Department of Medicine, Section of Pulmonary and Critical Care Medicine, The University of Chicago, Chicago, IL, 60637, USA.
Present address: Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
Microbiome. 2017 Jun 30;5(1):67. doi: 10.1186/s40168-017-0289-z.
Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct microbial community that decreases in richness and diversity with disease progression. Understanding the functional characteristics of the microbial community may aid in identifying potential therapies and may assist in management, but current methods are cumbersome. Here, we demonstrate the use of an oxidative metabolic assay as a complement to sequencing methods to describe the microbiome in the airways of patients with CF.
Expectorated sputum was collected from 16 CF subjects and 8 control subjects. The Biolog Gen III Microplate was used in a community-level physiological profiling (CLPP)-based assay to examine oxidative metabolic activity. 16S rRNA V4 amplicon sequencing was used to characterize the taxonomy and diversity of the samples. Correlations were then identified among the oxidative activity and taxonomy data. In an additional paired analysis, sputum from seven CF subjects were collected at two separate clinic visits and compared for oxidative activity, taxonomy, and diversity.
Significant differences in oxidative metabolic activity, microbial taxonomy, and diversity were found between the CF and control sputum samples. Oxidative activity correlated positively with total genera but not with other measures of diversity or taxonomy, demonstrating that the metabolic assay complements the structural aspects of the microbiome. As expected, Pseudomonas was significantly enriched in CF samples, while Streptococcus and Prevotella were similarly abundant in both CF and control samples. Paired analysis of CF samples at separate clinic visits revealed comparable oxidative activity that correlated with similar stability in taxonomy and diversity.
The CLPP assay used in this study complements existing sequencing methods to delineate the oxidative metabolic footprint of the CF airway bacterial community. This method may be useful to study the CF microbial community over time and with changes in disease state.
气道的进行性、慢性细菌感染是囊性纤维化（CF）患者死亡的主要原因。基于细菌 16S rRNA 基因测序的非培养方法描述了一种独特的微生物群落，随着疾病的进展，其丰富度和多样性逐渐降低。了解微生物群落的功能特征可能有助于确定潜在的治疗方法，并有助于管理，但目前的方法很繁琐。在这里，我们展示了一种氧化代谢测定法作为测序方法的补充，用于描述 CF 患者气道中的微生物组。
从 16 名 CF 患者和 8 名对照者中收集了咳出的痰液。使用 Biolog Gen III 微孔板进行社区水平生理特征分析（CLPP）基础测定，以检查氧化代谢活性。使用 16S rRNA V4 扩增子测序来描述样品的分类和多样性。然后鉴定氧化活性和分类数据之间的相关性。在额外的配对分析中，从 7 名 CF 患者收集了两次不同就诊时的痰液，并对氧化活性、分类和多样性进行了比较。
CF 和对照者的痰液样本之间存在氧化代谢活性、微生物分类和多样性的显著差异。氧化活性与总属呈正相关，但与其他多样性或分类测量值无关，这表明代谢测定法补充了微生物组的结构方面。不出所料，假单胞菌在 CF 样本中显著富集，而链球菌和普雷沃菌在 CF 和对照样本中同样丰富。在不同就诊时对 CF 样本的配对分析显示出可比较的氧化活性，与分类和多样性的相似稳定性相关。
本研究中使用的 CLPP 测定法补充了现有的测序方法，以描绘 CF 气道细菌群落的氧化代谢特征。这种方法可能有助于随着时间的推移和疾病状态的变化来研究 CF 微生物群落。
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