Department of Clinical Science, Faculty of Medicine, University of Bergen, Postboks 7804, 5020, Bergen, Norway.
Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway.
BMC Pulm Med. 2021 Nov 2;21(1):342. doi: 10.1186/s12890-021-01687-0.
Little is known concerning the stability of the lower airway microbiome. We have compared the microbiota identified by repeated bronchoscopy in healthy subjects and patients with ostructive lung diseaseases (OLD).
21 healthy controls and 41 patients with OLD completed two bronchoscopies. In addition to negative controls (NCS) and oral wash (OW) samples, we gathered protected bronchoalveolar lavage in two fractions (PBAL1 and PBAL2) and protected specimen brushes (PSB). After DNA extraction, we amplified the V3V4 region of the 16S rRNA gene, and performed paired-end sequencing (Illumina MiSeq). Initial bioinformatic processing was carried out in the QIIME-2 pipeline, identifying amplicon sequence variants (ASVs) with the DADA2 algorithm. Potentially contaminating ASVs were identified and removed using the decontam package in R and the sequenced NCS.
A final table of 551 ASVs consisted of 19 × 10 sequences. Alpha diversity was lower in the second exam for OW samples, and borderline lower for PBAL1, with larger differences in subjects not having received intercurrent antibiotics. Permutational tests of beta diversity indicated that within-individual changes were significantly lower than between-individual changes. A non-parametric trend test showed that differences in composition between the two exams (beta diversity) were largest in the PSBs, and that these differences followed a pattern of PSB > PBAL2 > PBAL1 > OW. Time between procedures was not associated with increased diversity.
The airways microbiota varied between examinations. However, there is compositional microbiota stability within a person, beyond that of chance, supporting the notion of a transient airways microbiota with a possibly more stable individual core microbiome.
人们对下呼吸道微生物组的稳定性知之甚少。我们比较了健康受试者和阻塞性肺疾病（OLD）患者通过重复支气管镜检查确定的微生物组。
21 名健康对照者和 41 名 OLD 患者完成了两次支气管镜检查。除了阴性对照（NCS）和口腔冲洗（OW）样本外，我们还分别采集了两个部分的保护性支气管肺泡灌洗（PBAL1 和 PBAL2）和保护性标本刷（PSB）。提取 DNA 后，我们扩增了 16S rRNA 基因的 V3V4 区，并进行了配对末端测序（Illumina MiSeq）。初始生物信息学处理是在 QIIME-2 管道中进行的，使用 DADA2 算法识别扩增子序列变异体（ASVs）。使用 R 中的 decontam 包和测序的 NCS 识别和去除潜在污染的 ASVs。
最终的 551 个 ASVs 表由 19×10 个序列组成。OW 样本第二次检查的 alpha 多样性较低，PBAL1 则处于边缘较低水平，未接受过中介抗生素的受试者差异更大。beta 多样性的置换检验表明，个体内变化明显低于个体间变化。非参数趋势检验表明，两次检查之间（beta 多样性）的组成差异在 PSB 中最大，并且这些差异遵循 PSB>PBAL2>PBAL1>OW 的模式。两次操作之间的时间间隔与多样性的增加无关。
气道微生物组在检查之间发生了变化。然而，在个体内存在组成微生物组的稳定性，超过了偶然的变化，支持了短暂的气道微生物组存在一个可能更稳定的个体核心微生物组的观点。
