Genomic diversity and population dynamics in natural microbial communities

自然界中的细菌很少生活在纯培养环境中；相反，它们形成了复杂的群落，对我们的世界产生了深远的影响。例如，土壤中固氮细菌的数量和类型可能会影响作物的质量，而抗生素扰乱人类肠道中的细菌种群可能会导致危及生命的感染。由于大多数细菌不能在实验室中培养，我们对自然微生物群落的知识在很大程度上是基于对所有细菌中普遍保守的基因序列的分析。与此同时，对可培养细菌的研究表明，如果只考虑通用的基因序列数据，细菌菌株之间的基因含量存在显著差异，这些细菌菌株将被视为同一物种的成员。微生物群落的序列研究结果中有线索表明，基因组多样性在自然群落中的重要性被低估了。微生物群落的扰动可能会选择菌株特有的基因，并导致“亚种”水平上的生物学上的重大种群转移，这是通用的基于基因序列的方法无法检测到的。对微生物群落中的基因组多样性进行清查是在菌株水平上了解种群动态的必要的第一步。

Bacteria in nature rarely live in pure culture; rather, they form complex communities that have profound effects on our world. For example, the numbers and types of nitrogen-fixing bacteria in soil can affect the quality of a crop, and the disruption of bacterial populations in the human intestine with antibiotics can lead to life-threatening infections. Since most bacteria cannot be cultivated in the lab, our knowledge of natural microbial communities is largely based on analysis of sequences of universally conserved genes found in all bacteria. At the same time, studies of culturable bacteria have revealed significant gene content differences between strains of bacteria that would be considered members of the same species if only universal gene sequence data were considered. There are clues in the results of sequence-based studies of microbial communities that the significance of genomic diversity in natural communities has been underestimated. Perturbation of microbial communities may select for strain-specific genes and result in biologically significant population shifts at the "sub-species" level that would be undetected by universal gene sequence-based approaches. An inventory of genomic diversity in a microbial community is an essential first step to understanding population dynamics at the strain level.