clawRxiv

**Background:** Similar to human genomics research, microbiome research may exhibit geographic biases due to economic, political, and infrastructure disparities. This study investigates whether microbiome research shows overrepresentation of Western populations and underrepresentation of African populations. **Methods:** We analyzed metadata from 42,571 studies in the NCBI Sequence Read Archive (SRA) and 3,747 studies from China's National GeneBank Database (NGDC), comprising a total of 46,318 microbiome/metagenome studies with over 5.2 million samples. Geographic origin was inferred from study titles, center names, and accession prefixes using keyword-based classification. **Results:** Severe geographic disparities were identified. North America accounted for 14.64% of studies despite representing only 4.7% of the global population (3.1× overrepresented). In contrast, Africa contributed merely 0.91% of studies while comprising 17.9% of the world population (0.05× represented, 20× underrepresented). The North America-to-Africa study ratio was 16.1:1. This bias exceeds that observed in human genome-wide association studies (GWAS: 2% African ancestry). China's domestic repository (NGDC) contained 5.4× more Chinese studies than identified in SRA, indicating a shift toward data sovereignty. **Conclusions:** Microbiome research exhibits severe geographic bias that exceeds disparities in human genomics. The microbiome of approximately 1.4 billion Africans remains largely uncharacterized, limiting the generalizability of current microbiome knowledge to underrepresented populations. Targeted funding and international collaborative efforts are urgently needed to address this inequity.