Are they for us, against us or just cohabiting? Itâs hard to know what to think about the microbes that live in and on us. In the same week that researchers announced that there is , the White House launched the National Microbiome Initiative. This $500 million âmoonshotâ is intended to understand the vast colonies of bacteria, fungi and viruses that coevolved with our bodies, lands and oceans. The hope is that it will lead to breakthroughs in health and many other fields of science.
âWe need the means to change dysfunctional microbiomes and make them functional,â says Jo Handelsman at the Obama administrationâs Office of Science and Technology Policy.
On the human health side, thousands of papers have been published over the last few years linking changes in gut flora composition to allergies, asthma, obesity, cancer to Parkinsonâs, Alzheimerâs, anorexia, autism, depression and even .
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The studies hint that we may one day be able to affect these conditions by tweaking our gut bugs. But thereâs quite a gap between this promise and the current science. That vacuum has been filled with misconceptions, snake oil and hype. Jonathan Eisen, a biologist at the University of California, Davis, calls it âmicrobiomaniaâ.
The , but it could be decades before its scientists can unpick the complex interplay of microbe and human biology to develop treatments. So in the meantime, what should we make of the dizzying array of touted medical links, the rise of DIY microbial transplants and the probiotic foods industry, which some estimates predict will be worth $96 billion by 2020? Not to mention the spectre of faeco-cosmetic treatments.
âThereâs a gap between the promise of the microbiome and the current science. It has been filled with misconceptions, snake oil and hype: microbiomaniaâ
Letâs start with that array of medical links. The intriguing associations we are seeing can be traced back to the trillion microbes in our guts producing chemicals that break down proteins and cell walls. This has downstream effects on aspects like chemical regulation, the immune system and the brain, the specific mechanisms of which are just starting to be decoded.
Although possible connections between bacterial products and medical conditions are multiplying fast, not everyone agrees that the bacteria are causing the observed effects, rather than the other way around. âNo doubt microbes drastically influence many aspects of our biology,â says Eisen, âbut as with brain scans, finding a difference between two groups of people doesnât tell you a lot.â
Whatâs more, says Mick Watson of the University of Edinburgh, UK, âa lot of people do really bad microbiome researchâ, without, for example, using control subjects.
And most of the good science is done in mice. Several experiments have suggested that autism-like behaviours and gastrointestinal ailments can be explained by microbiota, and in one case these behaviours were suspended by injecting microbes from neurotypical humans. But does that tell you much about autism? âNone of that makes any sense!â says Eisen. âMice donât have autism. This is not autism.â Nonetheless, it has led to headlines suggesting autism was cured by probiotics.
Much like Eisen, many microbiologists are worried about the premature applications of these studies. Another bugbear of his is microbial forensics. People are saying we should consider having criminalsâ microbiomes typed for a database, he says. âAre you kidding me? People have been executed based on bad forensics in the past.â
Swapping gut bugs
More immediately concerning is the rise of faecal transplantsÌęâ taking faeces from someone healthy and giving them, via rectal insertion, to someone else.
In the US and Canada, the transplantation is regulated as an investigational drug, which means its use is restricted to clinical trialsÌęâ the exception is treating Clostridium difficile infections, for which the transplants have a . In the UK, however, the , so can be done if a supervising physician agrees to it. The Taymount Clinic in Hitchin, UK, for example, offers them for ulcerative colitis, multiple sclerosis and Parkinsonâs disease, and its counterpart in the Bahamas is treating people with autism (see âFaecal tourismâ, below).
All the microbiologists żìĂš¶ÌÊÓÆ” spoke to vehemently warned against seeking out a clinic for this until trials have found conclusive evidence that the procedure works for the relevant condition and is safe. They were alarmed by the growing trend of Ìęâ people armed with a blender and an enema kit going it alone.
So if faecal transplants are an application too far, at least for now, and probiotics have little impact (see âSwallowing a myth?â, below), what can microbes do for us in the next few years?
âThink beyond the gut microbiome,â says Elisabeth Bik, a microbiologist at Stanford University in California. Researchers have long sought to manipulate oral microbiota for the treatment of bad breath or tooth decay. Osel, a company in California, is ; and at Washington University, researchers are . Bik sees these as legitimate applications that arenât too far off.
âMicrobiome research is incomplete. We simply do not know what many microbial genes doâ
The jury is still out on whether eye-catching disease cures will ever materialise. âItâs like the post-genome blues,â says Eisen. âWe spent $2 billion on the human genome, and it was sold as being critical to developing cures for all sorts of human ailments.â So far, it has led to more questions than answers.
Watson thinks the problem is that todayâs microbiome research is incomplete and focuses mainly on bacteria. âMost of it ignores fungi, protists, viruses and other parts of the microbiomeâ he says. Even if those were included, it wouldnât be enough â âfor many [microbial] genes, we simply do not know what they do,â he says. For microbiome research to develop, the field needs to become more focused, build standards and change from being a mostly observational science.
Thatâs exactly what the National Microbiome Initiative aims to do. âWeâre looking for the principles that govern the response of the microbiome,â says Handelsman.
In the meantime, scientists and press officers should take care to avoid hype. âYou canât put out a press release that says youâve solved autism â oh, footnote, it was in miceâ, says Eisen. Itâs naive to think this wonât send people to clinics to get a faecal transplant for an autistic child, he says.
While the big moonshot programmes unpick the impossible complexity of the microbiome, people will try to apply it by any means necessary.
Faecal tourism
The Taymount Clinic in Hitchin, UK, is the UKâs premier destination for those looking for a faecal transplant. It offers them for conditions such as ulcerative colitis, multiple sclerosis and Parkinsonâs disease. The faeces come from non-smoking, non-drinking, naturally slim donors.
Glenn Taylor, who runs Taymount, says rising demand has forced the clinic to build an extension that more than doubles its size.
Sixty per cent of its clients come from the US and Canada, so in July 2015, the clinic opened a branch in the Bahamas â âjust a half-hour flight from Florida, in a beautiful environmentsâ, says the website. Taylor says the Caribbean outpost has carried out faecal transplants on people with autism. âThey are changing the way that autistic patients present just by changing the microflora,â he says. And itâs the same with obesity: âWe hear all the time from patients with transplants who suddenly have no trouble losing weight.â
Not-so-clean break
The clinic is also developing a wellness treatment for healthy people as a kind of âspring cleaningâ for the gut, a week-long retreat involving a series of colonics followed by a selection of faecal transplants. âIt would freshen you up if you were feeling a little sluggish, or after a holidayâ, says Enid Taylor, a co-founder of the clinic.
However, so far, faecal transplants have been shown to work only for Clostridium difficile infections. The microbiologists żìĂš¶ÌÊÓÆ” spoke to were uniform in their condemnation of faecal transplants whose safety and efficacy hasnât been shown in clinical trials. Melanie Thomson, a microbiologist at Deakin University in Geelong, Australia, is concerned by âhyped hopesâ raised by practitioners. âBut I understand the frustration and hope that drives people to engage with [unproven] science in the hope of a âcureâ for intractable conditions,â she says.
Swallowing a myth?
Itâs tempting to think that regular doses of âfriendlyâ bacteria will keep your gut happy. This notion explains the wild success of probiotic drinks, yogurts and supplements.
But last week, the market got a black eye from a that found no evidence that taking probiotics benefits healthy people. In four of seven trials analysed, no effects were observed on the faecal microbiota composition when compared with a placebo.
There are several reasons why this could be. Some suppliers may use bacteria that are dead. Others donât put in the right mix, says Jonathan Eisen of the University of California, Davis. Even a well-made probiotic is unlikely to survive the enzymes that kill microbes traversing our bodies.
Three other studies did find some changes to the abundance of certain bacteria, but because of their poor design, no conclusions can be drawn.
This article will appear in print under the headline âMoonshot or mania?â
