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.

This data is freely available under the Creative Commons Attribution 4.0 International license (CC BY 4.0). If you use it in your work, please cite our publication:

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

Overview of the workflow

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 (shared in this repository) were then analysed to generate the article. The code used for that analysis can be found in this GitHub repository.