An anti-parasitic medication (ivermectin) shifted Amazonian villagers’ microbiomes toward an urban profile (May 2026, n=335) Rapid microbiome restructuring associated with medical exposure in remote Amazonian Indigenous communities Parasites

[Michael Harrop]

• https://www.the-scientist.com/medical-interventions-rapidly-change-isolated-indigenous-microbiomes-74501
• https://medicalxpress.com/news/2026-05-modern-medicine-gut-microbial-diversity.html
• https://www.cell.com/cell-reports/fulltext/S2211-1247(26)00421-3

Amerindian communities across southern Venezuela have remained isolated from Western medicine. Villages are often only accessible by river or air, and villagers rely on hunting and fishing for food. This isolation has a cost: These communities are among the last in the Americas to be affected by onchocerciasis, also known as river blindness. A parasite transmitted by black flies causes this condition, which can be treated by mass administration of the antiparasitic drug ivermectin. The Carter Center’s Onchocerciasis Elimination Program for the Americas (OEPA) has been delivering the drug across the Americas since 1993.

Now, an international research team has suggested that OEPA’s program may have had an unexpected impact by changing the microbiome of these isolated communities. Analysis of the microbiota living in and on the villagers showed that their diverse bacterial communities became more restricted and more alike to those seen in urban populations after just a handful of medical visits.

“The program offered a rare natural experiment,” said Maria G. Dominguez-Bello, a microbiologist at Rutgers University and coauthor of the new study, in a statement. “We know from studies in urban societies that antibiotics can have huge impacts on gut microbes,” she said. “But we didn’t know how even basic medicine might affect people with very limited exposure to medicine.”

Researchers from Dominguez-Bello’s group visited seven villages alongside the OEPA team in October 2015, before the medical program began, and again in February 2016. They collected over 1,500 samples from 335 participants, including fecal samples and swabs of the skin, nose, and mouth.

Click to shrink...

Highlights​

• Repeated medical exposure is associated with rapid microbiome restructuring
• Gut microbial diversity declines with repeated exposure especially in children
• Microbial taxa, networks, and gene functions shift with exposure
• Microbiome changes precede major lifestyle and dietary transition

Summary​

Many factors contribute to reduced microbial diversity associated with Westernization, complicating efforts to identify early drivers of microbiome change.

Here, we examine microbiome variation during the introduction of a sustained medical program into previously low-exposure remote Indigenous villages. We analyze fecal samples and body-site swabs from 335 Amerindians across multiple villages before and during repeated program visits, prior to major dietary or lifestyle transitions.

Low-exposure villages show higher baseline gut microbiota diversity than the medium-exposure village, and microbiota diversity declines over time in association with repeated exposure, particularly in children. Changes include loss of specific gut taxa, reduced bacterial network connectivity, and shifts in functional gene profiles toward those reported in urban populations. Oral microbiota diversity decreases, while skin and nasal diversity show modest changes.

These findings indicate that repeated exposure to basic medical interventions coincides with rapid microbiome restructuring during early stages of ecological transition.

Click to shrink...

 

[Michael Harrop]

I recall an earlier study that Martin Blaser was either involved in, or commented on, which found that anti-parasitic medications caused minimal changes to the gut microbiome. I can't find it now though. I tried a web search for "anti parasitic medication microbiome change minimal blaser".

The closest thing I found:
The effect of single dose albendazole (400 mg) treatment on the human gut microbiome of hookworm-infected Ghanaian individuals (2023) https://www.nature.com/articles/s41598-023-38376-3

Among treated individuals, there was also a significant variation in microbiota composition at 10–14 days following single-dose albendazole treatment. Individuals cured of hookworm infection after treatment showed a significant reduction in microbiota composition when compared to their pre-treatment state (ANOSIM; p = 0.02), whilst individuals who failed to clear the infection showed no change in microbiota composition (ANOSIM; p = 0.35). Uninfected individuals and those who were successfully treated were similar in their microbial composition and structure. We also found that the abundance of Clostridia spp. was increased in infected individuals pre- or post-treatment.

Click to shrink...

Not it:
Differential Effects of Two Common Antiparasitics on Microbiota Resilience (2023) https://academic.oup.com/jid/article/229/3/908/7456363. Mouse study showing minimal changes from albendazole.

Impact of Ivermectin on the Gut Microbial Ecosystem (2023) https://www.mdpi.com/1422-0067/24/22/16125 - used SHIME® (simulator of the human intestinal microbial ecosystem). Found minimal impacts.

Dynamic changes in human-gut microbiome in relation to a placebo-controlled anthelminthic trial in Indonesia (2018, n=150) https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0006620 - no differences from albendazole at a phylum level.

The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya (2019) https://journals.asm.org/doi/10.1128/mbio.00519-19 - treatment of hookworm infection with albendazole results in significant changes.

Gut microbiome of helminth-infected indigenous Malaysians is context dependent (2022) https://link.springer.com/article/10.1186/s40168-022-01385-x - Longitudinal changes in the microbiome in response to albendazole anthelmintic treatment were observed in both helminth infected and uninfected individuals.