The discovery suggested healthy bacteria might one day be used to treat obesity, they told the journal Cell.
By studying human twins, they found a type of bacteria that was not only associated with being thin but also seemed to run in families.
Transplanting some of these microbes into mice slowed down weight gain.
The study is the first to suggest certain types of naturally occurring gut bacteria are inherited.
Analysing faecal samples from 416 UK twin pairs, the researchers found the abundance of Christensenellaceae bacteria was more similar in identical twins, who share exact DNA, than in fraternal twins, who are genetically just like ordinary siblings.
The results also showed Christensenellaceae was more common in lean individuals.
When the researchers treated mice with a specific member of this bacterial family, isolated from the twin study, the animals gained less weight than mice that did not get this treatment.
Study leader Dr Ruth Ley, associate professor in the department of microbiology at Cornell University, said even though their initial findings had suggested the bacterium could be contributing to a "lean phenotype", they had been fairly stunned to see its effect in mice and had repeated the experiment several times.
They are now working to identify what genes seem to influence the presence of Christensenellaceae bacteria and why it would have this effect on weight.
"Once we have found out how it works in mice, if it seems like we can apply that to humans we can look into developing this as a probiotic to regulate weight."
However, Dr Ley pointed out that the overarching factor contributing to obesity was a sedentary lifestyle.
Prof David Haslam, chairman of the National Obesity Forum, said the results took the argument further away from poor personal choice "when you realise we have millions of gut bacteria that are making these decisions for us".
"It is very exciting data and a rapidly evolving field. It is like science fiction - these small creatures that we can't identify and we're full of them."
He added: "It begs so many questions like if you take too many antibiotics what does that do to your gut bacteria?"
Our genes influence whether we are fat or thin by shaping which types of microbes thrive in our gut, scientists say.