bitBiome, Inc., 513 Wasedatsurumaki-Cho, Shinjuku-Ku, Tokyo, 162-0041, Japan.
Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-Cho, Shinjuku-Ku, Tokyo, 162-8480, Japan.
Microbiome. 2024 Oct 2;12(1):188. doi: 10.1186/s40168-024-01903-z.
The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.
We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs.
The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community. Video Abstract.
宏基因组组装基因组 (MAGs) 的增加提高了我们对人类微生物组功能特征和分类学分配的理解。然而，作为群体共识基因组的 MAGs 常常聚集了物种和菌株之间的异质性，从而模糊了微生物宿主和移动遗传元件 (MGEs) 之间的精确关系。相比之下，通过单细胞基因组测序获得的单扩增基因组 (SAGs) 可以捕获单个基因组内容，包括 MGEs。
我们介绍了来自人类口腔和肠道微生物组的第一个大规模 SAG 数据集 (bbsag20)，其中包含 17202 个未经共组装的中等质量以上的 SAG。该数据集揭示了 312 种口腔和 647 种肠道物种中细菌谱系的多样性，其分类组成与 MAGs 不同。此外，SAGs 显示了口腔细菌向肠道转移的细胞水平证据。我们还鉴定了携带抗生素抗性基因 (ARGs) 的广泛宿主范围 MGEs，这些基因在 MAGs 中未被检测到。
SAG 和 MAG 之间的分类组成差异表明，结合这两种方法将有效地扩展基因组目录。通过在单个样本中连接移动组和抗性组，SAG 可以详细绘制 MGE 上 ARG 的动态网络，指出微生物群落中潜在的 ARG 库及其传播模式。
