When a member of the Amazon Matsés tribe develops the telltale sore of the parasitic disease leishmaniasis, the tribal shaman knows what to prescribe: heated scrapings from the outer bark of a particular vine. For untold generations, this indigenous group on the Peru-Brazil border has counted on the forest’s vast array of medicinal plants and animals to treat its maladies and enhance survival practices like hunting.

But the tribe’s self-sufficient healing tradition and the forest it depends on are under threat. Recent sustained contact with the outside world has rapidly led to cultural erosion, discrimination, and resource grabs by outsiders, hurting the tribe’s self-sufficiency and its relationship to the land. Worse, the elderly shamans who know the rainforest’s secrets are dying, and their knowledge is becoming lost even as the tribe depends on them for health care. And because of shame learned from missionaries who viewed traditional healing as “witchcraft,” until recently no younger Matsés were training to become shamans.

They are now. Thanks in part to Acaté Amazon Conservation, a nonprofit co-founded by Christopher N. Herndon, M.D. ’04, the tribe has captured and preserved its elders’ knowledge and inspired its youth by writing an encyclopedia, one intended for use in training the next generation of tribal healers. The encyclopedia—which Herndon believes is the first ethnobotanical inventory of an Amazonian tribe to be written by the indigenous people themselves—describes hundreds of plants in 500 pages of text, photographs, and illustrations. Filled with pride and optimism in the wake of the project, several young Matsés have now stepped up to apprentice to shamans, Herndon reported.

“With the medicinal plant knowledge disappearing fast among most indigenous groups and no one to write it down, the true losers in the end are tragically the indigenous stakeholders themselves,” Herndon said. “The methodology developed by the Matsés and Acaté can be a template for other indigenous cultures to safeguard their ancestral knowledge.”

That methodology was entirely homegrown. To compile the encyclopedia, five elderly shamans paired off with younger tribe members literate in the Matsés language. Over two years, the elders divulged all they knew about pharmaceutical organisms, diagnoses, and treatments, while the youths took notes and photographs. Last May, tribe members met to compile the information into a single document. Though Acaté provided support, including a laptop and help with formatting, the project was entirely led and undertaken by the Matsés.

Significantly, the tome is in the Matsés language—whose written version was developed by missionaries in order to translate the Bible—but it won’t be translated.

That’s a measure to protect this traditional body of knowledge from commercial exploitation, a practice some call biopiracy and one the Matsés are all too familiar with. The rainforest’s pharmaceutical gifts are legion, including the antimalarial drug quinine, the muscle relaxant curare, and the stimulant cocaine, among others. Westerners eager to explore them further don’t always take tribal interests into account. In the early 2000s, without permission from or sharing with the tribe, a Seattle company and others patented versions of several peptides from the Acaté frog (Phyllomedusa bicolor)—whose skin secretions the Matsés use to alter consciousness, heighten senses, and confer feelings of strength and courage—for use as painkillers. Another substance in the public domain used by the Matsés and neighboring tribes is bëcchëte, a type of milkwood whose secretions applied to the eyes are reported to help hunters better distinguish textures. Seeds from this plant are now sold on the Internet by non-Matsés. Herndon said he can’t disclose Matsés remedies due to Acaté’s agreement with the tribe.

Ethnobiology and ethnomedicine have long emphasized the importance of cataloging traditional plant uses, said Yale anthropology professor Claudia Valeggia, Ph.D., who studies the health of Latin American indigenous groups. What makes the encyclopedia unique, she said, is that its monolingual nature will keep it within the community. “This is an invaluable survival kit, not only literally—it can save lives and alleviate a lot of suffering—but also metaphorically as an important aspect of the Matsés culture.”

Herndon, a reproductive endocrinologist in Berkeley, Calif., has worked with indigenous South American tribes since he was in medical school, initially through a Downs Fellowship in the summer of his first year at Yale. For his medical student thesis, which was awarded the Ferris Prize on his graduation in 2004, he studied the Tiriyó people of Suriname, a small country on the northeastern coast of South America, and wrote about their knowledge of anatomy and disease as well as plants. This knowledge remains vitally important. Though Western medicine can be helpful in the Amazon, remote health stations are often understocked, personnel poorly trained, and treatment options expensive, impractical, or able to cause dangerous side effects.

Herndon met the Matsés in 2011 after completing his fellowship in reproductive endocrinology at the University of California, San Francisco. In 2012 he co-founded Acaté with William Park, an agroforester who helps the formerly seminomadic Matsés develop sustainable farming techniques to adapt to their now-more-permanent settlements.

Their health system too may soon become more sustainable. One of the young shamanic apprentices is also the local government health promoter, a vanguard of the Matsés’ next plan: to develop an integrated Western and tribal health system that offers the best of both worlds.