Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.
Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.
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DOI：
10.1128/spectrum.01501-23
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发表时间：
2023-08-17
影响因子：
3.7
通讯作者：
Yan, Zhen
中科院分区：
文献类型：
--
作者：
Huang, Ranran;Wang, Yafei;Liu, Daixi;Wang, Shaoyu;Lv, Haibo;Yan, Zhen
微生物次级代谢产物在微生物竞争、交流、资源获取、抗生素生产和其他各种生物技术过程中起着至关重要的作用。由于短读段测序的技术限制，从未培养的细菌中检索全长BGC（生物合成基因簇）序列是困难的，使得不可能确定BGC多样性。利用长读码测序和基因组挖掘技术，本研究回收了339个主要全长的BGC，阐明了中国黄海鳌山湾海水中发现的来自未培养谱系的广泛BGC。在细菌门如变形菌门、拟杆菌门、酸杆菌门和疣状微生物门以及以前未培养的古菌门“热浆菌门”中发现了许多极其多样的BGC。元转录组学数据显示，30.1%的次级代谢基因表达，并揭示了BGC核心生物合成基因和剪裁酶的表达模式。总之，我们的研究结果表明，长读宏基因组测序结合元转录组学分析提供了一个直接的观点到环境过程中的BGC的功能表达。重要性宏基因组数据的基因组挖掘已成为通过对次级代谢物潜力进行编目来进行新化合物生物勘探的首选方法。然而，BGC的准确检测需要未片段化的基因组组装，这在技术上一直难以从宏基因组获得，直到最近才采用新的长读技术。我们使用从长时间读取数据中生成的高质量宏基因组组装基因组来确定黄海地表水中发现的微生物的生物合成潜力。我们从大部分未培养和未充分探索的细菌和古菌门中回收了339个高度多样化且大部分全长的BGC。此外，我们提出了长读宏基因组测序结合元转录组分析作为一种潜在的方法，用于获得在大多数未培养的微生物中的专门代谢物基因簇的大部分未充分利用的遗传库。长读宏基因组学和元转录组学分析的组合是重要的，因为它可以更准确地评估微生物通过基于元转录组学数据的BGC表达来适应环境的机制。
Microbial secondary metabolites play crucial roles in microbial competition, communication, resource acquisition, antibiotic production, and a variety of other biotechnological processes. The retrieval of full-length BGC (biosynthetic gene cluster) sequences from uncultivated bacteria is difficult due to the technical constraints of short-read sequencing, making it impossible to determine BGC diversity. Using long-read sequencing and genome mining, 339 mainly full-length BGCs were recovered in this study, illuminating the wide range of BGCs from uncultivated lineages discovered in seawater from Aoshan Bay, Yellow Sea, China. Many extremely diverse BGCs were discovered in bacterial phyla such as Proteobacteria, Bacteroidota, Acidobacteriota, and Verrucomicrobiota as well as the previously uncultured archaeal phylum “Candidatus Thermoplasmatota.” The data from metatranscriptomics showed that 30.1% of secondary metabolic genes were being expressed, and they also revealed the expression pattern of BGC core biosynthetic genes and tailoring enzymes. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional expression of BGCs in environmental processes. IMPORTANCE Genome mining of metagenomic data has become the preferred method for the bioprospecting of novel compounds by cataloguing secondary metabolite potential. However, the accurate detection of BGCs requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until recently with new long-read technologies. We used high-quality metagenome-assembled genomes generated from long-read data to determine the biosynthetic potential of microbes found in the surface water of the Yellow Sea. We recovered 339 highly diverse and mostly full-length BGCs from largely uncultured and underexplored bacterial and archaeal phyla. Additionally, we present long-read metagenomic sequencing combined with metatranscriptomic analysis as a potential method for gaining access to the largely underutilized genetic reservoir of specialized metabolite gene clusters in the majority of microbes that are not cultured. The combination of long-read metagenomic and metatranscriptomic analyses is significant because it can more accurately assess the mechanisms of microbial adaptation to the environment through BGC expression based on metatranscriptomic data.
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影响因子：
5.5
作者：
Benjdia A;Balty C;Berteau O
通讯作者：
Berteau O
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
--
作者：
Milshteyn A;Schneider JS;Brady SF
通讯作者：
Brady SF
DOI：
10.1073/pnas.1714381115
发表时间：
2017-12-26
影响因子：
11.1
作者：
Amos, Gregory C. A.;Awakawa, Takayoshi;Jensen, Paul R.
通讯作者：
Jensen, Paul R.
影响因子：
16.6
作者：
Geller-McGrath, David;Mara, Paraskevi;Taylor, Gordon T. T.;Suter, Elizabeth;Edgcomb, Virginia;Pachiadaki, Maria
通讯作者：
Pachiadaki, Maria