The South American MicroBiome Archive (saMBA): Enriching the healthy microbiome concept by evaluating uniqueness and biodiversity of neglected populations

Abstract The composition and function of the human gut microbiome has been linked to multiple health outcomes across all world regions, often with region-specific associations. Unfortunately, the extent to which microbiomes from different populations are characterised is limited by their economic resources. Over 70% of the sequenced human microbiomes come from analyses of European and North American populations, skewing our understanding by focusing excessively on just 15% of the global population. Thus, entire continents rely on results from research conducted in wealthier countries whose main findings are unlikely to generalize across other world regions. Moreover, statistical models perform poorly when applied to minorities, a blind spot with serious consequences in biomedicine, and which can only be addressed by analysing microbiome data from currently neglected areas. To address this problem, we created saMBA— the largest archive of gut microbiomes from South America, one of the world’s most biodiverse regions in terms of the gut microbiome of its inhabitants, yet the one with the fewest samples. ‘saMBA’ includes 33 gut microbiome studies, ∼73% of which were incorporated in a microbiome archive for the first time. By leveraging this resource, we uncovered a high biodiversity within —and uniqueness between— gut microbiomes across the continent, expanding the concept of the healthy microbiome to be more globally representative. Additionally, our results highlight that the gut microbiome biodiversity of this region remains far from fully characterized. We demonstrate how saMBA can guide new sampling efforts to better capture this diversity. Finally, the code deployed to build saMBA is compatible with that of a previous global compendium and is openly available to researchers from other underrepresented regions, fostering the inclusion of other neglected populations to accelerate microbiome research globally. Competing Interest Statement JFC has been an invited speaker at conferences organized by Bromotech, Yakult and Nestle and has received research funding from Nutricia, Dupont/IFF, and Nestle. GC has received honoraria from Janssen, Probi, Apsen, and Ingelhem Boehringer as an invited speaker; is in receipt of research funding from Pharmavite, Fonterra, Reckitt, Nestle and Tate and Lyle; and has been paid for consultancy work by Yakult, Zentiva, Bayer Healthcare and Heel Pharmaceuticals. This support neither influenced nor constrained the contents of this manuscript. All other authors declare no conflicts of interest.