Including Indigenous peoples in microbiota research is both scientifically essential and ethically necessary. A new Science & Society article shows that understanding and respecting Indigenous knowledge is essential for ethical microbiota research and for uncovering knowledge that benefits everyone.

The article, published in Trends in Microbiology, describes a 15-year collaboration between researchers led by Raul Tito at KU Leuven in Belgium and the Matsés people of the Peru–Brazil border. The collaboration was rooted in community-based participatory research—an approach that treats Indigenous communities as equal partners rather than subjects of study. 

Like other Indigenous peoples, the Matsés have unique gut microbes that can help advance our understanding of human evolution and improve global health. Gaining this knowledge, however, requires ethical research and strong, trust-based partnerships.

Building partnerships

To establish this collaboration, the researchers first learned about Matsés leadership structures, health concerns, and cultural beliefs. Rather than using standard Western interview techniques, they held open community discussions that fit the Matsés’s way of making decisions. Recognizing the authority of the chief and local delegates was key to build trust among the Matsés, who are historically wary of outsiders.

The researchers learned that concepts such as consent and privacy have different meanings in Matsés culture. Health is seen as a communal right, not an individual issue, and participation in research was often viewed as a collective act of pride. 

The researchers also launched a voluntary screening program for intestinal worms and parasites. Coordinated with local health workers, the program provided medical benefits and opened dialogue about gut health and the human microbiota.

Sharing benefits 

In the guts of Matsés people, the researchers identified new microbial species, including a harmless Treponema strain found in ancestral human populations but largely absent in industrialized societies. This finding may help scientists understand how gut ecosystems evolved and how they influence health. 

Over time, the Matsés participants began to ask questions about the fate of their biological samples and the potential for commercial use. So, the researchers developed a benefit-sharing agreement that guarantees equal profit from any commercialization of microbial discoveries. 

Ethical research with Indigenous communities cannot rely only on external regulations, which are often incomplete or absent in low- and middle-income countries, the authors say. “Establishing genuine partnerships with Indigenous peoples requires sustained investment in trust-building, honest engagement with historical and structural injustices, and a recalibration of scientific practices to prioritize respect, autonomy, and justice,” they say. “Trust must be actively cultivated through shared purpose and mutual accountability.”