Computer Science Department, Indiana University, Bloomington, Indiana, United States of America.
PLoS Comput Biol. 2022 Mar 18;18(3):e1009397. doi: 10.1371/journal.pcbi.1009397. eCollection 2022 Mar.
Host-microbiome interactions and the microbial community have broad impact in human health and diseases. Most microbiome based studies are performed at the genome level based on next-generation sequencing techniques, but metaproteomics is emerging as a powerful technique to study microbiome functional activity by characterizing the complex and dynamic composition of microbial proteins. We conducted a large-scale survey of human gut microbiome metaproteomic data to identify generalist species that are ubiquitously expressed across all samples and specialists that are highly expressed in a small subset of samples associated with a certain phenotype. We were able to utilize the metaproteomic mass spectrometry data to reveal the protein landscapes of these species, which enables the characterization of the expression levels of proteins of different functions and underlying regulatory mechanisms, such as operons. Finally, we were able to recover a large number of open reading frames (ORFs) with spectral support, which were missed by de novo protein-coding gene predictors. We showed that a majority of the rescued ORFs overlapped with de novo predicted protein-coding genes, but on opposite strands or in different frames. Together, these demonstrate applications of metaproteomics for the characterization of important gut bacterial species.
宿主-微生物组相互作用和微生物群落对人类健康和疾病有广泛影响。大多数基于微生物组的研究都是基于下一代测序技术在基因组水平上进行的，但宏蛋白质组学作为一种强大的技术正在兴起，可以通过描述微生物蛋白质的复杂和动态组成来研究微生物组的功能活性。我们进行了一项大规模的人类肠道微生物组宏蛋白质组学数据调查，以鉴定在所有样本中普遍表达的通才物种和在与特定表型相关的一小部分样本中高度表达的专家。我们能够利用宏蛋白质组学质谱数据揭示这些物种的蛋白质景观，从而能够描述不同功能的蛋白质的表达水平和潜在的调控机制，如操纵子。最后，我们能够恢复大量具有光谱支持的开放阅读框 (ORF)，这些 ORF 被从头预测蛋白质编码基因预测器遗漏。我们表明，大多数恢复的 ORF 与从头预测的蛋白质编码基因重叠，但在相反的链上或不同的框架上。总之，这些都证明了宏蛋白质组学在表征重要肠道细菌物种方面的应用。
