Finding ways to manipulate the massive population of bacteria living inside our gut is turning out to be a tricky proposition for medical researchers. The ecology of our microbiome is enormously complex and we are only just learning of the broad effect gut bacteria has on our overall health.

A new study by a team at Stanford University has successfully shown how diet can be used to help propagate a specific species of gut bacteria. The research is an early step towards a future of precision medicine that can modulate the gut microbiome to help treat a variety of diseases and improve overall health.

"We're all endowed with a microbial community in our guts that assembled in a chaotic manner during our first few years of life," says Justin Sonnenburg, an author on the new study. "Although we continue to acquire new strains throughout life, this acquisition is a poorly orchestrated and not-well-understood process. This study suggests it could be possible to reshape our microbiome in a deliberate manner to enhance health and fight disease."

Until now, probiotics have generally been the most traditional way to modulate a person's gut microbiome. Essentially this means we consume certain strains of good bacteria to help maintain good health or treat conditions such as depression or allergies. But the team at Stanford wanted to understand how our diets could be altering the population of bacteria in our gut and whether consuming specific foods could help propagate certain bacterial strains.

To begin, the team tracked down a specific strain of gut bacteria that feeds on a carbohydrate called porphyran. This carbohydrate is found in seaweed often used in sushi rolls and the bacteria is perfect for study as seaweed is an ingredient rare in American diets.

"The genes that allow a bacterium to digest porphyran are exceedingly rare among humans that don't have seaweed as a common part of their diet," explains Sonnenburg. "This allowed us to test whether we could circumvent the rules of complex ecosystems by creating a privileged niche that could favor a single microbe by allowing it to exist in the absence of competition from the 30 trillion other microbes in the gut."

Further studies with different mouse models showed that levels of this bacteria in an animal's microbiome could be effectively manipulated by feeding them different volumes of seaweed. Excitingly, these levels could be precisely calibrated by simply increasing or decreasing the amount of porphyran-rich food ingested.

"The results of this dilution experiment blew us away," says Sonnenburg. "The direct effect of diet on the bacterial population was very clear."

The researchers then isolated the specific genes in the bacteria that enabled it to effectively digest porphyran. These genes were then transferred to another strain of the same bacteria without the same ability. In subsequent mouse models levels of the newly engineered bacteria were then effectively manipulated, again simply through diet.

What this research ultimately hopes to lead to is the development of a type of precision medicine whereby specific beneficial bacteria can be delivered to patients and then have its activity easily switched on or off through simple dietary measures.

"A physician whose patient is about to begin immunotherapy for cancer may choose to also administer a bacterial strain known to activate the immune system, for example," suggests Sonnenburg. "Conversely, a patient with an autoimmune disease may benefit from a different set of microbiota that can dial down an overactive immune response. They are just a very powerful lever to modulate our biology in health and disease."

The research was published in the journal Nature.