Inter-individual differences in the gene content of human gut bacterial species.
Inter-individual differences in the gene content of human gut bacterial species.
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人肠道细菌物种的基因含量的个体间差异。
DOI：
10.1186/s13059-015-0646-9
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发表时间：
2015-04-21
期刊：
影响因子：
12.3
通讯作者：
Bork P
中科院分区：
文献类型：
--
作者：
Zhu A;Sunagawa S;Mende DR;Bork P
人类肠道微生物的基因含量差异可能导致个体间的表型变异，如消化能力。目前还不清楚基因含量的变化是由微生物物种组成的差异或由同一物种的不同菌株的存在引起的;后者的基因含量变化的程度是未知的。与可培养菌株的泛基因组研究不同，宏基因组数据的使用可以通过在其自然栖息地（在这种情况下，每个个体的肠道）中测量肠道细菌菌株的结构变异来提供无偏见的观点，代表肠道细菌种群之间的天然边界。我们分析了来自粪便样本的公开的宏基因组数据，以表征肠道细菌物种的个体间差异。对11种丰富的肠道细菌物种的比较表明，来自同一物种的菌株的基因含量在个体之间平均相差13%。这个数字仅基于基因缺失，代表一个下限，但变异已经在与可培养物种的完全测序菌株之间观察到的相似范围内。我们发现，个体之间差异很大的辅助基因可以编码重要的功能，如多糖利用和荚膜多糖合成位点。宏基因组学可以深入了解复杂群落中菌株基因含量的变化，这是单靠系统发育标记基因无法预测的。基因含量的个体间变异性很大，这意味着必须考虑菌株分辨率，以充分评估个体人类肠道微生物组的功能潜力。本文的在线版本（doi：10.1186/s13059-015-0646-9）包含补充材料，可供授权用户使用。
Gene content differences in human gut microbes can lead to inter-individual phenotypic variations such as digestive capacity. It is unclear whether gene content variation is caused by differences in microbial species composition or by the presence of different strains of the same species; the extent of gene content variation in the latter is unknown. Unlike pan-genome studies of cultivable strains, the use of metagenomic data can provide an unbiased view of structural variation of gut bacterial strains by measuring them in their natural habitats, the gut of each individual in this case, representing native boundaries between gut bacterial populations. We analyzed publicly available metagenomic data from fecal samples to characterize inter-individual variation in gut bacterial species. A comparison of 11 abundant gut bacterial species showed that the gene content of strains from the same species differed, on average, by 13% between individuals. This number is based on gene deletions only and represents a lower limit, yet the variation is already in a similar range as observed between completely sequenced strains of cultivable species. We show that accessory genes that differ considerably between individuals can encode important functions, such as polysaccharide utilization and capsular polysaccharide synthesis loci. Metagenomics can yield insights into gene content variation of strains in complex communities, which cannot be predicted by phylogenetic marker genes alone. The large degree of inter-individual variability in gene content implies that strain resolution must be considered in order to fully assess the functional potential of an individual's human gut microbiome. The online version of this article (doi:10.1186/s13059-015-0646-9) contains supplementary material, which is available to authorized users.
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影响因子：
12.3
作者：
Hogg JS;Hu FZ;Janto B;Boissy R;Hayes J;Keefe R;Post JC;Ehrlich GD
通讯作者：
Ehrlich GD
影响因子：
14.9
作者：
Kanehisa M;Goto S;Sato Y;Furumichi M;Tanabe M
通讯作者：
Tanabe M
聚糖代谢如何塑造人类肠道微生物群。
DOI：
10.1038/nrmicro2746
发表时间：
2012-04-11
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
通讯作者：
--
影响因子：
3.2
作者：
Gordienko, Evgeny N.;Kazanov, Marat D.;Gelfand, Mikhail S.
通讯作者：
Gelfand, Mikhail S.
影响因子：
11.3
作者：
Juhas M;van der Meer JR;Gaillard M;Harding RM;Hood DW;Crook DW
通讯作者：
Crook DW