Is the microbiome as important for precision medicine as genetics?

Undoubtedly genetics plays a role in determining microbiome variation across populations and our genes may enable particular bacterial strains to thrive. However, the institute’s research had surprising results, indicating that a host's genetics account for just 2% of the variation between populations, and genes are less important in determining microbiome composition.

Instead it is diet and lifestyle that are the key influencers and our unique microbiomes grow and change with us throughout our lives. Though genetics is less of a determining factor, our unique colonies of fungi, bacteria and microorganisms are still able to interact with our genes to modify and influence many common health issues.

A huge advantage microbiome science has over genetics is that it is far more mutable,” says Kuntz. “While technologies like CRISPR (a family of DNA sequences in bacteria and archaea) allow for changing of genetics, safe usage of that in humans is far off, but we already ‘edit’ our microbiomes even through changes in diet.”

Kuntz also argues that the possible dawn of a ‘post-antibiotic’ age would make microbiome interventions for diseases a dire necessity.

“Even if this does not come to pass,” he continues, “microbiome-based medicine for infection may be part of preventing overuse of antibiotics or even – as has been seen in clostridium difficile infections – something that outperforms antibiotics currently.”

Understanding and implementing the correct changes in the microbiome (through diet or other means such as probiotics) is a lengthy and complicated process, but it is proving the efficacy, safety and economic viability of these interventions that is crucial to secure the necessary approvals to bring microbiome medicine to the global market.

“The latter is a current hurdle in fecal microbiota transplant (FMT) – the transplantation of fecal bacteria from a healthy person into a recipient,” says Kuntz. “FMT is possibly the easiest treatment to ensure a beneficial and large change in the microbiome, since understanding the inner workings is less important than the overall health status of the donor. This could be extremely helpful in a number of digestive diseases, which otherwise resist treatment.”

Perhaps the biggest issue facing microbiome precision medicine is to keep interest and funding high so that research can progress efficiently.

“Genomic medicine went through a significant bubble that when popped really limited the field despite its still promising applications to medicine,” explains Kuntz.

He believes the microbiome field faces a similar issue if it is considered a fad, or if a lack of immediate results is taken to indicate that results won’t eventually be forthcoming.

“So having enthusiasm and public support and knowledge – especially in traditionally underserved communities where microbiome driven disease may be highest – will be key to keeping the microbiome relevant,” he adds, “and ultimately having it implemented as standard, precision medicine.”

Kuntz and Gilbert would like to see the standardisation and expansion of collection of microbiome samples for medicine and research. Making microbiome sampling a basic and integral part of personal health would not only increase its diagnostic potential they say, by simply reaching more people, it would also improve research if those samples could be properly identified and used for further large-scale epidemiological research.

“The price-point for taking microbiome samples is already low enough that this is possible, but collection protocols, public awareness, and reticence from healthcare providers remain as roadblocks,” says Kuntz. “A similar hurdle has faced genomic medicine for some time, but we are hopeful that microbiome medicine might overcome these issues more quickly.”

In the longer term, the ultimate goal is to utilise this information along with further developing probiotic, prebiotic and microbiome targeting products to treat disease.

“This is further ahead due to the amount of research, especially on larger, more diverse cohorts, that must be first performed,” concludes Kuntz. “This isn’t to say some probiotic research won’t bear fruit sooner than ten to 15 years, but truly personalised therapies may take that long depending on what research breakthroughs are made and how research is handled now and in the future.”