Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library.
Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library.
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DOI：
10.3389/fmicb.2020.585398
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发表时间：
2020
影响因子：
5.2
通讯作者：
Liles MR
中科院分区：
文献类型：
--
作者：
Santana-Pereira ALR;Sandoval-Powers M;Monsma S;Zhou J;Santos SR;Mead DA;Liles MR
土壤微生物历来是发现天然产物的丰富资源，但其中大多数微生物仍未培养，其生物合成能力尚未得到充分开发。为了使用独立于培养的方法确定土壤微生物的生物合成潜力，我们从长期作物轮作实验 Cullars Rotation（美国阿拉巴马州奥本市）采样的表土中构建了大肠杆菌的大型插入宏基因组文库。使用 PCR 或 NGS（下一代测序）多重汇集策略筛选文库克隆的生物合成基因簇 (BGC)，并结合生物信息学分析来识别与每个宏基因组克隆相关的重叠群。从 19,200 个克隆中检测到总共 1,015 个 BGC，鉴定出 223 个克隆 (1.2%) 携带聚酮合酶 (PKS) 和/或非核糖体肽合成酶 (NRPS) 簇，与针对 I 型聚酮合酶 (KS) 结构域的 PCR 筛选相比，命中率显着提高。 NGS 鉴定的 NRPS 和 PKS 簇与 MIBiG 数据库中已知的 BGC 或 PCR 鉴定的 PKS 簇不同。同样，通过文库 NGS 获得的 16S rRNA 基因序列包括许多未通过 PCR 恢复的代表，与 KS 扩增子筛选中观察到的相同偏差一致。这项研究为天然产物的发现提供了新的资源，并规避了扩增偏差，从而可以对土壤宏基因组库进行注释，从而更全面地了解其功能和系统发育多样性。
Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in Escherichia coli from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.
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DOI：
10.1073/pnas.1402564111
发表时间：
2014-04-01
影响因子：
11.1
作者：
Howe, Adina Chuang;Jansson, Janet K.;Brown, C. Titus
通讯作者：
Brown, C. Titus
影响因子：
2.1
作者：
Bitok, J. Kipchirchir;Lemetre, Christophe;Brady, Sean F.
通讯作者：
Brady, Sean F.
影响因子：
3.7
作者：
Cheng, Jiujun;Romantsov, Tatyana;Charles, Trevor C.
通讯作者：
Charles, Trevor C.
影响因子：
14.8
作者：
Fisch, Katja M.;Gurgui, Cristian;Piel, Joern
通讯作者：
Piel, Joern
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T