May the Fiber Be with You: Gut Microbiomes from a remote Amazon village to the undergraduate lab

Katrine Whiteson

University of California Irvine School of Biological Sciences, co-Director, UCI Microbiome Center

Bacterial and viral colonization of the human body has profound implications for human health, yet our understanding of what constitutes a “healthy microbiome” remains incomplete—especially in the context of industrialization. Over the past century, global diets have shifted dramatically, with increased consumption of processed foods and a steep decline in dietary fiber intake. These changes have left our colons depleted of critical substrates that fuel gut microbial communities, with potential consequences for immune function, metabolic health, and chronic disease risk.

To explore what a less industrialized microbiome might look like, we studied the gut, oral, and fermented food microbiomes of women and children from 28 households in Conambo, a remote Indigenous community along the Conambo River in the Ecuadorian Amazon. This community is largely isolated from urban infrastructure, with minimal exposure to processed foods or modern medical care. Microbiome profiles from Conambo participants revealed high diversity and a dominance of microbial taxa such as Prevotellaceae.

We also analyzed chicha, a traditional fermented manioc beverage prepared by mastication of boiled cassava tubers. Our findings revealed microbial succession during fermentation and close taxonomic overlaps with oral and gut microbiota—underscoring the intimate links between diet, tradition, and microbial transmission. Within Conambo, household co-residence emerged as a strong driver of microbiome similarity across fecal, saliva, and chicha samples.

Finally, we contextualized the Conambo microbiomes by comparing them to global reference datasets, including UC Irvine undergraduates participating in dietary fiber intervention studies. Together, these datasets reveal how environmental exposure, diet, and social structure shape the human microbiome—and offer a lens into both human microbial history and the future of microbiome-informed health.