Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank.
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank.
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用培养的生物库揭示人类肠道微生物组的分类学黑暗。
DOI：
10.1186/s40168-021-01064-3
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发表时间：
2021-05-21
期刊：
影响因子：
15.5
通讯作者：
Liu SJ
中科院分区：
文献类型：
--
作者：
Liu C;Du MX;Abuduaini R;Yu HY;Li DH;Wang YJ;Zhou N;Jiang MZ;Niu PX;Han SS;Chen HH;Shi WY;Wu L;Xin YH;Ma J;Zhou Y;Jiang CY;Liu HW;Liu SJ
在肠道微生物组研究中，培养的肠道微生物资源发挥着重要作用，例如帮助阐明肠道微生物功能和宿主-微生物相互作用。尽管已经进行了几项主要研究来阐明培养的人类肠道微生物群，但迄今为止，高达70%的统一人类胃肠道基因组物种尚未培养。大规模的肠道微生物分离和鉴定以及公众可用性对于肠道微生物研究和进一步表征人类肠道微生物功能至关重要。在这项研究中，我们构建了一个人肠道微生物生物库（hGMB;主页：hgmb.nmdc.cn），通过培养来自健康中国志愿者的239份新鲜粪便样本的31个样本混合物中的10，558株菌株，并将代表400个不同物种的1170株菌株保藏在国际保藏管理局的培养物保藏中心，以供长期保存和全球公众访问。根据《国际原核生物命名规则》的规定，共鉴定和命名了102个新种，提出了28个新属和3个新科。hGMB代表了超过80%的常见和占优势的人类肠道微生物属和种，其特征来自全球人类肠道16 S rRNA基因扩增子数据（n = 11，647），并培养了人类微生物组计划提出的24个“最需要的”和“中等优先级”分类群。我们总共测序了115个基因组，代表102个新的分类群和13个以前已知的物种。进一步的计算机模拟分析显示，新测序的hGMB基因组代表了统一人类胃肠道基因组（UHGG）中22个以前未培养的物种，并贡献了24个UHGG尚未发现的潜在“黑暗类群”的代表。从hGMB基因组生成的非冗余基因目录覆盖了全球最大的人类肠道基因目录中超过50%的功能已知基因（KEGG直系同源物）和FUnkFams数据库中大约10%的“最想要的”功能未知蛋白质。建立了一个可公开访问的人类肠道微生物生物库（hGMB），其中包含1170种菌株，代表400种人类肠道微生物物种。hGMB通过增加102个新物种、28个新属、3个新科和115个人类肠道微生物的新基因组来扩展肠道微生物资源和基因组库。视频摘要在线版本包含补充材料，可在10. 1186/s40168-021-01064-3。
In gut microbiome studies, the cultured gut microbial resource plays essential roles, such as helping to unravel gut microbial functions and host-microbe interactions. Although several major studies have been performed to elucidate the cultured human gut microbiota, up to 70% of the Unified Human Gastrointestinal Genome species have not been cultured to date. Large-scale gut microbial isolation and identification as well as availability to the public are imperative for gut microbial studies and further characterizing human gut microbial functions. In this study, we constructed a human Gut Microbial Biobank (hGMB; homepage: hgmb.nmdc.cn) through the cultivation of 10,558 isolates from 31 sample mixtures of 239 fresh fecal samples from healthy Chinese volunteers, and deposited 1170 strains representing 400 different species in culture collections of the International Depository Authority for long-term preservation and public access worldwide. Following the rules of the International Code of Nomenclature of Prokaryotes, 102 new species were characterized and denominated, while 28 new genera and 3 new families were proposed. hGMB represented over 80% of the common and dominant human gut microbial genera and species characterized from global human gut 16S rRNA gene amplicon data (n = 11,647) and cultured 24 “most-wanted” and “medium priority” taxa proposed by the Human Microbiome Project. We in total sequenced 115 genomes representing 102 novel taxa and 13 previously known species. Further in silico analysis revealed that the newly sequenced hGMB genomes represented 22 previously uncultured species in the Unified Human Gastrointestinal Genome (UHGG) and contributed 24 representatives of potentially “dark taxa” that had not been discovered by UHGG. The nonredundant gene catalogs generated from the hGMB genomes covered over 50% of the functionally known genes (KEGG orthologs) in the largest global human gut gene catalogs and approximately 10% of the “most wanted” functionally unknown proteins in the FUnkFams database. A publicly accessible human Gut Microbial Biobank (hGMB) was established that contained 1170 strains and represents 400 human gut microbial species. hGMB expands the gut microbial resources and genomic repository by adding 102 novel species, 28 new genera, 3 new families, and 115 new genomes of human gut microbes. Video abstract The online version contains supplementary material available at 10.1186/s40168-021-01064-3.
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影响因子：
3
作者：
Bardou P;Mariette J;Escudié F;Djemiel C;Klopp C
通讯作者：
Klopp C
影响因子：
14.9
作者：
Federhen S
通讯作者：
Federhen S
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
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作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
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影响因子：
7.4
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通讯作者：
Holt PR
影响因子：
30.3
作者：
Caballero S;Kim S;Carter RA;Leiner IM;Sušac B;Miller L;Kim GJ;Ling L;Pamer EG
通讯作者：
Pamer EG