Culture of previously uncultured members of the human gut microbiota by culturomics
Culture of previously uncultured members of the human gut microbiota by culturomics
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DOI：
10.1038/nmicrobiol.2016.203
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发表时间：
2016-12-01
影响因子：
28.3
通讯作者：
Raoult, Didier
中科院分区：
文献类型：
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作者：
Lagier, Jean-Christophe;Khelaifia, Saber;Raoult, Didier
宏基因组学彻底改变了对人类微生物组，健康和疾病之间关系的理解，但产生了无数尚未分配给已知微生物的序列（1）。近几十年来被忽视的原核生物的纯培养对于阐明这些生物的作用仍然是必不可少的（2）。我们最近引入了微生物培养组学，这是一种使用多种培养条件和基质辅助激光解吸/电离-飞行时间和16 S rRNA进行鉴定的培养方法（2）。在这里，我们选择了最佳的培养条件来增加研究样品的数量，并应用了新的方案（新鲜样品接种;检测变形菌门和微需氧和嗜盐原核生物的小菌落和特定培养物）来解决以前研究的弱点（3-5）。我们鉴定了1，057种原核生物，从而为人类肠道库增加了531种物种：146种人类已知但不在肠道中的细菌，187种细菌和1种以前未在人类中分离的古细菌，以及197种潜在的新物种。对新物种进行了基因组测序。通过比较宏基因组学和文化组学分析的结果，我们表明，使用文化组学允许培养对应于先前未分配的序列的生物体。总之，文化组学使至少从人类肠道中分离出一次的物种数量翻了一番。
Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism(1). The pure culture of prokaryotes, neglected in recent decades, remains essential to elucidating the role of these organisms(2). We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization-time of flight and 16S rRNA for identification(2). Here, we have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies(3-5). We identified 1,057 prokaryotic species, thereby adding 531 species to the human gut repertoire: 146 bacteria known in humans but not in the gut, 187 bacteria and 1 archaea not previously isolated in humans, and 197 potentially new species. Genome sequencing was performed on the new species. By comparing the results of the metagenomic and culturomic analyses, we show that the use of culturomics allows the culture of organisms corresponding to sequences previously not assigned. Altogether, culturomics doubles the number of species isolated at least once from the human gut.