Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited in their ability to directly compare microbial metabolic function across samples and studies. We introduce Carnelian, an end-to-end pipeline for metabolic functional profiling uniquely suited to finding functional trends across diverse datasets. Carnelian is able to find shared metabolic pathways, concordant functional dysbioses, and distinguish Enzyme Commission (EC) terms missed by existing methodologies. We demonstrate Carnelian’s effectiveness on type 2 diabetes, Crohn’s disease, Parkinson’s disease, and industrialized and non-industrialized gut microbiome cohorts.

中文翻译：

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红玉髓从整个宏基因组测序读数中揭示了不同研究人群中隐藏的功能模式


微生物种群响应不同的周围环境而表现出功能变化。尽管整个宏基因组测序有望提供足够的原始数据来研究这些变化，但现有工具直接比较样本和研究中微生物代谢功能的能力有限。我们引入了红玉髓，这是一种用于代谢功能分析的端到端管道，特别适合在不同数据集中查找功能趋势。红玉髓能够找到共享的代谢途径、一致的功能失调，并区分现有方法中遗漏的酶委员会 (EC) 术语。我们证明了红玉髓对 2 型糖尿病、克罗恩病、帕金森病以及工业化和非工业化肠道微生物群的有效性。