Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China–association with asthma, rhinitis and rhinoconjunctivitis in high school students

Abstract

Background Studies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor microbiome exposure. Developing countries such as China have experienced rapid urbanization in past years, but no study has investigated microbiome exposure and urban-rural health effects in these countries. Methods Nine high schools from urban and rural areas were randomly selected in Shanxi Province, China, and classroom vacuum dust was collected for shotgun metagenomic sequencing. A self-administered questionnaire was collected from 1332 students for personal information and health data. Three-level logistic regression was performed between microbial richness/abundance/functional pathways and the occurrence of asthma and rhinitis symptoms. Results Consistent with developed countries, the prevalence of wheeze and rhinitis was higher in urban areas than in rural areas (p < 0.05). Metagenomic profiling revealed 8302 bacterial, 395 archaeal, 744 fungal, 524 protist and 1103 viral species in classroom dust. Actinobacteria (mean relative abundance 49.7%), Gammaproteobacteria (18.4%) and Alphaproteobacteria (10.0%) were the most abundant bacterial classes. The overall microbiome composition was significantly different between urban and rural schools (p = 0.001, Adonis). Species from Betaproteobactera, Gammaproteobacteria and Bacilli were enriched in urban schools, and species from Actinobacteria and Cyanobacteria were enriched in rural schools. Potential pathogens were present in higher abundance in urban schools than in rural schools (p < 0.05). Pseudoalteromonas, Neospora caninum and Microbacterium foliorum were positively associated with the occurrence of wheeze, rhinitis and rhinoconjunctivitis, and Brachybacterium was protectively (negatively) associated with rhinitis (p < 0.01). The abundance of human endocrine and metabolic disease pathways was positively associated with rhinitis (p = 0.008), and butyrate and propionate metabolic genes and pathways were significantly enriched in rural schools (p < 0.005), in line with previous findings that these short-chain fatty acids protect against inflammatory diseases in the human gut. Conclusions We conducted the first indoor microbiome survey in urban/rural environments with shotgun metagenomics, and the results revealed high-resolution microbial taxonomic and functional profiling and potential health effects.

Cow Farmers’ Homes Host More Diverse Airborne Bacterial Communities Than Pig Farmers’ Homes and Suburban Homes

“…According to the PCoA analysis, suburban homes had a distinct bacterial community, while the pig and cow farmers’ homes showed a minor overlap ( Figure 3 ). Different indoor bacterial community composition between suburban and farmers’ homes is in line with previous studies, which showed a difference in microbiota between farm and non-farm homes ( Kirjavainen et al, 2019 ; Fu et al, 2021 ). Even though there is an overlap in the community composition of cow and pig farmers’ homes, there was a significant difference in the community composition between cow and pig farmers’ homes.…”

Isolation and Identification of Talaromyces sp. Strain Q2 and Its Biocontrol Mechanisms Involved in the Control of Fusarium Wilt

“…The libraries were sequenced on the Illumina HiSeq X-ten platform. The raw sequencing reads were processed to obtain quality-filtered reads for further analyses followed by co-occurrence network analyses as reported previously (Zhang et al, 2018;Fu et al, 2021).…”

Update of the list of QPS‐recommended microbiological agents intentionally added to food or feed as notified to EFSA 16: suitability of taxonomic units notified to EFSA until March 2022

“…In the period between 2019 and 2022, only one relevant article was found related to the safety of M. foliorum. Fu et al (2021) studied the microbiological load of urban air dust by a metagenomic approach and found an association of M. foliorum with the occurrence of wheeze, rhinitis and rhinoconjunctivitis; a causal relationship was not investigated.…”