A groundbreaking study conducted by Justin Sonnenburg and his team at Stanford University in California has shed light on the stark differences in gut microbiomes among different populations. The research, using ultra-deep sequencing techniques, focused on the gut microbiomes of 167 Hadza people, average Californians, and farmers in Nepal.
The study revealed that the Hadza people exhibited a significantly higher average of 730 species in their gut microbiome compared to just 277 species in the average Californian population, while farmers in Nepal had an average of 436 microbe species. Moreover, the researchers discovered that the Hadza not only had diverse bacteria populations but also had varied bacteriophages and archaea.
The team documented that 124 gut-resident species were disappearing in industrialized populations, underscoring the distinct aspects of the Hadza gut microbiome in terms of in situ replication rates, signatures of selection, and strain sharing. The industrialized gut microbes, on the other hand, were found to be enriched in genes associated with oxidative stress, suggesting a potential correlation between microbiome adaptation and inflammatory processes.
Growing evidence suggests that the loss of microbial diversity in our gut microbiota is closely related to the increased prevalence of metabolic, cognitive, and immune diseases accompanying industrialization. The Microbiota Vault, spearheaded by Prof Martin Blaser (Rutgers) and Professors Rob Knight and Jack Gilbert (University of California at San Diego), has been proposed as a repository for human-associated microbes to preserve microbial biodiversity and potentially pave the way for novel probiotics to support health.
Among the groups studied for disappearing gut bacteria, the Hadza people in East Africa have been highly significant. Previous studies have shown that their gut microbiota is more diverse and resilient to challenges like antibiotics compared to Western populations.
Sonnenburg and his team employed ultra-deep metagenomic sequencing to analyze 351 fecal samples from the Hadza, as well as comparative populations in California and Nepal. This comprehensive sequencing effort resulted in over 90,000 genomes from various gut microbes, including bacteria, bacteriophages, archaea, and eukaryotes. Notably, 44% of these genomes were previously unrecorded in existing databases.
Furthermore, the researchers identified a bacterium called Treponema succinifaciens that was completely absent in the Californian samples and partially present in the Nepali samples, indicating its decreasing presence with industrialization.
The unique dataset generated from this study provides a critical reference point for microbiome scientists to understand the effects of industrialization on the gut microbiome. As the Hadza people face challenges linked to land dispossession, lack of resources, and socioeconomic inequality, the findings shed light on the impact of changing lifestyles on microbial diversity.
In conclusion, this study emphasizes the importance of preserving microbial diversity in the face of industrialization and highlights the potential implications for human health. The research underscores the significance of ongoing efforts to explore and understand the complex interactions between our gut microbiota and overall well-being.
Source: Cell (doi: 10.1016/j.cell.2023.05.046) “Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes” by M.M. Carter et al.