Analysing one’s stools was once a niche interest. A quick look at Amazon, however, reveals dozens of home tests designed to test the composition of your faeces. You can even buy kits for your pets.
Such products reflect a surge in public appetite for information about the gut microbiome. “Regardless of the country you are in, a lot of patients are coming to physicians asking about microbiota testing,” says at the Catholic University of Rome.
Whether these kits actually tell us anything useful is a matter of debate, given the inherent challenges in defining what comprises an optimum microbiome – and how to achieve it.
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Simply proving causality – that a particular community of organisms is directly implicated in a specific medical condition – has been a huge barrier. “We have some evidence from animal models and some evidence from intervention trials, but there are not many,” says at the University of Trento in Italy.
Even more challenging is the huge variation between people. “The gut microbiome is extremely personal to each of us,” says Segata. “If we compare my microbiome and your gut microbiome, on average, we will have 30 to 40 per cent of species in common, and the strains of those species can be extremely different.” Complicating matters further is the fact that the behaviour of each microbe will depend on its neighbours, your age and your diet. “None of the bacteria work in isolation,” says Segata.
For these reasons, it doesn’t make sense to talk about a single “healthy microbiome”, he says. There are many configurations that may each be associated with a higher or lower risk of certain conditions at different stages of life.
But some general patterns are becoming evident. One recent that used data collected by the nutrition company ZOE found that vegans have higher levels of bacteria in the family Lachnospiraceae and the genus Butyricicoccus, as well as the species Roseburia hominis, which all produce short-chain fatty acids like butyrate. “These compounds are very beneficial for us – they lower inflammation, keeping our immune system in a good shape, and [maintain] homeostasis of the gut barrier,” says Segata, who was one of the study’s authors and is a consultant for ZOE.
Diagnostic tests can already pick up on some of these differences. “We don’t have a fixed microbial health signature, but we have increasing data [showing] which are the keystones of health, such as the presence or absence of specific clusters [of bacteria],” says Ianiro.
But the reliability of these tests can vary from provider to provider. In a recent outlining the “expert consensus” on gut microbiome tests, Ianiro and his colleagues argue that we need better guidelines to ensure they do what they claim, and educational programmes to ensure that health professionals are able to interpret test results correctly.
The team is particularly wary of direct-to-consumer products, which are . “In our consensus, we said that the testing should be prescribed by a clinician,” says Ianiro.
at the Polytechnic University of Cartagena in Spain also thinks caution is necessary before we invest in at-home gut microbiome tests. They often don’t provide enough context to help consumers understand their results, which is perhaps due to the general difficulties of defining the optimum microbiome. “I have seen some of those reports, and they are just so high level – it’s not informative at all,” she says.
Despite all these concerns, the future could hold great potential. at the Duchossois Family Institute at the University of Chicago in Illinois has been working on a that measures metabolites produced by gut bacteria. These act as markers of overall microbiome function, rather than indicating the presence of individual species.
Sidebottom’s team has found that levels of metabolites such as butyrate and deoxycholic acid, derived from bile, can predict the in people with liver disease and those receiving a , which is probably a result of the microbiome’s influence on the immune system.
The test takes just a few hours, which would enable hospitals to quickly identify who is most at risk of an infection. “A patient can be admitted in the morning, and then by the afternoon, we can report back if their gut microbiome needs to be supported in any way, through dietary intervention or the introduction of specific microbes,” says Sidebottom.
Eventually, she hopes that measurements of the gut microbiome will be as routine as blood tests, but we still have a long way to go in deciphering the varied and complex nature of the bugs that live within us.
