A core human microbiome as viewed through 16S rRNA sequence clusters.
A core human microbiome as viewed through 16S rRNA sequence clusters.
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DOI：
10.1371/journal.pone.0034242
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Fodor AA
中科院分区：
文献类型：
--
作者：
Huse SM;Ye Y;Zhou Y;Fodor AA
我们使用扩增的V1-V3和V3-V5小亚基核糖体RNA（16 S）高变区序列探索了200多个个体中18个身体部位的微生物群，作为NIH共同基金人类微生物组项目的一部分。具有最大数量的核心OTU（定义为在95%或更多的个体中共享的OTU）的身体部位是口腔部位（唾液、舌头、脸颊、牙龈和喉咙），其次是鼻子、粪便和皮肤，而阴道部位具有在受试者之间共享的最少数量的OTU。我们发现，基于分类学的样本之间的共性有时可能掩盖亚属OTU水平的变异性。这在口腔中特别明显，其中给定的属可以存在于许多不同的口腔部位，但是亚属OTU显示出非常不同的部位选择，并且在阴道部位中特别明显，阴道部位始终由乳杆菌属主导，但是在受试者中具有明显不同的亚属V1-V3 OTU群体。不同的身体部位在估计的微生物丰富度方面显示出大约10倍的差异，粪便样本具有最高的估计丰富度，其次是口腔、喉咙和牙龈，然后是皮肤、鼻腔和阴道部位。通过V1-V3引物测量的丰富度始终高于通过V3-V5测量的丰富度。我们还表明，当这样一个大的队列在属的水平进行分析，大多数科目适合粪便“肠型”的配置文件，但其他科目是中间，模糊的肠型之间的区别。当在更精细的尺度上，OTU水平上分析时，很少或没有分离到粪便肠型，但在阴道中明显存在不同的生物型。最后，我们注意到，即使OTU存在于几乎每个受试者中，或者在一些样品中占主导地位，也显示出相对丰度的数量级变化，强调了个体之间的高度可变性。
We explore the microbiota of 18 body sites in over 200 individuals using sequences amplified V1–V3 and the V3–V5 small subunit ribosomal RNA (16S) hypervariable regions as part of the NIH Common Fund Human Microbiome Project. The body sites with the greatest number of core OTUs, defined as OTUs shared amongst 95% or more of the individuals, were the oral sites (saliva, tongue, cheek, gums, and throat) followed by the nose, stool, and skin, while the vaginal sites had the fewest number of OTUs shared across subjects. We found that commonalities between samples based on taxonomy could sometimes belie variability at the sub-genus OTU level. This was particularly apparent in the mouth where a given genus can be present in many different oral sites, but the sub-genus OTUs show very distinct site selection, and in the vaginal sites, which are consistently dominated by the Lactobacillus genus but have distinctly different sub-genus V1–V3 OTU populations across subjects. Different body sites show approximately a ten-fold difference in estimated microbial richness, with stool samples having the highest estimated richness, followed by the mouth, throat and gums, then by the skin, nasal and vaginal sites. Richness as measured by the V1–V3 primers was consistently higher than richness measured by V3–V5. We also show that when such a large cohort is analyzed at the genus level, most subjects fit the stool “enterotype” profile, but other subjects are intermediate, blurring the distinction between the enterotypes. When analyzed at the finer-scale, OTU level, there was little or no segregation into stool enterotypes, but in the vagina distinct biotypes were apparent. Finally, we note that even OTUs present in nearly every subject, or that dominate in some samples, showed orders of magnitude variation in relative abundance emphasizing the highly variable nature across individuals.
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影响因子：
3.7
作者：
Bogaert D;Keijser B;Huse S;Rossen J;Veenhoven R;van Gils E;Bruin J;Montijn R;Bonten M;Sanders E
通讯作者：
Sanders E
影响因子：
3.7
作者：
Schloss PD;Gevers D;Westcott SL
通讯作者：
Westcott SL
DOI：
10.1126/science.1208344
发表时间：
2011-10-07
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Wu GD;Chen J;Hoffmann C;Bittinger K;Chen YY;Keilbaugh SA;Bewtra M;Knights D;Walters WA;Knight R;Sinha R;Gilroy E;Gupta K;Baldassano R;Nessel L;Li H;Bushman FD;Lewis JD
通讯作者：
Lewis JD
影响因子：
64.8
作者：
Turnbaugh, Peter J.;Hamady, Micah;Yatsunenko, Tanya;Cantarel, Brandi L.;Duncan, Alexis;Ley, Ruth E.;Sogin, Mitchell L.;Jones, William J.;Roe, Bruce A.;Affourtit, Jason P.;Egholm, Michael;Henrissat, Bernard;Heath, Andrew C.;Knight, Rob;Gordon, Jeffrey I.
通讯作者：
Gordon, Jeffrey I.
DOI：
10.1126/science.1177486
发表时间：
2009-12-18
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Costello EK;Lauber CL;Hamady M;Fierer N;Gordon JI;Knight R
通讯作者：
Knight R