Researchers at King's College London and Cornell University in the US studied pairs of twins at King's Department of Twin Research.
They identified a specific, little known bacterial family that is highly heritable and more common in individuals with low body weight. This microbe also protected against weight gain when transplanted into mice.
The results, published in the journal Cell, could pave the way for personalised probiotic therapies that are optimised to reduce the risk of obesity-related diseases based on an individual's genetic make-up.
The abundances of specific types of microbes were found to be more similar in identical twins, who share 100 per cent of their genes, than in non-identical twins, who share on average only half of the genes that vary between people.
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These findings demonstrate that genes influence the composition of gut microbes.
The type of bacteria whose abundance was most heavily influenced by host genetics was a recently identified family called 'Christensenellaceae'.
Members of this health-promoting bacterial family were more abundant in individuals with a low body weight than in obese individuals.
"Our findings show that specific groups of microbes living in our gut could be protective against obesity - and that their abundance is influenced by our genes," said Professor Tim Spector, Head of the Department of Twin Research and Genetic Epidemiology at King's College London.
"The human microbiome represents an exciting new target for dietary changes and treatments aimed at combating obesity," he said.
"Up until now, variation in the abundances of gut microbes has been explained by diet, the environment, lifestyle, and health," said Ruth Ley, Associate Professor at Cornell University.