State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
Environ Int. 2020 Jun;139:105702. doi: 10.1016/j.envint.2020.105702. Epub 2020 Apr 2.
We spend ever-increasing time indoors along with urbanization; however, the geographical distribution patterns of microbiome and antibiotic resistome, and their driving forces in household environment remains poorly characterized. Here, we surveyed the bacterial and fungal communities, and the resistome in settled dust gathered from 82 homes located across Beijing, China, employing Illumina sequencing and high-throughput quantitative PCR techniques. There was no clear geographical distribution pattern in dust-related bacterial communities although a slight but significant (P < 0.05) distance-decay relationship occurred in its community similarity; by contrast, a relatively distinct geographical clustering and a stronger distance-decay relationship were observed in fungal communities at the local scale. The cross-domain (bacteria versus fungi) relationships in the microbiome of the dust samples were mostly observed as robust co-occurrence correlations. The bacterial communities were dominated by Proteobacteria and Actinobacteria phyla, with human skin, soil and plants being potential major sources. The fungal communities largely comprised potential allergens (a median 61% of the fungal sequences), with Alternaria genus within Ascomycota phylum being the most predominant taxa. The profile of dust-related bacterial communities was mainly affected by housing factors related to occupants and houseplants, while that of fungal communities was determined by georeferenced environmental factors, particularly vascular plant diversity. Additionally, a great diversity (1.96 on average for Shannon index) and normalized abundance (2.22 copies per bacterial cell on average) of antibiotic resistance genes were detected across the dust samples, with the dominance of genes resistant to vancomycin and Macrolide-Lincosamide-Streptogramin B. The resistome profile exhibited no distinct geographical pattern, and was primarily driven by certain bacterial phyla and occupancy-related factors. Overall, we underline the significance of anthropogenic impacts and house location in structuring bacterial and fungal communities inside homes, respectively, and suggest that household dust is an overlooked reservoir for antibiotic resistance.
我们在城市化进程中越来越多地待在室内；然而，家庭环境中微生物组和抗生素耐药组的地理分布模式及其驱动因素仍未得到充分描述。在这里，我们采用 Illumina 测序和高通量定量 PCR 技术，调查了采集自中国北京 82 户家庭的定居尘埃中的细菌和真菌群落以及耐药组。尘埃相关细菌群落没有明显的地理分布模式，尽管其群落相似性存在微弱但显著的（P<0.05）距离衰减关系；相比之下，真菌群落具有相对明显的地理聚类和更强的距离衰减关系。尘埃样本微生物组的跨域（细菌与真菌）关系主要表现为稳健的共现相关性。细菌群落主要由 Proteobacteria 和 Actinobacteria 门组成，人类皮肤、土壤和植物可能是其主要来源。真菌群落主要由潜在过敏原组成（真菌序列中位数为 61%），子囊菌门的交链孢属是最主要的类群。尘埃相关细菌群落的组成主要受与居住者和室内植物有关的住房因素影响，而真菌群落的组成则由地理参考环境因素决定，特别是维管束植物多样性。此外，在尘埃样本中检测到了大量的抗生素耐药基因（平均香农指数为 1.96）和归一化丰度（平均每细菌细胞 2.22 个拷贝），其中以万古霉素和大环内酯-林可酰胺-链阳性菌素 B 耐药基因为主。耐药组图谱没有明显的地理模式，主要受某些细菌门和与居住者有关的因素驱动。总体而言，我们强调了人为影响和家庭位置在分别构建家庭内部细菌和真菌群落方面的重要性，并提出家庭尘埃是抗生素耐药性被忽视的储库。
