He uses transdisciplinary methods to find new information and applications for improving conservation outcomes that also impact the protection of public health.

[4] As part of Aguirre's academic career, he was appointed as assistant professor in 1992 at Colorado State University for the Department of Fishery and Wildlife Biology.

His research is focused on uncovering the impact of emerging diseases in marine wildlife populations including manatees, monk seals and sea turtles.

He co-founded the emerging discipline of Conservation medicine, with Mary C. Pearl and Gary Tabor, expanding the One Health approach to the environment, animals and people.

[5][6] In a study Aguirre conducted in 2020, he searched for the exact origin of SARS-COV-2, which was unknown but the evidence pointed to the Wuhan wet market where several bats and wild animals were frequently stored and sold in close spaces and identified that in many pandemics in the past, bats were known for spreading zoonotic diseases and markets like these are the ideal conditions for viruses like COVID-19 to emerge.

[7] In another paper, he gave examples of vector-borne and parasitic diseases that have persisted, emerged and re-emerged in the environment, significantly harming human and animal populations all over the world.

He describes how specialists in the field of transdisciplinary and socio-ecological health umbrellas have collaborated and integrated new and established techniques for disease modelling, prediction, diagnosis, treatment, control, and prevention, and that approaches like these that mainly emphasize conservation of biodiversity for health protection provide novel opportunities for increasing the efficiency and probability of success.

[13] Further, Peter Hudson in the journal TREE stated "I like to think of conservation medicine as the consequence of the human footprint on the ecological balance of disease dynamics... and drive of its contributors highlight how interdisciplinary research should be undertaken".