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"It's opening a new door for developing mitigation strategies," Dr Sergio Morales, a University of Otago senior lecturer, said this week.
"Any piece of information that makes the picture a little bit clearer" would ultimately help to cut methane emissions, he said.
Latest research was "not a silver bullet" but he was more confident about finding an eventual solution.
The researchers had studied two types of sheep - those producing high amounts of methane and those producing less.
They found the most active hydrogen-consuming microbes differed between the sheep.
And, in the low methane-emitting sheep, hydrogen-consuming bacteria dominated, which did not produce methane.
The findings suggested that methane emissions could be reduced by controlling the hydrogen supply.
One strategy was to introduce feed supplements that encouraged non-methane producers to outcompete methanogens, which were micro-organisms that produced methane.
Dr Morales, of the Otago microbiology and immunology department, said researchers had already known that microbes helped control methane levels, but scientists now knew why.
They had clarified which microbes and enzymes controlled the supply of hydrogen, the main energy source for methane-producing microbes, known as methanogens.
Prof Greg Cook, also of the department, said this discovery was important because methane emissions from ruminant animals, including sheep and cattle, accounted for about a third of New Zealand's overall greenhouse gas emissions.
Prof Cook, Dr Morales, Dr Xochitl Morgan, Rowena Rushton-Green and PhD student Cecilia Wang, also of the department, were working as part of an international research collaboration, the Research Alliance on Agricultural Greenhouse Gases.
New processes that controlled methane production in the stomach of sheep and similar animals such as cattle and deer had also been identified.
The breakthrough research was recently published in scientific journal International Society for Microbial Ecology Journal.