基因组分辨率下不存在持续的昼夜振荡器：肠道微生物组动态中的伪相干性
No persistent circadian oscillator at genome resolution: pseudo-coherence in gut microbiome dynamics
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中文总结 AI 辅助
该研究通过分析小鼠肠道微生物组的小时级基因组分辨率时间序列，发现其动态为伪相干性而非存在持续昼夜振荡器，提出了可证伪的时钟基因敲除队列检验方法。
中文摘要 AI 辅助
肠道微生物组的昼夜节律通常被解读为宿主驱动的授时作用，或是微生物振荡器同步至共同时钟的证据。我们重新分析了小时级基因组分辨率（MAG水平）的小鼠肠道时间序列，并采用针对性诊断方法检验该解读。在该分辨率下，针对数据集中的两只小鼠，时频表示不存在持续脊；时间平均频谱在低频段增强、中频段减弱；滞后协方差呈现显著的时间不对称性，在数十小时附近存在全局不平衡峰；振幅调整的傅里叶替代检验在候选昼夜带中识别出弱的时间平均结构，但从未表现为固定的时频脊。携带推断的非正态放大的两个功能类群，通过两种推断动力学模式（波动被瞬时放大的反应模式、注入波动的非正态模式）的排名被独立识别，无需借助任何相位信息即可恢复拟杆菌门的主要多糖降解菌，以及厚壁菌门A的次要丁酸和丙酸发酵菌。这些特征的结合匹配稳定但强非正态的随机 regime，即伪相干性：几何放大将随机波动重塑到低维反应子空间，产生间歇性同步样事件、时间反演对称性破缺，以及无 underlying 振荡器的涌现时间平均特征尺度。我们提出通过高分辨率时钟基因敲除队列进行可证伪检验。
英文摘要
Diurnal rhythms in the gut microbiome are commonly read as evidence of host-driven entrainment or of microbial oscillators that synchronise to a common clock. We reanalyse hourly genome-resolved (MAG-level) mouse-gut time series with diagnostics tailored to test that interpretation. At this resolution and for both animals in the dataset, the time-frequency representation carries no persistent ridge; the time-averaged spectrum is enhanced at low frequencies and depleted at intermediate frequencies; the lagged covariance is markedly time-asymmetric, with a global imbalance peak near tens of hours; and an amplitude-adjusted Fourier surrogate test identifies a weak time-averaged construction in the candidate circadian band, never as a fixed time-frequency ridge. The two functional guilds that carry the inferred non-normal amplification are identified independently by the rankings of two inferred dynamical modes (the reaction mode, into which fluctuations are transiently amplified, and the non-normal mode, which injects them), and recover the primary polysaccharide degraders of Bacteroidota and the secondary butyrate and propionate fermenters of Bacillota A without invoking any phase information. The conjunction of these signatures matches a stable but strongly non-normal stochastic regime, that is, pseudo-coherence: geometric amplification reshapes stochastic fluctuations onto a low-dimensional reaction subspace, producing intermittent synchronisation-like episodes, broken time-reversal symmetry, and emergent time-averaged characteristic scales without an underlying oscillator. We propose a falsifiable test via high-resolution clock-gene-knockout cohorts.
