Insights from 15 years of collaborative microbiome research with Indigenous peoples in the Peruvian Amazon

Forming sustainable research partnerships with Indigenous peoples requires trust and mutual benefit, say microbiome researchers in an opinion paper publishing October 8 in the Cell Press journal Trends in Microbiology. The paper presents a framework for building this type of relationship based on insights from the team’s 15-year-long collaboration with the Matsés, a group of people who live in the Amazon rainforest on the border of Peru and Brazil. To build trust, the researchers worked in collaboration with the Matsés through all stages of the research project, from developing research methods to disseminating results. 

“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,” write the researchers, including physician Graciela Meza of the Universidad Nacional de la Amazonía Peruana (UNAP), microbiologists Raul Tito and Jeroen Raes of KU Leuven-VIB, Belgium, and anthropologist Cecil Lewis of the Oklahoma School of Science and Mathematics. 

By studying the microbiomes of the Matsés and other Indigenous peoples, the researchers hope to understand how the human gut microbiome evolved and how it is impacted by access to processed foods and pharmaceuticals. To establish their partnership, the researchers began by conducting cultural research with Matsés leaders, community members, local health personnel, and political authorities. They developed their microbiome research protocols in collaboration with the Matsés people. 

“Our evolving collaboration with the Matsés proposes a framework that prioritizes long-term partnership, transparency, and community oversight,” they write. “All research activities are co-developed with the community and initiated only after extensive consultation and approval by Matsés leadership. We maintain open dialogue throughout the research process, from early protocol development to dissemination of results, ensuring culturally appropriateness, ongoing consent, and accountability.” 

The researchers note that achieving trust and effective communication with Indigenous peoples in a research setting is about more than the language barrier: it also requires understanding key cultural differences and maintaining transparency. 

“For the Matsés, as for other Indigenous peoples, trust is often shaped by negative sociohistorical experiences,” they write. “Recognizing the authority of immediate leaders and the Apu (Matsés chief), was essential to establishing legitimacy and ensuring respectful engagement, especially given the Matsés’ deep wariness of outsiders.” 

The researchers also altered some of their methods to better suit the Matsés culture. For example, rather than conducting individual interviews, they surveyed groups of people in “mini assemblies” to allow for dialogue and reflection amongst community members. 

In response to concerns amongst the Matsés that their biological samples might be commercialized, the researchers introduced a benefit-sharing clause in their protocols, which they developed in collaboration with the Matsés, such that any net profits from the commercialization of microbial strains isolated from Matsés would be split evenly.  

“This oversight reinforces accountability and embeds long-term ethical stewardship within a formal, regulatory framework to ensure protections endure beyond the project timeline or team turnover,” they write. 

As another benefit to the Matsés, the researchers organized for community members to receive general health screenings, including for intestinal parasites to address a common concern in the region. The screenings conducted were open to all community members, independent of their participation in the study. 

“Our collaboration with the Matsés highlights that ethical research is more than compliance with external standards, it requires integrating the perspectives of all stakeholders,” they write. “Only through such collaborative frameworks can we responsibly access knowledge with potential global relevance.” 

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This research was supported by funding from the National Institutes of Health and the Fonds Wetenschappelijk Onderzoek – Vlaanderen. 

Trends in Microbiology, Tito et al., “Navigating trust and science: Microbiome research in the Amazon”  https://www.cell.com/trends/microbiology/fulltext/S0966-842X(25)00250-1

Trends in Microbiology, (@TrendsMicrobiol) published by Cell Press, is a monthly review journal that provides a multidisciplinary forum for the discussion of all aspects of microbiology—from cell biology and immunology to genetics and evolution—and ranges across virology, bacteriology, protozoology, and mycology. Visit http://www.cell.com/trends/microbiology. To receive Cell Press media alerts, please contact press@cell.com.