#FEMSmicroBlog: Characterizing the gut eukaryome of African children


Eukaryotes, such as fungi, protists, and helminths, live in the human gut alongside a complex community of bacteria and other microorganisms. While some eukaryotes are harmful pathogens, recent data show that others might be neutral or even beneficial. The research article “The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status” in microLife characterizes eukaryotic community members along the gastrointestinal tract in a large cohort, as explained by Pascale Vonaesch for the #FEMSmicroBlog. #FascinatingMicrobes


About the gut eukaryome of African children

Historically, eukaryotes in the human gut were considered harmful to their hosts. That’s why research has focused mainly on their roles in disease and how to get rid of them.

Over the years, the hypothesis emerged that gut eukaryotes could be beneficial for human health. For example, the most common eukaryote, the single-cell protist Blastocystis, resides in the guts of at least a billion people worldwide.

These microaerobes thrive in low oxygen levels. Higher oxygen levels are a sign of gut inflammation as found in patients with Crohn’s disease, who also carry lower levels of Blastocystis.

It is challenging to evaluate the role of the eukaryome in health since the diversity and ecology of gut eukaryotes remain poorly studied. The research article The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status” in microLife sheds light on the eukaryotic members of the human gut microbiome. The study is part of the “Afribiota” project.

The “Afribiota” project sampled roughly 1,000 children aged 2-5 years in Bangui (Central African Republic) and Antananarivo (Madagascar). The aim of the project was to identify the causes of stunting, impaired growth, and development of children due to chronic malnutrition or repeated infections. This condition affects at least 25% of children across the world and has negative long-term impacts on health and cognition.

This is the first study characterizing the eukaryome throughout the human gastrointestinal tract rather than only the eukaryome of the feces. The study describes that fungal communities in the stomach and duodenum are very different than fungal communities in feces.


Two special eukaryotic gut members in African children

The study used multiple amplicon sequencing approaches to identify the eukaryotes present in the gut. The identified eukaryotic gut members were then linked to diverse clinical factors, such as stunting, gut inflammation, and anemia.

The study found little association between the eukaryome overall and stunting or other clinical factors. In contrast, the bacterial microbiome is strongly correlated with clinical factors in children and in a wide array of other diseases.

While the eukaryome (the overall eukaryotic community) does not differ in children with or without stunting, two eukaryotes were associated with stunting: Fusarium equiseti and Blastocystis. The fungal plant pathogen Fusarium equiseti was more common in stunted individuals. But rather than living in the gut, this fungus is most likely a transient member of the gut microbiome after ingesting it with plant-derived food. Its link to stunting is yet unknown and could be related to mycotoxin production.

On the contrary, Blastocystis is a widespread gut resident and is less common in stunted individuals, echoing findings that it is uncommon in people with several immune-mediated diseases in industrialized populations. This suggests that Blastocystis might be an indicator of a healthy gut ecosystem.


Analyzing the human intestinal eukaryome

Notably, many of the fungi detected throughout the upper gastrointestinal tract are unlikely to be residents of the gut. Instead, they are probably transients acquired from the diet and environment. Differentiating between residents and transients gut inhabitants, as well as assessing their functional roles, represent some of the many open questions about the human gut eukaryome.

Identified species in the gut eukaryome of African children.
Identified species in the gut eukaryome of African children. From Vonaesch et al. (2023).

The eukaryomes of the children differ strongly between the two countries from which samples were taken (Central African Republic and Madagascar). Additionally, their eukaryomes seem to be more diverse than typically observed in industrialized countries, with helminths, fungi, and multiple types of common protists (including Blastocystis, amoebae, and flagellates) often found within an individual. Studying geographically diverse populations, particularly from the Global South, is important to better understand the common features of the human eukaryome in health and disease.

The results are consistent with the emerging viewpoint that eukaryotes in the human gut may be commensal and even beneficial. Uncovering the functional connections between the eukaryotes and the rest of the gut ecosystem promises new insights into human health.


About the author of this blog

Pascale Vonaesch is an Assistant Professor at the University of Lausanne and a Principal Investigator within the NCCR Microbiomes. She wrote her PhD thesis at the Institut of Microbiology at the ETH in Zürich (Switzerland) on host-pathogen interactions. Thereafter, she joined the Institut Pasteur in Paris (France) as a postdoctoral researcher, where she initiated and led the Afribiota project, a translational research project aimed at elucidating the pathophysiology underlying stunted child growth. Her lab focuses on fundamental and translational/clinical research on the human intestinal ecosystem and the contribution of the microbiota to health and disease.

About this blog section

The section #FascinatingMicrobes for the #FEMSmicroBlog explains the science behind a paper and highlights the significance and broader context of a recent finding. One of the main goals is to share the fascinating spectrum of microbes across all fields of microbiology.

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