Human microbiome studies remain focused on bacteria, as they comprise the dominant component of the microbiota. Recent advances in sequencing technology and optimization of amplicon sequencing protocols have allowed the description of other members of the microbiome, including eukaryotes (fungi) and, most recently, archaea. There are no known human-associated archaeal pathogens. Their diversity and contribution to health and chronic respiratory diseases, such as chronic rhinosinusitis (CRS), are unknown. Patients with CRS suffer from long-term sinus infections, and while the microbiota is hypothesized to play a role in its pathogenesis, the exact mechanism is poorly understood. In this cross-sectional study, we applied a recently optimized protocol to describe the prevalence, diversity and abundance of archaea in swab samples from the middle meatus of 60 individuals with and without CRS. A nested PCR approach was used to amplify the archaeal 16S rRNA gene for sequencing, and bacterial and archaeal load (also based on 16S rRNA genes) were estimated using Droplet Digital™ PCR (ddPCR). A total of 16 archaeal amplicon sequence variants (ASVs) from the phyla Euryarchaeota and Thaumarchaeota were identified. Archaeal ASVs were detected in 7/60 individuals, independent of disease state, whereas bacterial ASVs were detected in 60/60. Bacteria were also significantly more abundant than archaea. The ddPCR method was more sensitive than amplicon sequencing at detecting archaeal DNA in samples. Phylogenetic trees were constructed to visualize the evolutionary relationships between archaeal ASVs, isolates and clones. ASVs were placed into phylogenetic clades containing an apparent paucity of human-associated reference sequences, revealing how little studied the human archaeome is. This is the largest study to date to examine the human respiratory-associated archaeome, and provides the first insights into the prevalence, diversity and abundance of archaea in the human sinuses.

人类微生物组研究仍然集中在细菌上，因为它们构成了微生物群的主要组成部分。测序技术和扩增子测序方案优化的最新进展使得能够描述微生物组的其他成员，包括真核生物（真菌）和最近的古细菌。目前还没有已知的与人类相关的古菌病原体。它们的多样性以及对健康和慢性呼吸道疾病（例如慢性鼻窦炎（CRS））的贡献尚不清楚。 CRS 患者患有长期鼻窦感染，虽然假设微生物群在其发病机制中发挥作用，但确切机制尚不清楚。在这项横断面研究中，我们应用了最近优化的方案来描述 60 名患有和不患有 CRS 的个体中鼻道拭子样本中古细菌的流行情况、多样性和丰度。使用巢式 PCR 方法扩增古细菌 16S rRNA 基因进行测序，并使用 Droplet Digital™ PCR (ddPCR) 估计细菌和古细菌负荷（也基于 16S rRNA 基因）。来自该门的总共 16 个古菌扩增子序列变体 (ASV)广古菌门和奇古菌门被识别出来。在 7/60 的个体中检测到古菌 ASV，与疾病状态无关，而在 60/60 的个体中检测到细菌 ASV。细菌的数量也明显多于古细菌。 ddPCR 方法在检测样品中的古菌 DNA 方面比扩增子测序更灵敏。构建系统发育树以可视化古菌 ASV、分离株和克隆之间的进化关系。 ASV 被置于包含明显缺乏人类相关参考序列的系统发育分支中，这揭示了人类古基因组的研究是多么的少。这是迄今为止最大规模的研究人类呼吸道相关古细菌的研究，首次深入了解人类鼻窦中古细菌的流行程度、多样性和丰度。