Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, China.
School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China.
Microbiol Spectr. 2023 Aug 17;11(4):e0150123. doi: 10.1128/spectrum.01501-23. Epub 2023 Jul 6.
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 , , , and as well as the previously uncultured archaeal phylum " 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. 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.
微生物次生代谢产物在微生物竞争、通讯、资源获取、抗生素生产以及各种其他生物技术过程中发挥着关键作用。由于短读测序技术的限制，从未培养的细菌中检索全长 BGC（生物合成基因簇）序列非常困难，这使得 BGC 多样性无法确定。本研究采用长读测序和基因组挖掘技术，从中国黄海鳌山湾海水中未培养的谱系中回收了 339 个主要全长 BGC，阐明了从海水中发现的未培养谱系中广泛存在的 BGC 多样性。在细菌门如 、 、 、 和以前未培养的古菌门“Thermoplasmatota”中发现了许多极其多样化的 BGC。宏转录组学的数据表明，30.1%的次生代谢基因正在表达，它们还揭示了 BGC 核心生物合成基因和修饰酶的表达模式。总的来说，我们的研究结果表明，长读元基因组测序结合宏转录组分析为环境过程中 BGC 的功能表达提供了直接的视角。宏基因组数据分析的基因组挖掘已成为通过编目次生代谢物潜力来生物勘探新化合物的首选方法。然而，BGC 的准确检测需要未碎片化的基因组组装，直到最近，随着新的长读技术的出现，这在技术上一直难以从宏基因组中获得。我们使用从长读数据生成的高质量宏基因组组装基因组来确定黄海表层水中微生物的生物合成潜力。我们从主要未培养和探索不足的细菌和古菌门中回收了 339 个高度多样化和主要全长 BGC。此外，我们提出了长读元基因组测序结合宏转录组分析，作为一种潜在的方法，可以利用大多数未培养微生物中专门代谢基因簇的遗传库，这些基因簇在很大程度上尚未得到利用。长读元基因组和宏转录组分析的结合具有重要意义，因为它可以通过基于宏转录组数据的 BGC 表达更准确地评估微生物对环境的适应机制。
