Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy.
Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
Microbiome. 2017 Jul 14;5(1):79. doi: 10.1186/s40168-017-0293-3.
The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are consistently and constitutively expressed in the human gut in physiological conditions. Here, we selected a cohort of 15 healthy subjects from a native and highly monitored Sardinian population and analyzed their GMs using shotgun metaproteomics, with the aim of investigating GM functions actually expressed in a healthy human population. In addition, shotgun metagenomics was employed to reveal GM functional potential and to compare metagenome and metaproteome profiles in a combined taxonomic and functional fashion.
Metagenomic and metaproteomic data concerning the taxonomic structure of the GM under study were globally comparable. On the contrary, a considerable divergence between genetic potential and functional activity of the human healthy GM was observed, with the metaproteome displaying a higher plasticity, compared to the lower inter-individual variability of metagenome profiles. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several GM members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis, and short-chain fatty acid production). Noteworthy, Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the metabolic activity with the highest expression rate and the lowest inter-individual variability in the study cohort, in line with the previously reported importance of the biosynthesis of this microbial product for the gut homeostasis.
Our results provide detailed and taxon-specific information regarding functions and pathways actively working in a healthy GM. The reported discrepancy between expressed functions and functional potential suggests that caution should be used before drawing functional conclusions from metagenomic data, further supporting metaproteomics as a fundamental approach to characterize the human GM metabolic functions and activities.
通过宏基因组学的方法，对肠道微生物组（GM）的研究正在迅速向其功能特征研究转变。在这种情况下，对于在生理条件下哪些微生物功能在人类肠道中始终一致且组成性地表达，仍然没有共识。在这里，我们从一个原始且受到高度监测的撒丁岛人群中选择了 15 名健康受试者作为研究对象，并使用宏蛋白质组学分析了他们的 GM，目的是研究健康人群中 GM 实际上表达的功能。此外，我们还使用宏基因组学来揭示 GM 的功能潜力，并以分类和功能相结合的方式比较宏基因组和宏蛋白质组谱。
关于所研究 GM 的分类结构的宏基因组学和宏蛋白质组学数据在整体上是可比的。相反，观察到 GM 的遗传潜力与功能活性之间存在相当大的差异，与宏基因组谱较低的个体间变异性相比，宏蛋白质组显示出更高的可塑性。还检查了分类群特异性对功能活动和代谢任务的贡献，深入了解了 GM 成员在碳水化合物代谢（包括多糖降解、聚糖转运、糖酵解和短链脂肪酸生产）中的特殊作用。值得注意的是，梭菌驱动的丁酸生成（主要归因于粪杆菌属）被证明是研究队列中表达率最高且个体间变异性最低的代谢活性，这与先前报道的这种微生物产物对肠道稳态的生物合成的重要性一致。
我们的结果提供了关于健康 GM 中积极作用的功能和途径的详细且分类特异性信息。报告的表达功能和功能潜力之间的差异表明，在从宏基因组数据中得出功能结论之前应谨慎行事，进一步支持宏蛋白质组学作为一种基本方法来表征人类 GM 的代谢功能和活性。
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