Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes.
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes.
复制标题
人参考肠道微生物组目录，包括来自代表性不足的亚洲元基因组的新组装基因组。
DOI：
10.1186/s13073-021-00950-7
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发表时间：
2021-08-27
期刊：
影响因子：
12.3
通讯作者：
Lee I
中科院分区：
文献类型：
--
作者：
Kim CY;Lee M;Yang S;Kim K;Yong D;Kim HR;Lee I
地理位置和生活方式的宏基因组采样偏差是肠道微生物物种参考基因组目录不完整的部分原因。因此，来自目前代表性不足的群体的基因组组装可以有效地扩展参考肠道微生物组并改善分类和功能分析。我们使用公开的全宏基因组鸟枪测序（WMS）数据分别从印度和日本收集了110和645份粪便样本的基因组。此外，我们从韩国收集的90个粪便样本的新生成的WMS数据组装基因组。预期低丰度物种的基因组组装可能需要比通常使用的更深的测序，因此我们对来自韩国的粪便样本进行了超深WMS（> 30 Gbp或> 1亿个读取对）。因此，我们从三个代表性不足的亚洲国家的845个粪便宏基因组中组装了29，082个原核基因组，并将其与统一人类胃肠道基因组（UHGG）相结合，以生成一个扩展的目录，即人类参考肠道微生物组（HRGM）。HRGM包含5414个代表性原核生物物种的232，098个非冗余基因组，包括780个新物种，> 1.03亿个独特蛋白质和> 2.74亿个单核苷酸变体。这比UHGG增加了10%以上。新的780个物种丰富了拟杆菌科，包括与高纤维和海藻丰富的饮食有关的物种。单核苷酸变异密度与肠道微生物的物种形成率呈正相关。我们发现超深度测序促进了低丰度分类群的基因组组装，而深度测序（例如，> 2000万个读取对）可能需要用于低丰度分类群的概况分析。重要的是，HRGM显著改善了来自粪便样品的测序读数的分类学和功能分类。最后，对HRGM物种基因组上的人类自身抗原同源物的分析表明，具有高交叉反应性潜力的细菌分类群可能比那些具有低交叉反应性潜力的细菌分类群通过促进炎症状况而对肠道微生物组相关疾病的发病机制做出更多贡献。通过包括来自以前代表性不足的亚洲国家，韩国，印度和日本的肠道宏基因组，我们开发了一个大大扩展的微生物组目录，HRGM。微生物基因组和编码基因的信息是公开的（www.mbiomenet.org/HRGM/）。HRGM将有助于疾病相关肠道微生物群的识别和功能分析。在线版本包含补充材料，可通过10.1186/s13073-021-00950-7获得。
Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently under-represented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling. We assembled genomes using public whole-metagenomic shotgun sequencing (WMS) data for 110 and 645 fecal samples from India and Japan, respectively. In addition, we assembled genomes from newly generated WMS data for 90 fecal samples collected from Korea. Expecting genome assembly for low-abundance species may require a much deeper sequencing than that usually employed, so we performed ultra-deep WMS (> 30 Gbp or > 100 million read pairs) for the fecal samples from Korea. We consequently assembled 29,082 prokaryotic genomes from 845 fecal metagenomes for the three under-represented Asian countries and combined them with the Unified Human Gastrointestinal Genome (UHGG) to generate an expanded catalog, the Human Reference Gut Microbiome (HRGM). HRGM contains 232,098 non-redundant genomes for 5414 representative prokaryotic species including 780 that are novel, > 103 million unique proteins, and > 274 million single-nucleotide variants. This is an over 10% increase from the UHGG. The new 780 species were enriched for the Bacteroidaceae family, including species associated with high-fiber and seaweed-rich diets. Single-nucleotide variant density was positively associated with the speciation rate of gut commensals. We found that ultra-deep sequencing facilitated the assembly of genomes for low-abundance taxa, and deep sequencing (e.g., > 20 million read pairs) may be needed for the profiling of low-abundance taxa. Importantly, the HRGM significantly improved the taxonomic and functional classification of sequencing reads from fecal samples. Finally, analysis of human self-antigen homologs on the HRGM species genomes suggested that bacterial taxa with high cross-reactivity potential may contribute more to the pathogenesis of gut microbiome-associated diseases than those with low cross-reactivity potential by promoting inflammatory condition. By including gut metagenomes from previously under-represented Asian countries, Korea, India, and Japan, we developed a substantially expanded microbiome catalog, HRGM. Information of the microbial genomes and coding genes is publicly available (www.mbiomenet.org/HRGM/). HRGM will facilitate the identification and functional analysis of disease-associated gut microbiota. The online version contains supplementary material available at 10.1186/s13073-021-00950-7.
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影响因子：
10.7
作者：
Huerta-Cepas J;Forslund K;Coelho LP;Szklarczyk D;Jensen LJ;von Mering C;Bork P
通讯作者：
Bork P
影响因子：
9.2
作者：
Dhakan, D. B.;Maji, A.;Sharma, V. K.
通讯作者：
Sharma, V. K.
DOI：
10.1099/ijs.0.65504-0
发表时间：
2008-04-01
影响因子：
2.8
作者：
Chassard, Christophe;Delmas, Eve;Bernalier-Donadille, Annick
通讯作者：
Bernalier-Donadille, Annick
影响因子：
14.9
作者：
Huerta-Cepas, Jaime;Szklarczyk, Damian;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
12.3
作者：
Boulangé CL;Neves AL;Chilloux J;Nicholson JK;Dumas ME
通讯作者：
Dumas ME