Table_1_Assessing the Hybrid Effects of Neutral and Niche Processes on Gut Microbiome Influenced by HIV Infection.DOC

That both stochastic neutral and deterministic niche forces are in effect in shaping the community assembly and diversity maintenance is becoming an increasingly important consensus. However, assessing the effects of disease on the balance between the two forces in the human microbiome has not been explored to the best of our knowledge. In this article, we applied a hybrid model to address this issue by analyzing the potential effect of HIV infection on the human gut microbiome and adopted a further step of multimodality testing to improve the interpretation of their model. Our study revealed that although niche process is the dominant force in shaping human gut microbial communities, niche process- and neutral process-driven taxa could coexist in the same microbiome, confirming the notion of their joint responsibility. However, we failed to detect the effect of HIV infection in changing the balance. This suggests that the rule governing community assembly and diversity maintenance may be changed by the disturbance from HIV infection-caused dysbiosis. Although we admit that the general question of disease effect on community assembly and diversity maintenance may still be an open question, our study presents the first piece of evidence to reject the significant influence of diseases.

目前学界已逐渐达成一项愈发重要的共识：随机中性过程与确定性生态位过程共同发挥作用，参与群落构建与多样性维持的调控。然而，据我们所知，目前尚无研究探讨疾病如何影响人类微生物组（human microbiome）中这两种过程间的平衡。本文中，我们通过分析HIV感染对人类肠道微生物组的潜在影响，构建混合模型以解决该问题，并进一步采用多模态检验（multimodality testing）步骤优化模型的解读效果。本研究结果显示：尽管生态位过程是塑造人类肠道微生物群落的主导力量，但由生态位过程和中性过程共同调控的分类群（taxa）可在同一微生物组中共存，证实了二者共同发挥调控作用的观点。但我们未检测到HIV感染会改变这两种过程间的平衡。这表明，HIV感染引发的菌群失调（dysbiosis）所带来的扰动，或可改变调控群落构建与多样性维持的内在规律。尽管我们承认，疾病对群落构建与多样性维持的影响这一核心问题仍属于开放性议题，但本研究首次提供了驳斥疾病存在显著影响的实证证据。