Over the past two decades, the role of the microbiome in human health and disease has become better understood. However, generalizing findings across populations is challenging, in part because of compositional differences and a lack of studies in low- and middle-income countries. Early evidence shows that humans in Africa harbor diverse and distinct microbial communities, but few microbiome studies have been conducted on the continent thus far1,2,3.

The few studies on African microbiomes have largely been led by researchers in the Global North4. In some cases, these studies have not included intellectual and scholarly participation by African scholars, raising concerns regarding unequitable engagement and ‘scientific colonialism’. These disparities may be addressed through more equitable inter- and intracontinental collaborative research partnerships, local research leadership, and involvement of national governments with investments in research infrastructure, education and supportive policy development2,5,6. An implementation framework for such engagement is presented here, which will contribute to increasing the current knowledge on African microbiomes, while advancing global science (Table 1).

Table 1 Pillars of an implementation framework for African microbiome research

This implementation framework will provide guidance for African researchers, international partners, healthcare professionals, policymakers and stakeholders. The framework aims to facilitate effective engagement with diverse populations, accelerate research progress and maximize the influence of human microbiome research on healthcare outcomes in Africa. It emphasizes ethical considerations, community and national government involvement, capacity building, multidisciplinary collaboration, knowledge translation and standardization of workflows.

African leadership

Current research on African microbiomes is often intellectually driven by scientists from the Global North. Investments in education and mentorship programs are required to build capacity, which would empower local scientists and scholars and ensure that African microbiome research is well positioned to provide mechanistic insights, filling the current knowledge gap. For example, in genomics, initiatives such as the Human Heredity and Health in Africa (H3Africa)7 and the Pan-African Bioinformatics Network for H3Africa (H3ABioNet)8 have been instrumental for capacity development. These programs have provided training opportunities for early-career and senior researchers in Africa, with skills gained that include career mentorship and academic leadership; this helps nurture the next generation of researchers on the continent.

Having African researchers in key leadership roles in microbiome research initiatives can influence research priorities so that they are locally relevant and have global impact. Research leaders who possess an in-depth understanding of the unique challenges in conducting microbiome research on the continent can promote cultural and contextual understanding of the communities they serve. This alignment with local needs and knowledge can enhance the significance and effectiveness of this research.

African leadership may be promoted through the creation and strengthening of regional research networks5,6. Several relatively small projects have already started, and existing genomics projects and cohorts are being leveraged for microbiome research. To ensure that efforts are not duplicated, but rather coordinated for cumulative impact, platforms such as the H3Africa Microbiome Task Force and the African Microbiome Special Interest Group have been created to facilitate networking and collaboration among researchers with an interest in African microbiome research. These groups have organized the African Microbiome Day event annually, since 2022, to showcase ongoing microbiome research in African populations and to encourage collaborations and networking. The African Microbiome Institute has organized symposia and workshops to achieve similar goals9. Strengthening and synergizing such platforms for engagement will be instrumental in advancing microbiome research.

Local research leadership should tailor funding proposals to address specific community needs. Local leaders can be conduits for transparent communication between research projects and the community, ensuring that the research is clearly understood and embraced by the local population. As a result, the involvement of local research leadership in shaping and advising on funding proposals not only increases the likelihood of securing financial support but also fosters a sense of community ownership and engagement, promoting project success and sustainability.

Locally relevant but globally applicable

African microbiome research, though aiming for broad applications and contributing to the global body of scientific knowledge, should address the health challenges and issues prevalent in African populations, considering cultural, lifestyle, genetic, dietary and environmental factors that may differ from those in other regions10,11. This can be achieved with a good understanding of the local context, through collaboration and engagement with local researchers, multidisciplinary team composition and the adaptation of research methods to local conditions. Collaborations can lead to unique insights that may be applicable beyond Africa, with implications for global health, drug development and personalized medicine. Community-engaged, locally relevant research should be structured to allow the generation of knowledge and solutions that can be shared, adapted and scaled to address similar challenges in broader contexts.

Ethical partnerships

Global partnerships between Africa and the Global North can improve the quality of research carried out in Africa if local investigators are included in the early stages of research planning. Microbiome research in Africa is generally driven by partnerships with the Global North2. Although these partnerships are needed to advance microbiome research on the continent, they should be equitable in order to prevent discontentment and dissatisfaction among local researchers and to enable sustainable capacity building and knowledge sharing.

Inequity in research partnerships includes colonization of local research, where research priorities and questions are decided in the Global North2; extraction of valuable resources, such as biological samples, traditional knowledge or data, without equitable benefit-sharing; and lack of authorship in scientific journals, which prevents local researchers from gaining visibility and credibility. This inequity can be attributed, in part, to an imbalance in skills and resources between researchers in economically affluent countries and their African partners, which can relegate the latter to secondary roles in project conception and data analysis. Investment in African research infrastructure and the development of local skills is necessary for any partnership to ensure meaningful collaboration, with terms of the partnership transparently established before research begins.

An ethical framework for microbiome research in Africa should prioritize the principles of justice, trust, autonomy, respect and beneficence. It should engage local communities and stakeholders in a meaningful and respectful manner to conduct studies that are scientifically valuable, locally relevant, and socially and ethically responsive. Some key considerations for establishing and nurturing ethical partnership practices are outlined below.

Shared goals and objectives

Shared goals and objectives are needed for mutually respectful collaborations. The process of reaching a consensus on study goals and objectives requires a thorough consideration of the cultural, social and ethical contexts within the communities where the study will take place and where the study outcomes will initially be implemented. This approach to partnership must include diverse perspectives and expertise, potential challenges, and the unique strengths and inputs of stakeholders. This process promotes inclusiveness and fosters a sense of collective ownership and should include opportunities to reassess goals to accommodate evolving needs of the researchers, and the community where feasible.

Local ownership of data and samples

Exportation of data and biospecimens from Africa has been curtailed compared to that in the past but remains a concern. Stringent regulatory frameworks are needed to ensure that data and biological samples collected for microbiome studies remain under local control; a transparent and mutually agreed-upon framework should be in place for their use, benefit and protection. Local communities and institutions should be included in the discussions on how data and samples are used, for example via a data access committee. Data and material transfer agreements, where already in place, should be clear and implementable. Mechanisms for using collected samples beyond their initial research purpose should be unambiguous to minimize unintended exploitation12.

Long-term sustainability and collaboration

Successful partnerships are those that endure beyond individual projects, with sustained collaborations and impact. Long-term partnerships can enable long-term initiatives such as establishing repositories for specimen storage or data storage facilities. Long-term partnerships should build institutional and organizational capacity through joint initiatives, research initiatives and funding opportunities.

Standardized microbiome workflows

The interaction between the microbiome and health has proven controversial, with some variability of results between different laboratories. Diverse experimental processes and specimen types can introduce variability across laboratories, potentially resulting in biased microbial profiles. These differences arise in part from a lack of standardized practices, with even minor adjustments in DNA extraction or bioinformatics analysis causing distortions. The experiences of initiatives such as MetaHit13 and the Human Microbiome Project14, which have highlighted substantial discrepancies in results due to differences in the DNA extraction protocols, underscores the challenge of comparing study results between laboratories. Research consortia in Africa must prioritize setting standards to ensure reproducibility and consistency.

Standardized laboratory procedures such as sample preservation, DNA extraction and library preparation, and bioinformatics pipelines enhance the reliability of research and contribute to bridging the gap in technological access that has often hindered microbiome studies in Africa. Templates for metadata collection will facilitate consistency and enable future meta-analyses of study data. This aligns with the advocacy for transparency and the sharing of metadata, championed by the Genomic Standards Consortium, for enhancing reproducibility.

Government involvement

Governments can have a role in policy development, funding allocation and the creation of a conducive regulatory environment for microbiome research. Investments should be made in research infrastructure, science education and support for local researchers. The involvement of governments and health systems should include coordinated efforts in tackling public health issues related to microbiome research by facilitating the uptake and use of research outputs. Local researchers should identify relevant government agencies and include them as stakeholders in the design and implementation of microbiome research, so that research can be translated into national policies and practices, as with the Southern African Human Genome Programme, a national initiative that aimed to elucidate unique genetic characteristics of southern African populations to facilitate a better understanding of human genetic diversity15.


A comprehensive and collaborative approach is needed to advance microbiome research in Africa. This implementation framework is formed of equitable inter- and intracontinental partnerships, local research leadership, and active government involvement and serves as a guide for equitable collaborative research practices across continental boundaries. This holistic approach will catalyze microbiome research in Africa, promoting health equity, precision medicine, and contributing to global scientific advancements.