Shotgun metagenomics of dust microbiome from flight deck and cabin in civil aviation aircraft

Sun, Yu; Xi, Fu; Li, Yanling; Yuan, Qianqian; Ou, Zheyuan; Lindgren, Torsten; Deng, Yiqun; Norbäck, Dan

doi:10.1111/ina.12707

Cited by 25 publications

(26 citation statements)

References 63 publications

(135 reference statements)

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“…Shotgun metagenomic sequencing is an amplification-free approach to characterize microbial species and a whole catalogue of functional genes. This approach has been widely used in human gut microbiome studies but has been applied in only a few microbiome studies in built environments such as in commercial aircrafts, metros and hospitals [ 21 – 24 ]. However, no health data were collected in these studies, and thus, the health effects of the microbial species, functional genes and metabolic products were unclear.…”

Section: Introductionmentioning

confidence: 99%

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

Zhang

et al. 2021

Microbiome

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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.

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Section: Introductionmentioning

confidence: 99%

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

Zhang

et al. 2021

Microbiome

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“…GRiD measures the growth rate of uncharacterized bacteria or bacteria with low coverage samples and lowquality genome assemblies [37,38]. We filtered all GRiD estimates with strain heterogeneity above 0.5 as these estimates are likely to be inaccurate.…”

Section: Growth Rate Analysis (Gra)mentioning

confidence: 99%

A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

et al. 2021

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Background Clean rooms of the Space Assembly Facility (SAF) at the Jet Propulsion Laboratory (JPL) at NASA are the final step of spacecraft cleaning and assembly before launching into space. Clean rooms have stringent methods of air-filtration and cleaning to minimize microbial contamination for exoplanetary research and minimize the risk of human pathogens, but they are not sterile. Clean rooms make a selective environment for microorganisms that tolerate such cleaning methods. Previous studies have attempted to characterize the microbial cargo through sequencing and culture-dependent protocols. However, there is not a standardized metagenomic workflow nor analysis pipeline for spaceflight hardware cleanroom samples to identify microbial contamination. Additionally, current identification methods fail to characterize and profile the risk of low-abundance microorganisms. Results A comprehensive metagenomic framework to characterize microorganisms relevant for planetary protection in multiple cleanroom classifications (from ISO-5 to ISO-8.5) and sample types (surface, filters, and debris collected via vacuum devices) was developed. Fifty-one metagenomic samples from SAF clean rooms were sequenced and analyzed to identify microbes that could potentially survive spaceflight based on their microbial features and whether the microbes expressed any metabolic activity or growth. Additionally, an auxiliary testing was performed to determine the repeatability of our techniques and validate our analyses. We find evidence that JPL clean rooms carry microbes with attributes that may be problematic in space missions for their documented ability to withstand extreme conditions, such as psychrophilia and ability to form biofilms, spore-forming capacity, radiation resistance, and desiccation resistance. Samples from ISO-5 standard had lower microbial diversity than those conforming to ISO-6 or higher filters but still carried a measurable microbial load. Conclusions Although the extensive cleaning processes limit the number of microbes capable of withstanding clean room condition, it is important to quantify thresholds and detect organisms that can inform ongoing Planetary Protection goals, provide a biological baseline for assembly facilities, and guide future mission planning.

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“…The interactions between microbes and surfaces are affected by many factors such as surface hydrophobicity, charge, topography, and other physicochemical attributes [10][11][12][13]. Consequently, the abundances of specific taxa differ depending on the type of surfaces and materials [14,15]. Similarly, the metabolic functions of surface microbial communities and the synthesized metabolites also vary by surface type [8,14] and materials [7].…”

Section: Introductionmentioning

confidence: 99%

“…Consequently, the abundances of specific taxa differ depending on the type of surfaces and materials [14,15]. Similarly, the metabolic functions of surface microbial communities and the synthesized metabolites also vary by surface type [8,14] and materials [7].…”

Section: Introductionmentioning

confidence: 99%

Metagenomic Insights Into the Microbial Communities of Inert and Oligotrophic Outdoor Pier Surfaces of a Coastal City

Tong

Leung

Shen

et al. 2021

Preprint

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Background: Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in coastal areas, and due to their unique locations at the interface between terrestrial and aquatic ecosystems, pier surfaces are likely to harbor interesting microbiology. In this study, the microbiomes on the metal and concrete surfaces at nine piers located along the coastline of Hong Kong were investigated by metagenomic sequencing. The roles played by different factors in shaping the taxonomic composition and functional traits of the pier surface microbiomes were determined. Metagenome-assembled genomes were reconstructed and their putative biosynthetic gene clusters were characterized in detail.Results: Surface material was found to be the strongest factor in structuring the taxonomic and functional compositions of the pier surface microbiomes. Corrosion-related bacteria were significantly enriched on metal surfaces, consistent with the pitting corrosion observed. The differential enrichment of taxa mediating biodegradation suggests differences between the metal and concrete surfaces in terms of specific xenobiotics being potentially degraded. Genome-centric analysis detected the presence of many novel species, with the majority of them belonging to the phylum Proteobacteria. Genomic characterization showed that the potential metabolic functions and secondary biosynthetic capacity were largely governed by taxonomy, rather than surface attributes and geography. Conclusions: Pier surfaces are a rich reservoir of abundant novel bacterial species. Members of the surface microbial communities use different mechanisms to counter the stresses under oligotrophic conditions. A better understanding of the outdoor surface microbiomes located in different environments should enhance the ability to maintain outdoor surfaces of infrastructures.

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Shotgun metagenomics of dust microbiome from flight deck and cabin in civil aviation aircraft

Cited by 25 publications

References 63 publications

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

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

A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

Metagenomic Insights Into the Microbial Communities of Inert and Oligotrophic Outdoor Pier Surfaces of a Coastal City

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