Danone Nutricia Research, Gif-sur-Yvette, France.
Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
Nat Commun. 2023 Jun 20;14(1):3310. doi: 10.1038/s41467-023-38558-7.
The gut microbiome is important for human health, yet modulation requires more insight into inter-individual variation. Here, we explored latent structures of the human gut microbiome across the human lifespan, applying partitioning, pseudotime, and ordination approaches to >35,000 samples. Specifically, three major gut microbiome branches were identified, within which multiple partitions were observed in adulthood, with differential abundances of species along branches. Different compositions and metabolic functions characterized the branches' tips, reflecting ecological differences. An unsupervised network analysis from longitudinal data from 745 individuals showed that partitions exhibited connected gut microbiome states rather than over-partitioning. Stability in the Bacteroides-enriched branch was associated with specific ratios of Faecalibacterium:Bacteroides. We also showed that associations with factors (intrinsic and extrinsic) could be generic, branch- or partition-specific. Our ecological framework for cross-sectional and longitudinal data allows a better understanding of overall variation in the human gut microbiome and disentangles factors associated with specific configurations.
肠道微生物组对人类健康很重要，但要想对其进行调节，就需要更多地了解个体间的差异。在这里，我们通过对超过 35000 个样本应用分区、拟时和排序方法，探索了人类肠道微生物组在整个生命周期中的潜在结构。具体来说，我们确定了三个主要的肠道微生物组分支，在成人期内观察到多个分区，并且沿着分支存在物种的差异丰度。分支的末端具有不同的组成和代谢功能，反映了生态差异。来自 745 个人的纵向数据的无监督网络分析表明，分区表现出连接的肠道微生物组状态，而不是过度分区。富含拟杆菌的分支的稳定性与特定的双歧杆菌：拟杆菌比值有关。我们还表明，与因素（内在和外在）的关联可以是通用的、分支特异性的或分区特异性的。我们的跨截面和纵向数据的生态框架可以更好地理解人类肠道微生物组的整体变化，并分解与特定配置相关的因素。
