Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations.
Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations.
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作者：
关于微生物种群如何变化，有两种主要观点，不同的是适应主要是由基因中心或基因组中心的过程驱动的。在微生物相关时间尺度上进行纵向采样，即，几天到几周，对于区分这些机制至关重要。由于其对微生物生态学和人类健康的重要性及其可获得性和高水平的治疗，我们使用口腔微生物群来研究细菌种群内基因组动态。宏基因组通过对来自17名志愿者的健康舌头的总群落DNA进行鸟枪测序来生成，所述健康舌头在4至7个时间点获得，所述时间间隔为数天至数周。我们获得了来自55个属的390个高质量的宏基因组组装基因组（MAG）定义种群基因组。每个MAG中的绝大多数基因在2周的采样窗口内紧密连锁，表明大多数群体的基因组在MAG水平上是暂时稳定的。MAG定义的人群由多达5个菌株组成，由单核苷酸变异频率确定。虽然大多数菌株随着时间的推移是稳定的，但检测到携带100多个不同基因的单个菌株，这些基因在一段时间内从低丰度上升到群体中的优势。这些结果表明，这是一个全基因组的过程，而不是一个基因水平的种群变化过程。我们推断，全基因组的生态类型的选择是在口腔人口在短时间尺度的适应占主导地位的模式。
Two major viewpoints have been put forward for how microbial populations change, differing in whether adaptation is driven principally by gene-centric or genome-centric processes. Longitudinal sampling at microbially relevant timescales, i.e., days to weeks, is critical for distinguishing these mechanisms. Because of its significance for both microbial ecology and human health and its accessibility and high level of curation, we used the oral microbiota to study bacterial intrapopulation genome dynamics. Metagenomes were generated by shotgun sequencing of total community DNA from the healthy tongues of 17 volunteers at four to seven time points obtained over intervals of days to weeks. We obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes from 55 genera. The vast majority of genes in each MAG were tightly linked over the 2-week sampling window, indicating that the majority of the population’s genomes were temporally stable at the MAG level. MAG-defined populations were composed of up to 5 strains, as determined by single-nucleotide-variant frequencies. Although most were stable over time, individual strains carrying over 100 distinct genes that rose from low abundance to dominance in a population over a period of days were detected. These results indicate a genome-wide as opposed to a gene-level process of population change. We infer that genome-wide selection of ecotypes is the dominant mode of adaptation in the oral populations over short timescales.
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影响因子：
9.2
作者：
Hall MW;Singh N;Ng KF;Lam DK;Goldberg MB;Tenenbaum HC;Neufeld JD;G Beiko R;Senadheera DB
通讯作者：
Senadheera DB
影响因子：
3.7
作者：
Claesson MJ;O'Sullivan O;Wang Q;Nikkilä J;Marchesi JR;Smidt H;de Vos WM;Ross RP;O'Toole PW
通讯作者：
O'Toole PW
DOI：
10.1038/ismej.2015.241
发表时间：
2016-07
期刊：
The ISME journal
影响因子：
--
作者：
Bendall ML;Stevens SL;Chan LK;Malfatti S;Schwientek P;Tremblay J;Schackwitz W;Martin J;Pati A;Bushnell B;Froula J;Kang D;Tringe SG;Bertilsson S;Moran MA;Shade A;Newton RJ;McMahon KD;Malmstrom RR
通讯作者：
Malmstrom RR
影响因子：
14.9
作者：
Haft, DH;Loftus, BJ;White, O
通讯作者：
White, O
影响因子：
7.7
作者：
Evans, Daniel R.;Griffith, Marissa P.;Van Tyne, Daria
通讯作者：
Van Tyne, Daria