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Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota
Nature Microbiology ( IF 28.3 ) Pub Date : 2020-01-20 , DOI: 10.1038/s41564-019-0643-y
Fiona J Whelan 1 , Barbara Waddell 2 , Saad A Syed 3 , Shahrokh Shekarriz 3 , Harvey R Rabin 2, 4 , Michael D Parkins 2, 4 , Michael G Surette 2, 3, 5
Affiliation  

Amplicon sequencing (for example, of the 16S rRNA gene) identifies the presence and relative abundance of microbial community members. However, metagenomic sequencing is needed to identify the genetic content and functional potential of a community. Metagenomics is challenging in samples dominated by host DNA, such as those from the skin, tissue and respiratory tract. Here, we combine advances in amplicon and metagenomic sequencing with culture-enriched molecular profiling to study the human microbiota. Using the cystic fibrosis lung as an example, we cultured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abundance identified in direct sequencing of sputum samples; importantly, culture enrichment identified 63.3% more operational taxonomic units than direct sequencing. We developed the PLate Coverage Algorithm (PLCA) to determine a representative subset of culture plates on which to conduct culture-enriched metagenomics, resulting in the recovery of greater taxonomic diversity—including of low-abundance taxa—with better metagenome-assembled genomes, longer contigs and better functional annotations when compared to culture-independent methods. The PLCA is also applied as a proof of principle to a previously published gut microbiota dataset. Culture-enriched molecular profiling can be used to better understand the role of the human microbiota in health and disease.



中文翻译:

富含培养的宏基因组测序能够深入分析囊性纤维化肺微生物群

扩增子测序(例如,16S rRNA 基因)确定微生物群落成员的存在和相对丰度。然而,需要宏基因组测序来确定群落的遗传内容和功能潜力。宏基因组学在以宿主 DNA 为主的样本中具有挑战性,例如来自皮肤、组织和呼吸道的样本。在这里,我们将扩增子和宏基因组测序的进展与培养丰富的分子谱相结合,以研究人类微生物群。以囊性纤维化肺为例,我们平均培养了 82.13% 的操作分类单位,代表了痰样本直接测序中确定的相对丰度的 99.3%;重要的是,与直接测序相比,文化富集确定了 63.3% 的可操作分类单元。我们开发了 PLate Coverage Algorithm (PLCA) 来确定一个有代表性的培养板子集,在其上进行富集培养的宏基因组学,从而恢复更大的分类多样性——包括低丰度分类群——具有更好的宏基因组组装基因组、更长的时间与文化无关的方法相比,重叠群和更好的功能注释。PLCA 也被用作先前发表的肠道微生物群数据集的原理证明。文化丰富的分子谱分析可用于更好地了解人类微生物群在健康和疾病中的作用。与文化无关的方法相比,更长的重叠群和更好的功能注释。PLCA 也被用作先前发表的肠道微生物群数据集的原理证明。文化丰富的分子谱分析可用于更好地了解人类微生物群在健康和疾病中的作用。与文化无关的方法相比,更长的重叠群和更好的功能注释。PLCA 也被用作先前发表的肠道微生物群数据集的原理证明。文化丰富的分子谱分析可用于更好地了解人类微生物群在健康和疾病中的作用。

更新日期:2020-01-20
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