The "most wanted" taxa from the human microbiome for whole genome sequencing.
The "most wanted" taxa from the human microbiome for whole genome sequencing.
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DOI：
10.1371/journal.pone.0041294
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Earl AM
中科院分区：
文献类型：
--
作者：
Fodor AA;DeSantis TZ;Wylie KM;Badger JH;Ye Y;Hepburn T;Hu P;Sodergren E;Liolios K;Huot-Creasy H;Birren BW;Earl AM
人类微生物组计划(HMP)的目标是生成人类相关微生物的全面目录，包括代表最常见物种的参考基因组。为了实现这一目标，HMP使用16S rRNA基因(16S)测序对200多名健康志愿者队列中18个身体栖息地的微生物群落进行了表征，并从人类相关微生物中生成了近1000个参考基因组。为了确定当前的参考基因组集合如何很好地捕捉到在健康微生物组中观察到的多样性，并指导微生物组成员的分离和未来的测序，我们将HMP的16S数据集与几个参考16S集合进行了比较，以创建用于测序的“最想要的”分类群列表。我们的分析表明，HMP队列微生物组中常见分类群的多样性相对较小，这些OTU代表的新分类群很少，HMP志愿者中的许多常见分类群在不同的健康人群中重复出现。综上所述，这些结果表明，应该有可能对大部分人类微生物组进行全基因组测序，包括“最想要的”，这些序列应该有助于支持跨多个队列的微生物组研究。此外，与其他分类群形成鲜明对比的是，在培养物集合中，最受欢迎的生物体的代表性很低，这表明将需要新的基于培养和单细胞的方法来分离这些生物体进行测序。
The goal of the Human Microbiome Project (HMP) is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has characterized the microbial communities at 18 body habitats in a cohort of over 200 healthy volunteers using 16S rRNA gene (16S) sequencing and has generated nearly 1,000 reference genomes from human-associated microorganisms. To determine how well current reference genome collections capture the diversity observed among the healthy microbiome and to guide isolation and future sequencing of microbiome members, we compared the HMP’s 16S data sets to several reference 16S collections to create a ‘most wanted’ list of taxa for sequencing. Our analysis revealed that the diversity of commonly occurring taxa within the HMP cohort microbiome is relatively modest, few novel taxa are represented by these OTUs and many common taxa among HMP volunteers recur across different populations of healthy humans. Taken together, these results suggest that it should be possible to perform whole-genome sequencing on a large fraction of the human microbiome, including the ‘most wanted’, and that these sequences should serve to support microbiome studies across multiple cohorts. Also, in stark contrast to other taxa, the ‘most wanted’ organisms are poorly represented among culture collections suggesting that novel culture- and single-cell-based methods will be required to isolate these organisms for sequencing.
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影响因子：
5.8
作者：
DeSantis, TZ;Dubosarskiy, I;Andersen, GL
通讯作者：
Andersen, GL
DOI：
10.1126/science.1183605
发表时间：
2010-05-21
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Human Microbiome Jumpstart Reference Strains Consortium;Nelson KE;Weinstock GM;Highlander SK;Worley KC;Creasy HH;Wortman JR;Rusch DB;Mitreva M;Sodergren E;Chinwalla AT;Feldgarden M;Gevers D;Haas BJ;Madupu R;Ward DV;Birren BW;Gibbs RA;Methe B;Petrosino JF;Strausberg RL;Sutton GG;White OR;Wilson RK;Durkin S;Giglio MG;Gujja S;Howarth C;Kodira CD;Kyrpides N;Mehta T;Muzny DM;Pearson M;Pepin K;Pati A;Qin X;Yandava C;Zeng Q;Zhang L;Berlin AM;Chen L;Hepburn TA;Johnson J;McCorrison J;Miller J;Minx P;Nusbaum C;Russ C;Sykes SM;Tomlinson CM;Young S;Warren WC;Badger J;Crabtree J;Markowitz VM;Orvis J;Cree A;Ferriera S;Fulton LL;Fulton RS;Gillis M;Hemphill LD;Joshi V;Kovar C;Torralba M;Wetterstrand KA;Abouellleil A;Wollam AM;Buhay CJ;Ding Y;Dugan S;FitzGerald MG;Holder M;Hostetler J;Clifton SW;Allen-Vercoe E;Earl AM;Farmer CN;Liolios K;Surette MG;Xu Q;Pohl C;Wilczek-Boney K;Zhu D
通讯作者：
Zhu D
影响因子：
56.9
作者：
Huber, Julie A.;Mark Welch, David;Sogin, Mitchell L.
通讯作者：
Sogin, Mitchell L.
影响因子：
3.6
作者：
Burmolle, M;Hansen, LH;Sorensen, SJ
通讯作者：
Sorensen, SJ
影响因子：
3.7
作者：
Davis LM;Martínez I;Walter J;Goin C;Hutkins RW
通讯作者：
Hutkins RW