Australian infant gut microbiome metagenomics

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.

传统原住民社会与“西式”社会的肠道菌群在多样性与组成上存在显著差异。西式饮食会改变肠道菌群，进而诱发心血管代谢疾病，这类疾病对澳大利亚原住民的影响尤为显著。现有文献中关于原住民肠道菌群的研究相对匮乏，针对生活在传统与西式社会环境下的幼儿的对比研究更是空白，这限制了我们对不同文化背景下生命早期菌群发育的认知。为此，本研究针对50名居住于偏远地区、对西式食品可及性存在差异的澳大利亚原住民婴儿（中位年龄不足1岁）展开肠道宏基因组分析，并以居住在澳大利亚城市地区、年龄与性别与之匹配的非原住民婴儿作为对照。原住民婴儿展现出更高的α多样性（alpha diversity），且β多样性（beta diversity）存在显著差异，共有114个物种与38个属的丰度存在不同。部分微生物类群仅在原住民婴儿中存在；原住民婴儿在年幼时双歧杆菌（Bifidobacteria）的定植率更高，而在年长时普雷沃氏菌（Prevotella）的丰度也更高。与之相反，非原住民婴儿在各个年龄段中均拥有较高丰度的Phocaeicola（原归类为拟杆菌属Bacteroides）。值得注意的是，原住民婴儿的肠道病毒与真菌数量显著更高。上述研究结果表明，尽管面临不断加剧的西式化进程，这些原住民婴儿在生命早期仍拥有保留全球传统社会肠道菌群核心特征的微生物组。西式肠道菌群尚未实现跨代传递，也未在该群体中形成，这证明偏远地区环境与持久的传统生活方式对肠道菌群具有主导性影响。本研究为原住民群体的生命早期肠道菌群研究提供了关键见解，并强调了保留传统生活方式对维持肠道菌群多样性的重要意义。