The primate gut bacterial microbiome: a systematic review of research methodologies, taxonomic coverage, and conservation implications

Abstract

Primates are central to both human evolutionary research and ecosystem functioning, serving as seed dispersers, predators, pollinators, and prey. Despite their value to human and ecosystem science, global primate populations continue to decline, with [~]65% of species currently threatened with extinction. Conservation biology increasingly recognises that survival depends not only on protecting habitats and populations, but also on safeguarding the microbial communities that underpin host health, nutrition, and resilience. The gut bacterial microbiome plays a critical role in digestion, immune function, and adaptation to environmental change, making it an important dimension of primate conservation. Here, we systematically and quantitatively assessed the taxonomic and geographic coverage of primate gut bacterial microbiome research to identify key knowledge gaps relevant to primate conservation. Between 2001 and 2025, 261 articles were published across 100 journals. While taxonomic coverage is high at the family level, it declines substantially at the finer taxonomic scales. Currently, [~]34.5% of species have been studied, leaving gut bacterial biodiversity undocumented for 344 species. Moreover, approximately one-third of studied species have exclusively been studied in captivity, limiting insights into natural microbiome variation and reducing the conservation relevance of these findings. Geographic biases further hinder conservation applications, with megadiverse countries such as Brazil, the Democratic Republic of Congo, and Indonesia underrepresented. In addition, study methodology and reporting standards remain inconsistent. To address these challenges, a framework for the standardised reporting of a minimum set of data for primate gut bacterial microbiome research is included in this review. Adoption of this framework will improve transparency, comparability, and data accessibility, thereby enhancing the utility of microbiome research for primate conservation. By integrating microbial ecology into conservation biology, we highlight the microbiome as a potential critical frontier for safeguarding primate health, evolutionary potential, and long-term survival.