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Lin TH, Chou YH, Hsu TY, Hung CH, Lai CY. Association among polydisperse aerodynamic size of bioaerosols, biodiversity and urbanization in kindergartens. CHEMOSPHERE 2024; 359:142333. [PMID: 38759806 DOI: 10.1016/j.chemosphere.2024.142333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/17/2024] [Accepted: 05/12/2024] [Indexed: 05/19/2024]
Abstract
The aerodynamic sizes of bioaerosols may significantly affect their behaviors, respiratory deposition and biodiversity. The respirable bacterial size, biodiversity, and human-associated bacteria (HAB) related bioaerosols were evaluated at three kindergartens in Taiwan. Kindergartens A, B, and C were in urban, semi-urban, and rural areas, respectively. A six-stage viable Andersen cascade impactor was used to collect bioaerosols and to determine their size distributions. The geometric mean diameter (GMD), geometric standard deviation (GSD), heat maps, and uniformity were used to evaluate the association of bacteria characteristics. A BD Phoenix-100 automated interpretation system was used to identify the airborne bacteria species. The results revealed that 1425 colonies of the sampled airborne bacteria contained 63 species in 29 genera, and overall, 63.0% were HABs. The most abundant phylum was Actinobacteria (56.6 ± 22.2%) and Firmicutes (31.6 ± 22.3%), and from the taxonomic analysis, both airborne Micrococcus and the Staphylococcus aureus are the dominant genus. All the bacteria aerodynamic particle size distributions were polydisperse distributions. The heat map and uniformity analysis had revealed most of the sampled bioaerosols distributed between 1.1-3.3 μm, and most of the polydisperse airborne Streptococcus spp. had a size in the respirable range, due to urbanization, they have potentially contributed to respiratory risk in the kindergartens. The Shannon diversity index (H) and inverse Simpson diversity index (D) of the bioaerosols in urban kindergarten were negatively correlated with GMD and GSD. The Pearson correlations revealed that the kindergarten in the rural area, with a higher temperature, a lower relative humidity, and a lower CO2 concentration than the others, tended to have the largest H and D values (P < 0.05). Multiple and stepwise regression revealed that bioaerosol aerodynamic size was statistically significantly correlated with H (P = 0.001) and D values (P = 0.002). This study sheds light on the characteristics of bioaerosols and their associations with microbiome.
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Affiliation(s)
- Tzu-Hsien Lin
- Department of Public Health, China Medical University, Taichung, Taiwan.
| | - Ying-Hsiang Chou
- Department of Medical Imaging and Radiological Sciences, Chung Shan Medical University, Taichung, Taiwan; Department of Radiation Oncology, Chung Shan Medical University Hospital, Taichung, Taiwan; Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.
| | - Tzu-Yu Hsu
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung, Taiwan.
| | - Chun-Hui Hung
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung, Taiwan.
| | - Chane-Yu Lai
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung, Taiwan; Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan.
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Zampolli J, De Giani A, Rossi M, Finazzi M, Di Gennaro P. Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas. Front Microbiol 2024; 15:1380953. [PMID: 38863750 PMCID: PMC11165352 DOI: 10.3389/fmicb.2024.1380953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.
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Affiliation(s)
| | | | | | | | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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3
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Nastasi N, Haines SR, Bope A, Meyer ME, Horack JM, Dannemiller KC. Fungal diversity differences in the indoor dust microbiome from built environments on earth and in space. Sci Rep 2024; 14:11858. [PMID: 38789478 PMCID: PMC11126634 DOI: 10.1038/s41598-024-62191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Human occupied built environments are no longer confined to Earth. In fact, there have been humans living and working in low-Earth orbit on the International Space Station (ISS) since November 2000. With NASA's Artemis missions and the age of commercial space stations set to begin, more human-occupied spacecraft than ever will be in Earth's orbit and beyond. On Earth and in the ISS, microbes, especially fungi, can be found in dust and grow when unexpected, elevated moisture conditions occur. However, we do not yet know how indoor microbiomes in Earth-based homes and in the ISS differ due to their unique set of environmental conditions. Here we show that bacterial and fungal communities are different in dust collected from vacuum bags on Earth and the ISS, with Earth-based homes being more diverse (465 fungal OTUs and 237 bacterial ASVs) compared to the ISS (102 fungal OTUs and 102 bacterial ASVs). When dust from these locations were exposed to varying equilibrium relative humidity conditions (ERH), there were also significant fungal community composition changes as ERH and time elevated increased (Bray Curtis: R2 = 0.35, P = 0.001). These findings can inform future spacecraft design to promote healthy indoor microbiomes that support crew health, spacecraft integrity, and planetary protection.
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Affiliation(s)
- Nicholas Nastasi
- Environmental Science Graduate Program, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, College of Engineering, Environmental Health Sciences, The Ohio State University, 470 Hitchcock Hall, 2050 Neil Ave, Columbus, OH, 43210, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA
| | - Sarah R Haines
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Ashleigh Bope
- Environmental Science Graduate Program, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, College of Engineering, Environmental Health Sciences, The Ohio State University, 470 Hitchcock Hall, 2050 Neil Ave, Columbus, OH, 43210, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA
| | - Marit E Meyer
- NASA Glenn Research Center, Cleveland, OH, 44135, USA
| | - John M Horack
- Department of Mechanical and Aerospace Engineering, College of Engineering and John Glenn College of Public Affairs, Ohio State University, Columbus, OH, 43210, USA
| | - Karen C Dannemiller
- Department of Civil, Environmental and Geodetic Engineering, College of Engineering, Environmental Health Sciences, The Ohio State University, 470 Hitchcock Hall, 2050 Neil Ave, Columbus, OH, 43210, USA.
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA.
- Sustainability Institute, The Ohio State University, Columbus, OH, 43210, USA.
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Wang W, Qiu Z, Li H, Wu X, Cui Y, Xie L, Chang B, Li P, Zeng H, Ding T. Patient-derived pathogenic microbe deposition enhances exposure risk in pediatric clinics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171703. [PMID: 38490424 DOI: 10.1016/j.scitotenv.2024.171703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
Healthcare-associated infections (HAIs) pose significant risks to pediatric patients in outpatient settings. To prevent HAIs, understanding the sources and transmission routes of pathogenic microorganisms is crucial. This study aimed to identify the sources of opportunistic bacterial pathogens (OBPs) in pediatric outpatient settings and determine their transmission routes. Furthermore, assessing the public health risks associated with the core OBPs is important. We collected 310 samples from various sites in pediatric outpatient areas and quantified the bacteria using qPCR and CFU counting. We also performed 16S rRNA gene and single-bacterial whole-genome sequencing to profile the transmission routes and antibiotic resistance characteristics of OBPs. We observed significant variations in microbial diversity and composition among sampling sites in pediatric outpatient settings, with active communication of the microbiota between linked areas. We found that the primary source of OBPs in multi-person contact areas was the hand surface, particularly in pediatric patients. Five core OBPs, Staphylococcus epidermidis, Acinetobacter baumannii, Pseudomonas aeruginosa, Streptococcus mitis, and Streptococcus oralis, were mainly derived from pediatric patients and spread into the environment. These OBPs accumulated at multi-person contact sites, resulting in high microbial diversity in these areas. Transmission tests confirmed the challenging spread of these pathogens, with S. epidermidis transferring from the patient's hand to the environment, leading to an increased abundance and emergence of related strains. More importantly, S. epidermidis isolated from pediatric patients carried more antibiotic-resistance genes. In addition, two strains of multidrug-resistant A. baumannii were isolated from both a child and a parent, confirming the transmission of the five core OBPs centered around pediatric patients and multi-person contact areas. Our results demonstrate that pediatric patients serve as a significant source of OBPs in pediatric outpatient settings. OBPs carried by pediatric patients pose a high public health risk. To effectively control HAIs, increasing hand hygiene measures in pediatric patients and enhancing the frequency of disinfection in multi-person contact areas remains crucial. By targeting these preventive measures, the spread of OBPs can be reduced, thereby mitigating the risk of HAIs in pediatric outpatient settings.
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Affiliation(s)
- Wan Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Zongyao Qiu
- Center for Disease Control and Prevention of Nanhai District, Foshan 528200, China
| | - Hui Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xiaorong Wu
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Ying Cui
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Lixiang Xie
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Bozhen Chang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Peipei Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Hong Zeng
- Center for Disease Control and Prevention of Nanhai District, Foshan 528200, China.
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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Hao Y, Lu C, Xiang Q, Sun A, Su JQ, Chen QL. Unveiling the overlooked microbial niches thriving on building exteriors. ENVIRONMENT INTERNATIONAL 2024; 187:108649. [PMID: 38642506 DOI: 10.1016/j.envint.2024.108649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024]
Abstract
Rapid urbanization in the Asia-Pacific region is expected to place two-thirds of its population in concrete-dominated urban landscapes by 2050. While diverse architectural facades define the unique appearance of these urban systems. There remains a significant gap in our understanding of the composition, assembly, and ecological potential of microbial communities on building exteriors. Here, we examined bacterial and protistan communities on building surfaces along an urbanization gradient (urban, suburban and rural regions), investigating their spatial patterns and the driving factors behind their presence. A total of 55 bacterial and protist phyla were identified. The bacterial community was predominantly composed of Proteobacteria (33.7% to 67.5%). The protistan community exhibited a prevalence of Opisthokonta and Archaeplastida (17.5% to 82.1% and 1.8% to 61.2%, respectively). The composition and functionality of bacterial communities exhibited spatial patterns correlated with urbanization. In urban buildings, factors such as facade type, light exposure, and building height had comparatively less impact on bacterial composition compared to suburban and rural areas. The highest bacterial diversity and lowest Weighted Average Community Identity (WACI) were observed on suburban buildings, followed by rural buildings. In contrast, protists did not show spatial distribution characteristics related to facade type, light exposure, building height and urbanization level. The distinct spatial patterns of protists were primarily shaped by community diffusion and the bottom-up regulation exerted by bacterial communities. Together, our findings suggest that building exteriors serve as attachment points for local microbial metacommunities, offering unique habitats where bacteria and protists exhibit independent adaptive strategies closely tied to the overall ecological potential of the community.
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Affiliation(s)
- Yilong Hao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Changyi Lu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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Lu Y, Duan M, Li Y, Zhang S, Hu X, Liu L. Altitude-associated trends in bacterial communities in ultrahigh-altitude residences. ENVIRONMENT INTERNATIONAL 2024; 185:108503. [PMID: 38377724 DOI: 10.1016/j.envint.2024.108503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Indoor bacterial communities may change with altitude because their major contributors, outdoor bacterial communities, vary with altitude. People's health effects from bacteria inhalation exposure can also vary with altitude because human respiratory physiology changes with oxygen content in air. Accordingly, adjusting indoor bacterial communities may help to acclimate newcomers from low-altitude environments to ultrahigh-altitude environments. To lay the groundwork for further research, we aimed to first elucidate the bacterial communities in ultrahigh-altitude residences and the effects of altitude on these communities. We collected 187 environmental samples from residential communities at ultrahigh altitudes of 3811-4651 m in Ngari, China and sequenced bacterial 16S rRNA genes. RESULTS On one hand, when abundant genera in ultrahigh-altitude residences and those reported by previous studies on low-altitude residences were compared, nine genera were shared, whereas other five genera were abundant only at ultrahigh altitudes. On the other hand, when the bacterial communities of residences at different ultrahigh altitudes were further compared, the bacterial composition in indoor surface samples varied significantly with altitude. The relative abundance of five bacterial genera in indoor air samples and 10 genera and three phyla in indoor surface samples varied monotonically with altitude. CONCLUSIONS Altitude may be a long-neglected factor that shapes residential bacterial communities and thus warrants attention.
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Affiliation(s)
- Yiran Lu
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Mengjie Duan
- Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China; Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Yifan Li
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Shengyu Zhang
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaomin Hu
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Li Liu
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China.
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Hill MS, Gilbert JA. Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures. Microbiol Mol Biol Rev 2023; 87:e0012121. [PMID: 38047636 PMCID: PMC10732082 DOI: 10.1128/mmbr.00121-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.
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Affiliation(s)
- Megan S. Hill
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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Prado T, Magalhães MGP, Moreira DA, Brandão ML, Fumian TM, Ferreira FC, Chame M, Leomil L, Degrave WMS, Leite JPG, Miagostovich MP. Microbiome and virome on indoor surfaces of an Antarctic research ship. Mem Inst Oswaldo Cruz 2023; 118:e230084. [PMID: 37672426 PMCID: PMC10481937 DOI: 10.1590/0074-02760230084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods. OBJECTIVES AND METHODS We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity. FINDINGS Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae. MAIN CONCLUSIONS This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.
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Affiliation(s)
- Tatiana Prado
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Rio de Janeiro, RJ, Brasil
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Genômica Aplicada e BioInovações, Rio de Janeiro, RJ, Brasil
| | | | - Daniel Andrade Moreira
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Genômica Aplicada e BioInovações, Rio de Janeiro, RJ, Brasil
| | - Martha Lima Brandão
- Fundação Oswaldo Cruz-Fiocruz, Projeto FioAntar/VPPIS, Rio de Janeiro, RJ, Brasil
| | - Tulio Machado Fumian
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Fernando Cesar Ferreira
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
| | - Marcia Chame
- Fundação Oswaldo Cruz-Fiocruz, Plataforma Institucional para Biodiversidade e Saúde Animal, Rio de Janeiro, RJ, Brasil
| | - Luciana Leomil
- Serviço Nacional de Aprendizagem Industrial, Centro Tecnológico para Indústria Química e Têxtil, Biotecnologia, Parque Tecnológico da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | | | - José Paulo Gagliardi Leite
- Fundação Oswaldo Cruz-Fiocruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil
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Konecna E, Videnska P, Buresova L, Urik M, Smetanova S, Smatana S, Prokes R, Lanickova B, Budinska E, Klanova J, Borilova Linhartova P. Enrichment of human nasopharyngeal bacteriome with bacteria from dust after short-term exposure to indoor environment: a pilot study. BMC Microbiol 2023; 23:202. [PMID: 37525095 PMCID: PMC10391871 DOI: 10.1186/s12866-023-02951-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Indoor dust particles are an everyday source of human exposure to microorganisms and their inhalation may directly affect the microbiota of the respiratory tract. We aimed to characterize the changes in human nasopharyngeal bacteriome after short-term exposure to indoor (workplace) environments. METHODS In this pilot study, nasopharyngeal swabs were taken from 22 participants in the morning and after 8 h of their presence at the workplace. At the same time points, indoor dust samples were collected from the participants' households (16 from flats and 6 from houses) and workplaces (8 from a maternity hospital - NEO, 6 from a pediatric hospital - ENT, and 8 from a research center - RCX). 16S rRNA sequencing analysis was performed on these human and environmental matrices. RESULTS Staphylococcus and Corynebacterium were the most abundant genera in both indoor dust and nasopharyngeal samples. The analysis indicated lower bacterial diversity in indoor dust samples from flats compared to houses, NEO, ENT, and RCX (p < 0.05). Participants working in the NEO had the highest nasopharyngeal bacterial diversity of all groups (p < 0.05). After 8 h of exposure to the workplace environment, enrichment of the nasopharynx with several new bacterial genera present in the indoor dust was observed in 76% of study participants; however, no significant changes were observed at the level of the nasopharyngeal bacterial diversity (p > 0.05, Shannon index). These "enriching" bacterial genera overlapped between the hospital workplaces - NEO and ENT but differed from those in the research center - RCX. CONCLUSIONS The results suggest that although the composition of nasopharyngeal bacteriome is relatively stable during the day. Short-term exposure to the indoor environment can result in the enrichment of the nasopharynx with bacterial DNA from indoor dust; the bacterial composition, however, varies by the indoor workplace environment.
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Affiliation(s)
- Eva Konecna
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Petra Videnska
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Lucie Buresova
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Milan Urik
- Department of Pediatric Otorhinolaryngology, University Hospital Brno, Černopolní 9, 613 00 Brno, Czech Republic
- Department of Pediatric Otorhinolaryngology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, Czech Republic
| | - Sona Smetanova
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Stanislav Smatana
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Roman Prokes
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, Brno, Czech Republic
| | - Barbara Lanickova
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
- Department of Gynaecology and Obstetrics, University Hospital Brno, Obilni Trh 526/11, 602 00 Brno, Czech Republic
| | - Eva Budinska
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Jana Klanova
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
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Yanagi U, Kaihara N, Simazaki D, Bekki K, Homma Y, Iba C, Asai A, Hayashi M. Bacterial Flora on Mist Outlet Surfaces in 4D Theaters and Suspended Particle Concentration Characteristics during 4D Movie Screenings. Microorganisms 2023; 11:1856. [PMID: 37513027 PMCID: PMC10383669 DOI: 10.3390/microorganisms11071856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
In this study, we measured suspended particle concentrations during the screening of 4D movies (3 screens and 15 movies) and 2D movies (9 screens and 9 movies) in 3 movie theaters to obtain a more detailed understanding of the situation of suspended particle concentrations and adherent bacterial flora in 4D movie theaters, which have been introduced in increasing numbers in recent years. The adherent bacterial flora on the floor and mist outlet surfaces in the 4D movie theaters were collected and analyzed. During the movie showings, the concentrations of suspended particles in 4D movie theaters were significantly higher than those in 2D movie theaters (p < 0.001). A significant increase in suspended particle concentrations due to 4D movie effects was also observed. The results of the α-diversity and β-diversity analyses indicate that the bacterial flora on the surfaces of mist outlets in 4D movie theaters are similar. Moreover, there are many closely related species, and the bacterial flora are rich and contain rare bacterial species. Many of the bacterial genera that are dominant in 4D theaters are suited to aqueous environments, and bacteria in the water supply system may have an impact on the indoor environment.
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Affiliation(s)
- U Yanagi
- School of Architecture, Kogakuin University, Tokyo 163-8677, Japan
| | - Noriko Kaihara
- Department of Environmental Health, National Institute of Public Health, Wako 351-0197, Japan
| | - Dai Simazaki
- Department of Environmental Health, National Institute of Public Health, Wako 351-0197, Japan
| | - Kanae Bekki
- Department of Environmental Health, National Institute of Public Health, Wako 351-0197, Japan
| | - Yoshinori Homma
- Department of Environmental Health, National Institute of Public Health, Wako 351-0197, Japan
| | - Chiemi Iba
- Graduate School of Engineering, Kyoto University, Kyoto 615-8540, Japan
| | - Atsuto Asai
- Graduate School of Engineering, Kogakuin University, Tokyo 163-8677, Japan
| | - Motoya Hayashi
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
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11
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Wang Y, Thompson KN, Yan Y, Short MI, Zhang Y, Franzosa EA, Shen J, Hartmann EM, Huttenhower C. RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities. MICROBIOME 2023; 11:131. [PMID: 37312147 DOI: 10.1186/s40168-022-01449-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Characterization of microbial activity is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active ("viable") community members. Current sequence-based technologies can rarely differentiate microbial activity, due to their inability to distinguish live and dead sourced DNA. As a result, our understanding of microbial community structures and the potential mechanisms of transmission between humans and our surrounding environments remains incomplete. As a potential solution, 16S rRNA transcript-based amplicon sequencing (16S-RNA-seq) has been proposed as a reliable methodology to characterize the active components of a microbiome, but its efficacy has not been evaluated systematically. Here, we present our work to benchmark RNA-based amplicon sequencing for activity assessment in synthetic and environmentally sourced microbial communities. RESULTS In synthetic mixtures of living and heat-killed Escherichia coli and Streptococcus sanguinis, 16S-RNA-seq successfully reconstructed the active compositions of the communities. However, in the realistic environmental samples, no significant compositional differences were observed in RNA ("actively transcribed - active") vs. DNA ("whole" communities) spiked with E. coli controls, suggesting that this methodology is not appropriate for activity assessment in complex communities. The results were slightly different when validated in environmental samples of similar origins (i.e., from Boston subway systems), where samples were differentiated both by environment type as well as by library type, though compositional dissimilarities between DNA and RNA samples remained low (Bray-Curtis distance median: 0.34-0.49). To improve the interpretation of 16S-RNA-seq results, we compared our results with previous studies and found that 16S-RNA-seq suggests taxon-wise viability trends (i.e., specific taxa are universally more or less likely to be viable compared to others) in samples of similar origins. CONCLUSIONS This study provides a comprehensive evaluation of 16S-RNA-seq for viability assessment in synthetic and complex microbial communities. The results found that while 16S-RNA-seq was able to semi-quantify microbial viability in relatively simple communities, it only suggests a taxon-dependent "relative" viability in realistic communities. Video Abstract.
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Affiliation(s)
- Ya Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Kelsey N Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Meghan I Short
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
- Harvard T.H. Chan School of Public Health Microbiome Analysis Core, Building SPH1, 655 Huntington Avenue, Boston, MA, 02115, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, 665 Huntington Avenue, Boston, MA, 02115, USA.
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12
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Rolon ML, Tan X, Chung T, Gonzalez-Escalona N, Chen Y, Macarisin D, LaBorde LF, Kovac J. The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination. MICROBIOME 2023; 11:128. [PMID: 37271802 DOI: 10.1186/s40168-023-01544-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/06/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about microbiota that co-occurs with L. monocytogenes and its stability over seasons in tree fruit packing environments. In this 2-year longitudinal study, we aimed to characterize spatial and seasonal changes in microbiota composition and identify taxa indicative of L. monocytogenes contamination in wet processing areas of three tree fruit packing facilities (F1, F2, F3). METHODS A total of 189 samples were collected during two apple packing seasons from floors under the washing, drying, and waxing areas. The presence of L. monocytogenes was determined using a standard culturing method, and environmental microbiota was characterized using amplicon sequencing. PERMANOVA was used to compare microbiota composition among facilities over two seasons, and abundance-occupancy analysis was used to identify shared and temporal core microbiota. Differential abundance analysis and random forest were applied to detect taxa indicative of L. monocytogenes contamination. Lastly, three L. monocytogenes-positive samples were sequenced using shotgun metagenomics with Nanopore MinION, as a proof-of-concept for direct detection of L. monocytogenes' DNA in environmental samples. RESULTS The occurrence of L. monocytogenes significantly increased from 28% in year 1 to 46% in year 2 in F1, and from 41% in year 1 to 92% in year 2 in F3, while all samples collected from F2 were L. monocytogenes-positive in both years. Samples collected from three facilities had a significantly different microbiota composition in both years, but the composition of each facility changed over years. A subset of bacterial taxa including Pseudomonas, Stenotrophomonas, and Microbacterium, and fungal taxa, including Yarrowia, Kurtzmaniella, Cystobasidium, Paraphoma, and Cutaneotrichosporon, were identified as potential indicators of L. monocytogenes within the monitored environments. Lastly, the DNA of L. monocytogenes was detected through direct Nanopore sequencing of metagenomic DNA extracted from environmental samples. CONCLUSIONS This study demonstrated that a cross-sectional sampling strategy may not accurately reflect the representative microbiota of food processing facilities. Our findings also suggest that specific microorganisms are indicative of L. monocytogenes, warranting further investigation of their role in the survival and persistence of L. monocytogenes. Video Abstract.
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Affiliation(s)
- M Laura Rolon
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Xiaoqing Tan
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Taejung Chung
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Dumitru Macarisin
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Luke F LaBorde
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.
- Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA.
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13
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An XL, Xu JX, Xu MR, Zhao CX, Li H, Zhu YG, Su JQ. Dynamics of Microbial Community and Potential Microbial Pollutants in Shopping Malls. mSystems 2023; 8:e0057622. [PMID: 36602317 PMCID: PMC9948725 DOI: 10.1128/msystems.00576-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/17/2022] [Indexed: 01/06/2023] Open
Abstract
Shopping malls offer various niches for microbial populations, potentially serving as sources and reservoirs for the spread of microorganisms of public health concern. However, knowledge about the microbiome and the distribution of human pathogens in malls is largely unknown. Here, we examine the microbial community dynamics and genotypes of potential pathogens from floor and escalator surfaces in shopping malls and adjacent road dusts and greenbelt soils. The distribution pattern of microbial communities is driven primarily by habitats and seasons. A significant enrichment of human-associated microbiota in the indoor environment indicates that human interactions with surfaces might be another strong driver for mall microbiomes. Neutral community models suggest that the microbial community assembly is strongly driven by stochastic processes. Distinct performances of microbial taxonomic signatures for environmental classifications indicate the consistent differences of microbial communities of different seasons/habitats and the strong anthropogenic effect on homogenizing microbial communities of shopping malls. Indoor environments harbored higher concentrations of human pathogens than outdoor samples, also carrying a high proportion of antimicrobial resistance-associated multidrug efflux genes and virulence genes. These findings enhanced the understanding of the microbiome in the built environment and the interactions between humans and the built environment, providing a basis for tracking biothreats and communicable diseases and developing sophisticated early warning systems. IMPORTANCE Shopping malls are distinct microbial environments which can facilitate a constant transmission of microorganisms of public health concern between humans and the built environment or between human and human. Despite extensive investigation of the natural environmental microbiome, no comprehensive profile of microbial ecology has been reported in malls. Characterizing microbial distribution, potential pathogens, and antimicrobial resistance will enhance our understanding of how these microbial communities are formed, maintained, and transferred and help establish a baseline for biosurveillance of potential public health threats in malls.
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Affiliation(s)
- Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Jian-Xin Xu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Mei-Rong Xu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cai-Xia Zhao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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14
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Li H, Liu PQ, Luo QP, Ma JJ, Yang XR, Yan Y, Su JQ, Zhu YG. Spatiotemporal variations of microbial assembly, interaction, and potential risk in urban dust. ENVIRONMENT INTERNATIONAL 2022; 170:107577. [PMID: 36244231 DOI: 10.1016/j.envint.2022.107577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/08/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Community and composition of dust-borne microbes would affect human health and are regulated by microbial community assembly. The dust in kindergarten is always collected to evaluate the microbial exposure of children, yet the microbial assembly, their interactions, and potential pathogens in kindergarten dust remain unclear. Here, we aim to investigate the microbial community assembly and structures, and potential bacterial pathogens in outdoor dust of kindergartens, and reveal the factors influencing the assembly and composition of microbial community. A total of 118 urban dust samples were collected on the outdoor impervious surfaces of 59 kindergartens from different districts of Xiamen in January and June 2020. We extracted microbial genomic DNA in these dusts and characterized the microbial (i.e., bacteria and fungi) community compositions and diversities using target gene-based (16S rRNA genes for bacterial community and ITS 2 regions for fungal community) high-throughput sequencing. Potential bacterial pathogens were identified and the interactions between microbes were determined through a co-occurrence network analysis. Our results showed the predominance of Actinobacteria and α-Proteobacteria in bacterial communities and Capnodiales in fungal communities. Season altered microbial assembly, composition, and interactions, with both bacterial and fungal communities exhibiting a higher heterogeneity in summer than those in winter. Although stochastic processes predominated in bacterial and fungal community assembly, the season-depended environmental factors (e.g., temperature) and interactions between microbes play important roles in dust microbial community assembly. Potential bacterial pathogens were detected in all urban dust, with significantly higher relative abundance in summer than that in winter. These results indicated that season exerted more profound effects on microbial community composition, assembly, and interactions, and suggested the seasonal changes of potential risk of microbes in urban dust. Our findings provide new insights into microbial community, community assembly, and interactions between microbes in the urban dust, and indicate that taxa containing opportunistic pathogens occur commonly in urban dust.
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Affiliation(s)
- Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, Peoples R China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Pei-Qin Liu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Qiu-Ping Luo
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jin-Jin Ma
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, Peoples R China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yu Yan
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China.
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, Peoples R China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, Peoples R China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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15
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Watanabe K, Yanagi U, Shiraishi Y, Harada K, Ogino F, Asano K. Bacterial Communities in Various Parts of Air-Conditioning Units in 17 Japanese Houses. Microorganisms 2022; 10:microorganisms10112246. [PMID: 36422316 PMCID: PMC9697849 DOI: 10.3390/microorganisms10112246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
HVAC systems have a significant impact on the indoor environment, and microbial contamination in HVAC systems has a significant effect on the indoor air quality. In this study, to gain a better understanding of the microbial contamination inside ACs, we used NGS to analyze the 16S rRNA gene of bacteria adhering to AC filters, cooling coils, fans, and air outlet surfaces. The five phyla in terms of the highest relative abundance were Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria, and Bacteroidetes. The surface of an AC filter provides a history of indoor airborne bacterial contamination, and of the 10 bacterial genera we detected with the highest abundance (in the following order: Pseudomonas > Staphylococcus > Paracoccus > Corynebacterium > Acinetobacter > Streptococcus > Methylobacterium > Enhydrobacter > Sphingomonas > Actinotignum) on the filter surface, the top 6 genera were Gram-negative bacteria. Furthermore, the seventh-most abundant genus adhering to the filter surface (Methylobacterium) was the second-most abundant genus on the cooling coil and fan, and the ninth-most abundant genus on the air filter (Sphingomonas) was the third-most abundant genus on the cooling coil. Various factors impact the bacterial flora inside AC units, including the location of the house, AC unit usage, and occupant activity.
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Affiliation(s)
- Kensuke Watanabe
- Graduate School of Engineering, Kogakuin University, Tokyo 163 8677, Japan
| | - U Yanagi
- School of Architecture, Kogakuin University, Tokyo 163 8677, Japan
- Correspondence: ; Tel.: +81-(03)-3340-1468
| | - Yoshiki Shiraishi
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara 259 1193, Japan
| | - Kazuhiro Harada
- Research & Development, Duskin Co., Ltd., Osaka 564 0043, Japan
| | - Fumitoshi Ogino
- Research & Development, Duskin Co., Ltd., Osaka 564 0043, Japan
| | - Koichiro Asano
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara 259 1193, Japan
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16
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Hickman B, Kirjavainen PV, Täubel M, de Vos WM, Salonen A, Korpela K. Determinants of bacterial and fungal microbiota in Finnish home dust: Impact of environmental biodiversity, pets, and occupants. Front Microbiol 2022; 13:1011521. [PMID: 36419417 PMCID: PMC9676251 DOI: 10.3389/fmicb.2022.1011521] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2023] Open
Abstract
The indoors is where many humans spend most of their time, and are strongly exposed to indoor microbiota, which may have multifaceted effects on health. Therefore, a comprehensive understanding of the determinants of indoor microbiota is necessary. We collected dust samples from 295 homes of families with young children in the Helsinki region of Finland and analyzed the bacterial and fungal composition based on the 16S rRNA and ITS DNA sequences. Microbial profiles were combined with extensive survey data on family structure, daily life, and physical characteristics of the home, as well as additional external environmental information, such as land use, and vegetational biodiversity near the home. Using permutational multivariate analysis of variance we explained 18% of the variation of the relative abundance between samples within bacterial composition, and 17% of the fungal composition with the explanatory variables. The fungal community was dominated by the phyla Basidiomycota, and Ascomycota; the bacterial phyla Proteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria were dominant. The presence of dogs, multiple children, and firewood were significantly associated with both the fungal and bacterial composition. Additionally, fungal communities were associated with land use, biodiversity in the area, and the type of building, while bacterial communities were associated with the human inhabitants and cleaning practices. A distinction emerged between members of Ascomycota and Basidiomycota, Ascomycota being more abundant in homes with greater surrounding natural environment, and potential contact with the environment. The results suggest that the fungal composition is strongly dependent on the transport of outdoor environmental fungi into homes, while bacteria are largely derived from the inhabitants.
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Affiliation(s)
- Brandon Hickman
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pirkka V. Kirjavainen
- Environmental Health Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Martin Täubel
- Environmental Health Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Willem M. de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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17
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A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility. Microbiol Spectr 2022; 10:e0204522. [PMID: 35980043 PMCID: PMC9603805 DOI: 10.1128/spectrum.02045-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbial communities which persist in food processing facilities may have a detrimental impact on food safety and spoilage. In meat processing, Listeria monocytogenes is an organism of concern due to its ability to cause significant human illnesses and persist in refrigerated environments. The microbial ecology of Listeria spp. in small meat processing facilities has not been well characterized. Therefore, we collected samples from a newly constructed meat processing facility as an opportunity to investigate several research objectives: (i) to determine whether a stable, consistent microbiome develops in a small meat processing facility during the first 18 months of operation, (ii) to evaluate the environmental factors that drive microbial community formation, and (iii) to elucidate the relationship between microbial communities and the presence of Listeria species. We evaluated microbiomes using 16S rRNA gene sequencing and Listeria presence using quantitative PCR. We demonstrated that microbial communities differentiate by the functional room type, which is representative of several environmental differences such as temperature, sources of microbes, and activity. Temperature was an especially important factor; in rooms with low temperatures, communities were dominated by psychotrophs, especially Pseudomonas, while warmer rooms supported greater diversity. A stable core community formed in facility drains, indicating that mechanisms which cause persistence are present in the communities. The overall presence of Listeria in the facility was low but could be tied to specific organisms within a room, and the species of Listeria could be stratified by room function. IMPORTANCE This study provides critical knowledge to improve meat safety and quality from small meat processing facilities. Principally, it demonstrates the importance of facility design and room condition to the development of important microbial communities; temperature, sanitation regimen, and physical barriers all influence the ability of microorganisms to join the stable core community. It also demonstrates a relationship between the microbial community and Listeria presence in the facility, showing the importance of managing facility sanitation plans for not only pathogens, but also the general facility microbiome.
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18
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Li Z, Zheng N, An Q, Li X, Sun S, Zhang W, Ji Y, Wang S, Li P. Impact of environmental factors and bacterial interactions on dust mite allergens in different indoor dust. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157177. [PMID: 35803427 DOI: 10.1016/j.scitotenv.2022.157177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/11/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Indoor dust is the main carrier of indoor pollutants, especially dust mite allergens and bacteria, they can trigger asthma, rhinitis, eczema and other allergic diseases. However, the interactions between dust mite allergens and bacterial communities in different types of indoor dust are not clear. The study focused on particulate and flocculent fibrous dust, explored the concentrations of Der p 1 (Dermatophagoides pteronyssinus) and Der f 1 (D. farinae) in 46 households in Changchun and their environmental influences, characterized the bacterial communities by high-throughput sequencing, and the interactions between Der p 1, Der f 1 and bacterial communities were explored. The results showed that Der p 1 and Der f 1 tended to accumulate more in flocculent fibrous dust, and Der p 1 predominated in the indoor dust samples. The floor height, years of housing occupancy and the living areas all affected the concentrations of dust mite allergens. In bacterial community, Proteobacteria, Firmicutes and Actinobacteria were leading phyla in the two types of dust. Kocuria, Blastococcus and Massilia were dominating genera in particulate dust and Acinetobacter, Lactobacillus, Corynebacterium_1 were dominating genera in flocculent fibrous dust. The overall diversity and species richness of bacteria in particulate dust were significantly higher than those in flocculent dust (p < 0.001). The living area was an important environmental factor affecting the bacterial community in flocculent fibrous dust (p < 0.01). The interaction between the relative abundance of Proteobacteria, Firmicutes and Actinobacteria and dust mite allergen concentrations significantly differed between the two dust types, indicating that bacteria could be used both as food and to establish symbiotic relationships with household dust mites (HDMs) hosts and provide nutrition.
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Affiliation(s)
- Zimeng Li
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Na Zheng
- College of New Energy and Environment, Jilin University, Changchun, 130012, China; Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130012, China.
| | - Qirui An
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Xiaoqian Li
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Siyu Sun
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Wenhui Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Yining Ji
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Sujing Wang
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
| | - Pengyang Li
- College of New Energy and Environment, Jilin University, Changchun, 130012, China
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Fu X, Ou Z, Sun Y. Indoor microbiome and allergic diseases: From theoretical advances to prevention strategies. ECO-ENVIRONMENT & HEALTH (ONLINE) 2022; 1:133-146. [PMID: 38075599 PMCID: PMC10702906 DOI: 10.1016/j.eehl.2022.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 12/20/2023]
Abstract
The prevalence of allergic diseases, such as asthma, rhinitis, eczema, and sick building syndrome (SBS), has increased drastically in the past few decades. Current medications can only relieve the symptoms but not cure these diseases whose development is suggested to be greatly impacted by the indoor microbiome. However, no study comprehensively summarizes the progress and general rules in the field, impeding subsequent translational application. To close knowledge gaps between theoretical research and practical application, we conducted a comprehensive literature review to summarize the epidemiological, environmental, and molecular evidence of indoor microbiome studies. Epidemiological evidence shows that the potential protective indoor microorganisms for asthma are mainly from the phyla Actinobacteria and Proteobacteria, and the risk microorganisms are mainly from Bacilli, Clostridia, and Bacteroidia. Due to extremely high microbial diversity and geographic variation, different health-associated species/genera are detected in different regions. Compared with indoor microbial composition, indoor metabolites show more consistent associations with health, including microbial volatile organic compounds (MVOCs), lipopolysaccharides (LPS), indole derivatives, and flavonoids. Therefore, indoor metabolites could be a better indicator than indoor microbial taxa for environmental assessments and health outcome prediction. The interaction between the indoor microbiome and environmental characteristics (surrounding greenness, relative humidity, building confinement, and CO2 concentration) and immunology effects of indoor microorganisms (inflammatory cytokines and pattern recognition receptors) are briefly reviewed to provide new insights for disease prevention and treatment. Widely used tools in indoor microbiome studies are introduced to facilitate standard practice and the precise identification of health-related targets.
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Affiliation(s)
- Xi Fu
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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20
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Peimbert M, Alcaraz LD. Where environmental microbiome meets its host: subway and passenger microbiome relationships. Mol Ecol 2022; 32:2602-2618. [PMID: 35318755 DOI: 10.1111/mec.16440] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
Subways are urban transport systems with high capacity. Every day around the world, there are more than 150 million subway passengers. Since 2013, thousands of microbiome samples from various subways worldwide have been sequenced. Skin bacteria and environmental organisms dominate the subway microbiomes. The literature has revealed common bacterial groups in subway systems; even so, it is possible to identify cities by their microbiome. Low-frequency bacteria are responsible for specific bacterial fingerprints of each subway system. Furthermore, daily subway commuters leave their microbial clouds and interact with other passengers. Microbial exchange is quite fast; the hand microbiome changes within minutes, and after cleaning the handrails, the bacteria are re-established within minutes. To investigate new taxa and metabolic pathways of subway microbial communities, several high-quality metagenomic-assembled genomes (MAG) have been described. Subways are harsh environments unfavorable for microorganism growth. However, recent studies have observed a wide diversity of viable and metabolically active bacteria. Understanding which bacteria are living, dormant, or dead allows us to propose realistic ecological interactions. Questions regarding the relationship between humans and the subway microbiome, particularly the microbiome effects on personal and public health, remain unanswered. This review summarizes our knowledge of subway microbiomes and their relationship with passenger microbiomes.
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Affiliation(s)
- Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana. Ciudad de México, México
| | - Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
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21
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Ability of Essential Oil Vapours to Reduce Numbers of Culturable Aerosolised Coronavirus, Bacteria and Fungi. Antibiotics (Basel) 2022; 11:antibiotics11030393. [PMID: 35326856 PMCID: PMC8944824 DOI: 10.3390/antibiotics11030393] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Transmission of pathogens present in the indoor air can occur through aerosols. This study evaluated the efficacy of an evaporated mix of essential oils to reduce the numbers of culturable aerosolized coronavirus, bacterium and fungus. The essential oil-containing gel was allowed to vaporize inside a glass chamber for 10 or 20 min. Aerosols of a surrogate of SARS-CoV-2, murine hepatitis coronavirus MHV-1, Escherichia coli or Aspergillus flavus spores were produced using a collision nebuliser and passed through the essential oil vapours, then collected on a six-stage Andersen sampler. The six-stages of the impact sampler capture aerosols in sizes ranging from 7 to 0.65 µm. The number of culturable microbes present in the aerosols collected in the different stages were enumerated and compared to the number of culturable microbes in control microbial aerosols that were not exposed to the evaporated essential oils. After 10 and 20 min evaporation, the essential oils reduced the numbers of culturable aerosolized coronavirus by 48% (log10 reduction = 0.3; p = 0.002 vs. control) and 53% (log10 reduction = 0.3; p = 0.001 vs. control), respectively. The essential oils vaporised for 10 min, reduced the number of viable E. coli by 51% (log10 reduction = 0.3; p = 0.032 vs. control). The Aspergillus flavus spores were mostly observed in the larger aerosols (7.00 µm to 2.10 µm) and the essential oils vaporised for 10 min reduced the number of viable spores by 72% (log10 reduction = 0.6; p = 0.008 vs. control). The vapours produced by a gel containing naturally occurring essential oils were able to significantly reduce the viable numbers of aerosolized coronavirus, bacteria and fungal spores. The antimicrobial gel containing the essential oils may be able to reduce aerosol transmission of microbes when used in domestic and workplace settings.
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22
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Adi Wicaksono W, Reisenhofer-Graber T, Erschen S, Kusstatscher P, Berg C, Krause R, Cernava T, Berg G. Phyllosphere-associated microbiota in built environment: Do they have the potential to antagonize human pathogens? J Adv Res 2022; 43:109-121. [PMID: 36585101 PMCID: PMC9811327 DOI: 10.1016/j.jare.2022.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION The plant microbiota is known to protect its host against invasion by plant pathogens. Recent studies have indicated that the microbiota of indoor plants is transmitted to the local built environment where it might fulfill yet unexplored functions. A better understanding of the interplay of such microbial communities with human pathogens might provide novel cues related to natural inhibition of them. OBJECTIVE We studied the plant microbiota of two model indoor plants, Musa acuminata and Chlorophytum comosum, and their effect on human pathogens. The main objective was to identify mechanisms by which the microbiota of indoor plants inhibits human-pathogenic bacteria. METHODS Microbial communities and functioning were investigated using a comprehensive set of experiments and methods combining amplicon and shotgun metagenomic analyses with results from interaction assays. RESULTS A diverse microbial community was found to be present on Musa and Chlorophytum grown in different indoor environments; the datasets comprised 1066 bacterial, 1261 fungal, and 358 archaeal ASVs. Bacterial communities were specific for each plant species, whereas fungal and archaeal communities were primarily shaped by the built environment. Sphingomonas and Bacillus were found to be prevalent components of a ubiquitous core microbiome in the two model plants; they are well-known for antagonistic activity towards plant pathogens. Interaction assays indicated that they can also antagonize opportunistic human pathogens. Moreover, the native plant microbiomes harbored a broad spectrum of biosynthetic gene clusters, and in parallel, a variety of antimicrobial resistance genes. By conducting comparative metagenomic analyses between plants and abiotic surfaces, we found that the phyllosphere microbiota harbors features that are clearly distinguishable from the surrounding abiotic surfaces. CONCLUSIONS Naturally occurring phyllosphere bacteria can potentially act as a protective shield against opportunistic human pathogens. This knowledge and the underlying mechanisms can provide an important basis to establish a healthy microbiome in built environments.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | | | - Sabine Erschen
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria.
| | - Robert Krause
- Department of Internal Medicine, Medical University of Graz, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria; Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam, Potsdam, Germany; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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23
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Zhou Y, Leung MHY, Tong X, Lee JYY, Lee PKH. City-Scale Meta-Analysis of Indoor Airborne Microbiota Reveals that Taxonomic and Functional Compositions Vary with Building Types. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:15051-15062. [PMID: 34738808 DOI: 10.1021/acs.est.1c03941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Currently, there is a lack of understanding on the variations of the indoor airborne microbiotas of different building types within a city, and how operational taxonomic unit (OTU)- and amplicon sequence variant (ASV)-based analyses of the 16S rRNA gene sequences affect interpretation of the indoor airborne microbiota results. Therefore, in this study, the indoor airborne bacterial microbiotas between commercial buildings, residences, and subways within the same city were compared using both OTU- and ASV-based analytic methods. Our findings suggested that indoor airborne bacterial microbiota compositions were significantly different between building types regardless of the bioinformatics method used. The processes of ecological drift and random dispersal consistently played significant roles in the assembly of the indoor microbiota across building types. Abundant taxa tended to be more centralized in the correlation network of each building type, highlighting their importance. Taxonomic changes between the microbiotas of different building types were also linked to changes in their inferred metabolic function capabilities. Overall, the results imply that customized strategies are necessary to manage indoor airborne bacterial microbiotas for each building type or even within each specific building.
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Affiliation(s)
- You Zhou
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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24
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Tong X, Leung MHY, Shen Z, Lee JYY, Mason CE, Lee PKH. Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city. MICROBIOME 2021; 9:213. [PMID: 34724986 PMCID: PMC8562002 DOI: 10.1186/s40168-021-01166-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/20/2021] [Indexed: 05/25/2023]
Abstract
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 physical attributes and environmental 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 correlated with 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. Video Abstract.
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Affiliation(s)
- Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Zhiyong Shen
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
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25
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Haines SR, Hall EC, Marciniak K, Misztal PK, Goldstein AH, Adams RI, Dannemiller KC. Microbial growth and volatile organic compound (VOC) emissions from carpet and drywall under elevated relative humidity conditions. MICROBIOME 2021; 9:209. [PMID: 34666813 PMCID: PMC8524935 DOI: 10.1186/s40168-021-01158-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Microbes can grow in indoor environments if moisture is available, and we need an improved understanding of how this growth contributes to emissions of microbial volatile organic compounds (mVOCs). The goal of this study was to measure how moisture levels, building material type, collection site, and microbial species composition impact microbial growth and emissions of mVOCs. We subjected two common building materials, drywall, and carpet, to treatments with varying moisture availability and measured microbial communities and mVOC emissions. RESULTS Fungal growth occurred in samples at >75% equilibrium relative humidity (ERH) for carpet with dust and >85% ERH for inoculated painted drywall. In addition to incubated relative humidity level, dust sample collection site (adonis p=0.001) and material type (drywall, carpet, adonis p=0.001) drove fungal and bacterial species composition. Increased relative humidity was associated with decreased microbial species diversity in samples of carpet with dust (adonis p= 0.005). Abundant volatile organic compounds (VOCs) that accounted for >1% emissions were likely released from building materials and the dust itself. However, certain mVOCs were associated with microbial growth from carpet with dust such as C10H16H+ (monoterpenes) and C2H6SH+ (dimethyl sulfide and ethanethiol). CO2 production from samples of carpet with dust at 95% ERH averaged 5.92 mg hr-1 kg-1, while the average for carpet without dust at 95% ERH was 2.55 mg hr-1 kg-1. CONCLUSION Microbial growth and mVOC emissions occur at lower relative humidity in carpet and floor dust compared to drywall, which has important implications for human exposure. Even under elevated relative humidity conditions, the VOC emissions profile is dominated by non-microbial VOCs, although potential mVOCs may dominate odor production. Video Abstract.
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Affiliation(s)
- Sarah R. Haines
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, Ontario M5S 1A4 Canada
| | - Emma C. Hall
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712 USA
| | | | - Pawel K. Misztal
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712 USA
| | - Allen H. Goldstein
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720 USA
| | - Rachel I. Adams
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Karen C. Dannemiller
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, Ohio State University, Columbus, OH 43210 USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH 43210 USA
- Sustainability Institute, Ohio State University, Columbus, OH 43210 USA
- Department of Civil, Environmental & Geodetic Engineering, Environmental Health Sciences, Ohio State University, 470 Hitchcock Hall, 2070 Neil Ave, Columbus, OH 43210 USA
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26
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Andersson (AMA, Salo J, Mikkola R, Marik T, Kredics L, Kurnitski J, Salonen H. Melinacidin-Producing Acrostalagmus luteoalbus, a Major Constituent of Mixed Mycobiota Contaminating Insulation Material in an Outdoor Wall. Pathogens 2021; 10:pathogens10070843. [PMID: 34357993 PMCID: PMC8308789 DOI: 10.3390/pathogens10070843] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Occupants may complain about indoor air quality in closed spaces where the officially approved standard methods for indoor air quality risk assessment fail to reveal the cause of the problem. This study describes a rare genus not previously detected in Finnish buildings, Acrostalagmus, and its species A. luteoalbus as the major constituents of the mixed microbiota in the wet cork liner from an outdoor wall. Representatives of the genus were also present in the settled dust in offices where occupants suffered from symptoms related to the indoor air. One strain, POB8, was identified as A. luteoalbus by ITS sequencing. The strain produced the immunosuppressive and cytotoxic melinacidins II, III, and IV, as evidenced by mass spectrometry analysis. In addition, the classical toxigenic species indicating water damage, mycoparasitic Trichoderma, Aspergillus section Versicolores, Aspergillus section Circumdati, Aspergillus section Nigri, and Chaetomium spp., were detected in the wet outdoor wall and settled dust from the problematic rooms. The offices exhibited no visible signs of microbial growth, and the airborne load of microbial conidia was too low to explain the reported symptoms. In conclusion, we suggest the possible migration of microbial bioactive metabolites from the wet outdoor wall into indoor spaces as a plausible explanation for the reported complaints.
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Affiliation(s)
- (Aino) Maria A. Andersson
- Department of Civil Engineering, Aalto University, P.O. Box 12100, FI-00076 Aalto, Finland; (J.S.); (R.M.); (J.K.); (H.S.)
- Correspondence: ; Tel.: +358-405508934
| | - Johanna Salo
- Department of Civil Engineering, Aalto University, P.O. Box 12100, FI-00076 Aalto, Finland; (J.S.); (R.M.); (J.K.); (H.S.)
| | - Raimo Mikkola
- Department of Civil Engineering, Aalto University, P.O. Box 12100, FI-00076 Aalto, Finland; (J.S.); (R.M.); (J.K.); (H.S.)
| | - Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (L.K.)
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (T.M.); (L.K.)
| | - Jarek Kurnitski
- Department of Civil Engineering, Aalto University, P.O. Box 12100, FI-00076 Aalto, Finland; (J.S.); (R.M.); (J.K.); (H.S.)
- Department of Civil Engineering and Architecture, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Heidi Salonen
- Department of Civil Engineering, Aalto University, P.O. Box 12100, FI-00076 Aalto, Finland; (J.S.); (R.M.); (J.K.); (H.S.)
- International Laboratory for Air Quality and Health, Queensland University of Technology, 2 George Street, Brisbane, QLD 4001, Australia
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27
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Chatoutsidou SE, Saridaki A, Raisi L, Katsivela E, Tsiamis G, Zografakis M, Lazaridis M. Airborne particles and microorganisms in a dental clinic: Variability of indoor concentrations, impact of dental procedures, and personal exposure during everyday practice. INDOOR AIR 2021; 31:1164-1177. [PMID: 34080742 DOI: 10.1111/ina.12820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
This study presents for the first time comprehensive measurements of the particle number size distribution (10 nm to 10 μm) together with next-generation sequencing analysis of airborne bacteria inside a dental clinic. A substantial enrichment of the indoor environment with new particles in all size classes was identified by both activities to background and indoor/outdoor (I/O) ratios. Grinding and drilling were the principal dental activities to produce new particles in the air, closely followed by polishing. Illumina MiSeq sequencing of 16S rRNA of bioaerosol collected indoors revealed the presence of 86 bacterial genera, 26 of them previously characterized as potential human pathogens. Bacterial species richness and concentration determined both by qPCR, and culture-dependent analysis were significantly higher in the treatment room. Bacterial load of the treatment room impacted in the nearby waiting room where no dental procedures took place. I/O ratio of bacterial concentration in the treatment room followed the fluctuation of I/O ratio of airborne particles in the biology-relevant size classes of 1-2.5, 2.5-5, and 5-10 μm. Exposure analysis revealed increased inhaled number of particles and microorganisms during dental procedures. These findings provide a detailed insight on airborne particles of both biotic and abiotic origin in a dental clinic.
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Affiliation(s)
| | - Aggeliki Saridaki
- School of Environmental Engineering, Technical University of Crete, Chania, Greece
| | - Louiza Raisi
- School of Environmental Engineering, Technical University of Crete, Chania, Greece
- Department of Electronic Engineering, Hellenic Mediterranean University, Chania, Greece
| | - Eleftheria Katsivela
- Department of Electronic Engineering, Hellenic Mediterranean University, Chania, Greece
| | - George Tsiamis
- Department of Environmental Engineering, University of Patras, Agrinio, Greece
| | | | - Mihalis Lazaridis
- School of Environmental Engineering, Technical University of Crete, Chania, Greece
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28
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Leung MHY, Tong X, Bøifot KO, Bezdan D, Butler DJ, Danko DC, Gohli J, Green DC, Hernandez MT, Kelly FJ, Levy S, Mason-Buck G, Nieto-Caballero M, Syndercombe-Court D, Udekwu K, Young BG, Mason CE, Dybwad M, Lee PKH. Characterization of the public transit air microbiome and resistome reveals geographical specificity. MICROBIOME 2021; 9:112. [PMID: 34039416 PMCID: PMC8157753 DOI: 10.1186/s40168-021-01044-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/09/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized. RESULTS City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes. CONCLUSIONS Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.
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Affiliation(s)
- M H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - X Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - K O Bøifot
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - D Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - D J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - D C Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - J Gohli
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - D C Green
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - M T Hernandez
- Environmental Engineering Program, College of Engineering and Applied Science, University of Colorado, Boulder, CO, USA
| | - F J Kelly
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - S Levy
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - G Mason-Buck
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - M Nieto-Caballero
- Environmental Engineering Program, College of Engineering and Applied Science, University of Colorado, Boulder, CO, USA
| | - D Syndercombe-Court
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK
| | - K Udekwu
- Department of Aquatic Sciences & Assessment, Swedish University of Agriculture, Uppsala, Sweden
| | - B G Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - C E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - M Dybwad
- Comprehensive Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway.
- Department of Analytical, Environmental & Forensic Sciences, King's College London, London, UK.
| | - P K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
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29
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Skowron K, Bauza-Kaszewska J, Kraszewska Z, Wiktorczyk-Kapischke N, Grudlewska-Buda K, Kwiecińska-Piróg J, Wałecka-Zacharska E, Radtke L, Gospodarek-Komkowska E. Human Skin Microbiome: Impact of Intrinsic and Extrinsic Factors on Skin Microbiota. Microorganisms 2021; 9:543. [PMID: 33808031 PMCID: PMC7998121 DOI: 10.3390/microorganisms9030543] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
The skin is the largest organ of the human body and it protects the body from the external environment. It has become the topic of interest of researchers from various scientific fields. Microorganisms ensure the proper functioning of the skin. Of great importance, are the mutual relations between such microorganisms and their responses to environmental impacts, as dysbiosis may contribute to serious skin diseases. Molecular methods, used for microorganism identification, allow us to gain a better understanding of the skin microbiome. The presented article contains the latest reports on the skin microbiota in health and disease. The review discusses the relationship between a properly functioning microbiome and the body's immune system, as well as the impact of internal and external factors on the human skin microbiome.
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Affiliation(s)
- Krzysztof Skowron
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Justyna Bauza-Kaszewska
- Department of Microbiology and Food Technology, UTP University of Science and Technology, 85-029 Bydgoszcz, Poland;
| | - Zuzanna Kraszewska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Joanna Kwiecińska-Piróg
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
| | - Ewa Wałecka-Zacharska
- Department of Food Hygiene and Consumer Health, Wrocław University of Environmental and Life Sciences, 31 C.K. Norwida St., 50-375 Wrocław, Poland;
| | - Laura Radtke
- Faculty of Civil and Environmental Engineering and Architecture, UTP University of Science and Technology in Bydgoszcz, Al. prof. S. Kaliskiego 7, 85-796 Bydgoszcz, Poland;
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Nicolaus Copernicus University in Toruń, L. Rydygier Collegium Medicum in Bydgoszcz, 85-094 Bydgoszcz, Poland; (Z.K.); (N.W.-K.); (K.G.-B.); (J.K.-P.); (E.G.-K.)
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30
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Fu X, Li Y, Meng Y, Yuan Q, Zhang Z, Wen H, Deng Y, Norbäck D, Hu Q, Zhang X, Sun Y. Derived habitats of indoor microbes are associated with asthma symptoms in Chinese university dormitories. ENVIRONMENTAL RESEARCH 2021; 194:110501. [PMID: 33221308 DOI: 10.1016/j.envres.2020.110501] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
Increasing evidence from the home environment indicates that indoor microbiome exposure is associated with asthma development. However, indoor microbiome composition can be highly diverse and dynamic, and thus current studies fail to produce consistent results. Chinese university dormitories are special high-density dwellings with similar building and occupants characteristics, which facilitate to disentangle the complex interactions between microbes, environmental characteristics and asthma. Settled air dust and floor dust was collected from 87 dormitory rooms in Shanxi University. Bacterial communities were characterized by 16 S rRNA amplicon sequencing. Students (n = 357) were surveyed for asthma symptoms and measured for fractional exhaled nitric oxide (FeNO). Asthma was not associated with the overall bacterial richness but associated with specific phylogenetic classes. Taxa richness and abundance in Clostridia, including Ruminococcus, Blautia, Clostridium and Subdoligranulum, were positively associated with asthma (p < 0.05), and these taxa were mainly derived from the human gut. Taxa richness in Alphaproteobacteria and Actinobacteria were marginally protectively associated with asthma, and these taxa were mainly derived from the outdoor environment. Bacterial richness and abundance were not associated with FeNO levels. Building age was associated with overall bacterial community variation in air and floor dust (p < 0.05), but not associated with the asthma-related microorganisms. Our data shows that taxa from different phylogenetic classes and derived habitats have different health effects, indicating the importance of incorporating phylogenetic and ecological concepts in revealing patterns in the microbiome asthma association analysis.
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Affiliation(s)
- Xi Fu
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Yanling Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yi Meng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Qianqian Yuan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zefei Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China
| | - Huarong Wen
- Baling Health Center, Dangyang, Hubei, 444100, PR China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Dan Norbäck
- Occupational and Environmental Medicine, Dept. of Medical Science, University Hospital, Uppsala University, 75237, Uppsala, Sweden
| | - Qiansheng Hu
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, PR China.
| | - Xin Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China.
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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31
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Sindi AS, Geddes DT, Wlodek ME, Muhlhausler BS, Payne MS, Stinson LF. Can we modulate the breastfed infant gut microbiota through maternal diet? FEMS Microbiol Rev 2021; 45:6133472. [PMID: 33571360 DOI: 10.1093/femsre/fuab011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Initial colonisation of the infant gut is robustly influenced by regular ingestion of human milk, a substance that contains microbes, microbial metabolites, immune proteins, and oligosaccharides. Numerous factors have been identified as potential determinants of the human milk and infant gut microbiota, including maternal diet; however, there is limited data on the influence of maternal diet during lactation on either of these. Here, we review the processes thought to contribute to human milk and infant gut bacterial colonisation and provide a basis for considering the role of maternal dietary patterns during lactation in shaping infant gut microbial composition and function. Although only one observational study has directly investigated the influence of maternal diet during lactation on the infant gut microbiome, data from animal studies suggests that modulation of the maternal gut microbiota, via diet or probiotics, may influence the mammary or milk microbiota. Additionally, evidence from human studies suggests that the maternal diet during pregnancy may affect the gut microbiota of the breastfed infant. Together, there is a plausible hypothesis that maternal diet during lactation may influence the infant gut microbiota. If substantiated in further studies, this may present a potential window of opportunity for modulating the infant gut microbiome in early life.
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Affiliation(s)
- Azhar S Sindi
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Western Australia, Australia.,College of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Mary E Wlodek
- Department of Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Beverly S Muhlhausler
- CSIRO, Adelaide, South Australia, Australia.,School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew S Payne
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Western Australia, Australia
| | - Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
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32
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Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, Shen J, Vlamakis H, Hartmann EM, Huttenhower C. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. MICROBIOME 2021; 9:17. [PMID: 33478576 PMCID: PMC7819323 DOI: 10.1186/s40168-020-00961-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/06/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g., qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting "viable" communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark "PMA-seq" (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. RESULTS PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil, and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types, and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the "PMA-responsive" microbes, we compared our results with previous PMA-based studies and found that PMA responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. CONCLUSIONS This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities but provided only qualitative assessments in realistically complex community samples. Video abstract.
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Affiliation(s)
- Ya Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Kelsey N. Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Sena Bae
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
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33
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Grehn C, Eschenhagen P, Temming S, Düesberg U, Neumann K, Schwarz C. Frequent Pet Contact as Risk Factor for Allergic Bronchopulmonary Aspergillosis in Cystic Fibrosis. Front Cell Infect Microbiol 2021; 10:601821. [PMID: 33585274 PMCID: PMC7873990 DOI: 10.3389/fcimb.2020.601821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/24/2020] [Indexed: 01/13/2023] Open
Abstract
Aspergillus fumigatus (Af) frequently colonizes the respiratory tract of patients with cystic fibrosis (CF). Af is associated with loss of pulmonary function and allergic bronchopulmonary aspergillosis (ABPA), a hypersensitivity fungal lung disease. Environmental factors have impact on CF patients’ lung function variation. The aim of this nationwide questionnaire survey was to investigate the amount of CF patients with frequent pet contact including pet species and to examine the potential impact of frequent pet contact on the occurrence of Af colonization and ABPA diagnosis in these patients. The survey was carried out in 31 German CF centers in 2018. A total of 1232 who completed the surveys were included, and statistical analysis was performed by chi-squared test. Within the study cohort 49.8% of subjects (n = 614; CF patients < 18years: 49.4%, n = 234; ≥ 18years: 50.1%, n = 380) reported frequent contact to pets, of which 60.7% reported frequent contact to dogs, 42.3% to cats and other animals. Of those with frequent pet contact, 71.8% (n = 441) had contact to one pet or more pets from the same family. Af colonization was not significantly associated with frequent pet contact. ABPA diagnosis was documented in 16.7% (n = 206) of all included CF patients and was significantly associated with frequent pet contact (18.9%, n = 116, p = 0.042), confirming previous single center examinations. Particularly, patients with frequent contact to dogs showed an increased ABPA prevalence of 21.3%. Frequent pet contact might be a risk factor for ABPA. CF patients who are sensitized to Af should be informed about the increased risk to develop an ABPA by frequent pet contact. Patients with recurrent onset of ABPA should be evaluated in terms of frequent pet contact.
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Affiliation(s)
- Claudia Grehn
- Department of Pediatric Pneumology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Patience Eschenhagen
- Department of Pediatric Pneumology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Svenja Temming
- Department of Pediatric Pneumology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Konrad Neumann
- Institute for Biometry and Clinical Epidemiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Carsten Schwarz
- Department of Pediatric Pneumology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
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34
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Sibanda T, Selvarajan R, Ogola HJ, Obieze CC, Tekere M. Distribution and comparison of bacterial communities in HVAC systems of two university buildings: Implications for indoor air quality and public health. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:47. [PMID: 33415530 PMCID: PMC7790485 DOI: 10.1007/s10661-020-08823-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/27/2020] [Indexed: 06/12/2023]
Abstract
The installation of HVAC systems in building is meant to enhance indoor air quality as well as increase comfort to occupants. However, HVAC systems have also become a vehicle of contamination of indoor air with potentially pathogenic microorganisms. DNA was extracted from ten HVAC filter dust samples collected from two buildings and subjected to high throughput sequencing analysis to determine the bacterial community structure. Further, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) software was used to predict the potential functional capabilities of the bacterial communities. Sequencing analysis led to the identification of five major bacterial phyla, including Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes and Bacteroidetes. At genus level, Mycobacterium, Bacillus, Cupriavidus, Hyphomicrobium and Mesorhizobium were the most dominant. With the exception of the later two bacterial genera, the first three are potential pathogens whose presence in HVAC systems poses a significant public health risk, especially among immunocompromised individuals. Nine pathways associated with antibiotics resistance and bacterial pathogenicity were identified, including polymyxin resistance and peptidoglycan biosynthesis pathways. Further, investigation of the relationship between the detected bacterial meta-communities and predicted potential virulence factors (antibiotic resistance and pathogenic genes) led to the detection of 350 positive associations among 43 core bacteria, 2 pathogenic genes (sitA and uidA) and 14 resistance genes. Overall, the heterogeneous nature of microorganisms found in HVAC systems observed in this study shows that HVAC systems are the origin of airborne infections in indoor environments, and must be periodically cleaned and disinfected to avoid the build-up of pathogens, and the subsequent exposure of human occupants of these pathogens.
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Affiliation(s)
- Timothy Sibanda
- Department of Biological Sciences, University of Namibia, Mandume Ndemufayo Ave, Pionierspark, Windhoek, Namibia.
| | - Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Johannesburg, South Africa
| | - Henry Jo Ogola
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Johannesburg, South Africa
- Centre for Research, Innovation and Technology, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | | | - Memory Tekere
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Johannesburg, South Africa
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35
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Zhou Y, Leung MHY, Tong X, Lai Y, Tong JCK, Ridley IA, Lee PKH. Profiling Airborne Microbiota in Mechanically Ventilated Buildings Across Seasons in Hong Kong Reveals Higher Metabolic Activity in Low-Abundance Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:249-259. [PMID: 33346641 DOI: 10.1021/acs.est.0c06201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Metabolically active bacteria within built environments are poorly understood. This study aims to investigate the active airborne bacterial microbiota and compare the total and active microbiota in eight mechanically ventilated buildings over four consecutive seasons using the 16S rRNA gene (rDNA) and the 16S rRNA (rRNA), respectively. The relative abundances of the taxa of presumptive occupants and environmental origins were significantly different between the active and total microbiota. The Sloan neutral model suggested that ecological drift and random dispersal played a smaller role in the assembly of the active microbiota than the total microbiota. The seasonal nature of the active microbiota was consistent with that of the total microbiota in both indoor and outdoor environments, while only the indoor environment was significantly affected by geography. The relative abundances of the active and total taxa were positively correlated, suggesting that the high-abundance members were also the greatest contributors to the community-level metabolic activity. Based on the rRNA/rDNA ratio, the low-abundance members consistently had a higher taxon-level metabolic activity than the high-abundance members over seasons, suggesting that the low-abundance members may have the ability to survive and thrive in the indoor environment and their impact on the health of occupants cannot be overlooked.
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Affiliation(s)
- You Zhou
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Yonghang Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Jimmy C K Tong
- Building Sustainability Group, Arup, Hong Kong SAR, China
| | - Ian A Ridley
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
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36
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Grydaki N, Colbeck I, Mendes L, Eleftheriadis K, Whitby C. Bioaerosols in the Athens Metro: Metagenetic insights into the PM 10 microbiome in a naturally ventilated subway station. ENVIRONMENT INTERNATIONAL 2021; 146:106186. [PMID: 33126062 DOI: 10.1016/j.envint.2020.106186] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/30/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
To date, few studies have examined the aerosol microbial content in Metro transportation systems. Here we characterised the aerosol microbial abundance, diversity and composition in the Athens underground railway system. PM10 filter samples were collected from the naturally ventilated Athens Metro Line 3 station "Nomismatokopio". Quantitative PCR of the 16S rRNA gene and high throughput amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region was performed on DNA extracted from PM10 samples. Results showed that, despite the bacterial abundance (mean = 2.82 × 105 16S rRNA genes/m3 of air) being, on average, higher during day-time and weekdays, compared to night-time and weekends, respectively, the differences were not statistically significant. The average PM10 mass concentration on the platform was 107 μg/m3. However, there was no significant correlation between 16S rRNA gene abundance and overall PM10 levels. The Athens Metro air microbiome was mostly dominated by bacterial and fungal taxa of environmental origin (e.g. Paracoccus, Sphingomonas, Cladosporium, Mycosphaerella, Antrodia) with a lower contribution of human commensal bacteria (e.g. Corynebacterium, Staphylococcus). This study highlights the importance of both outdoor air and commuters as sources in shaping aerosol microbial communities. To our knowledge, this is the first study to characterise the mycobiome diversity in the air of a Metro environment based on amplicon sequencing of the ITS region. In conclusion, this study presents the first microbial characterisation of PM10 in the Athens Metro, contributing to the growing body of microbiome exploration within urban transit networks. Moreover, this study shows the vulnerability of public transport to airborne disease transmission.
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Affiliation(s)
- N Grydaki
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ Essex, UK
| | - I Colbeck
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ Essex, UK
| | - L Mendes
- Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety - Environmental Radioactivity Laboratory, N.C.S.R. "Demokritos", Aghia Paraskevi, 15310 Athens, Greece
| | - K Eleftheriadis
- Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety - Environmental Radioactivity Laboratory, N.C.S.R. "Demokritos", Aghia Paraskevi, 15310 Athens, Greece
| | - C Whitby
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ Essex, UK.
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37
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Grehn C, Eschenhagen P, Temming S, Düesberg U, Neumann K, Schwarz C. Urban Life as Risk Factor for Aspergillosis. Front Cell Infect Microbiol 2020; 10:601834. [PMID: 33224902 PMCID: PMC7667220 DOI: 10.3389/fcimb.2020.601834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Aspergillus fumigatus (Af) frequently colonizes the airways of patients with cystic fibrosis (CF) and can cause severe diseases, such as allergic bronchopulmonary aspergillosis, Af bronchitis or even Af pneumonia. However, risk factors, including environmental factors, for acquiring Af in the respiratory tract of patients with CF are rarely studied and described. The aim of this study was to investigate whether urban or rural life could affect colonization with Af in the respiratory tract of patients with CF. Due to privacy policy, registry data are usually not linked to patients´ home addresses. It is therefore very difficult to analyze the influence of the patient´s residential environment. This prospective questionnaire survey was carried out in 31 German CF centers in 2018. Only completed surveys, including a clearly assigned type of residential area were included. Statistical analysis was performed by chi-squared test and logistic regression models. A total of 1016 questionnaires were analyzed (Patients` age: 23 ± 13; 0–88 years; female gender: n=492; 48%). The majority of patients with CF live in large cities (n =314; 30.9%) or urban districts (n=461; 45.4%). Prevalence of 30.2% was found for Af, within the 12 months of investigation period. Af colonization was significantly associated with urban life (p=0.004). Urban live should be considered as possible new risk factor for colonization with Af in the respiratory tract of patients with CF. These new results may raise the awareness of the influence of environmental factors on patient outcomes and should be included in patient guidance and preventive measures.
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Affiliation(s)
- Claudia Grehn
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Patience Eschenhagen
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Svenja Temming
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Konrad Neumann
- Institute for Biometry and Clinical Epidemiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Carsten Schwarz
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, CF Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Li S, Yang Z, Hu D, Cao L, He Q. Understanding building-occupant-microbiome interactions toward healthy built environments: A review. FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING 2020; 15:65. [PMID: 33145119 PMCID: PMC7596174 DOI: 10.1007/s11783-020-1357-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/30/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Built environments, occupants, and microbiomes constitute a system of ecosystems with extensive interactions that impact one another. Understanding the interactions between these systems is essential to develop strategies for effective management of the built environment and its inhabitants to enhance public health and well-being. Numerous studies have been conducted to characterize the microbiomes of the built environment. This review summarizes current progress in understanding the interactions between attributes of built environments and occupant behaviors that shape the structure and dynamics of indoor microbial communities. In addition, this review also discusses the challenges and future research needs in the field of microbiomes of the built environment that necessitate research beyond the basic characterization of microbiomes in order to gain an understanding of the causal mechanisms between the built environment, occupants, and microbiomes, which will provide a knowledge base for the development of transformative intervention strategies toward healthy built environments. The pressing need to control the transmission of SARS-CoV-2 in indoor environments highlights the urgency and significance of understanding the complex interactions between the built environment, occupants, and microbiomes, which is the focus of this review.
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Affiliation(s)
- Shuai Li
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Zhiyao Yang
- Lyles School of Civil Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Da Hu
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Liu Cao
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Institute for a Secure & Sustainable Environment, University of Tennessee, Knoxville, TN 37996 USA
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Schnorr SL. The soil in our microbial DNA informs about environmental interfaces across host and subsistence modalities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190577. [PMID: 33012224 DOI: 10.1098/rstb.2019.0577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In this study, I use microbiome datasets from global soil samples and diverse hosts to learn whether soil microbial taxa are found in host microbiomes, and whether these observations fit the narrative that environmental interaction influences human microbiomes. A major motivation for conducting host-associated microbiome research is to contribute towards understanding how the environment may influence host physiology. The microbial molecular network is considered a key vector by which environmental traits may be transmitted to the host. Research on human evolution seeks evidence that can inform about the living experiences of human ancestors. This objective is substantially enhanced by recent work on ancient biomolecules from preserved microbial tissues, such as dental calculus, faecal sediments and whole coprolites. A challenge yet is to distinguish authentic biomolecules from environmental contaminants deposited contemporaneously, primarily from soil. However, we do not have sound expectations about the soil microbial elements arriving to host-associated microbiomes in a modern context. One assumption in human microbiome research is that proximity to the natural environment should affect biodiversity or impart genetic elements. I present evidence supporting the assumption that environmental soil taxa are found among host-associated gut taxa, which can recapitulate the surrounding host habitat ecotype. Soil taxa found in gut microbiomes relate to a set of universal 'core' taxa for all soil ecotypes, demonstrating that widespread host organisms may experience a consistent pattern of external environmental cues, perhaps critical for development. Observed differentiation of soil feature diversity, abundance and composition among human communities, great apes and invertebrate hosts also indicates that lifestyle patterns are inferable from an environmental signal that is retrievable from gut microbiome amplicon data. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Stephanie L Schnorr
- Department of Anthropology, University of Nevada, Las Vegas, NV, USA.,Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
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Fu X, Li Y, Meng Y, Yuan Q, Zhang Z, Norbäck D, Deng Y, Zhang X, Sun Y. Associations between respiratory infections and bacterial microbiome in student dormitories in Northern China. INDOOR AIR 2020; 30:816-826. [PMID: 32304333 DOI: 10.1111/ina.12677] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/17/2020] [Accepted: 04/10/2020] [Indexed: 05/14/2023]
Abstract
Recent studies reveal that the microbial diversity and composition in the respiratory tract are related to the susceptibility, development, and progression of respiratory infections. Indoor microorganisms can transmit into the respiratory tract through breathing, but their role in infections is unclear. Here, we present the first association study between the indoor microbiome and respiratory infections. In total, 357 students living in 86 dormitory rooms in Shanxi University were randomly selected to survey symptoms of infections. Settled air dust was collected to characterize bacterial compositions by 16S rRNA sequencing. The overall microbial richness was not associated with respiratory infections, but microorganisms from specific phylogenetic classes showed various associations. Taxa richness and abundance of Actinobacteria were protectively associated with infections (P < .05). The abundance of several genera in Gammaproteobacteria, including Haemophilus, Klebsiella, Buttiauxella, and Raoultella, was positively associated with infections (P < .005). The role of these microorganisms was consistent with previous human microbiota studies. Building age was associated with the overall microbial composition variation in dormitories and negatively associated with three potential risk genera in Proteobacteria (P < .05). The weight of vacuum dust was positively associated with a protective genus, Micrococcus in Actinobacteria (P < .05).
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Affiliation(s)
- Xi Fu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, PR China
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, PR China
| | - Yanling Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, PR China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, PR China
| | - Yi Meng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, PR China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, PR China
| | - Qianqian Yuan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, PR China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, PR China
| | - Zefei Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China
| | - Dan Norbäck
- Occupational and Environmental Medicine, Dept. of Medical Science, University Hospital, Uppsala University, Uppsala, Sweden
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, PR China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, PR China
| | - Xin Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, PR China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, PR China
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Coil DA, Neches RY, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton-Marcell J, Gilbert JA, Eisen JA. Bacterial communities associated with cell phones and shoes. PeerJ 2020; 8:e9235. [PMID: 32551196 PMCID: PMC7292020 DOI: 10.7717/peerj.9235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.
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Affiliation(s)
- David A Coil
- Genome Center, University of California, Davis, CA, United States of America
| | - Russell Y Neches
- Genome Center, University of California, Davis, CA, United States of America
| | - Jenna M Lang
- Genome Center, University of California, Davis, CA, United States of America
| | - Guillaume Jospin
- Genome Center, University of California, Davis, CA, United States of America
| | - Wendy E Brown
- Department of Biomedical Engineering, University of California, Irvine, CA, United States of America.,Science Cheerleaders, Inc., Philadelphia, PA, United States of America
| | - Darlene Cavalier
- Science Cheerleaders, Inc., Philadelphia, PA, United States of America.,SciStarter.org, Philadelphia, PA, United States of America
| | - Jarrad Hampton-Marcell
- Argonne National Laboratory, University of Chicago, Lemont, IL, United States of America
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, UC San Diego School of Medicine, San Diego, CA, United States of America
| | - Jonathan A Eisen
- Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States of America
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Guo J, Xiong Y, Shi C, Liu C, Li H, Qian H, Sun Z, Qin C. Characteristics of airborne bacterial communities in indoor and outdoor environments during continuous haze events in Beijing: Implications for health care. ENVIRONMENT INTERNATIONAL 2020; 139:105721. [PMID: 32305743 DOI: 10.1016/j.envint.2020.105721] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
There is solid evidence that haze pollution threatens human health owing to the abiotic pollutants it contains. However, the characteristics of airborne bacterial communities in indoor and outdoor environments exhibiting haze occurrence are still unknown. Thus, we examined variations in both indoor and outdoor airborne bacterial communities in Beijing from December 9-27, 2016, a period which included three haze events. The outdoor airborne bacterial communities were clustered into two main groups (Groups I and II), and they shifted between two typical bacterial communities regardless of the haze event. The Chao1, Shannon, and phylogenetic diversity indexes and abundance of dominant classes changed significantly, as did airborne bacterial community type. The indoor airborne bacterial community closely tracked the outdoor bacterial community type, forming two obvious groups supported by Adonis analysis, changes in dominant classes, and bacterial diversity compared to the outdoor group. Furthermore, we found that the airborne bacterial community type could affect the morbidity of respiratory diseases. Daily pneumonia cases were significantly higher in Group I (p = 0.035), whereas daily amygdalitis cases were significantly higher in Group II (p = 0.025). Interestingly, the enriched classes in the indoor environment were quite different from those in the typical airborne bacterial community environment, except for Clostridia, which had significantly higher abundance in both indoor environments. In conclusion, we found that the two indoor and outdoor airborne bacterial community types changed independently of haze events, and the special airborne bacterial community type was closely related to the incidence of pneumonia in the heavy haze season.
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Affiliation(s)
- Jianguo Guo
- NHC Key Laboratory of Human Disease Comparative Medicine (The Institute of Laboratory Animal Sciences, CAMS&PUMC), Beijing 100021, China; Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese Medicine, Beijing 100021, China
| | - Yi Xiong
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Changhua Shi
- NHC Key Laboratory of Human Disease Comparative Medicine (The Institute of Laboratory Animal Sciences, CAMS&PUMC), Beijing 100021, China; Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese Medicine, Beijing 100021, China
| | - Ce Liu
- Department of Infectious Disease, Beijing Chuiyangliu Hospital, Affiliated with Tsinghua University, Beijing 100022, China
| | - Hongwei Li
- NHC Key Laboratory of Human Disease Comparative Medicine (The Institute of Laboratory Animal Sciences, CAMS&PUMC), Beijing 100021, China; Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese Medicine, Beijing 100021, China
| | - Hua Qian
- School of Energy and Environment, Southeast University, Nanjing 211189, China
| | - Zongke Sun
- National Institute of Environmental Health, China CDC, Beijing 100021, China
| | - Chuan Qin
- NHC Key Laboratory of Human Disease Comparative Medicine (The Institute of Laboratory Animal Sciences, CAMS&PUMC), Beijing 100021, China; Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese Medicine, Beijing 100021, China.
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Moelling K, Broecker F. Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection. JOURNAL OF ENVIRONMENTAL AND PUBLIC HEALTH 2020; 2020:1646943. [PMID: 32565838 PMCID: PMC7256708 DOI: 10.1155/2020/1646943] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/06/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022]
Abstract
Polluted air poses a significant threat to human health. Exposure to particulate matter (PM) and harmful gases contributes to cardiovascular and respiratory diseases, including allergies and obstructive lung disease. Air pollution may also be linked to cancer and reduced life expectancy. Uptake of PM has been shown to cause pathological changes in the intestinal microbiota in mice and humans. Less is known about the effects of pollution-associated microbiota on human health. Several recent studies described the microbiomes of urban and rural air samples, of the stratosphere and sand particles, which can be transported over long distances, as well as the air of indoor environments. Here, we summarize the current knowledge on airborne bacterial, viral, and fungal communities and discuss their potential consequences on human health. The current data suggest that bacterial pathogens are typically too sparse and short-lived in air to pose a significant risk for infecting healthy people. However, airborne fungal spores may exacerbate allergies and asthma. Little information is available on viruses including phages, and future studies are likely to detect known and novel viruses with a yet unknown impact on human health. Furthermore, varying experimental protocols have been employed in the recent microbiome and virome studies. Therefore, standardized methodologies will be required to allow for better comparisons between studies. Air pollution has been linked to more severe outcomes of SARS (severe acute respiratory syndrome) coronavirus (SARS-CoV) infections. This may have contributed to severe SARS-CoV-2 outbreaks, especially those in China, Northern Italy, Iran, and New York City.
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Affiliation(s)
- Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France. Microorganisms 2020; 8:microorganisms8030341. [PMID: 32121209 PMCID: PMC7143953 DOI: 10.3390/microorganisms8030341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 02/25/2020] [Indexed: 12/28/2022] Open
Abstract
The indoor microbial community is a mixture of microorganisms resulting from outdoor ecosystems that seed the built environment. However, the biogeography of the indoor microbial community is still inadequately studied. Dust from more than 3000 dwellings across France was analyzed by qPCR using 17 targets: 10 molds, 3 bacteria groups, and 4 mites. Thus, the first spatial description of the main indoor microbial allergens on the French territory, in relation with biogeographical factors influencing the distribution of microorganisms, was realized in this study. Ten microorganisms out of 17 exhibited increasing abundance profiles across the country: Five microorganisms (Dermatophagoïdes pteronyssinus, Dermatophagoïdes spp., Streptomyces spp., Cladosporium sphaerospermum, Epicoccum nigrum) from northeast to southwest, two (Cryptococcus spp., Alternaria alternata) from northwest to southeast, Mycobacteria from east to west, Aspergillus fumigatus from south to north, and Penicillium chrysogenum from south to northeast. These geographical patterns were partly linked to climate and land cover. Multivariate analysis showed that composition of communities seemed to depend on landscapes, with species related to closed and rather cold and humid landscapes (forests, located in the northeast) and others to more open, hot, and dry landscapes (herbaceous and coastal regions, located in the west). This study highlights the importance of geographical location and outdoor factors that shape communities. In order to study the effect of microorganisms on human health (allergic diseases in particular), it is important to identify biogeographic factors that structure microbial communities on large spatial scales and to quantify the exposure with quantitative tools, such as the multi-qPCR approach.
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45
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Prussin AJ, Belser JA, Bischoff W, Kelley ST, Lin K, Lindsley WG, Nshimyimana JP, Schuit M, Wu Z, Bibby K, Marr LC. Viruses in the Built Environment (VIBE) meeting report. MICROBIOME 2020; 8:1. [PMID: 31901242 PMCID: PMC6942371 DOI: 10.1186/s40168-019-0777-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 12/18/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND During a period of rapid growth in our understanding of the microbiology of the built environment in recent years, the majority of research has focused on bacteria and fungi. Viruses, while probably as numerous, have received less attention. In response, the Alfred P. Sloan Foundation supported a workshop entitled "Viruses in the Built Environment (VIBE)," at which experts in environmental engineering, environmental microbiology, epidemiology, infection prevention, fluid dynamics, occupational health, metagenomics, and virology convened to synthesize recent advances and identify key research questions and knowledge gaps regarding viruses in the built environment. RESULTS Four primary research areas and funding priorities were identified. First, a better understanding of viral communities in the built environment is needed, specifically which viruses are present and their sources, spatial and temporal dynamics, and interactions with bacteria. Second, more information is needed about viruses and health, including viral transmission in the built environment, the relationship between virus detection and exposure, and the definition of a healthy virome. The third research priority is to identify and evaluate interventions for controlling viruses and the virome in the built environment. This encompasses interactions among viruses, buildings, and occupants. Finally, to overcome the challenge of working with viruses, workshop participants emphasized that improved sampling methods, laboratory techniques, and bioinformatics approaches are needed to advance understanding of viruses in the built environment. CONCLUSIONS We hope that identifying these key questions and knowledge gaps will engage other investigators and funding agencies to spur future research on the highly interdisciplinary topic of viruses in the built environment. There are numerous opportunities to advance knowledge, as many topics remain underexplored compared to our understanding of bacteria and fungi. Video abstract.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Jessica A. Belser
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Werner Bischoff
- Section on Infectious Diseases, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Kaisen Lin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - William G. Lindsley
- Health Effects Laboratory Division (HELD), National Institute for Occupational Safety and Health, Morgantown, WV 26505 USA
| | | | - Michael Schuit
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702 USA
| | - Zhenyu Wu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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Gohli J, Bøifot KO, Moen LV, Pastuszek P, Skogan G, Udekwu KI, Dybwad M. The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities. MICROBIOME 2019; 7:160. [PMID: 31856911 PMCID: PMC6924074 DOI: 10.1186/s40168-019-0772-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/20/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people. In order to gain a deeper understanding of microbiome dynamics in subways, we must identify variables that affect microbial composition and those microorganisms that are unique to specific habitats. METHODS We performed high-throughput 16S rRNA gene sequencing of air and surface samples from 16 subway stations in Oslo, Norway, across all four seasons. Distinguishing features across seasons and between air and surface were identified using random forest classification analyses, followed by in-depth diversity analyses. RESULTS There were significant differences between the air and surface bacterial communities, and across seasons. Highly abundant groups were generally ubiquitous; however, a large number of taxa with low prevalence and abundance were exclusively present in only one sample matrix or one season. Among the highly abundant families and genera, we found that some were uniquely so in air samples. In surface samples, all highly abundant groups were also well represented in air samples. This is congruent with a pattern observed for the entire dataset, namely that air samples had significantly higher within-sample diversity. We also observed a seasonal pattern: diversity was higher during spring and summer. Temperature had a strong effect on diversity in air but not on surface diversity. Among-sample diversity was also significantly associated with air/surface, season, and temperature. CONCLUSIONS The results presented here provide the first direct comparison of air and surface bacterial microbiomes, and the first assessment of seasonal variation in subways using culture-independent methods. While there were strong similarities between air and surface and across seasons, we found both diversity and the abundances of certain taxa to differ. This constitutes a significant step towards understanding the composition and dynamics of bacterial communities in subways, a highly important environment in our increasingly urbanized and interconnect world. Video abstract.
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Affiliation(s)
- Jostein Gohli
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway.
| | - Kari Oline Bøifot
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
- Department of Analytics, Environmental & Forensic Sciences, King's College London, 150 Stamford Street, London, SE1 9NH, UK
| | - Line Victoria Moen
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
| | - Paulina Pastuszek
- Department of Molecular Biosciences, Stockholm University, SE 10691, Stockholm, Sweden
| | - Gunnar Skogan
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
| | - Klas I Udekwu
- SoS BIOs Sweden, Tiundagatan 41, SE 752 30, Uppsala, Sweden
| | - Marius Dybwad
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
- Department of Analytics, Environmental & Forensic Sciences, King's College London, 150 Stamford Street, London, SE1 9NH, UK
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Sbihi H, Boutin RCT, Cutler C, Suen M, Finlay BB, Turvey SE. Thinking bigger: How early-life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease. Allergy 2019; 74:2103-2115. [PMID: 30964945 DOI: 10.1111/all.13812] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/27/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023]
Abstract
Imbalance, or dysbiosis, of the gut microbiome of infants has been linked to an increased risk of asthma and allergic diseases. Most studies to date have provided a wealth of data showing correlations between early-life risk factors for disease and changes in the structure of the gut microbiome that disrupt normal immunoregulation. These studies have typically focused on one specific risk factor, such as mode of delivery or early-life antibiotic use. Such "micro-level" exposures have a considerable impact on affected individuals but not necessarily the whole population. In this review, we place these mechanisms under a larger lens that takes into account the influence of upstream "macro-level" environmental factors such as air pollution and the built environment. While these exposures likely have a smaller impact on the microbiome at an individual level, their ubiquitous nature confers them with a large influence at the population level. We focus on features of the indoor and outdoor human-made environment, their microbiomes and the research challenges inherent in integrating the built environment microbiomes with the early-life gut microbiome. We argue that an exposome perspective integrating internal and external microbiomes with macro-level environmental factors can provide a more comprehensive framework to define how environmental exposures can shape the gut microbiome and influence the development of allergic disease.
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Affiliation(s)
- Hind Sbihi
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| | - Rozlyn CT. Boutin
- Department of Microbiology and Immunology, Michael Smith Laboratories The University of British Columbia Vancouver British Columbia Canada
| | - Chelsea Cutler
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| | - Mandy Suen
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
| | - B. Brett Finlay
- Department of Microbiology and Immunology, Michael Smith Laboratories The University of British Columbia Vancouver British Columbia Canada
| | - Stuart E. Turvey
- Department of Pediatrics, British Columbia Children’s Hospital The University of British Columbia Vancouver British Columbia Canada
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Valeriani F, Margarucci LM, Gianfranceschi G, Ciccarelli A, Tajani F, Mucci N, Ripani M, Romano Spica V. Artificial-turf surfaces for sport and recreational activities: microbiota analysis and 16S sequencing signature of synthetic vs natural soccer fields. Heliyon 2019; 5:e02334. [PMID: 31517095 PMCID: PMC6728760 DOI: 10.1016/j.heliyon.2019.e02334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/04/2019] [Accepted: 08/15/2019] [Indexed: 12/12/2022] Open
Abstract
Synthetic fibres are used in place of the natural grass worldwide, for realizing playgrounds, soccer fields and even domestic gardens or recreational structures. An intensive use of artificial turf is currently observed in sports facilities, due to lower costs, higher sustainability in recycling of materials, and advantages related to athletic practice and performance. However, even if chemical and physical risks were studied, the microbiological component was not fully addressed, especially considering a comprehensive evaluation of the microbiota in synthetic vs natural playground surfaces. Here, we investigated the microbial community present on soccer fields, using Next Generation Sequencing and a 16S amplicon sequencing approach. Artificial and natural turfs show own ecosystems with different microbial profiles and a mean Shannon's diversity value of 2.176 and 2.475, respectively. The bacterial community is significantly different between facilities (ANOSIM: R = 0.179; p < 0.001) and surface materials (ANOSIM: R = 0.172; p < 0.005). The relative abundance of potentially pathogenic bacterial OTUs was higher in synthetic than in natural samples (ANOVA, F = 2.2). Soccer fields are characterized by their own microbiota, showing a different 16S amplicon sequencing signature between natural and artificial turfs.
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Affiliation(s)
- Federica Valeriani
- University of Rome "Foro Italico", Department of Movement, Human and Health Sciences, Public Health Unit, Rome, Italy
| | - Lory Marika Margarucci
- University of Rome "Foro Italico", Department of Movement, Human and Health Sciences, Public Health Unit, Rome, Italy
| | - Gianluca Gianfranceschi
- University of Rome "Foro Italico", Department of Movement, Human and Health Sciences, Public Health Unit, Rome, Italy
| | - Antonello Ciccarelli
- University of Rome "Foro Italico", Department of Movement, Human and Health Sciences, Public Health Unit, Rome, Italy
| | - Filippo Tajani
- University of Rome "Foro Italico", Department of Movement, Human and Health Sciences, Public Health Unit, Rome, Italy
| | - Nicolina Mucci
- INAIL, Department of Technological Innovations and Safety of Plants, Products and Anthropic Settlements, Rome, Italy
| | - Maurizio Ripani
- University of Rome "Foro Italico", Department of Movement, Human and Health Sciences, Public Health Unit, Rome, Italy
| | - Vincenzo Romano Spica
- University of Rome "Foro Italico", Department of Movement, Human and Health Sciences, Public Health Unit, Rome, Italy
- Corresponding author.
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Chen C, He R, Cheng Z, Han M, Zha Y, Yang P, Yao Q, Zhou H, Zhong C, Ning K. The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities. Front Microbiol 2019; 10:1579. [PMID: 31354673 PMCID: PMC6636667 DOI: 10.3389/fmicb.2019.01579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/25/2019] [Indexed: 02/01/2023] Open
Abstract
Large-scale campus resembles a small “semi-open community,” harboring disturbances from the exchanges of people and vehicles, wherein stressors such as temperature and population density differ among the ground surfaces of functional partitions. Therefore, it represents a special ecological niche for the study on microbial ecology in the process of urbanization. In this study, we investigated outdoor microbial communities in four campuses in Wuhan, China. We obtained 284 samples from 55 sampling sites over six seasons, as well as their matching climatic and environmental records. The structure of campus outdoor microbial communities which influenced by multiple climatic factors featured seasonality. The dispersal influence of human activities on microbial communities also contributed to this seasonal pattern non-negligibly. However, despite the microbial composition alteration in response to multiple stressors, the overall predicted function of campus outdoor microbial communities remained stable across campuses. The spatial–temporal dynamic patterns on campus outdoor microbial communities and its predicted functions have bridged the gap between microbial and macro-level ecosystems, and provided hints toward a better understanding of the effects of climatic factors and human activities on campus micro-environments.
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Affiliation(s)
- Chaoyun Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ruiqiao He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangyu Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuguo Zha
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Yao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Zhou
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Chaofang Zhong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Abstract
Many studies have highlighted the importance of body site and individuality in shaping the composition of the human skin microbiome, but we still have a poor understanding of how extrinsic (e.g., lifestyle) and intrinsic (e.g., age) factors influence its composition. We characterized the bacterial microbiomes of North American volunteers at four skin sites and the mouth. We also collected extensive subject metadata and measured several host physiological parameters. Integration of host and microbial features showed that the skin microbiome was predominantly associated with demographic, lifestyle, and physiological factors. Furthermore, we uncovered reproducible associations between chronological age, skin aging, and members of the genus Corynebacterium. Our work provides new understanding of the role of host selection and lifestyle in shaping skin microbiome composition. It also contributes to a more comprehensive appreciation of the factors that drive interindividual skin microbiome variation. Despite recognition that biogeography and individuality shape the function and composition of the human skin microbiome, we know little about how extrinsic and intrinsic host factors influence its composition. To explore the contributions of these factors to skin microbiome variation, we profiled the bacterial microbiomes of 495 North American subjects (ages, 9 to 78 years) at four skin surfaces plus the oral epithelium using 16S rRNA gene amplicon sequencing. We collected subject metadata, including host physiological parameters, through standardized questionnaires and noninvasive biophysical methods. Using a combination of statistical modeling tools, we found that demographic, lifestyle, and physiological factors collectively explained 12 to 20% of the variability in microbiome composition. The influence of health factors was strongest on the oral microbiome. Associations between host factors and the skin microbiome were generally dominated by operational taxonomic units (OTUs) affiliated with the Clostridiales and Prevotella. A subset of the correlations between microbial features and host attributes were site specific. To further explore the relationship between age and the skin microbiome of the forehead, we trained a Random Forest regression model to predict chronological age from microbial features. Age was associated mostly with two mutually coexcluding Corynebacterium OTUs. Furthermore, skin aging variables (wrinkles and hyperpigmented spots) were independently correlated to these taxa.
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