The South American MicroBiome Archive (SAMBA)

Overview of saMBA The South American MicroBiome Archive (saMBA) is the result of a semi-automated search and automated analysis of microbiome studies characterising the gut microbiome of people living in South America. The computational workflow used to build saMBA is hosted in this GitHub repository and can be deployed using this Docker image. Instructions about how to use the software can be found the documentation. The outputs of deploying the workflow were then analysed to generate the published article. The code used for that analysis can be found in this GitHub repository. The data is freely available under the Creative Commons Attribution 4.0 International license (CC BY 4.0). If you use the workflow or the dataset it in your work, please cite our preprint: Valderrama, Benjamin., Calderon-Romero, Paulina., Bastiaanssen, Thomaz F.S., Lavelle, Aonghus., Clarke, Gerard., Cryan, John F., "The South American MicroBiome Archive (saMBA): Enriching the healthy microbiome concept by evaluating uniqueness and biodiversity of neglected populations.", BioRxiv, doi.org/10.1101/2025.04.03.647034