Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota
Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota
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DOI：
10.1073/pnas.1820594116
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发表时间：
2019-04-23
影响因子：
11.1
通讯作者：
Shi, Wenyuan
中科院分区：
文献类型：
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作者：
Baker, Jonathon L.;Hendrickson, Erik L.;Shi, Wenyuan
众所周知，许多细菌已经进化到利用多种机制在灾难性事件中生存，其中包括应激反应基因的表达、静止、坏死性营养以及通过突变获得的代谢优势。然而，个人利用这些能力在生态复杂的环境中获得竞争优势的动态仍未得到研究。在这项研究中，我们观察了长期饥饿的整个生态扰动过程中的唾液微生物组，只允许最有能力获取和使用有限资源的物种生存。在最初的几天里，群落经历了死亡阶段，导致活细胞数量减少-50-100倍。有趣的是，在这个死亡阶段之后，只有三个物种：肺炎克雷伯菌、产酸克雷伯菌和产碱普罗威登斯菌（肠杆菌科的所有成员）似乎具有转录活性并且可恢复。克雷伯氏菌是重要的人类病原体，通常对多种抗生素具有抗药性，最近，口腔克雷伯氏菌在肠道的异位定植被记录可引起生态失调和炎症。元组学分析为进一步研究肠杆菌科的生态成功提供了一些线索。这些分离物在稳定期等位基因的已知生长优势中积累了单核苷酸多态性，并产生与抗菌环缩酚肽非常相似的天然产物。这项研究的结果表明，当面临饥饿时，致病性肠杆菌科细菌在唾液微生物组中的存活时间比其更良性的邻居要长得多。鉴于被口腔液体污染的医院表面，尤其是水槽和排水管，是耐药肠杆菌科细菌爆发的明确来源，这一点尤其重要。
It is well-understood that many bacteria have evolved to survive catastrophic events using a variety of mechanisms, which include expression of stress-response genes, quiescence, necrotrophy, and metabolic advantages obtained through mutation. However, the dynamics of individuals leveraging these abilities to gain a competitive advantage in an ecologically complex setting remain unstudied. In this study, we observed the saliva microbiome throughout the ecological perturbation of long-term starvation, allowing only the species best equipped to access and use the limited resources to survive. During the first several days, the community underwent a death phase that resulted in a -50-100-fold reduction in the number of viable cells. Interestingly, after this death phase, only three species, Klebsiella pneumoniae, Klebsiella oxytoca, and Providencia alcalifaciens, all members of the family Enterobacteriaceae, appeared to be transcriptionally active and recoverable. Klebsiella are significant human pathogens, frequently resistant to multiple antibiotics, and recently, ectopic colonization of the gut by oral Klebsiella was documented to induce dysbiosis and inflammation. MetaOmics analyses provided several leads for further investigation regarding the ecological success of the Enterobacteriaceae. The isolates accumulated single nucleotide polymorphisms in known growth advantage in stationary phase alleles and produced natural products closely resembling antimicrobial cyclic depsipeptides. The results presented in this study suggest that pathogenic Enterobacteriaceae persist much longer than their more benign neighbors in the salivary microbiome when faced with starvation. This is particularly significant, given that hospital surfaces contaminated with oral fluids, especially sinks and drains, are well-established sources of outbreaks of drug-resistant Enterobacteriaceae.