Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.
Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.
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DOI：
10.1186/s40168-017-0290-6
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发表时间：
2017-07-10
期刊：
影响因子：
15.5
通讯作者：
Hettich RL
中科院分区：
文献类型：
--
作者：
Xiong W;Brown CT;Morowitz MJ;Banfield JF;Hettich RL
人类肠道微生物区系的建立在出生时就开始了。这种生命早期的微生物区系发育可能会在婴儿期甚至整个生命周期影响宿主的生理。然而，肠道微生物区系在最初定植期间的功能稳定性和种群结构仍然知之甚少。代谢蛋白质组学是一项大规模表征复杂微生物群落(肠道微生物区系)代谢功能的新兴技术。我们应用元基因组信息的代谢蛋白质组学方法研究了早产儿肠道微生物定植过程中代谢功能的时间和个体间差异。通过分析30个单独的粪便样本，我们为四个婴儿中的每个人确定了多达12,568个蛋白质组，包括人类和微生物蛋白质。利用基因组分辨的匹配元基因组学，可以在物种/菌株水平上自信地鉴定蛋白质。对于丰富的生物，蛋白质组检测到的最大百分比为~45%。微生物与人类蛋白质的相对丰度随时间的增加表明，在生命早期的头几周，微生物的定殖率不断增加。我们观察到这些早产肠道群落中每个有机体的相对蛋白质丰度的显着变化和时间变化。由于群落的不同，在所有样本中只观察到81个微生物蛋酒同源组和57个人类蛋白质。这些保守的微生物蛋白参与了碳水化合物、能量、氨基酸和核苷酸的代谢，而保守的人类蛋白与免疫反应和粘膜成熟有关。我们为这些群落确定了七个蛋白质组簇，并显示婴儿肠道蛋白质组图谱随着时间的推移是不稳定的，并且不是个体特有的。应用肠道特定代谢模块(GMM)分析，我们发现肠道群落主要在营养(碳水化合物、脂肪和氨基酸)利用和短链脂肪酸产生方面的贡献不同。总体而言，这项研究报告了人类肠道微生物区系在早期定居期间的物种特定蛋白质组图谱和代谢功能。特别是，我们的工作有助于揭示在早产儿肠道定植期间三种主要营养来源和短链脂肪酸代谢的微生物区系相关的转移和变化。本文的在线版本(doi：10.1186/s401680170290-6)包含补充材料，授权用户可以使用。
Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. However, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota). We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants’ gut. By analyzing 30 individual fecal samples, we identified up to 12,568 protein groups for each of four infants, including both human and microbial proteins. With genome-resolved matched metagenomics, proteins were confidently identified at the species/strain level. The maximum percentage of the proteome detected for the abundant organisms was ~45%. A time-dependent increase in the relative abundance of microbial versus human proteins suggested increasing microbial colonization during the first few weeks of early life. We observed remarkable variations and temporal shifts in the relative protein abundances of each organism in these preterm gut communities. Given the dissimilarity of the communities, only 81 microbial EggNOG orthologous groups and 57 human proteins were observed across all samples. These conserved microbial proteins were involved in carbohydrate, energy, amino acid and nucleotide metabolism while conserved human proteins were related to immune response and mucosal maturation. We identified seven proteome clusters for the communities and showed infant gut proteome profiles were unstable across time and not individual-specific. Applying a gut-specific metabolic module (GMM) analysis, we found that gut communities varied primarily in the contribution of nutrient (carbohydrates, lipids, and amino acids) utilization and short-chain fatty acid production. Overall, this study reports species-specific proteome profiles and metabolic functions of human gut microbiota during early colonization. In particular, our work contributes to reveal microbiota-associated shifts and variations in the metabolism of three major nutrient sources and short-chain fatty acid during colonization of preterm infant gut. The online version of this article (doi:10.1186/s40168-017-0290-6) contains supplementary material, which is available to authorized users.
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