Uneven global coverage of halophilic metagenomes limits comparative analyses of microbial adaptation to saline environments

Abstract

Halophilic microorganisms are central to biotechnology, bioremediation, and astrobiology because they persist under extreme and polyextreme conditions analogous to extraterrestrial environments. Although metagenomics has transformed the study of halophilic biodiversity, available datasets remain fragmented and unevenly documented. To assess how halophilic metagenomic research reflects the global exploration of hypersaline environments, we analyzed PubMed-indexed studies and associated sequencing metadata deposited at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using a curation workflow. Our quantitative analysis reveals a severe geographic bias linked to uneven global research investment (Gini coefficient = 0.736), with a small number of countries contributing to many publicly available datasets. In contrast, the environmental distribution of these samples showed moderate ecological uniformity (Pielou’s Evenness = 0.818), though we identified pervasive gaps in metadata completeness that hinder dataset interoperability. Our curated dataset highlights a strong research focus on polyextremophilic habitats, positioning these ecosystems as prime targets for biotechnological and astrobiological bioprospecting. Additionally, the geographical bias highlights the need for interoperable global data frameworks and more equitable investment in data generation and analysis, especially in underrepresented regions of the Global South.

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