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Chibwe K, Sundararaju S, Zhang L, Tsui C, Tang P, Ling F. Intra-hospital microbiome variability is driven by accessibility and clinical activities. Microbiol Spectr 2024; 12:e0029624. [PMID: 38940596 PMCID: PMC11302010 DOI: 10.1128/spectrum.00296-24] [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: 02/08/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024] Open
Abstract
The hospital environmental microbiome, which can affect patients' and healthcare workers' health, is highly variable and the drivers of this variability are not well understood. In this study, we collected 37 surface samples from the neonatal intensive care unit (NICU) in an inpatient hospital before and after the operation began. Additionally, healthcare workers collected 160 surface samples from five additional areas of the hospital. All samples were analyzed using 16S rRNA gene amplicon sequencing, and the samples collected by healthcare workers were cultured. The NICU samples exhibited similar alpha and beta diversities before and after opening, which indicated that the microbiome there was stable over time. Conversely, the diversities of samples taken after opening varied widely by area. Principal coordinate analysis (PCoA) showed the samples clustered into two distinct groups: high alpha diversity [the pediatric intensive care unit (PICU), pathology lab, and microbiology lab] and low alpha diversity [the NICU, pediatric surgery ward, and infection prevention and control (IPAC) office]. Least absolute shrinkage and selection operator (LASSO) classification models identified 156 informative amplicon sequence variants (ASVs) for predicting the sample's area of origin. The testing accuracy ranged from 86.37% to 100%, which outperformed linear and radial support vector machine (SVM) and random forest models. ASVs of genera that contain emerging pathogens were identified in these models. Culture experiments had identified viable species among the samples, including potential antibiotic-resistant bacteria. Though area type differences were not noted in the culture data, the prevalences and relative abundances of genera detected positively correlated with 16S sequencing data. This study brings to light the microbial community temporal and spatial variation within the hospital and the importance of pathogenic and commensal bacteria to understanding dispersal patterns for infection control. IMPORTANCE We sampled surface samples from a newly built inpatient hospital in multiple areas, including areas accessed by only healthcare workers. Our analysis of the neonatal intensive care unit (NICU) showed that the microbiome was stable before and after the operation began, possibly due to access restrictions. Of the high-touch samples taken after opening, areas with high diversity had more potential external seeds (long-term patients and clinical samples), and areas with low diversity and had fewer (short-term or newborn patients). Classification models performed at high accuracy and identified biomarkers that could be used for more targeted surveillance and infection control. Though culturing data yielded viability and antibiotic-resistance information, it disproportionately detected the presence of genera relative to 16S data. This difference reinforces the utility of 16S sequencing in profiling hospital microbiomes. By examining the microbiome over time and in multiple areas, we identified potential drivers of the microbial variation within a hospital.
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Affiliation(s)
- Kaseba Chibwe
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Lin Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Clement Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Singapore
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Fangqiong Ling
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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Ye Z, Huang J, Liang Z, Liu S, Lei J, Deng S, Zheng B, Hong C, Wang Y, Wang X, Gao Q, Yang Y. A case study showing highly traceable sources of bacteria on surfaces of university buildings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 281:116632. [PMID: 38959791 DOI: 10.1016/j.ecoenv.2024.116632] [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: 05/10/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024]
Abstract
University students predominantly spend their time indoors, where prolonged exposure raises the risk of contact with microorganisms of concern. However, our knowledge about the microbial community characteristics on university campus and their underpinnings is limited. To address it, we characterized bacterial communities from the surfaces of various built environments typical of a university campus, including cafeterias, classrooms, dormitories, offices, meeting rooms, and restrooms, in addition to human skin. The classrooms harbored the highest α-diversity, while the cafeterias had the lowest α-diversity. The bacterial community composition varied significantly across different building types. Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Cyanobacteria were common phyla in university buildings, accounting for more than 90 % of total abundance. Staphylococcus aureus was the most abundant potential pathogen in classrooms, dormitories, offices, restrooms, and on human skin, indicating a potential risk for skin disease infections in these buildings. We further developed a new quantitative pathogenic risk assessment method according to the threat of pathogens to humans and found that classrooms exhibited the highest potential risk. The fast expectation-maximization algorithm identified 59 %-86 % of bacterial sources in buildings, with the human skin as the largest bacterial source for most buildings. As the sources of bacteria were highly traceable, we showed that homogeneous selection, dispersal limitation, and ecological drift were major ecological forces that drove community assembly. Our findings have important implications for predicting the distribution and sources of indoor dust bacterial communities on university campus.
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Affiliation(s)
- Zhencheng Ye
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jide Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zhengxiong Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Suo Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Sihang Deng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Bo Zheng
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Chaopeng Hong
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Yong Wang
- Institute for Ocean Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xiaoxiong Wang
- Institute for Ocean Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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3
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Cocker D, Birgand G, Zhu N, Rodriguez-Manzano J, Ahmad R, Jambo K, Levin AS, Holmes A. Healthcare as a driver, reservoir and amplifier of antimicrobial resistance: opportunities for interventions. Nat Rev Microbiol 2024:10.1038/s41579-024-01076-4. [PMID: 39048837 DOI: 10.1038/s41579-024-01076-4] [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: 07/27/2024]
Abstract
Antimicrobial resistance (AMR) is a global health challenge that threatens humans, animals and the environment. Evidence is emerging for a role of healthcare infrastructure, environments and patient pathways in promoting and maintaining AMR via direct and indirect mechanisms. Advances in vaccination and monoclonal antibody therapies together with integrated surveillance, rapid diagnostics, targeted antimicrobial therapy and infection control measures offer opportunities to address healthcare-associated AMR risks more effectively. Additionally, innovations in artificial intelligence, data linkage and intelligent systems can be used to better predict and reduce AMR and improve healthcare resilience. In this Review, we examine the mechanisms by which healthcare functions as a driver, reservoir and amplifier of AMR, contextualized within a One Health framework. We also explore the opportunities and innovative solutions that can be used to combat AMR throughout the patient journey. We provide a perspective on the current evidence for the effectiveness of interventions designed to mitigate healthcare-associated AMR and promote healthcare resilience within high-income and resource-limited settings, as well as the challenges associated with their implementation.
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Affiliation(s)
- Derek Cocker
- David Price Evans Infectious Diseases & Global Health Group, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Gabriel Birgand
- Centre d'appui pour la Prévention des Infections Associées aux Soins, Nantes, France
- National Institute for Health and Care Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, London, UK
- Cibles et medicaments des infections et de l'immunitée, IICiMed, Nantes Universite, Nantes, France
| | - Nina Zhu
- National Institute for Health and Care Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jesus Rodriguez-Manzano
- National Institute for Health and Care Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Raheelah Ahmad
- National Institute for Health and Care Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, London, UK
- Department of Health Services Research & Management, City University of London, London, UK
- Dow University of Health Sciences, Karachi, Pakistan
| | - Kondwani Jambo
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Anna S Levin
- Department of Infectious Disease, School of Medicine & Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - Alison Holmes
- David Price Evans Infectious Diseases & Global Health Group, University of Liverpool, Liverpool, UK.
- National Institute for Health and Care Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, London, UK.
- Department of Infectious Disease, Imperial College London, London, UK.
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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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5
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Eidem T, Nordgren T, Hernandez M. Bioaerosol Exposures and Respiratory Diseases in Cannabis Workers. Curr Allergy Asthma Rep 2024; 24:395-406. [PMID: 38878249 PMCID: PMC11233357 DOI: 10.1007/s11882-024-01157-7] [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] [Accepted: 06/10/2024] [Indexed: 07/10/2024]
Abstract
PURPOSE OF REVIEW This review investigates occupational inhalation hazards associated with biologically derived airborne particles (bioaerosols) generated in indoor cannabis cultivation and manufacturing facilities. RECENT FINDINGS Indoor cannabis production is growing across the US as are recent reports of respiratory diseases among cannabis workers, including occupational asthma morbidity and mortality. More information is needed to understand how bioaerosol exposure in cannabis facilities impacts worker health and occupational disease risk. Preliminary studies demonstrate a significant fraction of airborne particles in cannabis facilities are comprised of fungal spores, bacteria, and plant material, which may also contain hazardous microbial metabolites and allergens. These bioaerosols may pose pathogenic, allergenic, toxigenic, and pro-inflammatory risks to workers. The absence of multi-level, holistic bioaerosol research in cannabis work environments necessitates further characterization of the potential respiratory hazards and effective risk prevention methods to safeguard occupational health as the cannabis industry continues to expand across the US and beyond.
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Affiliation(s)
- Tess Eidem
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309-0428, US.
| | - Tara Nordgren
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523-1601, US
| | - Mark Hernandez
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309-0428, US
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Yamaguchi M, Imai K, Chen D, Seong YA, Jo K, Ito K. The Similarities in Microbial and Chemical Patterns of Fermentation in Two Open Environments were Promoted by Using 150-Year-Old Nukadoko as Starters. Curr Microbiol 2024; 81:250. [PMID: 38951184 PMCID: PMC11217091 DOI: 10.1007/s00284-024-03760-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/01/2024] [Indexed: 07/03/2024]
Abstract
Nukadoko, a fermented rice bran employed in traditional Japanese pickling, uses lactic acid bacteria to ferment vegetables. Here, we report the microbial and chemical data of a mixture of matured 150-year-old nukadoko and commercially available rice bran placed in two open environments over 29 days. Across the two environments, Loigolactobacillus was identified as the dominant microbial genera in the later stages of fermentation in nukadoko. The period of increase in the relative abundance of Loigolactobacillus correlated with a decrease in pH and Oxidation-Reduction Potential (ORP) values. While the two environments showed a difference in the rate of change in microbial diversity, they shared the common process through which Loigolactobacillus outcompeted adventitious bacteria in nukadoko, as indicated by the alpha and beta diversity index. Thus, the similarities in microbial and chemical data across two open environments during fermentation using starters indicate that starters contribute to the stability of fermentation in open environments.
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Affiliation(s)
- Marin Yamaguchi
- BIOTA Inc., Tokyo, 101-0022, Japan
- Faculty of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-8654, Japan
- College of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Kota Imai
- BIOTA Inc., Tokyo, 101-0022, Japan
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, 610-0394, Japan
| | - Dominique Chen
- Faculty of Letters, Arts and Sciences, Waseda University, Tokyo, 162-8644, Japan.
| | - Young Ah Seong
- Faculty of Engineering and Design, Hosei University, Tokyo, 102-8160, Japan
| | - Kazuhiro Jo
- Faculty of Design, Kyushu University, Fukuoka, 815-8540, Japan
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7
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D'Accolti M, Soffritti I, Bini F, Mazziga E, Caselli E. Tackling transmission of infectious diseases: A probiotic-based system as a remedy for the spread of pathogenic and resistant microbes. Microb Biotechnol 2024; 17:e14529. [PMID: 39045894 PMCID: PMC11267305 DOI: 10.1111/1751-7915.14529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 07/04/2024] [Indexed: 07/25/2024] Open
Abstract
Built environments (BEs) currently represent the areas in which human beings spend most of their life. Consistently, microbes populating BEs mostly derive from human occupants and can be easily transferred from BE to occupants. The hospital microbiome is a paradigmatic example, representing a reservoir for harmful pathogens that can be transmitted to susceptible patients, causing the healthcare-associated infections (HAIs). Environmental cleaning is a crucial pillar in controlling BE pathogens and preventing related infections, and chemical disinfectants have been largely used so far towards this aim. However, despite their immediate effect, chemical-based disinfection is unable to prevent recontamination, has a high environmental impact, and can select/increase antimicrobial resistance (AMR) in treated microbes. To overcome these limitations, probiotic-based sanitation (PBS) strategies were recently proposed, built on the use of detergents added with selected probiotics able to displace surrounding pathogens by competitive exclusion. PBS was reported as an effective and low-impact alternative to chemical disinfection, providing stable rebalance of the BE microbiome and significantly reducing pathogens and HAIs compared to disinfectants, without exacerbating AMR and pollution concerns. This minireview summarizes the most significant results obtained by applying PBS in sanitary and non-sanitary settings, which overall suggest that PBS may effectively tackle the infectious risk meanwhile preventing the further spread of pathogenic and resistant microbes.
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Affiliation(s)
- Maria D'Accolti
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
| | - Irene Soffritti
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
| | - Francesca Bini
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
| | - Eleonora Mazziga
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
| | - Elisabetta Caselli
- Section of Microbiology, Department of Chemical, Pharmaceutical and Agricultural Sciences, and LTTAUniversity of FerraraFerraraItaly
- CIAS Research CenterUniversity of FerraraFerraraItaly
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8
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Benton LD, Lopez-Galvez N, Herman C, Caporaso JG, Cope EK, Rosales C, Gameros M, Lothrop N, Martínez FD, Wright AL, Carr TF, Beamer PI. Environmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border. Sci Rep 2024; 14:12803. [PMID: 38834753 PMCID: PMC11150412 DOI: 10.1038/s41598-024-63356-6] [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: 09/04/2023] [Accepted: 05/28/2024] [Indexed: 06/06/2024] Open
Abstract
We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs. 8.4%). This investigation assessed differences in microbial dust composition in relation to demographic and housing characteristics on both sides of the US-MX Border. Forty homes were recruited in the US and MX. Home visits collected floor dust and documented occupants' demographics, asthma prevalence, housing structure, and use characteristics. US households were more likely to have inhabitants who reported asthma when compared with MX households (30% vs. 5%) and had significantly different flooring types. The percentage of households on paved roads, with flushing toilets, with piped water and with air conditioning was higher in the US, while dust load was higher in MX. Significant differences exist between countries in the microbial composition of the floor dust. Dust from Mexican homes was enriched with Alishewanella, Paracoccus, Rheinheimera genera and Intrasporangiaceae family. A predictive metagenomics analysis identified 68 significantly differentially abundant functional pathways between US and MX. This study documented multiple structural, environmental, and demographic differences between homes in the US and MX that may contribute to significantly different microbial composition of dust observed in these two countries.
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Affiliation(s)
- Lauren D Benton
- Department of Pediatrics, Steele Children's Research Center, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA.
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA.
| | - Nicolas Lopez-Galvez
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
- San Diego State University Research Foundation, San Diego State University, 5250 Campanile Dr, San Diego, CA, 92182, USA
| | - Chloe Herman
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, 1350 S Knoles Dr, Flagstaff, AZ, 86011, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, 1350 S Knoles Dr, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily K Cope
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, 1350 S Knoles Dr, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Cecilia Rosales
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
| | - Mercedes Gameros
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
| | - Nathan Lothrop
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
| | - Fernando D Martínez
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
| | - Anne L Wright
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
| | - Tara F Carr
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
| | - Paloma I Beamer
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
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9
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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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10
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Guerrieri F, Libert C. The invisible life. Front Microbiol 2024; 15:1401487. [PMID: 38832115 PMCID: PMC11144902 DOI: 10.3389/fmicb.2024.1401487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Affiliation(s)
- Francesca Guerrieri
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 - CNRS 5286, Lyon, France
| | - Cédric Libert
- Ecole Nationale Superieure d'Architecture de Saint-Etienne, Saint-Etienne, France
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11
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Bosch TCG, Wigley M, Colomina B, Bohannan B, Meggers F, Amato KR, Azad MB, Blaser MJ, Brown K, Dominguez-Bello MG, Ehrlich SD, Elinav E, Finlay BB, Geddie K, Geva-Zatorsky N, Giles-Vernick T, Gros P, Guillemin K, Haraoui LP, Johnson E, Keck F, Lorimer J, McFall-Ngai MJ, Nichter M, Pettersson S, Poinar H, Rees T, Tropini C, Undurraga EA, Zhao L, Melby MK. The potential importance of the built-environment microbiome and its impact on human health. Proc Natl Acad Sci U S A 2024; 121:e2313971121. [PMID: 38662573 PMCID: PMC11098107 DOI: 10.1073/pnas.2313971121] [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] [Indexed: 05/18/2024] Open
Abstract
There is increasing evidence that interactions between microbes and their hosts not only play a role in determining health and disease but also in emotions, thought, and behavior. Built environments greatly influence microbiome exposures because of their built-in highly specific microbiomes coproduced with myriad metaorganisms including humans, pets, plants, rodents, and insects. Seemingly static built structures host complex ecologies of microorganisms that are only starting to be mapped. These microbial ecologies of built environments are directly and interdependently affected by social, spatial, and technological norms. Advances in technology have made these organisms visible and forced the scientific community and architects to rethink gene-environment and microbe interactions respectively. Thus, built environment design must consider the microbiome, and research involving host-microbiome interaction must consider the built-environment. This paradigm shift becomes increasingly important as evidence grows that contemporary built environments are steadily reducing the microbial diversity essential for human health, well-being, and resilience while accelerating the symptoms of human chronic diseases including environmental allergies, and other more life-altering diseases. New models of design are required to balance maximizing exposure to microbial diversity while minimizing exposure to human-associated diseases. Sustained trans-disciplinary research across time (evolutionary, historical, and generational) and space (cultural and geographical) is needed to develop experimental design protocols that address multigenerational multispecies health and health equity in built environments.
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Affiliation(s)
- Thomas C. G. Bosch
- Zoological Institute, University of Kiel, Kiel24118, Germany
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
| | - Mark Wigley
- Graduate School of Architecture, Planning and Preservation, Columbia University, New York, NY10027
| | - Beatriz Colomina
- School of Architecture, Princeton University, Princeton, NJ08544
| | - Brendan Bohannan
- The Institute of Ecology and Evolution, University of Oregon, Eugene, OR97403-5289
| | - Forrest Meggers
- Princeton University School of Architecture & Andlinger Center for Energy and the Environment, Princeton, NJ08540
| | - Katherine R. Amato
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Anthropology, Northwestern University, Evanston, IL60208
| | - Meghan B. Azad
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3E 0Z3, Canada
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Martin J. Blaser
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, MBR3E 3P4, Canada
- Center for Advanced Biotechnology and Medicine at Rutgers Biomedical and Health Sciences, Rutgers University, Piscataway, NJ08854-8021
| | - Kate Brown
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Program in Science, Technology and Society, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Maria Gloria Dominguez-Bello
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ08901
- Department of Anthropology, Rutgers University, New Brunswick, NJ08901
| | - Stanislav Dusko Ehrlich
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Institute of Neurology, University College London, LondonWC1N 3RX, United Kingdom
| | - Eran Elinav
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Systems Immunology Department, Weizmann Institute of Science, Rehovot761000, Israel
- Division of Microbiome & Cancer, Deutsches Krebsforschungszentrum, 69120Heidelberg, Germany
| | - B. Brett Finlay
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
| | - Kate Geddie
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Medical and Related Sciences Centre, The Canadian Institute for Advanced Research, Toronto, ONM5G 1L7, Canada
| | - Naama Geva-Zatorsky
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Technion Integrated Cancer Center, Technion-Israel Institute of Technology, Haifa3525433, Israel
- Department of Cell Biology and Cancer Science, Technion-Israel Institute of Technology, Haifa3525433, Israel
| | - Tamara Giles-Vernick
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Anthropology & Ecology of Disease Emergence, Institut Pasteur, Université Paris Cité, Paris75015, France
| | - Philippe Gros
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Biochemistry, McGill University, Montreal, QCH3G 1Y6, Canada
| | - Karen Guillemin
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Institute of Molecular Biology, University of Oregon, Eugene, OR97403
| | - Louis-Patrick Haraoui
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, CanadaJ1E 4K8
| | - Elizabeth Johnson
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- College of Human Ecology, Cornell University, IthakaNY14853
| | - Frédéric Keck
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Laboratoire d’Anthropologie Sociale, Collège de France, Paris75005, France
| | - Jamie Lorimer
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- School of Geography and the Environment, University of Oxford, OX1 3QY, United Kingdom
| | - Margaret J. McFall-Ngai
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA91125
| | - Mark Nichter
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- School of Anthropology, University of Arizona, Tucson, AZ85721
| | - Sven Pettersson
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Nanyang Technological University, Singapore637715, Singapore
| | - Hendrik Poinar
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4M4, Canada
| | - Tobias Rees
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- LIMN, Berkeley, CA94708
| | - Carolina Tropini
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Microbiology and Immunology and School of Biomedical Engineering, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Eduardo A. Undurraga
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Santiago7820436, Chile
| | - Liping Zhao
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ08901
| | - Melissa K. Melby
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ONM5G 1M1, Canada
- Department of Anthropology, University of Delaware, Newark, DE19716
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12
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Perdijk O, Azzoni R, Marsland BJ. The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract. Physiol Rev 2024; 104:835-879. [PMID: 38059886 DOI: 10.1152/physrev.00020.2023] [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: 05/02/2023] [Revised: 11/07/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The last decade of microbiome research has highlighted its fundamental role in systemic immune and metabolic homeostasis. The microbiome plays a prominent role during gestation and into early life, when maternal lifestyle factors shape immune development of the newborn. Breast milk further shapes gut colonization, supporting the development of tolerance to commensal bacteria and harmless antigens while preventing outgrowth of pathogens. Environmental microbial and lifestyle factors that disrupt this process can dysregulate immune homeostasis, predisposing infants to atopic disease and childhood asthma. In health, the low-biomass lung microbiome, together with inhaled environmental microbial constituents, establishes the immunological set point that is necessary to maintain pulmonary immune defense. However, in disease perturbations to immunological and physiological processes allow the upper respiratory tract to act as a reservoir of pathogenic bacteria, which can colonize the diseased lung and cause severe inflammation. Studying these host-microbe interactions in respiratory diseases holds great promise to stratify patients for suitable treatment regimens and biomarker discovery to predict disease progression. Preclinical studies show that commensal gut microbes are in a constant flux of cell division and death, releasing microbial constituents, metabolic by-products, and vesicles that shape the immune system and can protect against respiratory diseases. The next major advances may come from testing and utilizing these microbial factors for clinical benefit and exploiting the predictive power of the microbiome by employing multiomics analysis approaches.
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Affiliation(s)
- Olaf Perdijk
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Rossana Azzoni
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
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13
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Kwak S, Usyk M, Beggs D, Choi H, Ahdoot D, Wu F, Maceda L, Li H, Im EO, Han HR, Lee E, Wu AH, Hayes RB, Ahn J. Sociobiome - Individual and neighborhood socioeconomic status influence the gut microbiome in a multi-ethnic population in the US. NPJ Biofilms Microbiomes 2024; 10:19. [PMID: 38467678 PMCID: PMC10928180 DOI: 10.1038/s41522-024-00491-y] [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: 03/24/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Lower socioeconomic status (SES) is related to increased incidence and mortality due to chronic diseases in adults. Association between SES variables and gut microbiome variation has been observed in adults at the population level, suggesting that biological mechanisms may underlie the SES associations; however, there is a need for larger studies that consider individual- and neighborhood-level measures of SES in racially diverse populations. In 825 participants from a multi-ethnic cohort, we investigated how SES shapes the gut microbiome. We determined the relationship of a range of individual- and neighborhood-level SES indicators with the gut microbiome. Individual education level and occupation were self-reported by questionnaire. Geocoding was applied to link participants' addresses with neighborhood census tract socioeconomic indicators, including average income and social deprivation in the census tract. Gut microbiome was measured using 16SV4 region rRNA gene sequencing of stool samples. We compared α-diversity, β-diversity, and taxonomic and functional pathway abundance by SES. Lower SES was significantly associated with greater α-diversity and compositional differences among groups, as measured by β-diversity. Several taxa related to low SES were identified, especially an increasing abundance of Prevotella copri and Catenibacterium sp000437715, and decreasing abundance of Dysosmobacter welbionis in terms of their high log-fold change differences. In addition, nativity and race/ethnicity have emerged as ecosocial factors that also influence the gut microbiota. Together, these results showed that lower SES was strongly associated with compositional and taxonomic measures of the gut microbiome, and may contribute to shaping the gut microbiota.
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Affiliation(s)
- Soyoung Kwak
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Mykhaylo Usyk
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Dia Beggs
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Heesun Choi
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Dariush Ahdoot
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Feng Wu
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Lorraine Maceda
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Huilin Li
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Eun-Ok Im
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
| | - Hae-Ra Han
- Johns Hopkins University School of Nursing, Baltimore, MD, USA
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Eunjung Lee
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anna H Wu
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Richard B Hayes
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Jiyoung Ahn
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA.
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14
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Li LJ, Xu F, Xu JX, Yan Y, Su JQ, Zhu YG, Li H. Spatiotemporal Changes of Antibiotic Resistance, Potential Pathogens, and Health Risk in Kindergarten Dust. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:3919-3930. [PMID: 38353611 DOI: 10.1021/acs.est.3c07935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The microorganisms present in kindergartens are extremely important for children's health during their three-year preschool education. To assess the risk of outdoor dust in kindergartens, the antibiotic resistome and potential pathogens were investigated in dust samples collected from 59 kindergartens in Xiamen, southeast China in both the winter and summer. Both high-throughput quantitative PCR and metagenome analysis revealed a higher richness and abundance of antibiotic resistance genes (ARGs) in winter (P < 0.05). Besides, the bloom of ARGs and potential pathogens was evident in the urban kindergartens. The co-occurrence patterns among ARGs, mobile genetic elements (MGEs), and potential pathogens suggested some bacterial pathogens were potential hosts of ARGs and MGEs. We found a large number of high-risk ARGs in the dust; the richness and abundance of high-risk ARGs were higher in winter and urban kindergartens compared to in summer and peri-urban kindergartens, respectively. The results of the co-occurrence patterns and high-risk ARGs jointly reveal that urbanization will significantly increase the threat of urban dust to human beings and their risks will be higher in winter. This study unveils the close association between ARGs/mobile ARGs and potential pathogens and emphasizes that we should pay more attention to the health risks induced by their combination.
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Affiliation(s)
- Li-Juan Li
- 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
| | - Fei Xu
- 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
| | - Jian-Xin Xu
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - 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
- 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
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - 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
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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15
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Imai K, Niwa R, Fujioka M, Ito K. Understanding the quality and safety of food production through the lens of The Microbiome of The Built Environment. Biosci Biotechnol Biochem 2024; 88:254-259. [PMID: 37994666 DOI: 10.1093/bbb/zbad164] [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: 10/02/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023]
Abstract
The Microbiome of the Built Environment (MoBE) is profoundly implicated in various sectors, including food science. The balance between beneficial and pathogenic microbes in these facilities directly influences product quality and public health. Maintaining a careful check on MoBE and external microbes is vital to the food industry to ensure quality control. There is also a risk of contamination in the meat processing facility as well. However, over-sanitization can increase drug-resistant microbes, highlighting the importance of balanced microbial management. Additionally, facility design, influenced by understanding MoBE, can optimize the growth of beneficial microbes and inhibit pathogenic microbes. Microbial mapping, an emerging practice, offers insights into microbial hotspots within facilities, resulting in targeted interventions. As the food industry evolves, the intricate understanding and management of MoBE will be pivotal to ensuring optimal food quality, safety, and innovation.
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Affiliation(s)
- Kota Imai
- BIOTA Inc., Tokyo, Japan
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Ryo Niwa
- BIOTA Inc., Tokyo, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Fujioka
- BIOTA Inc., Tokyo, Japan
- Department of Molecular Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
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16
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Wallace M, Cummings, Jr. DA, Roberts AG, Puri AW. A widespread methylotroph acyl-homoserine lactone synthase produces a new quorum sensing signal that regulates swarming in Methylobacterium fujisawaense. mBio 2024; 15:e0199923. [PMID: 38085021 PMCID: PMC10790750 DOI: 10.1128/mbio.01999-23] [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: 07/28/2023] [Accepted: 10/31/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacteria known as pink-pigmented facultative methylotrophs colonize many diverse environments on earth, play an important role in the carbon cycle, and in some cases promote plant growth. However, little is known about how these organisms interact with each other and their environment. In this work, we identify one of the chemical signals commonly used by these bacteria and discover that this signal controls swarming motility in the pink-pigmented facultative methylotroph Methylobacterium fujisawaense DSM5686. This work provides new molecular details about interactions between these important bacteria and will help scientists predict these interactions and the group behaviors they regulate from genomic sequencing information.
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Affiliation(s)
- Mike Wallace
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
| | - Dale A. Cummings, Jr.
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
| | - Andrew G. Roberts
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Aaron W. Puri
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, USA
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17
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Gottel NR, Hill MS, Neal MJ, Allard SM, Zengler K, Gilbert JA. Biocontrol in built environments to reduce pathogen exposure and infection risk. THE ISME JOURNAL 2024; 18:wrad024. [PMID: 38365248 PMCID: PMC10848226 DOI: 10.1093/ismejo/wrad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.
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Affiliation(s)
- Neil R Gottel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
| | - Megan S Hill
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Maxwell J Neal
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
| | - Sarah M Allard
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Karsten Zengler
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
| | - Jack A Gilbert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
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18
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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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19
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Xie J, Acosta EM, Gitai Z. Bacterial viability in the built environment of the home. PLoS One 2023; 18:e0288092. [PMID: 37939059 PMCID: PMC10631670 DOI: 10.1371/journal.pone.0288092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/15/2023] [Indexed: 11/10/2023] Open
Abstract
The built environment (BE) consists of human-made structures and, much like living organisms, is colonized by bacteria that make up the BE microbiome. The BE microbiome can potentially affect human health because of the constant proximity of these bacteria to humans. This has led to increasing public concern of whether the bacteria in the BE are harmful. Previous studies have used approaches based on DNA sequencing to assess the composition of the BE microbiome. However, the extent to which the bacterial DNA in the BE represents viable bacterial cells that could infect human hosts remains unknown. To address this open question we used both culture-based and culture-independent molecular methods to profile bacterial viability of the microbiomes from several BE sites. As part of an undergraduate-led project, we found that the vast majority of the bacterial DNA from the BE is not associated with viable bacteria, suggesting that most bacteria in the BE are dead. To begin to understand the determinants of bacterial viability in the BE we used mock bacterial communities to investigate the effects of temperature, relative humidity, and human interaction on bacterial viability. We found that relative humidity, temperature, and surface material did not have statistically significant effects on BE microbiome viability, but environmental exposure decreased bacterial viability. These results update our conception of the BE microbiome and begin to define the factors that affect BE microbiome viability.
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Affiliation(s)
- Joy Xie
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Ellen M. Acosta
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
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20
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Young GR, Sherry A, Smith DL. Built environment microbiomes transition from outdoor to human-associated communities after construction and commissioning. Sci Rep 2023; 13:15854. [PMID: 37740013 PMCID: PMC10516947 DOI: 10.1038/s41598-023-42427-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/10/2023] [Indexed: 09/24/2023] Open
Abstract
The microbiota of the built environment is linked to usage, materials and, perhaps most importantly, human health. Many studies have attempted to identify ways of modulating microbial communities within built environments to promote health. None have explored how these complex communities assemble initially, following construction of new built environments. This study used high-throughput targeted sequencing approaches to explore bacterial community acquisition and development throughout the construction of a new build. Microbial sampling spanned from site identification, through the construction process to commissioning and use. Following commissioning of the building, bacterial richness and diversity were significantly reduced (P < 0.001) and community structure was altered (R2 = 0.14; P = 0.001). Greater longitudinal community stability was observed in outdoor environments than indoor environments. Community flux in indoor environments was associated with human interventions driving environmental selection, which increased 10.4% in indoor environments following commissioning. Increased environmental selection coincided with a 12% reduction in outdoor community influence on indoor microbiomes (P = 2.00 × 10-15). Indoor communities became significantly enriched with human associated genera including Escherichia, Pseudomonas, and Klebsiella spp. These data represent the first to characterize the initial assembly of bacterial communities in built environments and will inform future studies aiming to modulate built environment microbiota.
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Affiliation(s)
- Gregory R Young
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, NE1 8ST, UK
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle, NE1 8ST, UK
| | - Angela Sherry
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, NE1 8ST, UK
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle, NE1 8ST, UK
| | - Darren L Smith
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, NE1 8ST, UK.
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle, NE1 8ST, UK.
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Bruno A, Sandionigi A, Panio A, Rimoldi S, Orizio F, Agostinetto G, Hasan I, Gasco L, Terova G, Labra M. Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets. BMC Microbiol 2023; 23:248. [PMID: 37674159 PMCID: PMC10481543 DOI: 10.1186/s12866-023-02990-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Sustainable aquaculture relies on multiple factors, including water quality, fish diets, and farmed fish. Replacing fishmeal (FM) with alternative protein sources is key for improving sustainability in aquaculture and promoting fish health. Indeed, great research efforts have been made to evaluate novel feed formulations, focusing especially on the effects on the fish gut microbiome. Few studies have explored host-environment interactions. In the present study, we evaluated the influence of novel insect-based (Tenebrio molitor) fish diets on the microbiome at the water-fish interface in an engineered rainbow trout (Oncorhynchus mykiss) farming ecosystem. Using 16S rRNA gene metabarcoding, we comprehensively analyzed the microbiomes of water, tank biofilm, fish intestinal mucus, fish cutis, and feed samples. RESULTS Core microbiome analysis revealed the presence of a highly reduced core shared by all sample sources, constituted by Aeromonas spp., in both the control and novel feed test groups. Network analysis showed that samples were clustered based on the sample source, with no significant differences related to the feed formulation tested. Thus, the different diets did not seem to affect the environment (water and tank biofilm) and fish (cutis and intestinal mucus) microbiomes. To disentangle the contribution of feed at a finer scale, we performed a differential abundance analysis and observed differential enrichment/impoverishment in specific taxa, comparing the samples belonging to the control diet group and the insect-based diet group. CONCLUSIONS Omic exploration of the water-fish interface exposes patterns that are otherwise undetected. These data demonstrate a link between the environment and fish and show that subtle but significant differences are caused by feed composition. Thus, the research presented here is a step towards positively influencing the aquaculture environment and its microbiome.
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Affiliation(s)
- Antonia Bruno
- ZooPlantLab, Biotechnology and Biosciences Department, University of Milano-Bicocca, Milan, Italy.
| | | | - Antonella Panio
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Milan, Italy
| | - Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Flavio Orizio
- ZooPlantLab, Biotechnology and Biosciences Department, University of Milano-Bicocca, Milan, Italy
| | - Giulia Agostinetto
- ZooPlantLab, Biotechnology and Biosciences Department, University of Milano-Bicocca, Milan, Italy
| | - Imam Hasan
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Laura Gasco
- Department of Agricultural, Forest and Food Sciences, University of Turin, Torino, Italy
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Massimo Labra
- ZooPlantLab, Biotechnology and Biosciences Department, University of Milano-Bicocca, Milan, Italy
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Abstract
Emerging evidence suggest a major role for the gut microbiome in wound infections. A Trojan Horse mechanism of surgical site infections has been hypothesized to occur when pathogens in the gut, gums, and periodontal areas enter an immune cell and silently travel to the wound site where they release their infectious payload. Genetic tracking of microbes at the strain level is now possible with genetic sequencing techniques and can clarify the origin of microbes that cause wound infections. An emerging field of dietary prehabilitation to modulate the microbiome before surgery is being described to improve infection-related outcomes from surgery.
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Affiliation(s)
- Sanjiv Hyoju
- Department of Surgery, University of Chicago, Pritzker School of Medicine, 5841 South Maryland, Chicago, IL 60637, USA
| | - Kaylie Machutta
- University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, NV 89557, USA
| | - Monika A Krezalek
- Northshore University Health Systems, 1000 Central Street Suite 800, Evanston, IL 60201, USA
| | - John C Alverdy
- Department of Surgery, University of Chicago, Pritzker School of Medicine, 5841 South Maryland, Chicago, IL 60637, USA.
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23
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Youngblom MA, Imhoff MR, Smyth LM, Mohamed MA, Pepperell CS. Portrait of a generalist bacterium: pathoadaptation, metabolic specialization and extreme environments shape diversity of Staphylococcus saprophyticus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553882. [PMID: 37645846 PMCID: PMC10462137 DOI: 10.1101/2023.08.18.553882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Staphylococcus saprophyticus is a Gram-positive, coagulase-negative staphylococcus found in diverse environments including soil and freshwater, meat, and dairy foods. S. saprophyticus is also an important cause of urinary tract infections (UTIs) in humans, and mastitis in cattle. However, the genetic determinants of virulence have not yet been identified, and it remains unclear whether there are distinct sub-populations adapted to human and animal hosts. Using a diverse sample of S. saprophyticus isolates from food, animals, environmental sources, and human infections, we characterized the population structure and diversity of global populations of S. saprophyticus . We found that divergence of the two major clades of S. saprophyticus is likely facilitated by barriers to horizontal gene transfer (HGT) and differences in metabolism. Using genome-wide association study (GWAS) tools we identified the first Type VII secretion system (T7SS) described in S. saprophyticus and its association with bovine mastitis. Finally, we found that in general, strains of S. saprophyticus from different niches are genetically similar with the exception of built environments, which function as a 'sink' for S. saprophyticus populations. This work increases our understanding of the ecology of S. saprophyticus and of the genomics of bacterial generalists. Data summary Raw sequencing data for newly sequenced S. saprophyticus isolates have been deposited to the NCBI SRA under the project accession PRJNA928770. A list of all genomes used in this work and their associated metadata are available in the supplementary material. Custom scripts used in the comparative genomics and GWAS analyses are available here: https://github.com/myoungblom/sapro_genomics . Impact statement It is not known whether human and cattle diseases caused by S. saprophyticus represent spillover events from a generalist adapted to survive in a range of environments, or whether the capacity to cause disease represents a specific adaptation. Seasonal cycles of S. saprophyticus UTIs and molecular epidemiological evidence suggest that these infections may be environmentally-acquired rather than via transmission from person to person. Using comparative genomics and genome wide association study tools, we found that S. saprophyticus appears adapted to inhabit a wide range of environments (generalist), with isolates from animals, food, natural environments and human infections being closely related. Bacteria that routinely switch environments, particularly between humans and animals, are of particular concern when it comes to the spread of antibiotic resistance from farm environments into human populations. This work provides a framework for comparative genomic analyses of bacterial generalists and furthers our understanding of how bacterial populations move between humans, animals, and the environment.
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24
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Rappaport HB, Oliverio AM. Extreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology. Nat Commun 2023; 14:4959. [PMID: 37587119 PMCID: PMC10432404 DOI: 10.1038/s41467-023-40657-4] [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: 03/23/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
Research in extreme environments has substantially expanded our understanding of the ecology and evolution of life on Earth, but a major group of organisms has been largely overlooked: microbial eukaryotes (i.e., protists). In this Perspective, we summarize data from over 80 studies of protists in extreme environments and identify focal lineages that are of significant interest for further study, including clades within Echinamoebida, Heterolobosea, Radiolaria, Haptophyta, Oomycota, and Cryptophyta. We argue that extreme environments are prime sampling targets to fill gaps in the eukaryotic tree of life and to increase our understanding of the ecology, metabolism, genome architecture, and evolution of eukaryotic life.
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Affiliation(s)
| | - Angela M Oliverio
- Department of Biology, Syracuse University, Syracuse, NY, 13210, USA.
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25
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Bartmanski BJ, Rocha M, Zimmermann-Kogadeeva M. Recent advances in data- and knowledge-driven approaches to explore primary microbial metabolism. Curr Opin Chem Biol 2023; 75:102324. [PMID: 37207402 PMCID: PMC10410306 DOI: 10.1016/j.cbpa.2023.102324] [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: 12/28/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023]
Abstract
With the rapid progress in metabolomics and sequencing technologies, more data on the metabolome of single microbes and their communities become available, revealing the potential of microorganisms to metabolize a broad range of chemical compounds. The analysis of microbial metabolomics datasets remains challenging since it inherits the technical challenges of metabolomics analysis, such as compound identification and annotation, while harboring challenges in data interpretation, such as distinguishing metabolite sources in mixed samples. This review outlines the recent advances in computational methods to analyze primary microbial metabolism: knowledge-based approaches that take advantage of metabolic and molecular networks and data-driven approaches that employ machine/deep learning algorithms in combination with large-scale datasets. These methods aim at improving metabolite identification and disentangling reciprocal interactions between microbes and metabolites. We also discuss the perspective of combining these approaches and further developments required to advance the investigation of primary metabolism in mixed microbial samples.
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Affiliation(s)
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, Braga, Portugal
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26
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Iancu L, Muslim A, Aazmi S, Jitaru V. Postmortem skin microbiome signatures associated with human cadavers within the first 12 h at the morgue. Front Microbiol 2023; 14:1234254. [PMID: 37564294 PMCID: PMC10410280 DOI: 10.3389/fmicb.2023.1234254] [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: 06/04/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023] Open
Abstract
Introduction Forensic microbiome studies expanded during the last decade, aiming to identify putative bacterial biomarkers to be used for the postmortem interval (PMI) estimation. Bacterial diversity and dynamics during decomposition are influenced by each individual's micro and macroenvironment, ante and postmortem conditions, varying across body sites and time. The skin, the largest organ of the human body, hosts a diverse microbial diversity, representing the first line of defense of a living individual. Targeting the investigation of the postmortem skin microbiome could help understanding the role of microbes during decomposition, and association with the ante and postmortem conditions. Methods The current study aimed to identify the postmortem skin microbiome signatures associated with eight human bodies, received at the Institute of Legal Medicine Iasi, Romania, during April and May 2021. A total of 162 samples (including triplicate) representing face and hands skin microbiome were investigated via Illumina MiSeq, upon arrival at the morgue (T0) and after 12 hours (T1). Results The taxonomic characteristics of the skin microbiota varied across different body sites. However, there were no significant differences in taxonomic profiles between collection time, T0 and T1, except for some dynamic changes in the abundance of dominant bacteria. Moreover, different microbial signatures have been associated with a specific cause of death, such as cardiovascular disease, while an elevated blood alcohol level could be associated with a decrease in bacterial richness and diversity. Discussion The places where the bodies were discovered seemed to play an important role in explaining the bacterial diversity composition. This study shows promising results towards finding common postmortem bacterial signatures associated with human cadavers within the first 12h at the morgue.
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Affiliation(s)
- Lavinia Iancu
- Department of Criminal Justice, University of North Dakota, Grand Forks, ND, United States
| | - Azdayanti Muslim
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, Selangor, Malaysia
- Institute for Biodiversity and Sustainable Development, Universiti Teknologi MARA (UiTM), Selangor, Malaysia
- Microbiome Health and Environment (MiHeaRT), Faculty of Applied Sciences, Universiti Teknologi MARA, Selangor, Malaysia
| | - Shafiq Aazmi
- Microbiome Health and Environment (MiHeaRT), Faculty of Applied Sciences, Universiti Teknologi MARA, Selangor, Malaysia
- School of Biology, Faculty of Applied Science, Universiti Teknologi MARA, Selangor, Malaysia
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Lu Y, Yang J, Zhang L, Chen F, Han P, Fu Y. Characteristics of bacterial community and ARG profiles in the surface and air environments in a spacecraft assembly cleanroom. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121613. [PMID: 37087089 DOI: 10.1016/j.envpol.2023.121613] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/13/2023] [Accepted: 04/09/2023] [Indexed: 05/03/2023]
Abstract
Understanding the microbial communities and antibiotic resistance genes (ARGs) in spacecraft assembly cleanrooms is crucial for spacecraft microbial control and astronaut safety. However, there have been few reports of ARG profiles and their relationship with microbiomes in such environments. In the present study, we assessed the bacterial community and ARGs in the air dust and surface environments of a typical spacecraft assembly cleanroom. Our results show a significant difference in bacterial composition between surfaces and air dust, as they belong to two distinct ecostates. Bacillus and Acinetobacter were significantly enriched in the air samples. Bacterial community network analysis revealed lower topological parameters and robustness of bacterial networks in the air samples. We also observed different distribution patterns of some typical ARGs between surface and air dust samples. Notably, the ermB gene exhibited a relatively high copy number and was enriched in the surface environment, compared to that in the air. Overall, our study provides insight into the complex microbial community and the distribution and transfer of ARGs in spacecraft assembly cleanrooms, and offers important input for developing control strategies against ARGs.
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Affiliation(s)
- Yueying Lu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Jianlou Yang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Lantao Zhang
- Institute of Manned Space System and Engineering, China Academy of Space Technology, Beijing, 100094, China.
| | - Fangqi Chen
- Shen Yuan Honors College, Beihang University, Beijing, 100191, China.
| | - Pei Han
- Laboratory of Space Utilization, Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, Beijing, 100094, China.
| | - Yuming Fu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China; International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China.
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28
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Shiwa Y, Baba T, Sierra MA, Kim J, Mason CE, Suzuki H. Evaluation of rRNA depletion methods for capturing the RNA virome from environmental surfaces. BMC Res Notes 2023; 16:142. [PMID: 37420286 DOI: 10.1186/s13104-023-06417-9] [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: 12/17/2022] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
OBJECTIVE Metatranscriptomic analysis of RNA viromes on built-environment surfaces is hampered by low RNA yields and high abundance of rRNA. Therefore, we evaluated the quality of libraries, efficiency of rRNA depletion, and viral detection sensitivity using a mock community and a melamine-coated table surface RNA with levels below those required (< 5 ng) with a library preparation kit (NEBNext Ultra II Directional RNA Library Prep Kit). RESULTS Good-quality RNA libraries were obtained from 0.1 ng of mock community and table surface RNA by changing the adapter concentration and number of PCR cycles. Differences in the target species of the rRNA depletion method affected the community composition and sensitivity of virus detection. The percentage of viral occupancy in two replicates was 0.259 and 0.290% in both human and bacterial rRNA-depleted samples, a 3.4 and 3.8-fold increase compared with that for only bacterial rRNA-depleted samples. Comparison of SARS-CoV-2 spiked-in human rRNA and bacterial rRNA-depleted samples suggested that more SARS-CoV-2 reads were detected in bacterial rRNA-depleted samples. We demonstrated that metatranscriptome analysis of RNA viromes is possible from RNA isolated from an indoor surface (representing a built-environment surface) using a standard library preparation kit.
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Affiliation(s)
- Yuh Shiwa
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan.
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan.
| | - Tomoya Baba
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
- Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Tokyo, Japan
| | - Maria A Sierra
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- 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
| | - 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
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.
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29
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Jeste DV, Malaspina D, Bagot K, Barch DM, Cole S, Dickerson F, Dilmore A, Ford CL, Karcher NR, Luby J, Rajji T, Pinto-Tomas AA, Young LJ. Review of Major Social Determinants of Health in Schizophrenia-Spectrum Psychotic Disorders: III. Biology. Schizophr Bull 2023; 49:867-880. [PMID: 37023360 PMCID: PMC10318888 DOI: 10.1093/schbul/sbad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
BACKGROUND Social determinants of health (SDoHs) are nonmedical factors that significantly impact health and longevity. We found no published reviews on the biology of SDoHs in schizophrenia-spectrum psychotic disorders (SSPD). STUDY DESIGN We present an overview of pathophysiological mechanisms and neurobiological processes plausibly involved in the effects of major SDoHs on clinical outcomes in SSPD. STUDY RESULTS This review of the biology of SDoHs focuses on early-life adversities, poverty, social disconnection, discrimination including racism, migration, disadvantaged neighborhoods, and food insecurity. These factors interact with psychological and biological factors to increase the risk and worsen the course and prognosis of schizophrenia. Published studies on the topic are limited by cross-sectional design, variable clinical and biomarker assessments, heterogeneous methods, and a lack of control for confounding variables. Drawing on preclinical and clinical studies, we propose a biological framework to consider the likely pathogenesis. Putative systemic pathophysiological processes include epigenetics, allostatic load, accelerated aging with inflammation (inflammaging), and the microbiome. These processes affect neural structures, brain function, neurochemistry, and neuroplasticity, impacting the development of psychosis, quality of life, cognitive impairment, physical comorbidities, and premature mortality. Our model provides a framework for research that could lead to developing specific strategies for prevention and treatment of the risk factors and biological processes, thereby improving the quality of life and increasing the longevity of people with SSPD. CONCLUSIONS Biology of SDoHs in SSPD is an exciting area of research that points to innovative multidisciplinary team science for improving the course and prognosis of these serious psychiatric disorders.
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Affiliation(s)
- Dilip V Jeste
- Department of Psychiatry, University of California, San Diego (Retired), CA, USA
| | - Dolores Malaspina
- Departments of Psychiatry, Neuroscience and Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kara Bagot
- Department of Psychiatry, Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deanna M Barch
- Departments of Psychological and Brain Sciences, Psychiatry, and Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Steve Cole
- Departments of Psychiatry and Biobehavioral Sciences, and Medicine, University of California, Los Angeles, CA, USA
| | - Faith Dickerson
- Department of Psychology, Sheppard Pratt, Baltimore, MD, USA
| | - Amanda Dilmore
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Charles L Ford
- Center for Translational Social Neuroscience, Department of Psychiatry, Emory University, Atlanta, GA, USA
| | - Nicole R Karcher
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Joan Luby
- Department of Psychiatry (Child), Washington University in St. Louis, St. Louis, MO, USA
| | - Tarek Rajji
- Adult Neurodevelopment and Geriatric Psychiatry Division, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Adrián A Pinto-Tomas
- Biochemistry Department, School of Medicine, Universidad de Costa Rica, San José, Costa Rica
| | - Larry J Young
- Center for Translational Social Neuroscience, Department of Psychiatry, Emory University, Atlanta, GA, USA
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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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31
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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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32
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Han SY, Yun G, Cha HM, Lee MK, Lee H, Kang EK, Hong SP, Teahan KA, Park M, Hwang H, Lee SS, Kim M, Choi IS. A Natural Virucidal and Microbicidal Spray Based on Polyphenol-Iron Sols. ACS APPLIED BIO MATERIALS 2023; 6:1981-1991. [PMID: 37083357 PMCID: PMC10152399 DOI: 10.1021/acsabm.3c00195] [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: 03/14/2023] [Accepted: 04/09/2023] [Indexed: 04/22/2023]
Abstract
Numerous disinfection methods have been developed to reduce the transmission of infectious diseases that threaten human health. However, it still remains elusively challenging to develop eco-friendly and cost-effective methods that deactivate a wide range of pathogens, from viruses to bacteria and fungi, without doing any harm to humans or the environment. Herein we report a natural spraying protocol, based on a water-dispersible supramolecular sol of nature-derived tannic acid (TA) and Fe3+, which is easy-to-use and low-cost. Our formulation effectively deactivates viruses (influenza A viruses, SARS-CoV-2, and human rhinovirus) as well as suppressing the growth and spread of pathogenic bacteria (Escherichia coli, Salmonella typhimurium, Staphylococcus aureus, and Acinetobacter baumannii) and fungi (Pleurotus ostreatus and Trichophyton rubrum). Its versatile applicability in a real-life setting is also demonstrated against microorganisms present on the surfaces of common household items (e.g., air filter membranes, disposable face masks, kitchen sinks, mobile phones, refrigerators, and toilet seats).
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Affiliation(s)
| | - Gyeongwon Yun
- Department of Chemistry,
KAIST, Daejeon 34141, Korea
| | - Hyeon-Min Cha
- Infectious Diseases Therapeutic Research Center,
KRICT, Daejeon 34114, Korea
- Graduate School of New Drug Discovery and Development,
Chungnam National University, Daejeon 34134,
Korea
| | - Myoung Kyu Lee
- Infectious Diseases Therapeutic Research Center,
KRICT, Daejeon 34114, Korea
| | - Hojae Lee
- Department of Chemistry, Hallym
University, Chuncheon 24252, Korea
| | | | - Seok-Pyo Hong
- Department of Chemistry,
KAIST, Daejeon 34141, Korea
| | - Kirsty A. Teahan
- School of Chemistry and Institute for Life Sciences,
Highfield Campus, University of Southampton, Southampton SO17
1BJ, United Kingdom
| | - Minjeong Park
- Hansol RootOne, Inc., 165
Myeoncheon-ro, Dangjin 31803, Korea
| | - Hansol Hwang
- Hansol RootOne, Inc., 165
Myeoncheon-ro, Dangjin 31803, Korea
| | - Seung Seo Lee
- School of Chemistry and Institute for Life Sciences,
Highfield Campus, University of Southampton, Southampton SO17
1BJ, United Kingdom
| | - Meehyein Kim
- Infectious Diseases Therapeutic Research Center,
KRICT, Daejeon 34114, Korea
- Graduate School of New Drug Discovery and Development,
Chungnam National University, Daejeon 34134,
Korea
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33
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Zhou JC, Wang YF, Zhu D, Zhu YG. Deciphering the distribution of microbial communities and potential pathogens in the household dust. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162250. [PMID: 36804982 DOI: 10.1016/j.scitotenv.2023.162250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
The reliance of modern society on indoor environments increasing has made them crucial sites for human exposure to microbes. Extensive research has identified ecological drivers that influence indoor microbial assemblages. However, few studies have examined the dispersion of microbes in different locations of identical indoor environments. In this study, we employed PacBio Sequel full-length amplicon sequencing to examine the distribution of microbes at distinct locations in a single home and to identify the potential pathogens and microbial functions. Microbial communities differed considerably among the indoor sampling sites (P < 0.05). In addition, bacterial diversity was influenced by human activities and contact with the external environment at different sites, whereas fungal diversity did not significantly differ among the sites. Potential pathogens, including bacteria and fungi, were significantly enriched on the door handle (P < 0.05), suggesting that door handles may be hotpots for potential pathogens in the household. A high proportion of fungal allergens (34.37 %-56.50 %), which can cause skin diseases and asthma, were observed. Co-occurrence network analysis revealed the essential ecological role of microbial interactions in the development of a healthy immune system. Overall, we revealed the differences in microbial communities at different sampling sites within a single indoor environment, highlighting the distribution of potential pathogens and ecological functions of microbes, and providing a new perspective and information for assessing indoor health from a microbiological viewpoint.
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Affiliation(s)
- Jia-Cheng Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; International School of Beijing, Beijing 101318, China
| | - Yi-Fei Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment 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.
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment 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
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment 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; University of the Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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34
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Du S, Tong X, Lai ACK, Chan CK, Mason CE, Lee PKH. Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution. Nat Commun 2023; 14:2676. [PMID: 37160974 PMCID: PMC10169181 DOI: 10.1038/s41467-023-38400-0] [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: 11/02/2022] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assesses viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes are found to be habitat dependent. Caudoviricetes species are ubiquitous on surface habitats in the BEs, and some of them are distinct from those present in other environments. Antimicrobial resistance genes are identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants' skin. Diverse CRISPR/Cas immunity systems and anti-CRISPR proteins are found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus-host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner is identified through a unique gene insertion. This work illustrates that virus-host interactions occur frequently in BEs and that viruses are integral members of BE microbiomes.
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Affiliation(s)
- Shicong Du
- 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
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, P. R. China
| | - Alvin C K Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Chak K Chan
- 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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35
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Ahn J, Kwak S, Usyk M, Beggs D, Choi H, Ahdoot D, Wu F, Maceda L, Li H, Im EO, Han HR, Lee E, Wu A, Hayes R. Sociobiome - Individual and neighborhood socioeconomic status influence the gut microbiome in a multi-ethnic population in the US. RESEARCH SQUARE 2023:rs.3.rs-2733916. [PMID: 37131763 PMCID: PMC10153375 DOI: 10.21203/rs.3.rs-2733916/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Lower socioeconomic status (SES) is related to increased incidence and mortality due to chronic diseases in adults. Association between SES variables and gut microbiome variation has been observed in adults at the population level, suggesting that biological mechanisms may underlie the SES associations; however, there is a need for larger U.S. studies that consider individual- and neighborhood-level measures of SES in racially diverse populations. In 825 participants from a multi-ethnic cohort, we investigated how SES shapes the gut microbiome. We determined the relationship of a range of several individual- and neighborhood-level SES indicators with the gut microbiome. Individual education level and occupation were self-reported by questionnaire. Geocoding was applied to link participants' addresses with neighborhood census tract socioeconomic indicators, including average income and social deprivation in the census tract. Gut microbiome was measured using 16SV4 region rRNA gene sequencing of stool samples. We compared α-diversity, β-diversity, and taxonomic and functional pathway abundance by socioeconomic status. Lower SES was significantly associated with greater α-diversity and compositional differences among groups, as measured by β-diversity. Several taxa related to low SES were identified, especially an increasing abundance of Genus Catenibacterium and Prevotella copri. The significant association between SES and gut microbiota remained even after considering the race/ethnicity in this racially diverse cohort. Together, these results showed that lower socioeconomic status was strongly associated with compositional and taxonomic measures of the gut microbiome, suggesting that SES may shape the gut microbiota.
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Affiliation(s)
| | | | | | - Dia Beggs
- Department of Population Health, NYU Grossman School of Medicine
| | | | | | - Feng Wu
- Perlmutter Cancer Center, NYU Langone Health
| | | | | | | | - Hae-Ra Han
- Johns Hopkins University School of Nursing
| | | | - Anna Wu
- University of Southern California
| | - Richard Hayes
- Department of Population Health, NYU Grossman School of Medicine
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36
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Conz A, Salmona M, Diomede L. Effect of Non-Nutritive Sweeteners on the Gut Microbiota. Nutrients 2023; 15:nu15081869. [PMID: 37111090 PMCID: PMC10144565 DOI: 10.3390/nu15081869] [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: 03/20/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The human gut microbiota, a complex community of microorganisms living in the digestive tract, consists of more than 1500 species distributed in more than 50 different phyla, with 99% of bacteria coming from about 30-40 species. The colon alone, which contains the largest population of the diverse human microbiota, can harbor up to 100 trillion bacteria. The gut microbiota is essential in maintaining normal gut physiology and health. Therefore, its disruption in humans is often associated with various pathological conditions. Different factors can influence the composition and function of the gut microbiota, including host genetics, age, antibiotic treatments, environment, and diet. The diet has a marked effect, impacting the gut microbiota composition, beneficially or detrimentally, by altering some bacterial species and adjusting the metabolites produced in the gut environment. With the widespread use of non-nutritive sweeteners (NNS) in the diet, recent investigations have focused on their effect on the gut microbiota as a mediator of the potential impact generated by gastrointestinal-related disturbances, such as insulin resistance, obesity, and inflammation. We summarized the results from pre-clinical and clinical studies published over the last ten years that examined the single effects of the most consumed NNS: aspartame, acesulfame-K, sucralose, and saccharin. Pre-clinical studies have given conflicting results for various reasons, including the administration method and the differences in metabolism of the same NNS among the different animal species. A dysbiotic effect of NNS was observed in some human trials, but many other randomized controlled trials reported a lack of significant impacts on gut microbiota composition. These studies differed in the number of subjects involved, their dietary habits, and their lifestyle; all factors related to the baseline composition of gut microbiota and their response to NNS. The scientific community still has no unanimous consensus on the appropriate outcomes and biomarkers that can accurately define the effects of NNS on the gut microbiota.
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Affiliation(s)
- Andrea Conz
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Mario Salmona
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Luisa Diomede
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
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37
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D’Accolti M, Soffritti I, Bini F, Mazziga E, Arnoldo L, Volta A, Bisi M, Antonioli P, Laurenti P, Ricciardi W, Vincenti S, Mazzacane S, Caselli E. Potential Use of a Combined Bacteriophage–Probiotic Sanitation System to Control Microbial Contamination and AMR in Healthcare Settings: A Pre-Post Intervention Study. Int J Mol Sci 2023; 24:ijms24076535. [PMID: 37047510 PMCID: PMC10095405 DOI: 10.3390/ijms24076535] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/24/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
Microbial contamination in the hospital environment is a major concern for public health, since it significantly contributes to the onset of healthcare-associated infections (HAIs), which are further complicated by the alarming level of antimicrobial resistance (AMR) of HAI-associated pathogens. Chemical disinfection to control bioburden has a temporary effect and can favor the selection of resistant pathogens, as observed during the COVID-19 pandemic. Instead, probiotic-based sanitation (probiotic cleaning hygiene system, PCHS) was reported to stably abate pathogens, AMR, and HAIs. PCHS action is not rapid nor specific, being based on competitive exclusion, but the addition of lytic bacteriophages that quickly and specifically kill selected bacteria was shown to improve PCHS effectiveness. This study aimed to investigate the effect of such combined probiotic–phage sanitation (PCHSφ) in two Italian hospitals, targeting staphylococcal contamination. The results showed that PCHSφ could provide a significantly higher removal of staphylococci, including resistant strains, compared with disinfectants (−76%, p < 0.05) and PCHS alone (−50%, p < 0.05). Extraordinary sporadic chlorine disinfection appeared compatible with PCHSφ, while frequent routine chlorine usage inactivated the probiotic/phage components, preventing PCHSφ action. The collected data highlight the potential of a biological sanitation for better control of the infectious risk in healthcare facilities, without worsening pollution and AMR concerns.
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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; (M.D.)
- 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; (M.D.)
- 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; (M.D.)
- 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; (M.D.)
- CIAS Research Center, University of Ferrara, 44122 Ferrara, Italy
| | - Luca Arnoldo
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Antonella Volta
- CIAS Research Center, University of Ferrara, 44122 Ferrara, Italy
| | - Matteo Bisi
- CIAS Research Center, University of Ferrara, 44122 Ferrara, Italy
| | - Paola Antonioli
- Department of Infection Prevention Control and Risk Management, S. Anna University Hospital, 44124 Ferrara, Italy
| | - Patrizia Laurenti
- Department of Health Sciences and Public Health, Section of Hygiene, Catholic University of the Sacred Heart, 00168 Rome, Italy
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Walter Ricciardi
- Department of Health Sciences and Public Health, Section of Hygiene, Catholic University of the Sacred Heart, 00168 Rome, Italy
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Sara Vincenti
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, 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; (M.D.)
- CIAS Research Center, University of Ferrara, 44122 Ferrara, Italy
- Correspondence:
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38
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Xiong G, Ji L, Cheng M, Ning K. Niche-Based Microbial Community Assemblage in Urban Transit Systems and the Influence of City Characteristics. Microbiol Spectr 2023; 11:e0016723. [PMID: 36916942 PMCID: PMC10101094 DOI: 10.1128/spectrum.00167-23] [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: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 03/16/2023] Open
Abstract
Microbiota residing on the urban transit systems (UTSs) can be shared by travelers and have niche-specific assemblage. However, it remains unclear how the assemblages are influenced by city characteristics, rendering city-specific and microbial-aware urban planning challenging. Here, we analyzed 3,359 UTS microbial samples collected from 16 cities around the world. We found the stochastic process dominated in all UTS microbiota assemblages, with the explanation rate (R2) of the neutral community model (NCM) higher than 0.7. Moreover, city characteristics predominantly drove such assemblage, largely responsible for the variation in the stochasticity ratio (50.1%). Furthermore, by utilizing an artificial intelligence model, we quantified the ability of UTS microbes in discriminating between cities and found that the ability was also strongly affected by city characteristics, especially climate and continent. From these, we found that although the NCM R2 of the New York City UTS microbiota was 0.831, the accuracy of the microbial-based city characteristic classifier was higher than 0.9. This is the first study to demonstrate the effects of city characteristics on the UTS microbiota assemblage, paving the way for city-specific and microbial-aware applications. IMPORTANCE We analyzed the urban transit system microbiota assemblage across 16 cities. The stochastic process was dominant in the urban transit system microbiota assemblage. The urban transit system microbe's ability in discriminating between cities was quantified using transfer learning based on random forest (RF) methods. Certain urban transit system microbes were strongly affected by city characteristics.
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Affiliation(s)
- Guangzhou Xiong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lei Ji
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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39
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Sah GP, Kovalick G, Chopyk J, Kuo P, Huang L, Ghatbale P, Das P, Realegeno S, Knight R, Gilbert JA, Pride DT. Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic. Microbiol Spectr 2023; 11:e0450922. [PMID: 36916973 PMCID: PMC10100919 DOI: 10.1128/spectrum.04509-22] [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: 11/20/2022] [Accepted: 02/11/2023] [Indexed: 03/15/2023] Open
Abstract
The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.
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Affiliation(s)
- Govind Prasad Sah
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Grace Kovalick
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Jessica Chopyk
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Lina Huang
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Pooja Ghatbale
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Promi Das
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
| | - Susan Realegeno
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
- Department of Computer Science & Engineering, University of California San Diego, San Diego, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
- Scripps Institution of Oceanography and Department of Pediatrics, University of California San Diego, San Diego, California, USA
| | - David T. Pride
- Department of Pathology, University of California San Diego, San Diego, California, USA
- Department of Medicine, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
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40
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Impact of high altitude on composition and functional profiling of oral microbiome in Indian male population. Sci Rep 2023; 13:4038. [PMID: 36899053 PMCID: PMC10006418 DOI: 10.1038/s41598-023-30963-8] [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: 09/12/2022] [Accepted: 03/03/2023] [Indexed: 03/12/2023] Open
Abstract
The oral cavity of human contains bacteria that are critical for maintaining the homeostasis of the body. External stressors such as high altitude (HA) and low oxygen affect the human gut, skin and oral microbiome. However, compared to the human gut and skin microbiome, studies demonstrating the impact of altitude on human oral microbiota are currently scarce. Alterations in the oral microbiome have been reported to be associated with various periodontal diseases. In light of the increased occurrence of HA oral health related problems, the effect of HA on the oral salivary microbiome was investigated. We conducted a pilot study in 16 male subjects at two different heights i.e., H1 (210 m) and H2 (4420 m). Total of 31 saliva samples,16 at H1 and 15 at H2 were analyzed by utilizing the 16S rRNA high-throughput sequencing, to explore the relationship between the HA environment and salivary microbiota. The preliminary results suggesting that, the most abundant microbiome at the phylum level are: Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Interestingly, 11 genera were identified at the both heights with different relative abundances. In addition, the salivary microbiome was more diverse at H1 compared to H2 as demonstrated by decreased alpha diversity. Further, predicted functional results indicate that microbial metabolic profiles significantly decreased at H2 as compared to H1, including two major metabolic pathways involving carbohydrates, and amino acids. Our findings show that HA induces shifts in the composition and structure of human oral microbiota which can affect host health homeostasis.
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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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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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Neidhöfer C, Sib E, Benhsain AH, Mutschnik-Raab C, Schwabe A, Wollkopf A, Wetzig N, Sieber MA, Thiele R, Döhla M, Engelhart S, Mutters NT, Parčina M. Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes. Microorganisms 2023; 11:microorganisms11010185. [PMID: 36677477 PMCID: PMC9867353 DOI: 10.3390/microorganisms11010185] [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: 11/22/2022] [Revised: 01/02/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023] Open
Abstract
Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms propagate how and where in hospitals are undoubtedly beneficial for preventing hospital-acquired infections, there are, to date, no standardized procedures on how to best study the hospital microbiome. Our study aimed to investigate the microbiome of hospital sanitary facilities, outlining the extent to which hospital microbiome analyses differ according to sample-preparation protocol. For this purpose, fifty samples were collected from two separate hospitals-from three wards and one hospital laboratory-using two different storage media from which DNA was extracted using two different extraction kits and sequenced with two different primer pairs (V1-V2 and V3-V4). There were no observable differences between the sample-preservation media, small differences in detected taxa between the DNA extraction kits (mainly concerning Propionibacteriaceae), and large differences in detected taxa between the two primer pairs V1-V2 and V3-V4. This analysis also showed that microbial occurrences and compositions can vary greatly from toilets to sinks to showers and across wards and hospitals. In surgical wards, patient toilets appeared to be characterized by lower species richness and diversity than staff toilets. Which sampling sites are the best for which assessments should be analyzed in more depth. The fact that the sample processing methods we investigated (apart from the choice of primers) seem to have changed the results only slightly suggests that comparing hospital microbiome studies is a realistic option. The observed differences in species richness and diversity between patient and staff toilets should be further investigated, as these, if confirmed, could be a result of excreted antimicrobials.
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Affiliation(s)
- Claudio Neidhöfer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Correspondence:
| | - Esther Sib
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Al-Harith Benhsain
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | | | - Anna Schwabe
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Alexander Wollkopf
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Nina Wetzig
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Martin A. Sieber
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Ralf Thiele
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, 53757 Sankt Augustin, Germany
| | - Manuel Döhla
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56072 Koblenz, Germany
| | - Steffen Engelhart
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Nico T. Mutters
- Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany
| | - Marijo Parčina
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
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Bruno A, Cafiso A, Sandionigi A, Galimberti A, Magnani D, Manfrin A, Petroni G, Casiraghi M, Bazzocchi C. Red mark syndrome: Is the aquaculture water microbiome a keystone for understanding the disease aetiology? Front Microbiol 2023; 14:1059127. [PMID: 36922974 PMCID: PMC10010170 DOI: 10.3389/fmicb.2023.1059127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/01/2023] [Indexed: 03/02/2023] Open
Abstract
Aquaculture significantly contributes to the growing demand for food worldwide. However, diseases associated with intensive aquaculture conditions, especially the skin related syndromes, may have significant implications on fish health and industry. In farmed rainbow trout, red mark syndrome (RMS), which consists of multiple skin lesions, currently lacks recognized aetiological agents, and increased efforts are needed to elucidate the onset of these conditions. Most of the past studies were focused on analyzing skin lesions, but no study focused on water, a medium constantly interacting with fish. Indeed, water tanks are environmental niches colonized by microbial communities, which may be implicated in the onset of the disease. Here, we present the results of water and sediment microbiome analyses performed in an RMS-affected aquaculture facility, bringing new knowledge about the environmental microbiomes harbored under these conditions. On the whole, no significant differences in the bacterial community structure were reported in RMS-affected tanks compared to the RMS-free ones. However, we highlighted significant differences in microbiome composition when analyzing different samples source (i.e., water and sediments). Looking at the finer scale, we measured significant changes in the relative abundances of specific taxa in RMS-affected tanks, especially when analyzing water samples. Our results provide worthwhile insight into a mostly uncharacterized ecological scenario, aiding future studies on the aquaculture built environment for disease prevention and monitoring.
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Affiliation(s)
- Antonia Bruno
- ZooPlantLab, Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Alessandra Cafiso
- Department of Veterinary Medicine and Animal Science, University of Milan, Lodi, Italy
| | | | - Andrea Galimberti
- ZooPlantLab, Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Davide Magnani
- ZooPlantLab, Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Amedeo Manfrin
- Experimental Zooprophylactic Institute of the Venezie (IZSVe), Legnaro, Italy
| | | | - Maurizio Casiraghi
- ZooPlantLab, Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Chiara Bazzocchi
- Department of Veterinary Medicine and Animal Science, University of Milan, Lodi, Italy
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Highlander SK, Wood JM, Gillece JD, Folkerts M, Fofanov V, Furstenau T, Singh NK, Guan L, Seuylemezian A, Benardini JN, Engelthaler DM, Venkateswaran K, Keim PS. Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition. PLoS One 2023; 18:e0282428. [PMID: 36947490 PMCID: PMC10032485 DOI: 10.1371/journal.pone.0282428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/14/2023] [Indexed: 03/23/2023] Open
Abstract
The National Aeronautics and Space Administration (NASA) has been monitoring the microbial burden of spacecraft since the 1970's Viking missions. Originally culture-based and then focused 16S sequencing techniques were used, but we have now applied whole metagenomic sequencing to a variety of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools to contrast marker, k-mer, and true alignment approaches. Hierarchical clustering analysis of the data separated vacuum particles from other SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO (International Standards Organization) compliant facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals Cutibacterium acnes and Corynebacterium spp. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particles and SAF samples contained strong signals of the tricarboxylic acid cycle and of amino acid biosynthesis, suggesting that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 samples generated high quality metagenome assembled genomes (MAG), which were dominated by Moraxella osloensis or Malassezia restricta. One M. osloensis MAG was assembled into a single circular scaffold and gene annotated. This study includes a rigorous quantitative determination of microbial loads and a qualitative dissection of microbial composition. Assembly of multiple specimens led to greater confidence for the identification of particular species and their predicted functional roles.
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Affiliation(s)
- Sarah K Highlander
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jason M Wood
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - John D Gillece
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Megan Folkerts
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Viacheslav Fofanov
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Tara Furstenau
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Lisa Guan
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Arman Seuylemezian
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - James N Benardini
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - David M Engelthaler
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Paul S Keim
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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46
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Birgand G, Ahmad R, Bulabula ANH, Singh S, Bearman G, Sánchez EC, Holmes A. Innovation for infection prevention and control-revisiting Pasteur's vision. Lancet 2022; 400:2250-2260. [PMID: 36528378 PMCID: PMC9754656 DOI: 10.1016/s0140-6736(22)02459-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Louis Pasteur has long been heralded as one of the fathers of microbiology and immunology. Less known is Pasteur's vision on infection prevention and control (IPC) that drove current infection control, public health, and much of modern medicine and surgery. In this Review, we revisited Pasteur's pioneering works to assess progress and challenges in the process and technological innovation of IPC. We focused on Pasteur's far-sighted conceptualisation of the hospital as a reservoir of microorganisms and amplifier of transmission, aseptic technique in surgery, public health education, interdisciplinary working, and the protection of health services and patients. Examples from across the globe help inform future thinking for IPC innovation, adoption, scale up and sustained use.
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Affiliation(s)
- Gabriel Birgand
- Centre d'appui pour la Prévention des Infections Associées aux Soins, Nantes, France; National Institute for Health and Care Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London, London, UK
| | - Raheelah Ahmad
- National Institute for Health and Care Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London, London, UK; School of Health and Psychological Sciences, City University of London, London, UK; Institute of Business and Health Management, Dow University of Health Sciences, Karachi, Pakistan
| | | | - Sanjeev Singh
- Department of Medicine, Amrita Institute of Medical Sciences, Amrita University, Kerala, India
| | - Gonzalo Bearman
- Division of Infectious Diseases, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Enrique Castro Sánchez
- National Institute for Health and Care Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London, London, UK; College of Nursing, Midwifery and Healthcare, Richard Wells Centre, University of West London, London, UK
| | - Alison Holmes
- National Institute for Health and Care Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London, London, UK; Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.
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47
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Fakunle AG, Jafta N, Smit LAM, Naidoo RN. Indoor bacterial and fungal aerosols as predictors of lower respiratory tract infections among under-five children in Ibadan, Nigeria. BMC Pulm Med 2022; 22:471. [PMID: 36494686 PMCID: PMC9733100 DOI: 10.1186/s12890-022-02271-w] [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: 08/26/2021] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study aimed to investigate the association between exposure to diverse indoor microbial aerosols and lower respiratory tract infections (LRTI) among children aged 1 to 59 months in Ibadan, Nigeria. METHODS One hundred and seventy-eight (178) hospital-based LRTI cases among under-five children were matched for age (± 3 months), sex and geographical location with 180 community-based controls (under-five children without LRTI). Following consent from caregivers of eligible participants, a child's health questionnaire, clinical proforma and standardized home-walkthrough checklist were used to collect data. Participant homes were visited and sampled for indoor microbial exposures using active sampling approach by Anderson sampler. Indoor microbial count (IMC), total bacterial count (TBC), and total fungal count (TFC) were estimated and dichotomized into high (> median) and low (≤ median) exposures. Alpha diversity measures including richness (R), Shannon (H) and Simpson (D) indices were also estimated. Conditional logistic regression models were used to test association between exposure to indoor microbial aerosols and LRTI risk among under-five children. RESULTS Significantly higher bacterial and fungal diversities were found in homes of cases (R = 3.00; H = 1.04; D = 2.67 and R = 2.56; H = 0.82; D = 2.33) than homes of controls (R = 2.00; H = 0.64; D = 1.80 and R = 1.89; H = 0.55; D = 1.88) p < 0.001, respectively. In the multivariate models, higher categories of exposure to IMC (aOR = 2.67, 95% CI 1.44-4.97), TBC (aOR = 2.51, 95% CI 1.36-4.65), TFC (aOR = 2.75, 95% CI 1.54-4.89), bacterial diversity (aOR = 1.87, 95% CI 1.08-3.24) and fungal diversity (aOR = 3.00, 95% CI 1.55-5.79) were independently associated with LRTI risk among under-five children. CONCLUSIONS This study suggests an increased risk of LRTI when children under the age of five years are exposed to high levels of indoor microbial aerosols.
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Affiliation(s)
- Adekunle Gregory Fakunle
- grid.16463.360000 0001 0723 4123Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban, 4041 South Africa ,grid.412422.30000 0001 2045 3216Department of Public Health, College of Health Sciences, Osun State University, Osogbo, Osun State Nigeria
| | - Nkosana Jafta
- grid.16463.360000 0001 0723 4123Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban, 4041 South Africa
| | - Lidwien A. M. Smit
- grid.5477.10000000120346234Institute for Risk Assessment (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Rajen N. Naidoo
- grid.16463.360000 0001 0723 4123Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban, 4041 South Africa
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48
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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49
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Weisser WW, Hensel M, Barath S, Culshaw V, Grobman YJ, Hauck TE, Joschinski J, Ludwig F, Mimet A, Perini K, Roccotiello E, Schloter M, Shwartz A, Hensel DS, Vogler V. Creating ecologically sound buildings by integrating ecology, architecture and computational design. PEOPLE AND NATURE 2022. [DOI: 10.1002/pan3.10411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wolfgang W. Weisser
- Technical University of Munich Terrestrial Ecology Research Group Department of Life Science Systems School of Life Sciences Freising Germany
| | - Michael Hensel
- Department for Digital Architecture and Planning Technical University Vienna Vienna Austria
| | - Shany Barath
- Faculty of Architecture and Town Planning, Technion Israel Institute of Technology Haifa Israel
| | - Victoria Culshaw
- Technical University of Munich Terrestrial Ecology Research Group Department of Life Science Systems School of Life Sciences Freising Germany
| | - Yasha J. Grobman
- Faculty of Architecture and Town Planning, Technion Israel Institute of Technology Haifa Israel
| | - Thomas E. Hauck
- Department for Landscape Architecture and Landscape Planning Technical University Vienna Vienna Austria
| | | | - Ferdinand Ludwig
- Green Technologies in Landscape Architecture, School of Engineering and Design Technical University of Munich Munich Germany
| | - Anne Mimet
- Technical University of Munich Terrestrial Ecology Research Group Department of Life Science Systems School of Life Sciences Freising Germany
| | - Katia Perini
- Architecture and design Department University of Genoa Genoa Italy
| | - Enrica Roccotiello
- Department of Earth, Environment and Life Sciences (DISTAV) University of Genoa Genoa Italy
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich Oberschleissheim Germany
| | - Assaf Shwartz
- Faculty of Architecture and Town Planning, Technion Israel Institute of Technology Haifa Israel
| | - Defne Sunguroğlu Hensel
- Green Technologies in Landscape Architecture, School of Engineering and Design Technical University of Munich Munich Germany
| | - Verena Vogler
- Research and Development Department, McNeel Europe S.L. Barcelona Spain
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50
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Alfy MM, El Sayed SB, El-Shokry M. Assessing decontamination practices at a medical microbiology research laboratory. JOURNAL OF BIOSAFETY AND BIOSECURITY 2022. [DOI: 10.1016/j.jobb.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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