Jin Hao, Quan Keyu, He Qiuwen, Kwok Lai-Yu, Ma Teng, Li Yalin, Zhao Feiyan, You Lijun, Zhang Heping, Sun Zhihong
Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
Nat Microbiol. 2023 Jan;8(1):150-161. doi: 10.1038/s41564-022-01270-1. Epub 2023 Jan 5.
Metagenome-based resources have revealed the diversity and function of the human gut microbiome, but further understanding is limited by insufficient genome quality and a lack of samples from typically understudied populations. Here we used hybrid long-read PromethION and short-read HiSeq sequencing to characterize the faecal microbiota of 60 Inner Mongolian individuals (n = 180 samples over three time points) who were part of a probiotic yogurt intervention trial. We present the Inner Mongolian Gut Genome catalogue, comprising 802 closed and 5,927 high-quality metagenome-assembled genomes. This approach achieved high genome continuity and substantially increased the resolution of genomic elements, including ribosomal RNA operons, metabolic gene clusters, prophages and insertion sequences. Particularly, we report the ribosomal RNA operon copy numbers for uncultured species, over 12,000 previously undescribed gut prophages and the distribution of insertion sequence elements across gut bacteria. Overall, these data provide a high-quality, large-scale resource for studying the human gut microbiota.
基于宏基因组的资源已揭示了人类肠道微生物群的多样性和功能，但由于基因组质量不足以及缺乏来自典型研究不足人群的样本，进一步的了解受到限制。在这里，我们使用了长读长的PromethION和短读长的HiSeq测序技术，对60名内蒙古个体（在三个时间点共180个样本）的粪便微生物群进行了特征分析，这些个体参与了一项益生菌酸奶干预试验。我们展示了内蒙古肠道基因组目录，其中包括802个封闭基因组和5927个高质量的宏基因组组装基因组。这种方法实现了高基因组连续性，并大幅提高了基因组元件的分辨率，包括核糖体RNA操纵子、代谢基因簇、原噬菌体和插入序列。特别是，我们报告了未培养物种的核糖体RNA操纵子拷贝数、超过12000个以前未描述的肠道原噬菌体以及插入序列元件在肠道细菌中的分布。总体而言，这些数据为研究人类肠道微生物群提供了高质量、大规模的资源。
