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.

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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.

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[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.

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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.

 

[SFBayFMT5]

It seems to me that the authors of the first paper are not arguing that it is specifically the ivermectin that caused the changes, but rather "contact with the modern medical system". I agree this is a weird way to describe it (at least, I gather from how you present this that you also think it's weird) because it's an ill-defined concept that doesn't provide any potential leads as to mechanism, it almost borders on the magical.

To tell you the truth, I don't know how much the authors think that the ivermectin is or isn't responsible. It's possible that they think it IS, but feel they can't come out and say it because nobody visited the same doctors and didn't receive the drug. Alternatively, it's possible that there are previous studies showing that ivermectin doesn't affect the microbiome, so they don't think this is the reason but have nothing else to blame.

I wouldn't extrapolate from albendazole to ivermectin or vice versa in terms of direct effects as they have completely different targets (microtubules vs. ion channels) and very different structures. Neither of their targets should be present in the gut microbiome, there are some distant relatives of both in bacteria but these drugs are selective enough to target invertebrate forms of the proteins over their mammalian relatives, which are much less separated than either is from bacteria.

Obviously, an explanation is the fact of being sick with parasites itself having an effect on the microbiome. This is very plausible, and given the fact that only one of your citations showed an effect in people or animals NOT infected with parasitic worms adds weight to this interpretation. Even that study occurred in a population with a high burden of the worms, so one could postulate that even the "uninfected" people are frequently exposed to the worms, or that there is a change in the microbiome of the whole village when some members are cured of their parasites. This also goes along with the fact that the treated villagers became more "Westernized" in their microbiome--few Westerners ever need to take anti-worm medications, but that is because few of them are ever infected with the worms in the first place. If it were the treatment itself having the effect rather than the lack of worms, then it isn't immediately clear why it should approach the US/European microbiome.

This raises an important caveat of all "traditional microbiome" studies. Yes, we all agree that antibiotic overuse is bad for the gut, and so is highly processed food, and people in developed countries get a lot of both of them. Thus it can be tempting to look to cultures that don't have these things as an example of what we could become if we cut back on these things. However, while there's very likely a greater burden of chronic disease in industrialized nations, there are other types of ill health that are much more prevalent in traditional societies, including infections (with things like malaria and parasitic worms), leading to much higher infant mortality and shorter life expectancy.

Thus, it's not good to assume without proof that all microbiome differences between developed and more traditional societies are due to the latter being "less damaged" by things like bad diets and antibiotics. It's also very possible that some of them are due to the higher parasite load in the less modern cultures. These are not all necessarily bad, some may be protective microbes whose presence guards against parasites being an even bigger problem for those societies than they already are, but many of them could well be reflective of a different kind of poor health than the Western one, not of optimal health.