New insights from uncultivated genomes of the global human gut microbiome
New insights from uncultivated genomes of the global human gut microbiome
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DOI：
10.1038/s41586-019-1058-x
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发表时间：
2019-04-25
期刊：
影响因子：
64.8
通讯作者：
Kyrpides, Nikos C.
中科院分区：
文献类型：
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作者：
Nayfach, Stephen;Shi, Zhou Jason;Kyrpides, Nikos C.
人类肠道微生物组的许多物种的基因组序列仍然未知，主要是由于在实验室条件下培养微生物的挑战。在这里，我们通过从3，810个粪便宏基因组中重建60，664个原核基因组草案来解决这个问题，这些基因组来自地理和表型多样的人类。这些基因组为2，058个新鉴定的物种水平操作分类单位（OTU）提供了参考点，这比先前已知的测序肠道细菌的系统发育多样性增加了50%。平均而言，新发现的OTU包括每个个体33%的丰富度和28%的物种丰度，并且在农村人口中富集。临床肠道微生物组研究的荟萃分析指出了新发现的OTU的许多疾病关联，这些OTU有可能改善预测模型。最后，我们的分析表明，未培养的肠道物种经历了基因组减少，导致某些生物合成途径的丧失，这可能为未来改进培养策略提供线索。
The genome sequences of many species of the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3,810 faecal metagenomes, from geographically and phenotypically diverse humans. These genomes provide reference points for 2,058 newly identified species-level operational taxonomic units (OTUs), which represents a 50% increase over the previously known phylogenetic diversity of sequenced gut bacteria. On average, the newly identified OTUs comprise 33% of richness and 28% of species abundance per individual, and are enriched in humans from rural populations. A meta-analysis of clinical gut-microbiome studies pinpointed numerous disease associations for the newly identified OTUs, which have the potential to improve predictive models. Finally, our analysis revealed that uncultured gut species have undergone genome reduction that has resulted in the loss of certain biosynthetic pathways, which may offer clues for improving cultivation strategies in the future.