Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, UK.
Microb Genom. 2023 Mar;9(3). doi: 10.1099/mgen.0.000917.
The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognizes insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterized. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.
微生物插入序列的多样性是微生物基因组多样性产生的关键移动遗传元件，需要在当前的微生物数据库中得到更好的体现。在微生物组群落中识别这些序列存在一些重大问题，导致它们的代表性不足。在这里，我们提出了一个名为 Palidis 的生物信息学管道，该管道通过从混合微生物群落基因组中识别反向末端重复区域，快速识别宏基因组序列数据中的插入序列。将 Palidis 应用于 264 个人类宏基因组，鉴定出 879 个独特的插入序列，其中 519 个是新的，以前没有被描述过。将这个目录查询大型分离株基因组数据库揭示了跨细菌类别的水平基因转移事件的证据。我们将继续更广泛地应用这个工具，构建插入序列目录，这是希望查询其微生物基因组中插入序列的研究人员的宝贵资源。
