The study, led by researchers at the Stanford University School of Medicine, reports that consumption of seaweed could help establish a specific strain of Bacteroides in our gut – adding that a specific carbohydrate found in nori could selectively favour the growth.
"We're all endowed with a microbial community in our guts that assembled in a chaotic manner during our first few years of life," commented senior author Dr Justin Sonnenburg – and associate professor of microbiology and immunology. "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."
Sonnenburg and colleagues used a mouse model to demonstrate that it is possible to favour certain bacterial strains over others through the inclusion of certain dietary compounds.
While many pre-existing and widely recognised prebiotic fibres are known to work in similar ways, in this case the team were looking for a way to manipulate and encourage the growth and ‘engraftment’ of one specific bacterial strain over multiple others through the use of a specific compound – which could also allow control over the level of growth by calibrating dietary levels.
To investigate, the team visited a waste-water treatment facility, in a bid to find members of the Bacteroides genus able to digest nori seaweed – something that is not widely consumed in many western populations.
Sonnenburg and his colleagues specifically screened the bacteria they collected for an ability to use a carbohydrate found in nori called porphyran.
"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," said Sonnenburg. "This allowed us to test whether we could circumvent the rules of complex ecosystems by creating a privileged niche that could favour a single microbe by allowing it to exist in the absence of competition from the 30 trillion other microbes in the gut."
Once they had found a strain of Bacteroides that was able to feast on the nori carbohydrate, the team then attempted to introduce it into three groups of laboratory mice: two groups of which had their own gut bacteria wiped out and replaced with that of healthy human donors, and one which kept a conventional mouse microbiome.
When the mice were fed a typical diet of mouse chow, the team reported that the porphyran-digesting strain of Bacteroides was able to populate two groups to ‘varying and limited degrees’ while one group rejected the new strain completely.
However, when the mice were fed a porphyran-rich diet, the results were dramatically different, said Sonnenburg.
When fed nori, the strain populated the guts ‘robustly’ at similar levels in all the mice, said the team.
Furthermore, the team found they could precisely calibrate the population size of the newly introduced bacteria by increasing or decreasing the amount of nori the animals were fed.
"The results of this dilution experiment blew us away," commented Sonnenburg. "The direct effect of diet on the bacterial population was very clear."
In addition to showing it is possible to favour the growth of the specific nori-feeding bacterial strain, the US-based team went one step further by demonstrating that the genes necessary to enable the digestion of porphyran exist as a unit that can be engineered into other Bacteroides strains – thus giving them the same advantages.
"We can use these gene modules to develop a vast toolkit to make therapeutic microbial treatments a reality," Sonnenburg said. "Porphyran-digesting genes and a diet rich in seaweed is the first pair, but there could potentially be hundreds more.
“We'd like to expand this simple paradigm into an array of dietary components and microbes,” he added – noting that the team are now working to identify other genes that have similar abilities.
"It's become very clear over the last 10 years that gut microbes are not only wired to many aspects of our biology, but that they are also very malleable," Sonnenburg added. "Our growing ability to manipulate them is going to change how precision health is practiced.”
Published online ahead of print, doi: 10.1038/s41586-018-0092-4
“An exclusive metabolic niche enables strain engraftment in the gut microbiota”
Authors: Elizabeth Stanley Shepherd, et al