The indoor environment - a potential source for intact human-associated anaerobes

Background. People in westernised countries spend most of their time indoors. A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. For this reason, the built environment (BE) might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes. Methods. We sampled ten households and used propidium monoazide (PMA) to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. Results. Quantitative and qualitative analysis revealed that most of the microbial taxa in the BE samples are of human origin. Less than 25% of the prokaryotic signatures originate from intact cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. However, we also confirmed the presence of intact, strictly anaerobic taxa on bathroom floors, including methanogenic archaea. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that human-associated methanogens can survive oxic conditions for at least 6 h. Conclusions. This study enabled us to collect strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.

研究背景。西化国家的人群绝大多数时间都处于室内环境。健康的人体微生物组依赖于人体与所处环境之间发生的微生物相互作用与交换过程。基于此，建成环境（built environment, BE）可能是共生微生物的重要潜在来源。由于目前研究者尚未明确人体微生物组如何获取对氧气敏感的微生物，因此厌氧微生物尤为受关注。

研究方法。本研究对10户家庭开展采样，并使用叠氮溴化丙锭（propidium monoazide, PMA）评估所采集原核生物的活性。基于16S rRNA基因测序技术对比微生物组特征，并通过遗传学分析与培养组学分析验证了实验结果。

研究结果。定量与定性分析显示，建成环境样本中的绝大多数微生物类群均源自人体。仅不到25%的原核生物特征序列来自完整活细胞，这表明需氧类群与抗胁迫类群具有明显的生存优势。不过，本研究也在浴室地面检测到了完整的专性厌氧微生物类群，包括产甲烷古菌（methanogenic archaea）。由于产甲烷菌被认为对有氧环境高度敏感，本研究使用人体来源分离株开展耐氧性实验以验证其存活能力，结果显示人体来源的产甲烷菌可在有氧环境中存活至少6小时。

研究结论。本研究获取了强有力的证据，支持“专性厌氧微生物类群可在建成环境中短期存活”这一假说。这表明建成环境可作为厌氧型人体共生微生物的潜在来源。