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Gilbert JA, Hartmann EM. The indoors microbiome and human health. Nat Rev Microbiol 2024:10.1038/s41579-024-01077-3. [PMID: 39030408 DOI: 10.1038/s41579-024-01077-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 07/21/2024]
Abstract
Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.
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Affiliation(s)
- Jack A Gilbert
- Department of Paediatrics, University of California San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
- Department of Medicine, Division of Pulmonary Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
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2
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Harnpicharnchai P, Siriarchawatana P, Mayteeworakoon S, Ingsrisawang L, Likhitrattanapisal S, Eurwilaichitr L, Ingsriswang S. Interplay of xenobiotic-degrading and antibiotic-resistant microorganisms among the microbiome found in the air, handrail, and floor of the subway station. ENVIRONMENTAL RESEARCH 2024; 247:118269. [PMID: 38246293 DOI: 10.1016/j.envres.2024.118269] [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: 10/30/2023] [Revised: 01/11/2024] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
Investigating the quality of the subway environment, especially regarding antibiotic resistance genes (ARGs) and xenobiotics, conveys ecological and health impacts. In this study, compositions and relations of microorganisms harboring ARGs and xenobiotic degradation and metabolism genes (XDGs) in the Sukhumvit subway station (MRT-SKV) in Bangkok was assessed by analyzing the taxonomic and genetic diversity of the microbiome in the air and on the surfaces of floor and handrail. The major bacteria in the MRT-SKV (including Moraxella, which was abundant in the bioaerosol and handrail samples, and Staphylococcus, which was abundant in the bioaerosol samples) were found to contain both ARGs and XDGs. The co-abundance correlation network revealed notable relationships among bacteria harboring antibiotic resistance genes (ARGs) and xenobiotic degradation genes (XDGs). Significant associations were observed between ARGs linked to glycopeptide and fluoroquinolone resistance and genes associated with benzoate, styrene, and atrazine degradation pathways, as well as between ARGs related to cephamycin, cephalosporin, and MLS resistance and XDGs associated with the cytochrome P450-dependent drug metabolism pathway. These correlations suggested that selective pressure exerted by certain xenobiotics and antibiotics can simultaneously affect both ARGs and XDGs in the environment and should favor correlations and co-survival among ARG- and XDG-containing bacteria in the environments. The correlations may occur via shared mechanisms of resistance to both xenobiotics and antibiotics. Finally, different correlation pairs were seen in different niches (air, handrail, floor) of the subway environment or different geolocations. Thus, the relationship between ARG and XDG pairs most likely depends on the unique characteristics of the niches and on the prominent types of xenobiotics and antibiotics in the subway environment. The results indicated that interactions and connections between microbial communities can impact how they function. These microorganisms can have profound effects on accumulation of xenobiotics and ARGs in the MRT-SKV.
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Affiliation(s)
- Piyanun Harnpicharnchai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Paopit Siriarchawatana
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Sermsiri Mayteeworakoon
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Lily Ingsrisawang
- Department of Statistics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Somsak Likhitrattanapisal
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Lily Eurwilaichitr
- National Energy Technology Center, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Supawadee Ingsriswang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand.
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3
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Williams TC, Asselin E, Mazzulli T, Woznow T, Hamzeh H, Nahkaie D, Waisman D, Stojkova B, Dixon R, Bryce E, Charles M. One-year trial evaluating the durability and antimicrobial efficacy of copper in public transportation systems. Sci Rep 2024; 14:6765. [PMID: 38514805 PMCID: PMC10958017 DOI: 10.1038/s41598-024-56225-9] [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: 12/26/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024] Open
Abstract
Surfaces on transit vehicles are frequently touched and could potentially act as reservoirs for micro-organism transmission. Regular cleaning and disinfection to minimize the spread of micro-organisms is operationally challenging due to the need to keep vehicles in circulation. The application of copper (Cu) alloys to high- touch surfaces could help reduce the risk of cross-contamination, however, little is known about the durability and efficacy of engineered copper surfaces after prolonged use. Three Cu products (decal, thermal fabrication, and alloy covers) were assessed over a 12-month period. These Cu products were randomly installed on 110 stanchions on three buses and four train (SkyTrain) cars in Vancouver and three buses, two subway cars, and two streetcars in Toronto with mirrored control surfaces directly opposite. Bacterial counts (Colony forming units, CFU) and ATP bioluminescence (ATPB) were measured every two months after peak morning routes. Durability of the Cu products were assessed monthly through visual inspection and colorimetry assays or by ex-situ microscopy. Cu products on stanchions reduced the mean colony forming units (CFU) of all vehicles by 42.7% in the mean CFU (0.573 (CI 95% 0.453-0.726), p-value < 0.001) compared to control surfaces. The three Cu products exhibited an overall 87.1% reduction in the mean ATPB readings (0.129 (CI 95% 0.059-0.285, p-value < 0.001) compared to controls. Surface Cu concentration for all three products was consistent throughout the 12-month period. Electron microscopy (SEM) and Energy-dispersive X-ray Spectroscopy (EDS) cross-sectional analysis showed no change in thickness or dealloying of Cu products, however SEM top-down analysis revealed substantial carbon accumulation on all surfaces. Cu products installed on transit vehicles maintained antimicrobial efficacy and durability after 12 months of use.
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Affiliation(s)
- Teresa C Williams
- Division of Medical Microbiology and Infection Prevention, Vancouver Coastal Health, Vancouver, BC, Canada
| | - Edouard Asselin
- Department of Materials Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Tony Mazzulli
- Department of Microbiology, Mount Sinai Hospital, Toronto, Canada
| | - Tracey Woznow
- Division of Medical Microbiology and Infection Prevention, Vancouver Coastal Health, Vancouver, BC, Canada
| | - Hadi Hamzeh
- Department of Microbiology, Mount Sinai Hospital, Toronto, Canada
| | - Davood Nahkaie
- Department of Materials Engineering, University of British Columbia, Vancouver, BC, Canada
| | | | - Biljana Stojkova
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
| | - Richard Dixon
- Community & Healthcare Acquired Infection Reduction (CHAIR), Vancouver, Canada
| | - Elizabeth Bryce
- Division of Medical Microbiology and Infection Prevention, Vancouver Coastal Health, Vancouver, BC, Canada
| | - Marthe Charles
- Division of Medical Microbiology and Infection Prevention, Vancouver Coastal Health, Vancouver, BC, Canada.
- Division of Medical Microbiology and Infection Prevention, Vancouver General Hospital, 1116 - 855 West 12th Avenue, Vancouver, BC, V5Z 1M9, Canada.
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An XL, Xu MR, Pan XF, Cai GJ, Zhao CX, Li H, Ye ZL, Zhu YG, Su JQ. Local environment, surface characteristics and stochastic processes shape the dynamics of urban dustbin surface microbiome. ENVIRONMENT INTERNATIONAL 2023; 177:108004. [PMID: 37295164 DOI: 10.1016/j.envint.2023.108004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Dustbins function as critical infrastructures for urban sanitation, creating a distinct breeding ground for microbial assemblages. However, there is no information regarding the dynamics of microbial communities and the underlying mechanism for community assembly on dustbin surfaces. Here, surface samples were collected from three sampling zones (business building, commercial street and residential community) with different types (kitchen waste, harmful waste, recyclables, and others) and materials (metallic and plastic); and distribution pattern and assembly of microbial communities were investigated by high-throughput sequencing. Bacterial and fungal communities showed the distinct community variations across sampling zones and waste sorting. Core community and biomarker species were significantly correlated with the spatial distribution of overall community. The detection of pathogens highlighted the potential risk of surface microbiome. Human skin, human feces and soil biomes were the potential source environments of the surface microbiomes. Neutral model prediction suggested that microbial community assembly was significantly driven by stochastic processes. Co-association patterns varied with sampling zones and waste types, and neutral amplicon sequence variants (ASVs) that fall within the 95 % confidence intervals of neutral model were largely involved in the stability of microbial networks. These findings improve our understanding of the distribution pattern and the underlying assembly of microbial community on the dustbin surface, thus enabling prospective prediction and assessment of urban microbiomes and their impacts on human health.
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Affiliation(s)
- Xin-Li An
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Mei-Rong Xu
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiao-Fang Pan
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guan-Jing Cai
- College of Science, Shantou University, Shantou, 515063, China
| | - Cai-Xia Zhao
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hu Li
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhi-Long Ye
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Satari L, Iglesias A, Porcar M. The Microbiome of Things: Appliances, Machines, and Devices Hosting Artificial Niche-Adapted Microbial Communities. Microorganisms 2023; 11:1507. [PMID: 37375009 DOI: 10.3390/microorganisms11061507] [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: 05/03/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
As it is the case with natural substrates, artificial surfaces of man-made devices are home to a myriad of microbial species. Artificial products are not necessarily characterized by human-associated microbiomes; instead, they can present original microbial populations shaped by specific environmental-often extreme-selection pressures. This review provides a detailed insight into the microbial ecology of a range of artificial devices, machines, and appliances, which we argue are specific microbial niches that do not necessarily fit in the "build environment" microbiome definition. Instead, we propose here the Microbiome of Things (MoT) concept analogous to the Internet of Things (IoT) because we believe it may be useful to shed light on human-made, but not necessarily human-related, unexplored microbial niches.
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Affiliation(s)
- Leila Satari
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Alba Iglesias
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Manuel Porcar
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
- Darwin Bioprospecting Excellence SL., Parc Científic, Universitat de València, 46980 Paterna, Spain
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D'Accolti M, Soffritti I, Bini F, Mazziga E, Cason C, Comar M, Volta A, Bisi M, Fumagalli D, Mazzacane S, Caselli E. Shaping the subway microbiome through probiotic-based sanitation during the COVID-19 emergency: a pre-post case-control study. MICROBIOME 2023; 11:64. [PMID: 36991513 PMCID: PMC10060134 DOI: 10.1186/s40168-023-01512-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/07/2023] [Indexed: 05/11/2023]
Abstract
BACKGROUND The COVID-19 pandemic has highlighted the extent to which the public transportation environment, such as in subways, may be important for the transmission of potential pathogenic microbes among humans, with the possibility of rapidly impacting large numbers of people. For these reasons, sanitation procedures, including massive use of chemical disinfection, were mandatorily introduced during the emergency and remain in place. However, most chemical disinfectants have temporary action and a high environmental impact, potentially enhancing antimicrobial resistance (AMR) of the treated microbes. By contrast, a biological and eco-sustainable probiotic-based sanitation (PBS) procedure was recently shown to stably shape the microbiome of treated environments, providing effective and long-term control of pathogens and AMR spread in addition to activity against SARS-CoV-2, the causative agent of COVID-19. Our study aims to assess the applicability and impact of PBS compared with chemical disinfectants based on their effects on the surface microbiome of a subway environment. RESULTS The train microbiome was characterized by both culture-based and culture-independent molecular methods, including 16S rRNA NGS and real-time qPCR microarray, for profiling the train bacteriome and its resistome and to identify and quantify specific human pathogens. SARS-CoV-2 presence was also assessed in parallel using digital droplet PCR. The results showed a clear and significant decrease in bacterial and fungal pathogens (p < 0.001) as well as of SARS-CoV-2 presence (p < 0.01), in the PBS-treated train compared with the chemically disinfected control train. In addition, NGS profiling evidenced diverse clusters in the population of air vs. surface while demonstrating the specific action of PBS against pathogens rather than the entire train bacteriome. CONCLUSIONS The data presented here provide the first direct assessment of the impact of different sanitation procedures on the subway microbiome, allowing a better understanding of its composition and dynamics and showing that a biological sanitation approach may be highly effective in counteracting pathogens and AMR spread in our increasingly urbanized and interconnected environment. Video Abstract.
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Affiliation(s)
- Maria D'Accolti
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTA, University of Ferrara, 44121, Ferrara, Italy
- CIAS Research Center, University of Ferrara, 44122, Ferrara, Italy
| | - Irene Soffritti
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTA, University of Ferrara, 44121, Ferrara, Italy
- CIAS Research Center, University of Ferrara, 44122, Ferrara, Italy
| | - Francesca Bini
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTA, University of Ferrara, 44121, Ferrara, Italy
- CIAS Research Center, University of Ferrara, 44122, Ferrara, Italy
| | - Eleonora Mazziga
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTA, University of Ferrara, 44121, Ferrara, Italy
- CIAS Research Center, University of Ferrara, 44122, Ferrara, Italy
| | - Carolina Cason
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - Manola Comar
- Department of Advanced Translational Microbiology, Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Antonella Volta
- CIAS Research Center, University of Ferrara, 44122, Ferrara, Italy
| | - Matteo Bisi
- CIAS Research Center, University of Ferrara, 44122, Ferrara, Italy
| | - Daniele Fumagalli
- Facility Management Unit, Azienda Trasporti Milanesi S.P.A, 20121, Milan, Italy
| | - Sante Mazzacane
- CIAS Research Center, University of Ferrara, 44122, Ferrara, Italy
| | - Elisabetta Caselli
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTA, University of Ferrara, 44121, Ferrara, Italy.
- CIAS Research Center, University of Ferrara, 44122, Ferrara, Italy.
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Siriarchawatana P, Pumkaeo P, Harnpicharnchai P, Likhitrattanapisal S, Mayteeworakoon S, Boonsin W, Zhou X, Liang J, Cai L, Ingsriswang S. Temporal, compositional, and functional differences in the microbiome of Bangkok subway air environment. ENVIRONMENTAL RESEARCH 2023; 219:115065. [PMID: 36535389 DOI: 10.1016/j.envres.2022.115065] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
With the growing numbers of the urban population, an increasing number of commuters have relied on subway systems for rapid transportation in daily life. Analyzing the temporal distribution of air microbiomes in subway environments is crucial for the assessment and monitoring of air quality in the subway system, especially with regard to public health. This study employed culture-independent metabarcode sequencing to analyze bacterial diversity and variations in bacterial compositions associated with bioaerosols collected from a subway station in Bangkok over a four-month period. The bacteria obtained were found to consist primarily of Proteobacteria, Firmicutes, and Actinobacteria, with variations at the family, genus, and species levels among samples obtained in different months. The vast majority of these bacteria are most likely derived from outside environments and human body sources. Many of the bacteria found in Bangkok subway station were also identified as "core microorganisms" of subway environments around the world, as suggested by the MetaSUB Consortium. The diversity of bacterial communities was shown to be influenced by several air quality variables, especially ambient temperature and the quantity of particulate matters, which showed positive correlations with several bacterial species such as Acinetobacter lwoffii, Staphylococcus spp., and Moraxella osloensis. In addition, metabolic profiles inferred from metabarcode-derived bacterial diversity showed significant variations across different sampling times and sites and can be used as a starting point to further explore the functional roles of specific groups of bacteria in the subway environment. This study thus introduced the information required for surveillance of microbiological impacts and their contributions to the well-being of subway commuters in Bangkok.
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Affiliation(s)
- Paopit Siriarchawatana
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Panyapon Pumkaeo
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Piyanun Harnpicharnchai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Somsak Likhitrattanapisal
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Sermsiri Mayteeworakoon
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Worawongsin Boonsin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Xin Zhou
- Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Junmin Liang
- Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Lei Cai
- Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Supawadee Ingsriswang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
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Seasonal variations of the airborne microbial assemblages of the Seoul subway, South Korea from 16S and ITS gene profiles with chemical analysis. Sci Rep 2022; 12:18456. [PMID: 36323743 PMCID: PMC9630434 DOI: 10.1038/s41598-022-21120-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 09/22/2022] [Indexed: 11/07/2022] Open
Abstract
In this study, we determined the seasonal airborne microbial diversity profiles at SMRT stations by sequencing the 16S rRNA and ITS. Particulate matter samples were collected from air purifiers installed in the platform area of the SMRT subway stations. Three stations that included the most crowded one were selected for the sampling. The sampling was done at each season during 2019. After extracting the total DNA from all seasonal samples, PCR was performed with Illumina overhang adapter primers for the V3-V4 region of the 16S rRNA gene and ITS2 region of the ITS gene. The amplified products were further purified, and sequencing libraries were made. Sequencing was carried with the Illumina Miseq Sequencing system (Illumina, USA) followed by in-depth diversity analyses. The elemental composition of the particulate matter samples collected from the different subway stations were obtained using a WD-XRF spectrometer. The SMRT microbiome showed extensive taxonomic diversity with the most common bacterial genera at the subway stations associated with the skin. Overall, the stations included in this study harbored different phylogenetic communities based on α- and β-diversity comparisons. Microbial assemblages also varied depending upon the season in which the samples were taken and the station. Major elements present at the subway stations were from aerosols generated between wheels and brake cushions and between the catenaries and the pantographs. This study shows that the microbial composition of the SMRT subway stations comes from a diverse combination of environmental and human sources, the season and the lifestyle of commuters.
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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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Antimicrobial Photodynamic Coatings Reduce the Microbial Burden on Environmental Surfaces in Public Transportation—A Field Study in Buses. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19042325. [PMID: 35206511 PMCID: PMC8872155 DOI: 10.3390/ijerph19042325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 12/17/2022]
Abstract
Millions of people use public transportation daily worldwide and frequently touch surfaces, thereby producing a reservoir of microorganisms on surfaces increasing the risk of transmission. Constant occupation makes sufficient cleaning difficult to achieve. Thus, an autonomous, permanent, antimicrobial coating (AMC) could keep down the microbial burden on such surfaces. A photodynamic AMC was applied to frequently touched surfaces in buses. The microbial burden (colony forming units, cfu) was determined weekly and compared to equivalent surfaces in buses without AMC (references). The microbial burden ranged from 0–209 cfu/cm2 on references and from 0–54 cfu/cm2 on AMC. The means were 13.4 ± 29.6 cfu/cm2 on references and 4.5 ± 8.4 cfu/cm2 on AMC (p < 0.001). The difference in microbial burden on AMC and references was almost constant throughout the study. Considering a hygiene benchmark of 5 cfu/cm2, the data yield an absolute risk reduction of 22.6% and a relative risk reduction of 50.7%. In conclusion, photodynamic AMC kept down the microbial burden, reducing the risk of transmission of microorganisms. AMC permanently and autonomously contributes to hygienic conditions on surfaces in public transportation. Photodynamic AMC therefore are suitable for reducing the microbial load and closing hygiene gaps in public transportation.
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11
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Pochtovyi AA, Vasina DV, Verdiev BI, Shchetinin AM, Yuzhakov AG, Ovchinnikov RS, Tkachuk AP, Gushchin VA, Gintsburg AL. Microbiological Characteristics of Some Stations of Moscow Subway. BIOLOGY 2022; 11:biology11020170. [PMID: 35205037 PMCID: PMC8869165 DOI: 10.3390/biology11020170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 01/08/2023]
Abstract
Simple Summary Public transport facilities, including subway systems, provide the most suitable conditions for the transfer of microorganisms between people and the environment, contributing to the pathogenic potential of the urban habitat. Investigation of microbiome diversity and description of its characteristic properties, e.g., antibiotic-resistance profiles, leads to understanding of these interactions. In this study, we aimed to conduct an extended analysis of the bioaerosol and surface microbiome of the Moscow subway, using 16S rRNA gene sample sequencing and classical microbiology methods. The microbiomes of two subway stations (Novokosino and Cherkizovskaya) were reconstructed which differ in terms of passenger traffic and duration of exploitation. It was shown that most bacterial genera were ubiquitous; however, the unique genera were presented in aerosol samples. The relatively older Cherkizovskaya station possessed greater diversity in antibiotic resistance among the identified microorganisms compared to Novokosino station. We also provided a comparative analysis of these results with the previously published data, which allowed us to identify the distribution of microorganisms associated with the human microbiome and the environment regardless of the seasonal fluctuations. The obtained results provide valuable information on the diversity of bacterial communities in the Moscow subway, one of the most socially important facilities in metropolitan areas. Abstract The subway is one of the most actively used means of transport in the traffic infrastructure of large metropolitan areas. More than seven million passengers use the Moscow subway every day, which promotes the exchange of microorganisms between people and the surrounding subway environment. In this research, a study of the bacterial communities of two Moscow subway stations was conducted and the common subway microbiome was determined. However, there were differences in microbiological and antibiotic-resistance profiles, depending on the station. The station’s operational period since opening correlated with the taxonomic diversity and resistance of the identified bacteria. Moreover, differences between aerosol and surface bacterial communities were found at the two subway stations, indicating the importance of diversified sampling during the microbiome profiling of public areas. In this study, we also compared our data with previously published results obtained for the Moscow subway. Despite sample collection at different stations and seasons, we showed the presence of 15 common genera forming the core microbiome of the Moscow subway, which represents human commensal species, as well as widespread microorganisms from the surrounding environment.
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Affiliation(s)
- Andrei A. Pochtovyi
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (A.A.P.); (V.A.G.); Tel.: +7-499-193-30-01 (A.A.P.)
| | - Daria V. Vasina
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
| | - Bakhtiyar I. Verdiev
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
| | - Alexey M. Shchetinin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
| | - Anton G. Yuzhakov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Laboratory of Biochemistry and Molecular Biology, Federal State Budget Scientific Institution “Federal Scientific Center VIEV”, 109428 Moscow, Russia
| | - Roman S. Ovchinnikov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Laboratory of Mycology and Antibiotics, Federal Research Center “All-Russian Research Institute of Experimental Veterinary Medicine (VIEV) Named after K.I. Skryabin and Y.R. Kovalenko“ of Russian Academy of Science, 109428 Moscow, Russia
| | - Artem P. Tkachuk
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
| | - Vladimir A. Gushchin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (A.A.P.); (V.A.G.); Tel.: +7-499-193-30-01 (A.A.P.)
| | - Alexander L. Gintsburg
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (D.V.V.); (B.I.V.); (A.M.S.); (A.G.Y.); (R.S.O.); (A.P.T.); (A.L.G.)
- Department of Infectiology and Virology, Federal State Autonomous Educational Institution of Higher Education I M Sechenov, First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119435 Moscow, Russia
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Hernández-Álvarez C, García-Oliva F, Cruz-Ortega R, Romero MF, Barajas HR, Piñero D, Alcaraz LD. Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150136. [PMID: 34818799 DOI: 10.1016/j.scitotenv.2021.150136] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/10/2023]
Abstract
Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.
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Affiliation(s)
- Cristóbal Hernández-Álvarez
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Mexico
| | - Rocío Cruz-Ortega
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Miguel F Romero
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Hugo R Barajas
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Luis D Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico.
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Mills S, Ross RP. Colliding and interacting microbiomes and microbial communities - consequences for human health. Environ Microbiol 2021; 23:7341-7354. [PMID: 34390616 DOI: 10.1111/1462-2920.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022]
Abstract
Living 'things' coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world - paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.
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Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Vargas-Robles D, Gonzalez-Cedillo C, Hernandez AM, Alcaraz LD, Peimbert M. Passenger-surface microbiome interactions in the subway of Mexico City. PLoS One 2020; 15:e0237272. [PMID: 32813719 PMCID: PMC7437895 DOI: 10.1371/journal.pone.0237272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/22/2020] [Indexed: 01/02/2023] Open
Abstract
Interaction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces and compare regular and women-only wagons. We also explored the effect of surface cleaning on microbial resettling. Finally, we studied passenger behavior and characterized microbial changes after traveling. Most passengers (99%), showed some type of surface interaction during a wagon trip, mostly with the hands (92%). We found microbiome differences associated with surfaces, probably reflecting diverse surface materials and usage frequency. The platform floor was the most bacterial diverse surface, while the stair handrail and pole were the least diverse ones. After pole cleaning, the resettling of microbial diversity was fast (5–30 minutes); however, it did not resemble the initial composition. After traveling, passengers significantly increased their hand microbial diversity and converged to a similar microbial composition among passengers. Additionally, passenger hand microbiomes resembled subway surfaces in diversity. However, microbial fingerprints were preserved within passengers after traveling.
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Affiliation(s)
- Daniela Vargas-Robles
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Carolina Gonzalez-Cedillo
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Apolinar M. Hernandez
- 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
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
- * E-mail:
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