Fonterra subsidiary ViaLactia Biosciences worked with scientists from German biotech firm GBF and Spanish firm CSIC to develop 'metagenomic technology'.
The technology allows them to identify new natural enzymes by isolating genetic information for all microbes present in a living organism. And the researchers said an examination of cows' stomachs "has produced some amazing results".
"It is clear that the rumen [a cow's first stomach] is a wellspring of unusual and valuable enzymes, none of which have been studied before," said Manuel Ferrer, of CSIC.
Ferrer said researchers had discovered a range of novel enzymes using metagenomics.
"The rumen offers a promising starting-point for new products and processes that were until recently hidden from us, for example the synthesis of novel nutritional lipids with therapeutic properties."
Kieran Elborough, ViaLactia's chief forage scientist, said the new enzymes found in the rumen also offered the chance to better understand a cow's digestive system.
From this, it may be possible to adapt feed to suit digestion, even using enzymes to do this, so as to reduce pressure on pastoral systems.
"We could expect further benefits for environmental sustainability, due to reduced need for irrigation and fertilisers," said Elborough.
Fonterra said it was also now looking at metagenomics in cows as a way of breaking into New Zealand's $2bn industrial enzymes market.
"Rumen metagenomics is no longer a future possibility, it is a functioning technology," said Elborough. "We're exploring a new frontier, and identifying new value in New Zealand's dairy herd."
Interest in genomics is growing across the dairy industry. Over the next two days, the California Dairy Research Foundation will host its second "Symposium on Milk Genomics and Human Health".
A number of high-profile researchers are expected to attend, including Martin Grigorov of the Nestlé Research Centre in Switzerland.
A University of California project has spent the last year building up a databank containing the different genes making up milk. Researchers from the US, Canada, Australia, New Zealand, Ireland, the Netherlands and Switzerland have all taken part.