Faeces reveals the bacteria in our gut, but we don’t yet know which are optimal

STEVE GSCHMEISSNER/Science Photo Library/Alamy

The science of our gut microbiome is often painted as one of the hottest new areas of medicine, but there have also been claims that the research is being overhyped. The latest aspect of this field to come under the spotlight is testing kits that let you send away a stool sample to learn if your gut bacteria could be affecting your health.

An analysis has now found that these kits make claims that aren’t supported by evidence and their testing procedures aren’t rigorous enough. So should companies even be allowed to sell them?

Microbiome research started taking off about two decades ago, as advances in DNA sequencing allowed scientists to find out more about the bacteria that live on and inside us.

Doctors have long known that some infectious conditions are caused by an overgrowth of harmful pathogens. The revolutionary idea was that more subtle microbiome disturbances could cause conditions that are usually seen as having nothing to do with our gut, such as obesity, cancer and depression.

Despite the hype, the field hasn’t yet transformed the world of medicine. Faecal transplants – when stool from one person is transferred into another to boost their beneficial bacteria – have so far been licensed for just one rare medical condition, a severe form of diarrhoea that typically affects hospital patients who are taking strong antibiotics. And probiotic products – purported to deliver “good bacteria” to the gut – have generally not yet been shown to work in randomised trials, the gold standard of medical evidence.

But that hasn’t stopped some firms from selling microbiome-related products directly to the public. This prompted the US National Institutes of Health to set up an investigation into the public’s growing use of faecal testing kits.

Diane Hoffmann at the University of Maryland and her colleagues identified 31 companies around the world offering direct-to-consumer microbiome analysis kits. Based on the results of these analyses, users are given reports that may give a broad indication of their gut health, for instance in the form of a numerical score, or they may be told they have gut bacteria linked with a particular medical condition.

A big problem is that the science behind faecal DNA analysis isn’t yet advanced enough to produce reliable conclusions, says Hoffmann. Previous research has shown that identical samples given to different laboratories can give varying results. This may be because of differences in how the sample is processed or which reference databases the firms use to judge someone’s microbiome.

The companies generally don’t give details about how they do their analyses, considering it commercially sensitive. “They’re not required to give out the information,” says Hoffmann.

A further issue is that even if we could accurately quantify how much of each bacterial species someone has in their faeces, there is no consensus among doctors about which bacteria are linked with specific medical conditions or a healthy gut, says Hoffmann. “They don’t have the data necessary to say that someone’s gut microbiome is healthy or unhealthy.”

Some of the companies selling these tests also have a conflict of interest. The team found that nearly half of the manufacturers sell supplements or probiotic products claimed to improve gut health, which they recommend to consumers based on their test results.

The findings don’t surprise Lesley Hoyles at Nottingham Trent University in the UK, who co-authored a review of the field in Nature Microbiology last year, which concluded it was prone to “hype and misinformation”. When it comes to faecal testing, “there’s so much natural variation between individuals, it’s meaningless,” she says. “We don’t know what a healthy microbiome is.”

It might be tempting to think that if people want to waste their money on faecal test kits, they should be allowed to. But many other kinds of direct-to-consumer medical tests, such as those for pregnancy or covid-19, are regulated by government agencies, which require good supporting evidence. It is time for microbiome tests to meet the same standards, says Hoffmann.

No one is arguing that microbiome research should be abandoned. The field has great promise, but it is clearly only in its infancy. So, for now, it may be wise to carry on just flushing our faeces down the toilet.


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