Animal scientist uses AI to build climate-smart cattle production

Curiosity has always been strong driver for Dr. Limei Lin, especially when it came to understanding why animals exhibit special traits, such as the ability of birds to fly.

Now she is part of an international research group that aims to reduce methane production in cattle, receiving a prestigious UBC Killam Postdoctoral Fellowship for her work. Last September, Dr. Lin joined Dr. Leluo Guan’s (Tier 1 Canada Research Chair) lab, which is leading a $7.9-million, five-year research collaboration between major institutions and researchers called Novel and Adaptive Rumen Microbiome targeted solutions for GHG mitigation in cattle.

Dr. Lin brings to the research group a background in rumen microbe–host interactions. She is examining data from 10,000 beef and dairy cattle, which were provided by universities and dairy research centres from across Canada. These datasets contain the microbiome, genomics, and the production traits (also known as phenotype) of cattle. Dr. Lin is using these datasets to train prediction models that will eventually lead to an understanding of how the rumen microbiome and host genotype jointly influence key traits, such as feed efficiency and methane emissions.

Dr. Lin says, “I am harnessing artificial intelligence (machine learning and deep learning) to advance our understanding of the rumen microbiome and its central role in balancing food security and environmental impacts.”

“I am harnessing artificial intelligence…to advance our understanding of the rumen microbiome and its central role in balancing food security and environmental impacts.”

– Dr. Limei Lin

Ruminants are herbivorous grazers that extract nutrients from food through microbial degradation and fermentation in a specialized forestomach. This process relies on a diverse microbiome consisting of bacteria, archaea, protozoa, and fungi. The term ‘ruminant’ derives from their unique habit of regurgitating and re-chewing their feed to enhance digestion efficiency.

Dr. Lin explains that ruminants host one of the most complex microbial ecosystems in nature, with the rumen microbiome acting like an ‘engine’ that transforms fibrous plant material into energy, providing up to 70% of the host’s energy requirements. However, microbial interactions also generate large amounts of methane, a potent greenhouse gas that has 28 times the global warming potential than carbon dioxide. Methane not only contributes to climate change but also leads to energy loss for cattle.

Since arriving at UBC, Dr. Lin taught herself to use artificial intelligence and informatics to build predictive models in three months using resources such as GitHub, Bilibili, YouTube, and other online sites.

Now she is excited to embark on deep learning to explore the ‘microbial dark matter’ of the rumen – hoping to make new discoveries related to uncharacterized enzymes and novel microbial lineages that play potential roles in carbon cycling and industrial biotechnology.

Dr. Lin earned her MSc and PhD from Nanjing Agricultural University under the supervision of Professor Shengyong Mao, where she researched the gastrointestinal microbiome of ruminants. During this period, she explored how dietary changes reshape the microbial ecosystems of the whole gastrointestinal tract.

Her early studies on diet–microbiome–host crosstalk, together with genome-centric analyses in dairy cows, uncovered the microbial drivers of bile acid metabolism, vitamin biosynthesis, fiber degradation, and volatile fatty acid formation.

“My Killam Postdoctoral Fellow at UBC now extends this work, applying larger animal cohorts and advanced machine learning to explore how the rumen microbiome and host genetics together shape efficiency and sustainability in cattle production.”

Ultimately, she hopes to translate AI-driven discoveries into actionable strategies that enhance feed efficiency, reduce methane emissions, and redefine sustainable livestock production.

“By bridging artificial intelligence, microbial ecology, and animal science, this research aims to unlock new opportunities for climate-smart agriculture and global food security,” says Dr. Lin.

More Research in Applied Animal Biology