The field of microbiome research has never ceased to fascinate me. A recent study published in Nature Communications introduced the South American MicroBiome Archive (saMBA), a landmark project led by Benjamín Valderrama, a PhD student and computational biologist at APC Microbiome Ireland, University of Cork. This project curated one of the largest and most diverse datasets of human gut microbiomes, with a special focus on underrepresented populations from South and Central America. The study offers several critical insights that deserve careful consideration:
“Including neglected populations is not a matter of morality or ethics, it’s a matter of scientific rigour.”
Most large-scale human microbiome studies are disproportionately skewed towards European and North American populations. Conversely, populations from low-income regions such as Africa and South America remain severely underrepresented, often due to limited funding, infrastructure, and resources for sampling and sequencing.
The Human Microbiome Compendium analysis initially excluded the studies with fewer than 50 samples, inadvertently omitting valuable data from smaller South American studies. However, these populations are vital to improving the scientific validity and generalisability of microbiome research.
As microbiome-targeted diagnostics and therapies advance rapidly, the continued underrepresentation of diverse populations risks skewing results and diminishing clinical relevance. Findings derived from Western populations may not directly translate to those in different genetic, environmental, and cultural contexts. Thus, including diverse populations is not just equitable; it’s essentially a cornerstone of robust science.
“We need to take samples also from non-urbanised areas. That’s probably what can inform us the best or the most about the real biodiversity in the region.”
While the concept of a “healthy” gut microbiome remains complex and nuanced, microbial diversity is widely regarded as an important indicator of gut health. What is clear, however, is that non-industrialised populations consistently show higher microbial diversity compared to their industrialised counterparts.
The saMBA analysis revealed that rural and traditional communities in South and Central America harbour more diverse gut microbiota. Interestingly, populations in Central America and the Caribbean region displayed even greater diversity than those in South America. This is likely driven by traditional diets, less westernisation, and differng sanitation practices.
Overreliance on Western cohorts risks overlooking the full extent of global microbial diversity. Furthermore, the resilient and diverse microbiomes in these regions may also serve as reservoirs of antibiotic resistance genes, offering invaluable insight into microbial adaptation and global health threats such as antimicrobial resistance.
“The most challenging thing is first to find good quality available data, and then to find metadata associated with that data. That’s not always the case.”
A persistent barrier in microbiome research is the lack of high-quality, comprehensive metadata accompanying sequence data. While datasets from Europe and North America tend to be well-annotated, Latin American and Caribbean samples exhibit the highest number of unidentified taxa, despite showing high microbial diversity.
From a data preprocessing perspective, many published studies lack basic metadata, such as gender, age, and ethnicity. This limits the depth and precision of analyses. Most importantly, these details are crucial for stratified analysis and for uncovering more nuanced insights.
Researchers are strongly encouraged to ensure that metadata is complete, standardised, and publicly accessible, thereby enabling the scientific community to maximise the value extracted from these datasets.
Addressing these challenges requires more than goodwill. It demands concerted action from funding agencies and international consortia to: provide financial support to microbiome researchers in under-resourced regions; offer training and technical infrastructure, including standardised sampling and sequencing protocols; and promote policies that encourage open data sharing, inclusive of both sequence data and comprehensive metadata.
Through capacity building and fostering inclusivity, we can achieve scientifically rigorous, globally representative microbiome research. Only then can we understand the true diversity and function of the human gut microbiome in health and disease.
Further reading:
Integration of 168,000 samples reveals global patterns of the human gut microbiome | Cell
Structure, function and diversity of the healthy human microbiome | Nature
Examining the healthy human microbiome concept | Nature Reviews Microbiology
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