Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization

The gut microbiomes of traditional Indigenous and 'Western' societies differ markedly in diversity and composition. The Western diet modifies the gut microbiome, promoting cardiometabolic disorders that disproportionately affect Indigenous Australians. Studies of Indigenous gut microbiomes are underrepresented in the literature and comparative studies in young children living in traditional and Western societies are lacking, limiting our understanding of early-life microbiome development in different cultural contexts. Therefore, we analyzed gut metagenomes of 50 Indigenous Australian infants (median age < one year) living remotely with variable access to Western foods, compared to age- and sex-matched non-Indigenous infants living in urban Australia. Indigenous infants exhibited greater alpha diversity and significant differences in beta diversity, with 114 species and 38 genera differing in abundance. Some taxa were unique to Indigenous infants, who had higher carriage of Bifidobacteria at younger ages and Prevotella at older ages. In contrast, non-Indigenous infants had a high abundance of Phocaeicola ( Bacteroides ) across ages. Notably, Indigenous infants had markedly higher numbers of gut viruses and fungi. These findings reveal that despite encroaching Westernization, these Indigenous infants begin life with a gut microbiome that retains key features of traditional societies worldwide. The Western gut microbiome has not been transmitted inter-generationally and has not yet emerged, attesting to the dominant influence of a remote environment and enduring traditional lifestyle. This study provides crucial insights into the early-life microbiome in an Indigenous population and highlights the importance of preserving traditional lifestyles to maintain microbiome diversity.