Lim Yan Wei, Schmieder Robert, Haynes Matthew, Willner Dana, Furlan Mike, Youle Merry, Abbott Katelynn, Edwards Robert, Evangelista Jose, Conrad Douglas, Rohwer Forest
Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
Computational Science Research Center, San Diego State University, San Diego, CA, 92182, USA.
J Cyst Fibros. 2013 Mar;12(2):154-64. doi: 10.1016/j.jcf.2012.07.009. Epub 2012 Aug 28.
Samples collected from CF patient airways often contain large amounts of host-derived nucleic acids that interfere with recovery and purification of microbial and viral nucleic acids. This study describes metagenomic and metatranscriptomic methods that address these issues.
Microbial and viral metagenomes, and microbial metatranscriptomes, were successfully prepared from sputum samples from five adult CF patients.
Contaminating host DNA was dramatically reduced in the metagenomes. Each CF patient presented a unique microbiome; in some Pseudomonas aeruginosa was replaced by other opportunistic bacteria. Even though the taxonomic composition of the microbiomes is very different, the metabolic potentials encoded by the community are very similar. The viral communities were dominated by phages that infect major CF pathogens. The metatranscriptomes reveal differential expression of encoded metabolic potential with changing health status.
Microbial and viral metagenomics combined with microbial transcriptomics characterize the dynamic polymicrobial communities found in CF airways, revealing both the taxa present and their current metabolic activities. These approaches can facilitate the development of individualized treatment plans and novel therapeutic approaches.
从囊性纤维化（CF）患者气道采集的样本通常含有大量宿主来源的核酸，这会干扰微生物和病毒核酸的回收与纯化。本研究描述了可解决这些问题的宏基因组学和宏转录组学方法。
成功从5名成年CF患者的痰液样本中制备了微生物和病毒宏基因组以及微生物宏转录组。
宏基因组中污染性宿主DNA显著减少。每位CF患者都呈现出独特的微生物群；在某些患者中，铜绿假单胞菌被其他机会致病菌所取代。尽管微生物群的分类组成差异很大，但群落编码的代谢潜能非常相似。病毒群落以感染主要CF病原体的噬菌体为主。宏转录组揭示了随着健康状况变化编码代谢潜能的差异表达。
微生物和病毒宏基因组学与微生物转录组学相结合，可表征CF气道中发现的动态多微生物群落，揭示存在的分类群及其当前的代谢活动。这些方法有助于制定个性化治疗方案和新型治疗方法。
