Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces.
Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces.
复制标题
长读元基因组学从狗的粪便中检索完整的单序列细菌基因组。
DOI：
10.1186/s12864-021-07607-0
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发表时间：
2021-05-06
期刊：
影响因子：
4.4
通讯作者：
Francino O
中科院分区：
文献类型：
--
作者：
Cuscó A;Pérez D;Viñes J;Fàbregas N;Francino O
宏基因组学中的长读测序有助于从复杂的微生物群落中组装完整的基因组。这些基因组包括基本的生物信息，如核糖体基因或移动遗传元件，这些通常是短读缺失的。我们应用长读宏基因组学和纳米孔测序技术从狗粪便样本中检索高质量的宏基因组组装基因组（HQ MAGs）。我们使用纳米孔长读宏基因组学和移码感知校正技术对犬粪便样本进行了校正，并检索了8个单组份HQ MAGs，这些MAGs的完整性为bb0 - 90%，污染< 5%，包含大多数核糖体基因和trna。在技术层面上，我们证明了高分子量DNA提取提高了宏基因组组装的连续性，rRNA操作子的恢复，以及作为潜在HQ mag的较长和圆形的contigs的检索。这些HQ MAGs对应于琥珀弧菌属、苏氏菌属、普氏菌属、Phascolarctobacterium属、Catenibacterium属、Blautia属和肠球菌属。将我们的结果与之前的胃肠道微生物组报告（元基因组或基于16S rrna）联系起来，我们发现胃肠道上的一些细菌物种似乎更具有犬类特异性- succinivibrio， Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345 -，而其他细菌物种则更广泛地分布在动物和人类微生物组中- sutterella， Catenibacterium， Enterococcus和Blautia sp003287895。Sutterella HQ MAG可能是第一个报道的Sutterella stercoricanis基因组组装，由16S rRNA基因相似性分配。此外，我们发现长读取对于检测移动功能至关重要，而短读取的mag通常会遗漏这些功能。我们用纳米孔长读法从健康犬的粪便中回收了8个单组份HQ mag。我们还从这些以前在公共数据库中缺失的特定细菌物种中检索了相关的生物学见解，例如完整的核糖体操纵子和移动组功能。高分子量的DNA提取提高了装配体的邻接性，而高精度的碱基调用、原始读取错误校正、装配体抛光和移码校正则降低了插入和删除错误。实验和分析步骤确保了完整细菌基因组的检索。在线版本包含补充材料，可在10.1186/s12864-021-07607-0获得。
Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample. We used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific –Succinivibrio, Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345–, whereas others are more broadly distributed among animal and human microbiomes –Sutterella, Catenibacterium, Enterococcus, and Blautia sp003287895. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Moreover, we show that long reads are essential to detect mobilome functions, usually missed in short-read MAGs. We recovered eight single-contig HQ MAGs from canine feces of a healthy dog with nanopore long-reads. We also retrieved relevant biological insights from these specific bacterial species previously missed in public databases, such as complete ribosomal operons and mobilome functions. The high-molecular-weight DNA extraction improved the assembly’s contiguity, whereas the high-accuracy basecalling, the raw read error correction, the assembly polishing, and the frameshift correction reduced the insertion and deletion errors. Both experimental and analytical steps ensured the retrieval of complete bacterial genomes. The online version contains supplementary material available at 10.1186/s12864-021-07607-0.
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