The Ecuadorian Microbiome Project: a plea to strengthen microbial genomic research

Abstract

A technological revolution provides nations with access to unprecedented quantities of molecular information, and this is particularly evident in the vast and yet poorly understood realm of the microbiome. Traditionally, many developing countries in Asia, Africa, and South America remain marginal participants in the global flow of biodata, which will eventually affect their productivity and economies. Here, we present the Ecuadorian Microbiome Project (EcuMP) as an integrative initiative to close the research gap in the microbiome for Ecuador. We discuss the relevance that the study of the microbiome has for our understanding of diversity and new forms of production and biocapital. We also evaluate the state of research in metagenomics and the microbiome for South America, with emphasis on Ecuador as a small but biodiverse country. In the strict sense of access, understanding, and technological innovation based on molecular data, we propose the definition of bioliteracy. As indirect estimates of bioliteracy, we measured the number of indexed publications, BioProjects, monthly global internet traffic to GenBank, and patent applications in Espacenet. South America has a notable unevenness in scientific productivity related to the microbiome and metagenomics. Brazil leads productivity, with most of the measured parameters remaining one order of magnitude higher than other countries in the region. Participation of South American countries in the global flow of genomic information dwarfs when compared to the US. To reduce the effects of technological dependency and the associated lack of economic productivity, Ecuador should address the technological gap in the study of the microbiome. Our assessment reveals the urgency to translate the study of microbiomes into a source of technological prowess and the basis for local biocapitals.

Public human microbiome data are dominated by highly developed countries

“…The Pan-African Bioinformatics Network (H3ABioNet), which has worked extensively in genomics research capacity building in Africa, also recently hosted a hackathon wherein they began work on a data portal for African microbiome samples [ 52 ]. In South America, the Brazilian Microbiome project and the recently proposed Ecuadorian Microbiome project both seek to advance microbiome research capacity in their respective countries and create local infrastructure to support these goals [ 53 , 54 ]. Initiatives such as H3Africa’s African Collaborative Center for Microbiome and Genomics Research (ACCME) [ 55 ] may be ideally positioned to make progress in these trends, although as research activity grows in these underrepresented countries, using public metadata may become a less viable measure of these disparities: ACCME’s 2 existing microbiome publications, for example, do not have information about data availability [ 56 , 57 ], and ongoing discussions about issues such as data sovereignty [ 58 ] raise important questions about whether making data publicly available is a just and sustainable approach to biomedical research in countries or populations with comparatively little power in the global research ecosystem [ 59 – 61 ].…”

Soil Bacterial Community Along an Altitudinal Gradient in the Sumaco, a Stratovolcano in the Amazon Region

“…Our study sets the diversity profile for further and more detailed explorations of the features, potentials, and value of the bacteria occurring along the environmental gradient of the Sumaco, as a unique and seldom explored tropical stratovolcano. The study of the soil bacterial community of extreme environments, as the Sumaco volcano, will further contribute to the Ecuadorian Microbiome Project (EcuMP), which is an ambitious long-term initiative to research the bacterial diversity of Ecuador (Díaz et al, 2021).…”

Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit

“…However, no concrete information can be found on the project interface. The website has not been updated for several years and the initiative seems to have been abandoned or neglected in favour of other initiatives, such as the EMP (Díaz et al, 2021). This underlines the importance of long-term support for such initiatives, as the maintainance of online infrastructure over the long term is a big challenge in biological research (Bastow and Leonelli, 2010).…”