Advancing microbial ecology, microbiomes, and One Health in Africa: from regional initiatives to pan-African flagship programs.

Microbial ecology and microbiome science are increasingly central to global "One Health" efforts, a framework that recognizes the interconnected health of humans, animals, and the environment. In Africa, these fields are particularly important for addressing interconnected challenges in public health, agriculture, and ecosystem resilience. Discussions at the ISME Africa Morocco 2025 regional meeting highlighted both progress and persistent gaps in African microbiome research. Initiatives such as the African BioGenome Project and Human Heredity and Health in Africa demonstrate the feasibility of population-representative studies, regional training, networking, and open-science frameworks; however, the research landscape remains fragmented, with limited intra-African collaboration and continued reliance on external funding and leadership. The development of Africa-specific reference genomes, population-based microbiome datasets, is essential to address these gaps and ensure global representation. This perspective synthesizes current evidence and outlines strategic priorities to transition from toward coordinated pan-African research networks and flagship programs. Key recommendations include developing Africa-specific genome reference datasets, establishing pan-continental consortia, fostering equitable African-non-African partnerships, integrating microbiome science into policy frameworks, and adopting FAIR open-science practices. Strengthening bioinformatics and computational capacity will be essential to transform fragmented data into high-impact, coordinated insights. Advancing these priorities will accelerate translation into One Health outcomes, including antimicrobial resistance surveillance, food security, climate-resilient agriculture, and precision medicine. Africa's rich microbial diversity offers significant potential for antibiotic discovery, improved crop productivity, and sustainable agricultural systems. Collectively, strengthening Africa-led, collaborative microbiome research will enable the continent's microbial diversity to drive impactful solutions with regional and global relevance.