- Step 1: Get a testing kit.

I started by buying a test kit. An online search for “buy gut microbiome test” yields pages of possibilities. Testing kits range in cost from $US100 to several hundreds of dollars and are not covered by most health insurance because they are not ordered by a physician. Gut microbiome test kits are also not considered diagnostic, so they are not overseen or approved by the US Food and Drug Administration. (The founders of one defunct gut microbiome testing company were indicted in March for conspiracy to commit health-care fraud based on the company’s practices of seeking health-insurance reimbursement for its tests.)

I selected one that cost $US149. After receiving it in the mail, I went to the company’s website to register. I was asked to agree to the company’s 33-page privacy policy. I didn’t want to give a company free rein over my personal health information, including allowing the company to give third parties my “individual-level Personal Information, without explicit consent . . . for marketing and communication purposes.” Allowing the firm to tell anyone anything for marketing purposes after I’ve paid the company $US149 seemed unreasonable, so I dumped that kit. I found another one that didn’t require my agreeing to turn over so much personal information, although it cost more.

- Step 2: Taking the test.

To test your gut microbiome at home, you provide a sample of what comes out of your microbiome - a stool sample - and send it back. The kit included a small vial and scooper and it was pretty easy to manage if you’re not too squeamish. After getting the sample, I put the vial in an included postage-paid plastic envelope and sent it off.

- Step 3: The report.

Four weeks later, I received an email telling me my 31-page report was ready. The first page stated, in bold lettering, “These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease.”

The report said that only 46.83 per cent of taxa (groupings of microbes, such as a family or species) in my gut were identified, labeling 53.17 per cent as “unknown.” So at best, the list of my community of microbes was worse than half complete. “This is considered normal,” the report read, next to the number of unidentified microorganisms.

Researchers say that there are many species of microbes in our gut microbiome that haven’t been identified yet; without knowing anything about those microbes, it’s impossible to say how they might affect a person’s health.

I showed my report to microbiologist Peter Turnbaugh, head of the Turnbaugh Lab at the University of California at San Francisco, which studies the gut microbiome. He was surprised that the company couldn’t identify half of the sequences at the phylum level, which is a level of identification in biology just below kingdom.

For example, if we were talking about animals instead of bacteria, the company would have been able to tell me something was in the animal kingdom, but not whether it was a sponge or chordate (the group to which humans belong).

- Step 4: Acting on the report.

So what did that analysis of bacteria mean for my health going forward?

The report suggested I buy the company’s probiotics, which can help maintain good gut health - although the analysis of my microbiome had declared my current probiotic level “optimal.”

It also recommended a company-made B-vitamin supplement because, the report said, “your test results indicated that your gut microbial population is not contributing significantly to your daily need of one or more of the B vitamins.”

My last B vitamin tests were 18 months ago, but they were normal. And it said I should get a company fibre supplement. Research shows that fibre is indeed great for the microbiome, but I’m not sure why they would recommend it to me specifically, based on my personal test results.

What about conditions that may not produce immediate symptoms but might be lurking out there in the future if I don’t correct my microbiome?

According to the report, I have a high level of bacteria associated with gut inflammation. That does not mean I have gut inflammation - it just means “a high level of inflammatory potential in your gut,” the report said. Actual inflammation, it said, would have to be “diagnosed through a colonoscopy.” Gut inflammation is associated with symptoms such as constipation, fatigue and bloating.

Coincidentally, I had a colonoscopy scheduled for just a couple of months later. I told my gastroenterologist about my report and asked him to look specifically for inflammation. After the procedure, he said he had found just one “tiny” patch of inflammation, out of approximately five feet of intestine. He said this was normal. After hearing about my diet, which is generally high in whole foods, he did not recommend any other course of action.

My report also included dietary recommendations that, peer-reviewed evidence shows, supports gut microbiome generally (i.e., no need for testing): consuming whole foods, fibre and fermented foods. Great advice, but definitely generic advice I’d heard before handing over $US349 for information specifically tailored to me.

“None of those pills or probiotics or anything will in any way replace the critical role of what we do many times a day in terms of putting fuel into our body and the complexity of what that fuel does and how it works in our body,” Jacka says. “It’s not even close. You’re talking about these thousands of bacteria, you’re talking about very complex methodologies that we’re only just beginning to get right. . . . In the meantime, people can just get on with having a healthy diet that will best support their microbiome to do all of the things that it does to influence their health and metabolic processes and the way their genes express themselves.”

Turnbaugh had another concern.

“A lot of people assume that if you have a microbiome profile it’s predictive - that it’s going to tell you that you’re at risk of autism or obesity,” he says. But “most of the things you’re measuring in those profiles are bacteria that are largely unstudied. . . . We don’t really know very much about what they’re actually doing in the gut or why at a more molecular, cellular level, they matter for disease.”

“It’s understandable that you want to get your microbiome tested,” Turnbaugh says. “As long as you do it with the spirit of discovery, not absolute solutions. If you get your microbiome tested, we don’t even know what to do with that information.”

He says evidence definitely supports a whole foods diet, lots of fibre and fermented foods like yoghurt.

I asked Turnbaugh if he eats differently based on the research he’s done.

“I definitely eat yoghurt every day, but I don’t know if I’m eating it because of the data,” he says. “I just really like yoghurt.”

The Washington Post

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