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Alabiso A, Frasca S, Cantelmo V, Braglia R, Scuderi F, Costa F, Congestri R, Migliore L. From kitchen to crop: The efficacy and safety of the microbial consortium treated dishwasher wastewater for the Zero Mile system. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108967. [PMID: 39053313 DOI: 10.1016/j.plaphy.2024.108967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
A microbial consortium, based on the functional integration of photosynthetic and heterotrophic microorganisms, is the core of the Zero Mile System. This system is designed for reusing and upcycling household greywaters, a still untapped water resource. The previous challenges of dishwasher wastewater bioremediation demonstrated the capability of an ad hoc consortium (including a photosynthetic cyanobacterium and three heterotrophic bacterial isolates from dishwasher wastewater) to reclaim the wastewater at small/medium scale. In this study the wastewater treatment demonstrated to be effective in nutrient recycling and upcycling at a larger scale, i.e. 4 L (in three replicates to treat the total amount of wastewater discharged by the dishwasher), by removing high percentage of N and P from the wastewater (70% nitrogen, 50% phosphorous, respectively). Again, the reclaimed wastewater successfully fertilized lettuce plants both indoor (in the Zero Mile System demonstrator) and outdoor (in open field). Plants showed a significant higher biomass productivity in fresh weight compared to control plants and comparable or better values of the pigments and quality indices (e.g., soluble solids, total phenols, total flavonoids). Furthermore, the safety of the reclaimed wastewater is demonstrated by the analysis of the metabolic/ecologically relevant functions of the microbial communities in both untreated and treated wastewater. Colonizers were mainly organic matter degraders and bacteria involved in nitrogen cycling. The human related genera are quite few and no pathogens or potential microbiological contaminants of water bodies (as E. coli), were found. Hence, the utilization of treated dishwasher wastewater does not imply biological risks to agricultural products, soil, or groundwater.
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Affiliation(s)
- Annamaria Alabiso
- PhD Program in Evolutionary Biology and Ecology, Tor Vergata University of Rome, 00133, Rome, Italy; Department of Biology, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Sara Frasca
- PhD Program in Evolutionary Biology and Ecology, Tor Vergata University of Rome, 00133, Rome, Italy; Department of Biology, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Valerio Cantelmo
- Department of Biology, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Roberto Braglia
- Department of Biology, Tor Vergata University of Rome, 00133, Rome, Italy; eCampus University, 22060, Novedrate, (CO), Italy
| | - Francesco Scuderi
- Department of Biology, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Fiammetta Costa
- Department of Design, Polytechnic of Milan, 20133, Milan, Italy
| | - Roberta Congestri
- Department of Biology, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Luciana Migliore
- Department of Biology, Tor Vergata University of Rome, 00133, Rome, Italy; eCampus University, 22060, Novedrate, (CO), Italy.
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2
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Chen Y, Liang Z, Li G, An T. Indoor/Outdoor airborne microbiome characteristics in residential areas across four seasons and its indoor purification. ENVIRONMENT INTERNATIONAL 2024; 190:108857. [PMID: 38954924 DOI: 10.1016/j.envint.2024.108857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 06/04/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
Bioaerosols are more likely to accumulate in the residential environment, and long-term inhalation may lead to a variety of diseases and allergies. Here, we studied the distribution, influencing factors and diffusion characteristics of indoor and outdoor microbiota pollution in six residential buildings in Guangzhou, southern China over a period of one year. The results showed that the particle sizes of bioaerosol were mainly in the range of inhalable particle size (<4.7 μm) with a small difference among four seasons (74.61 % ± 2.17 %). The microbial communities showed obvious seasonal differences with high abundance in summer, but no obvious geographical differences. Among them, the bacteria were more abundant than the fungi. The dominant microbes in indoor and outdoor environments were similar, with Anoxybacillu, Brevibacillus and Acinetobacter as the dominant bacteria, and Cladosporium, Penicillium and Alternaria as the dominant fungi. The airborne microbiomes were more sensitive to temperature and particulate matter (PM2.5, PM10) concentrations. Based on the Sloan neutral model, bacteria were more prone to random diffusion than fungi, and the airborne microbiome can be randomly distributed in indoor and outdoor environments and between the two environments in each season. Bioaerosol in indoor was mainly from outdoor. The health risk evaluation showed that the indoor inhalation risks were higher than those outdoor. The air purifier had a better removal efficiency on 1.1-4.7 μm microorganisms, and the removal efficiency on Gram-negative bacteria was better than that on Gram-positive bacteria. This study is of great significance for the risk assessment and control of residential indoor bioaerosol exposure.
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Affiliation(s)
- Yuying Chen
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhishu Liang
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiying Li
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Taicheng An
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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3
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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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4
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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [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: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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5
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Lu Y, Duan M, Li Y, Zhang S, Hu X, Liu L. Altitude-associated trends in bacterial communities in ultrahigh-altitude residences. ENVIRONMENT INTERNATIONAL 2024; 185:108503. [PMID: 38377724 DOI: 10.1016/j.envint.2024.108503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Indoor bacterial communities may change with altitude because their major contributors, outdoor bacterial communities, vary with altitude. People's health effects from bacteria inhalation exposure can also vary with altitude because human respiratory physiology changes with oxygen content in air. Accordingly, adjusting indoor bacterial communities may help to acclimate newcomers from low-altitude environments to ultrahigh-altitude environments. To lay the groundwork for further research, we aimed to first elucidate the bacterial communities in ultrahigh-altitude residences and the effects of altitude on these communities. We collected 187 environmental samples from residential communities at ultrahigh altitudes of 3811-4651 m in Ngari, China and sequenced bacterial 16S rRNA genes. RESULTS On one hand, when abundant genera in ultrahigh-altitude residences and those reported by previous studies on low-altitude residences were compared, nine genera were shared, whereas other five genera were abundant only at ultrahigh altitudes. On the other hand, when the bacterial communities of residences at different ultrahigh altitudes were further compared, the bacterial composition in indoor surface samples varied significantly with altitude. The relative abundance of five bacterial genera in indoor air samples and 10 genera and three phyla in indoor surface samples varied monotonically with altitude. CONCLUSIONS Altitude may be a long-neglected factor that shapes residential bacterial communities and thus warrants attention.
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Affiliation(s)
- Yiran Lu
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Mengjie Duan
- Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China; Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Yifan Li
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Shengyu Zhang
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaomin Hu
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Li Liu
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China.
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6
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Kocurek B, Ramachandran P, Grim CJ, Morin P, Howard L, Ottesen A, Timme R, Leonard SR, Rand H, Strain E, Tadesse D, Pettengill JB, Lacher DW, Mammel M, Jarvis KG. Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities. Microbiol Spectr 2023; 11:e0148223. [PMID: 37812012 PMCID: PMC10714831 DOI: 10.1128/spectrum.01482-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/18/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE In developed countries, the human diet is predominated by food commodities, which have been manufactured, processed, and stored in a food production facility. Little is known about the application of metagenomic sequencing approaches for detecting foodborne pathogens, such as L. monocytogenes, and characterizing microbial diversity in food production ecosystems. In this work, we investigated the utility of 16S rRNA amplicon and quasimetagenomic sequencing for the taxonomic and phylogenetic classification of Listeria culture enrichments of environmental swabs collected from dairy and seafood production facilities. We demonstrated that single-nucleotide polymorphism (SNP) analyses of L. monocytogenes metagenome-assembled genomes (MAGs) from quasimetagenomic data sets can achieve similar resolution as culture isolate whole-genome sequencing. To further understand the impact of genome coverage on MAG SNP cluster resolution, an in silico downsampling approach was employed to reduce the percentage of target pathogen sequence reads, providing an initial estimate of required MAG coverage for subtyping resolution of L. monocytogenes.
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Affiliation(s)
- Brandon Kocurek
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Paul Morin
- Office of Regulatory Science, Northeast Food and Feed Laboratory, U.S. Food and Drug Administration, Jamaica, New York, USA
| | - Laura Howard
- Office of Regulatory Science, Northeast Food and Feed Laboratory, U.S. Food and Drug Administration, Jamaica, New York, USA
| | - Andrea Ottesen
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Ruth Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Susan R. Leonard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Hugh Rand
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Errol Strain
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Daniel Tadesse
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - James B. Pettengill
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - David W. Lacher
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Mark Mammel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Karen G. Jarvis
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
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7
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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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8
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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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9
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Yong SS, Lee JI, Kang DH. Bacterial composition of refrigerators in households and inactivation of airborne Staphylococcus aureus using a TiO 2-UVLED module in a 512 L aerobiology chamber. Food Microbiol 2023; 114:104274. [PMID: 37290863 DOI: 10.1016/j.fm.2023.104274] [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: 02/15/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 06/10/2023]
Abstract
This study aimed to investigate the microbiota in the air and on the surface of a refrigerator and to inactivate aerosolized Staphylococcus aureus using a TiO2-UVLED module. A total of 100 L of the air and 5000 cm2 surfaces in seven household refrigerators were collected using an air sampler and a swab, respectively. Samples were subjected to microbiota analysis as well as quantitative analyses of aerobic or anaerobic bacteria. The level of airborne aerobic bacteria was 4.26 log CFU/vol (100 L), while that of surface aerobic bacteria was 5.27 log CFU/surface (5000 cm2). PCoA based on the Bray-Curtis metric revealed that the bacterial composition differed between samples collected from refrigerators with and without a vegetable drawer. Moreover, pathogenic bacteria containing genera and order from each sample were found, such as Enterobacaterales, Pseudomonas, Staphylococcus, Listeria, and Bacillus. Among them, Staphylococcus aureus was determined to be a core hazardous pathogen in air. Therefore, three S. aureus strains isolated from the air in refrigerators, as well as a reference strain of S. aureus (ATCC 6538P), were inactivated by a TiO2-UVLED module in a 512 L aerobiology chamber. All aerosolized S. aureus were reduced over 1.6 log CFU/vol after treatment with TiO2 under UVA (365 nm) light at 40 J/cm2. These findings suggest that TiO2-UVLED modules have the potential to be used to control airborne bacteria in household refrigerators.
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Affiliation(s)
- So-Seum Yong
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Ik Lee
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong-Hyun Kang
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang-gun, Gangwon-do, 25354, Republic of Korea.
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10
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Chauhan BV, Higgins Jones D, Banerjee G, Agrawal S, Sulaiman IM, Jia C, Banerjee P. Indoor Bacterial and Fungal Burden in "Moldy" versus "Non-Moldy" Homes: A Case Study Employing Advanced Sequencing Techniques in a US Metropolitan Area. Pathogens 2023; 12:1006. [PMID: 37623966 PMCID: PMC10457890 DOI: 10.3390/pathogens12081006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
The presence of fungi in the indoor environment is associated with allergies and other respiratory symptoms. The aim of this study was to use sequencing and molecular methods, including next-generation sequencing (NGS) approaches, to explore the bacterial and fungal communities and their abundance in the indoor environment of houses (n = 20) with visible "moldy" (HVM) and nonvisible "non-moldy" (HNM) in Memphis, TN, USA. Dust samples were collected from air vents and ground surfaces, and the total DNA was analyzed for bacteria and fungi by amplifying 16S rRNA and ITS genes on the Illumina Miseq. Results indicated that Leptosphaerulina was the most abundant fungal genus present in the air vent and ground samples from HNM and HVM. At the same time, the most abundant bacterial genera in the air vent and ground samples were Propionibacterium and Streptococcus. The fungi community diversity was significantly different in the air vent samples. The abundance of fungal species known to be associated with respiratory diseases in indoor dust samples was similar, regardless of the visibility of fungi in the houses. The existence of fungi associated with respiratory symptoms was compared with several parameters like dust particulate matter (PM), CO2 level, temperature, and humidity. Most of these parameters are either positively or negatively correlated with the existence of fungi associated with respiratory diseases; however, none of these correlations were significant at p = 0.05. Our results indicate that implementing molecular methods for detecting indoor fungi may strengthen common exposure and risk assessment practices.
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Affiliation(s)
- Bhavin V. Chauhan
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | | | - Goutam Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Saumya Agrawal
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Irshad M. Sulaiman
- Southeast Regional Laboratory, U.S. Food and Drug Administration, Atlanta, GA 30309, USA
| | - Chunrong Jia
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Pratik Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
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11
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Saima S, Ferdous J, Sultana R, Rashid RB, Almeida S, Begum A, Jensen PKM. Detecting Enteric Pathogens in Low-Risk Drinking Water in Dhaka, Bangladesh: An Assessment of the WHO Water Safety Categories. Trop Med Infect Dis 2023; 8:321. [PMID: 37368739 DOI: 10.3390/tropicalmed8060321] [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: 02/13/2023] [Revised: 05/24/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The microbiological quality of water is usually assessed by fecal coliform bacteria, and the presence of E. coli as an indicator of fecal contamination is widely recommended by international guidelines. This study aimed to assess the prevalence of diarrheagenic pathogens, in both public and personal domain water sources and examine the reliance on the WHO drinking water risk assessment guidelines. This study was conducted in a low-income urban community in Dhaka, Bangladesh between September 2014 and October 2015. Polymerase chain reaction (PCR) was used to detect the marker and virulence genes of Escherichia coli, Vibrio cholerae, Salmonella species, and Campylobacter species, and the culture method was employed for the quantitative assessment of E. coli. According to the WHO guidelines, 48% of the public domain source water and 21% of the personal domain point-of-drinking water were classified in the low-risk group, i.e., 0 CFU of E. coli/100 mL. However, when using PCR, we detected pathogens in 39% (14/36) of the point-of-drinking water samples and 65% (74/114) of the public domain water source samples classified in the low-risk group. Our study showed that relying solely on E. coli detection as a measure of water quality may overlook the presence of other pathogens in the drinking water. In addition to the culture-based method, the detection of virulence genes by PCR should also be considered to add more scrutiny to the detection of diverse types of pathogens.
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Affiliation(s)
- Sabera Saima
- Department of Microbiology, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Jannatul Ferdous
- Department of Microbiology, University of Dhaka, 1000 Dhaka, Bangladesh
- Copenhagen Center for Disaster Research, Section for Global Health, Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, 1229 Dhaka, Bangladesh
| | - Rebeca Sultana
- Copenhagen Center for Disaster Research, Section for Global Health, Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
- icddr,b, 1212 Dhaka, Bangladesh
- Institute of Health Economics, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Ridwan Bin Rashid
- Department of Microbiology, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Sara Almeida
- Copenhagen Center for Disaster Research, Section for Global Health, Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
| | - Anowara Begum
- Department of Microbiology, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Peter Kjær Mackie Jensen
- Copenhagen Center for Disaster Research, Section for Global Health, Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
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12
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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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13
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Hoisington AJ, Stamper CE, Bates KL, Stanislawski MA, Flux MC, Postolache TT, Lowry CA, Brenner LA. Human microbiome transfer in the built environment differs based on occupants, objects, and buildings. Sci Rep 2023; 13:6446. [PMID: 37081054 PMCID: PMC10116103 DOI: 10.1038/s41598-023-33719-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/18/2023] [Indexed: 04/22/2023] Open
Abstract
Compared to microbiomes on other skin sites, the bacterial microbiome of the human hand has been found to have greater variability across time. To increase understanding regarding the longitudinal transfer of the hand microbiome to objects in the built environment, and vice versa, 22 participants provided skin microbiome samples from their dominant hands, as well as from frequently and infrequently touched objects in their office environments. Additional longitudinal samples from home environments were obtained from a subset of 11 participants. We observed stability of the microbiomes of both the hand and built environments within the office and home settings; however, differences in the microbial communities were detected across the two built environments. Occupants' frequency of touching an object correlated to that object having a higher relative abundance of human microbes, yet the percent of shared microbes was variable by participants. Finally, objects that were horizontal surfaces in the built environment had higher microbial diversity as compared to objects and the occupants' hands. This study adds to the existing knowledge of microbiomes of the built environment, enables more detailed studies of indoor microbial transfer, and contributes to future models and building interventions to reduce negative outcomes and improve health and well-being.
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Affiliation(s)
- Andrew J Hoisington
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA.
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA.
- Department of Systems Engineering and Management, US Air Force Institute of Technology, Wright-Patterson Air Force Base, OH, 45433, USA.
| | - Christopher E Stamper
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA
| | - Katherine L Bates
- Department of Biology, US Air Force Academy, USAF Academy, CO, 80840, USA
| | - Maggie A Stanislawski
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Eastern Colorado Health Care System, Veterans Affairs, Denver, CO, 80220, USA
| | - Michael C Flux
- Department of Psychology and Center for Neuroscience, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Teodor T Postolache
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Veterans Health Administration, Mental Illness Research Education and Clinical Center (MIRECC), Baltimore VA Annex, VISN 5, Baltimore, MD, 21201, USA
| | - Christopher A Lowry
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, Boulder, CO, 80309, USA
- Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Lisa A Brenner
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), VISN 19, Aurora, CO, 80045, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Aurora, CO, 80045, USA
- Departments of Psychiatry and Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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14
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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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15
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Ito K, Niwa R, Kobayashi K, Nakagawa T, Hoshino G, Tsuchida Y. A dark matter in sake brewing: Origin of microbes producing a Kimoto-style fermentation starter. Front Microbiol 2023; 14:1112638. [PMID: 36819013 PMCID: PMC9933502 DOI: 10.3389/fmicb.2023.1112638] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction In Kimoto-style fermentation, a fermentation starter is produced before the primary brewing process to stabilize fermentation. Nitrate-reducing bacteria, mainly derived from brewing water, produce nitrite, and lactic acid bacteria such as Leuconostoc can proliferate because of their tolerance toward low temperature and their low nutritional requirements. Later, Lactobacillus becomes the dominant genus, leading to weakly acidic conditions that contribute to control yeasts and undesired bacterial contaminants. However, the sources of these microorganisms that play a pivotal role in Sake brewing have not yet been revealed. Thus, comprehensive elucidation of the microbiome is necessary. Methods In this study, we performed 16S rRNA amplicon sequencing analysis after sampling from floor, equipment surfaces, and raw materials for making fermentation starters, including koji, and water in Tsuchida Sake brewery, Gunma, Japan. Results Amplicon sequence variants (ASVs) between the external environments and the fermentation starter were compared, and it was verified that the microorganisms in the external environments, such as built environments, equipment surfaces, and raw materials in the sake brewery, were introduced into the fermentation starter. Furthermore, various adventitious microbes present in the fermentation starter of early days and from the external environments were detected in a nonnegligible proportion in the starter, which may impact the taste and flavor. Discussion These findings illuminate the uncharacterized microbial dark matter of sake brewing, the sources of microbes in Kimoto-style fermentation.
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Affiliation(s)
- Kohei Ito
- BIOTA Inc., Tokyo, Japan,*Correspondence: Kohei Ito, ✉
| | - Ryo Niwa
- BIOTA Inc., Tokyo, Japan,Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Tomoyuki Nakagawa
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
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16
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Cui J, Chen C, Gan Q, Wang T, Li W, Zeng W, Xu X, Chen G, Wang L, Lu Z, Li J, Jin B. Indoor microplastics and bacteria in the atmospheric fallout in urban homes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158233. [PMID: 36007647 DOI: 10.1016/j.scitotenv.2022.158233] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Humans may be exposed to microplastics (MPs) through food, drink, and air. Although several studies have examined indoor environmental MPs, none have yet compared atmospheric MP and bacterial deposition characteristics among rooms in homes. We investigated indoor airborne MPs and bacteria in five room types (bedroom, dining room, living room, bathroom, and study) based on the duration of usage of each room. We identified synthetic polymers (23,889 MP particles of 21 types) and bacterial communities (383 genera belong to 24 phyla) collected through atmospheric deposition in various rooms of 20 homes. The abundance and composition of MPs are related to the duration of usage, human activities, goods, cleanliness, and the composition of occupants (family members) in households. In addition, the homes of elderly families (age 68-81 years) showed higher bacterial concentrations than those of young families (age 28-35 years), indicating that age markedly affects the structure of household microbiota. Furthermore, a significant correlation between MP concentration and bacterial community structure was observed. The abundances of polyamide (PA), polyurethane (PU), and polyethylene (PE) showed positive correlations with the relative abundances of major bacterial phyla. Taken together, our results suggest that various rooms in the home exhibit distinct MP abundances and bacterial structures that may be affected by age, cleanliness, and human activities.
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Affiliation(s)
- Jiawen Cui
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Chen Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Quan Gan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Tongfei Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Wei Li
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Wen Zeng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Xiaowen Xu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Gang Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Li Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Zhaogeng Lu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
| | - Jiana Li
- Ningbo Academy of Ecological and Environmental Sciences, Ningbo 315000, China
| | - Biao Jin
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
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17
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Qiu Y, Zhou Y, Chang Y, Liang X, Zhang H, Lin X, Qing K, Zhou X, Luo Z. The Effects of Ventilation, Humidity, and Temperature on Bacterial Growth and Bacterial Genera Distribution. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192215345. [PMID: 36430064 PMCID: PMC9691097 DOI: 10.3390/ijerph192215345] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND Bacteria are readily nourished in airtight environments with high humidity, such as storage cabinets, clothing closets, and corners, where ventilation is normally low and humidity is high. OBJECTIVES We characterized the role of humidity and ventilation in bacterial growth and genus distribution at different temperatures (26 °C and 34 °C). METHODS Fresh pork, which was used as the substrate for bacterial culture, was placed in storage cabinets. Bacterial growth and genera distribution on the surface of pork placed in a storage cabinet under different temperatures (26 °C and 34 °C); relative humidity levels (RH: 50%, 70%, 90%); and ventilation conditions (no ventilation and low, medium, and high levels of ventilation) were assessed by rDNA sequencing. RESULTS Increased ventilation and reduced humidity significantly decreased bacterial growth at 26 °C and 34 °C. The contribution of increased ventilation to the reduction in bacterial growth exceeded that of decreased humidity. Ventilation had the greatest effect on reducing bacterial growth compared to the unventilated conditions at 70% RH. At 34 °C, medium and high levels of ventilation were required to reduce bacterial growth. High temperatures greatly increased bacterial growth, but ventilation could reduce the degree of this increase.
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Affiliation(s)
- Yujia Qiu
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
| | - Yan Zhou
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
- Correspondence: (Y.Z.); (Z.L.)
| | - Yanfen Chang
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
| | - Xinyue Liang
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
| | - Hui Zhang
- Center for the Built Environment, University of California at Berkeley, Berkeley, CA 2506, USA
| | - Xiaorui Lin
- China Vanke Co., Ltd., Changsha 410000, China
| | - Ke Qing
- China Vanke Co., Ltd., Changsha 410000, China
| | - Xiaojie Zhou
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao 266061, China
| | - Ziqiang Luo
- Department of Physiology, The School of Basic Medicine Science, Central South University, Changsha 410000, China
- Correspondence: (Y.Z.); (Z.L.)
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18
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Seasonal variations of the airborne microbial assemblages of the Seoul subway, South Korea from 16S and ITS gene profiles with chemical analysis. Sci Rep 2022; 12:18456. [PMID: 36323743 PMCID: PMC9630434 DOI: 10.1038/s41598-022-21120-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 09/22/2022] [Indexed: 11/07/2022] Open
Abstract
In this study, we determined the seasonal airborne microbial diversity profiles at SMRT stations by sequencing the 16S rRNA and ITS. Particulate matter samples were collected from air purifiers installed in the platform area of the SMRT subway stations. Three stations that included the most crowded one were selected for the sampling. The sampling was done at each season during 2019. After extracting the total DNA from all seasonal samples, PCR was performed with Illumina overhang adapter primers for the V3-V4 region of the 16S rRNA gene and ITS2 region of the ITS gene. The amplified products were further purified, and sequencing libraries were made. Sequencing was carried with the Illumina Miseq Sequencing system (Illumina, USA) followed by in-depth diversity analyses. The elemental composition of the particulate matter samples collected from the different subway stations were obtained using a WD-XRF spectrometer. The SMRT microbiome showed extensive taxonomic diversity with the most common bacterial genera at the subway stations associated with the skin. Overall, the stations included in this study harbored different phylogenetic communities based on α- and β-diversity comparisons. Microbial assemblages also varied depending upon the season in which the samples were taken and the station. Major elements present at the subway stations were from aerosols generated between wheels and brake cushions and between the catenaries and the pantographs. This study shows that the microbial composition of the SMRT subway stations comes from a diverse combination of environmental and human sources, the season and the lifestyle of commuters.
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19
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Manus MB. Ecological Processes and Human Behavior Provide a Framework for Studying the Skin Microbial Metacommunity. MICROBIAL ECOLOGY 2022; 84:689-702. [PMID: 34636925 DOI: 10.1007/s00248-021-01884-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Metacommunity theory dictates that a microbial community is supported both by local ecological processes and the dispersal of microbes between neighboring communities. Studies that apply this perspective to human-associated microbial communities are thus far limited to the gut microbiome. Yet, the skin serves as the primary barrier between the body and the external environment, suggesting frequent opportunities for microbial dispersal to the variable microbial communities that are housed across skin sites. This paper applies metacommunity theory to understand the dispersal of microbes to the skin from the physical and social environment, as well as between different skin sites on an individual's body. This includes highlighting the role of human behavior in driving microbial dispersal, as well as shaping physiological properties of skin that underscore local microbial community dynamics. By leveraging data from research on the skin microbiomes of amphibians and other animals, this paper provides recommendations for future research on the skin microbial metacommunity, including generating testable predictions about the ecological underpinnings of the skin microbiome.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
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20
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Carstens CK, Salazar JK, Sharma SV, Chan W, Darkoh C. Evaluation of the kitchen microbiome and food safety behaviors of predominantly low-income families. Front Microbiol 2022; 13:987925. [PMID: 36246211 PMCID: PMC9557297 DOI: 10.3389/fmicb.2022.987925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial pathogens in the domestic environment present a risk to residents, particularly among susceptible populations. However, the impact of consumer demographic characteristics and food handling methods on kitchen microbiomes is not fully understood. The domestic kitchen bacterial communities of ten predominantly low-income families in Houston, TX, were assessed in conjunction with a cross-sectional food safety survey to evaluate differences in household and surface-specific microbiomes and bacterial foodborne pathogen presence. Three kitchen surfaces within each household, including the sink drain, the refrigerator handle, and the counter, were environmentally sampled and metataxonomically evaluated via targeted 16S rRNA sequencing. Disposable dish sponges were also acquired and examined. Results indicated that alpha diversity did not vary by the households, sampling locations, or demographic characteristics evaluated. Significant differences in beta diversity were observed among the bacterial communities of five pairs of households and between refrigerator handle and disposable dish sponge microbiomes. A total of 89 unique bacterial foodborne pathogens were identified across surface types. Each household contained at least one contaminated surface, and the most common bacterial foodborne pathogens identified were Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae. All parents reported washing their hands before meal preparation, washing fresh fruits and vegetables, and washing cutting boards with soap after use to prepare raw animal proteins. Gaps in food safety behaviors identified included a lack of serious concern for food contamination with germs and inappropriate handwashing, food handling, and cleaning behaviors. The number of unique bacterial foodborne pathogens identified within households was significantly higher among households whose respondent parent reported that they did not consider food contamination with germs to be a serious food safety problem (median: 41.0 species) compared to households whose respondent parent did consider food contamination to be a serious food safety problem (median: 3.0 species; p value = 0.0218). These results demonstrate that domestic kitchen taxonomic abundance profiles vary according to household and surface type. Data suggest that low-income consumers may be at risk of foodborne pathogen exposure from contaminated home kitchen surfaces, and that food safety attitudes may directly contribute to this hazard.
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Affiliation(s)
- Christina K. Carstens
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, United States
| | - Joelle K. Salazar
- Division of Food Processing Science and Technology, U.S. Food and Drug Administration, Bedford Park, IL, United States
| | - Shreela V. Sharma
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, United States
| | - Wenyaw Chan
- Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center, Houston, TX, United States
| | - Charles Darkoh
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, United States,Microbiology and Infectious Diseases Program, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States,*Correspondence: Charles Darkoh,
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21
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Brandau L, Jacksch S, Weis S, Schnell S, Egert M. Minority report: small-scale metagenomic analysis of the non-bacterial kitchen sponge microbiota. Arch Microbiol 2022; 204:363. [PMID: 35661258 PMCID: PMC9167186 DOI: 10.1007/s00203-022-02969-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Kitchen sponges are particularly well known to harbor a high number and diversity of bacteria, including pathogens. Viruses, archaea, and eukaryotes in kitchen sponges, however, have not been examined in detail so far. To increase knowledge on the non-bacterial kitchen sponge microbiota and its potential hygienic relevance, we investigated five used kitchen sponges by means of metagenomic shot-gun sequencing. Viral particles were sought to be enriched by a filter step during DNA extraction from the sponges. Data analysis revealed that ~ 2% of the sequences could be assigned to non-bacterial taxa. Each sponge harbored different virus (phage) species, while the present archaea were predominantly affiliated with halophilic taxa. Among the eukaryotic taxa, besides harmless algae, or amoebas, mainly DNA from food-left-overs was found. The presented work offers new insights into the complex microbiota of used kitchen sponges and contributes to a better understanding of their hygienic relevance.
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Affiliation(s)
- Lena Brandau
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Susanne Jacksch
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Sylvia Schnell
- Research Centre for BioSystems, Land Use, and Nutrition (IFZ), Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
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22
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Dong M, Feng H. Microbial Community Analysis and Food Safety Practice Survey-Based Hazard Identification and Risk Assessment for Controlled Environment Hydroponic/Aquaponic Farming Systems. Front Microbiol 2022; 13:879260. [PMID: 35663856 PMCID: PMC9161294 DOI: 10.3389/fmicb.2022.879260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022] Open
Abstract
Hydroponic and aquaponic farming is becoming increasingly popular as a solution to address global food security. Plants in hydroponic systems are grown hydroponically under controlled environments and are considered to have fewer food safety concerns than traditional field farming. However, hydroponics and aquaponics might have very different sources of microbial food safety risks that remain under-examined. In this study, we investigated the microbiomes, microbial hazards, and potential bacterial transmission routes inside two commercial hydroponic and aquaponic farming systems using 16S-ITS-23S rRNA sequencing and a hydroponic food safety practice survey. The hydroponic farming system microbiome was analyzed from the fresh produce, nutrient solution, tools, and farmworkers. Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes were the main components of hydroponic/aquaponic farming systems, with Pseudomonas being the most abundant genus in fresh produce samples. We further identified the presence of multiple spoilage bacteria and potential human, plant, and fish pathogens at the subspecies level. Spoilage Pseudomonas spp. and spoilage Clostridium spp. were abundant in the hydroponic microgreen farm and aquaponic lettuce farm, respectively. Moreover, we demonstrated the mapping of Escherichia coli 16s-ITS-23s rRNA sequence reads (∼2,500 bp) to small or large subunit rRNA databases and whole-genome databases to confirm pathogenicity and showed the potential of using 16s-ITS-23s rRNA sequencing for pathogen identification. With the SourceTracker and overlapping amplicon sequence variants, we predicted the bidirectional transmission route between plants and the surrounding environment and constructed the bacteria transmission map, which can be implemented in future food safety risk control plans.
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Affiliation(s)
| | - Hao Feng
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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23
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Zeng S, Cui J, Xiong J, Yuan S, Yue X, Guan W, Gao L, Liu J, Zuo J, Wang Q. The Microbial Metagenome of Eluates Obtained From the Surface of Broccoli Heads Subjected to Different Light Treatments. Front Microbiol 2022; 13:820419. [PMID: 35495709 PMCID: PMC9043960 DOI: 10.3389/fmicb.2022.820419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/22/2022] [Indexed: 12/01/2022] Open
Abstract
Foodborne illnesses present a major threat to public health and are frequently attributed to foodborne pathogens present on fresh produce. Some opportunistic pathogens of broccoli are also responsible for causing head rot. Three different light treatments, UV-C, red LED (50 μml/m2/s), and UV-C + LED were used to treat broccoli prior to or during storage. Following the light treatments, microorganisms present in eluates obtained from the surface of broccoli heads were characterized using a metagenomic approach. Metagenomic DNA libraries were subjected to high-throughput sequencing on an Illumina Hiseq platform. Results indicated that the combined treatment of LED red light and UV-C provided the best sensory preservation of broccoli, followed by LED red light and then UV-C. The bacterial communities in the eluates obtained from the surface of broccoli heads in all three light treatments were primarily represented at the phylum level by Proteobacteria and Firmicutes, while fungal communities were primarily represented by Ascomycota and Basidiomycota. Further analysis indicated that the all three light treatments reduced the presence of foodborne pathogens and bacterial taxa responsible for broccoli spoilage. While UV-C had a significant inhibitory effect on Botrytis cinerea, the light treatments increased the relative abundance of Pseudomonas fluorescens. Results indicate that a metagenomic approach can be used to detect pathogenic bacteria and fungi on fresh vegetables and assess the impact of management practices, such as light treatments, designed to maintain postharvest quality, on the composition of the microbiome present on the surface of harvested produce.
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Affiliation(s)
- Shixian Zeng
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,College of Life Sciences, Dalian Minzu University, Dalian, China
| | - Jingchun Cui
- College of Life Sciences, Dalian Minzu University, Dalian, China
| | - Jinliang Xiong
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Tianjin Key Laboratory of Food Biotechnology, Tianjin University of Commerce, Tianjin, China
| | - Shuzhi Yuan
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiaozhen Yue
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wenqiang Guan
- Tianjin Key Laboratory of Food Biotechnology, Tianjin University of Commerce, Tianjin, China
| | - Lipu Gao
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, China
| | - Jinhua Zuo
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qing Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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24
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Peimbert M, Alcaraz LD. Where environmental microbiome meets its host: subway and passenger microbiome relationships. Mol Ecol 2022; 32:2602-2618. [PMID: 35318755 DOI: 10.1111/mec.16440] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
Subways are urban transport systems with high capacity. Every day around the world, there are more than 150 million subway passengers. Since 2013, thousands of microbiome samples from various subways worldwide have been sequenced. Skin bacteria and environmental organisms dominate the subway microbiomes. The literature has revealed common bacterial groups in subway systems; even so, it is possible to identify cities by their microbiome. Low-frequency bacteria are responsible for specific bacterial fingerprints of each subway system. Furthermore, daily subway commuters leave their microbial clouds and interact with other passengers. Microbial exchange is quite fast; the hand microbiome changes within minutes, and after cleaning the handrails, the bacteria are re-established within minutes. To investigate new taxa and metabolic pathways of subway microbial communities, several high-quality metagenomic-assembled genomes (MAG) have been described. Subways are harsh environments unfavorable for microorganism growth. However, recent studies have observed a wide diversity of viable and metabolically active bacteria. Understanding which bacteria are living, dormant, or dead allows us to propose realistic ecological interactions. Questions regarding the relationship between humans and the subway microbiome, particularly the microbiome effects on personal and public health, remain unanswered. This review summarizes our knowledge of subway microbiomes and their relationship with passenger microbiomes.
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Affiliation(s)
- Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana. Ciudad de México, México
| | - Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
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25
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Yang J, Fu Y, Liu H. Microbiomes of air dust collected during the ground-based closed bioregenerative life support experiment "Lunar Palace 365". ENVIRONMENTAL MICROBIOME 2022; 17:4. [PMID: 35081988 PMCID: PMC8793263 DOI: 10.1186/s40793-022-00399-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/07/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND Understanding the dynamics of airborne microbial communities and antibiotic resistance genes (ARGs) in space life support systems is important because potential pathogens and antibiotic resistance pose a health risk to crew that can lead to mission failure. There have been few reports on the distribution patterns of microbiomes and ARGs in space life support systems. In particular, there have been no detailed investigations of microbiomes and/or antibiotic resistance based on molecular methods in long-term confined bioregenerative life support systems (BLSSs). Therefore, in the present study, we collected air dust samples from two crew shifts, different areas, and different time points in the "Lunar Palace 365" experiment. We evaluated microbial diversity, species composition, functional potential, and antibiotic resistance by combining cultivation-independent analyses (amplicon, shot-gun sequencing, and qPCR). RESULTS We found that the bacterial community diversity in the Lunar Palace1 (LP1) system was higher than that in a controlled environment but lower than that in an open environment. Personnel exchange led to significant differences in bacterial community diversity, and source tracking analysis revealed that most bacteria in the air derived from the cabin crew and plants, but no differences in microbial function or antibiotic resistance were observed. Thus, human presence had the strongest effect on the succession of microbial diversity in the BLSSs. CONCLUSIONS Our results highlight that microbial diversity in BLSSs is heavily influenced by changes in crew and is unique from other open and controlled environments. Our findings can be used to help develop safe, enclosed BLSS that meet the requirements of human survival and habitation in outer space. In addition, our results can further enhance our understanding of the indoor air microbial community and effectively maintain a safe working and living environment, including plant growth.
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Affiliation(s)
- Jianlou Yang
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, No. 37 Xueyuan Road, Beijing, 100191, China
| | - Yuming Fu
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, No. 37 Xueyuan Road, Beijing, 100191, China.
- State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100191, China.
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beihang University, Beijing, 100191, China.
| | - Hong Liu
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, No. 37 Xueyuan Road, Beijing, 100191, China.
- State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100191, China.
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beihang University, Beijing, 100191, China.
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26
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Gouello A, Dunyach-Remy C, Siatka C, Lavigne JP. Analysis of Microbial Communities: An Emerging Tool in Forensic Sciences. Diagnostics (Basel) 2021; 12:diagnostics12010001. [PMID: 35054168 PMCID: PMC8774847 DOI: 10.3390/diagnostics12010001] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/16/2023] Open
Abstract
The objective of forensic sciences is to find clues in a crime scene in order to reconstruct the scenario. Classical samples include DNA or fingerprints, but both have inherent limitations and can be uninformative. Another type of sample has emerged recently in the form of the microbiome. Supported by the Human Microbiome Project, the characteristics of the microbial communities provide real potential in forensics. They are highly specific and can be used to differentiate and classify the originating body site of a human biological trace. Skin microbiota is also highly specific and different between individuals, leading to its possibility as an identification tool. By extension, the possibilities of the microbial communities to be deposited on everyday objects has also been explored. Other uses include the determination of the post-mortem interval or the analysis of soil communities. One challenge is that the microbiome changes over time and can be influenced by many environmental and lifestyle factors. This review offers an overview of the main methods and applications to demonstrate the benefit of the microbiome to provide forensically relevant information.
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Affiliation(s)
- Audrey Gouello
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95037 Cergy-Pontoise, France;
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | - Catherine Dunyach-Remy
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | | | - Jean-Philippe Lavigne
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
- Correspondence: ; Tel.: +33-466683202
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27
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Koide T, Tamura M. Effect of diglyceryl dicaprylate on Candida albicans growth and pathogenicity. Biosci Biotechnol Biochem 2021; 85:2334-2342. [PMID: 34508624 DOI: 10.1093/bbb/zbab159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/07/2021] [Indexed: 01/06/2023]
Abstract
The antifungal effect of diglyceryl dicaprylate, one of the emulsifiers used as a food additive, on Candida albicans that is a pathogenic fungus that is predominant in the oral cavity was investigated. This component did not affect C. albicans growth; however, it suppressed some virulence factors in a concentration-dependent manner. Furthermore, the suppression of pathogenic factors, such as biofilm formation, adhesion, highly pathogenic dimorphism, and ability to produce proteolytic enzymes, was due to reduction in mRNA expression levels of genes involved in fungal pathogenicities. From these results, this emulsifier could potentially prevent the development of intraoral and extraoral diseases involving C. albicans and could potentially use in oral care and improvement of quality of life.
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Affiliation(s)
- Tomojiro Koide
- Department of Food Ingredients Development, Riken Vitamin Co., Ltd., Mihama-ku Chiba-City, Chiba, Japan
| | - Muneaki Tamura
- Department of Microbiology, Nihon University School of Dentistry, Kanda-surugadai Chiyoda-ku, Tokyo, Japan
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28
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Fei N, Choo-Kang C, Reutrakul S, Crowley SJ, Rae D, Bedu-Addo K, Plange-Rhule J, Forrester TE, Lambert EV, Bovet P, Riesen W, Korte W, Luke A, Layden BT, Gilbert JA, Dugas LR. Gut microbiota alterations in response to sleep length among African-origin adults. PLoS One 2021; 16:e0255323. [PMID: 34495955 PMCID: PMC8425534 DOI: 10.1371/journal.pone.0255323] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
Sleep disorders are increasingly being characterized in modern society as contributing to a host of serious medical problems, including obesity and metabolic syndrome. Changes to the microbial community in the human gut have been reportedly associated with many of these cardiometabolic outcomes. In this study, we investigated the impact of sleep length on the gut microbiota in a large cohort of 655 participants of African descent, aged 25-45, from Ghana, South Africa (SA), Jamaica, and the United States (US). The sleep duration was self-reported via a questionnaire. Participants were classified into 3 sleep groups: short (<7hrs), normal (7-<9hrs), and long (≥9hrs). Forty-seven percent of US participants were classified as short sleepers and 88% of SA participants as long sleepers. Gut microbial composition analysis (16S rRNA gene sequencing) revealed that bacterial alpha diversity negatively correlated with sleep length (p<0.05). Furthermore, sleep length significantly contributed to the inter-individual beta diversity dissimilarity in gut microbial composition (p<0.01). Participants with both short and long-sleep durations exhibited significantly higher abundances of several taxonomic features, compared to normal sleep duration participants. The predicted relative proportion of two genes involved in the butyrate synthesis via lysine pathway were enriched in short sleep duration participants. Finally, co-occurrence relationships revealed by network analysis showed unique interactions among the short, normal and long duration sleepers. These results suggest that sleep length in humans may alter gut microbiota by driving population shifts of the whole microbiota and also specific changes in Exact Sequence Variants abundance, which may have implications for chronic inflammation associated diseases. The current findings suggest a possible relationship between disrupted sleep patterns and the composition of the gut microbiota. Prospective investigations in larger and more prolonged sleep researches and causally experimental studies are needed to confirm these findings, investigate the underlying mechanism and determine whether improving microbial homeostasis may buffer against sleep-related health decline in humans.
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Affiliation(s)
- Na Fei
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Candice Choo-Kang
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
| | - Sirimon Reutrakul
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
| | - Stephanie J. Crowley
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
| | - Dale Rae
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Kweku Bedu-Addo
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Jacob Plange-Rhule
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Terrence E. Forrester
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Estelle V. Lambert
- Department of Physiology, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Pascal Bovet
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | - Walter Riesen
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | - Wolfgang Korte
- Center for Laboratory Medicine, Canton Hospital, St. Gallen, Switzerland
| | - Amy Luke
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
| | - Brian T. Layden
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America
| | - Jack A. Gilbert
- University of California San Diego, San Diego, California, United States of America
| | - Lara R. Dugas
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
- Division of Epidemiology & Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
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29
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Zambom AZ, Wang Q. Testing independence between discrete random variables. COMMUN STAT-THEOR M 2021. [DOI: 10.1080/03610926.2021.1934026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Adriano Z. Zambom
- Department of Mathematics, California State University, Northridge, Northridge, California, USA
| | - Qing Wang
- Department of Mathematics, Wellesley College, Wellesley, Massachusetts, USA
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30
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Kuddus M, Khatoon F, Saleem M, Anwar S, Alam Shahid SM, Ginawi T, Hossain A, Malaqi Alnabri AA, Alshammari ZF, Mohammed Alrabie A, Jehad Alenazi SS, F Alshammari MM, Kausar MA. Assessment of bio-contaminants during COVID-19 outbreak from the indoor environment of Hail city, Kingdom of Saudi Arabia. Bioinformation 2021; 17:541-549. [PMID: 35095228 PMCID: PMC8770406 DOI: 10.6026/97320630017541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/23/2021] [Accepted: 05/23/2021] [Indexed: 11/23/2022] Open
Abstract
Biocontaminants are minute particles derived from different biological materials. Indoor biocontaminants are associated with major public health problems. In Gulf countries, it is more precarious due to the harsh climatic conditions, including high ambient temperatures and relative humidity. In addition, due to COVID-19 pandemic, most of the time public is inside their home. Therefore, the aim of the study was to determine the load of biocontaminants in the indoor environment of Hail city. The results showed that most of the bacteria are gram-positive and higher in polymicrobial (87.1%) than monomicrobial (62.7%) association. There was no significant association with sample collection time and types of isolates. The most abundant microbes found in all samples were Staphylococcus aureus followed by Bacillus spp. Among Gram-negative bacterial isolates, E. coli was most common in tested indoor air samples. The study will be useful to find the biocontaminants associated with risk factors and their impact on human health in indoor environment, especially during the COVID-19 pandemic. These results indicate the need to implement health care awareness programs in the region to improve indoor air quality.
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Affiliation(s)
- Mohammed Kuddus
- Department of Biochemistry, College of Medicine, University of Hail, Hail, KSA
| | - Fahmida Khatoon
- Department of Biochemistry, College of Medicine, University of Hail, Hail, KSA
| | - Mohd Saleem
- Department of Pathology, College of Medicine, University of Hail, Hail, KSA
| | - Sadaf Anwar
- Department of Biochemistry, College of Medicine, University of Hail, Hail, KSA
| | | | - Tarig Ginawi
- Department of Biochemistry, College of Medicine, University of Hail, Hail, KSA
| | - Ashfaque Hossain
- Department of Medical Microbiology and Immunology, RAK Medical and Health Sciences University, UAE
| | | | | | | | | | | | - Mohd Adnan Kausar
- Department of Biochemistry, College of Medicine, University of Hail, Hail, KSA
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31
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Manus MB, Kuthyar S, Perroni-Marañón AG, de la Mora AN, Amato KR. Comparing different sample collection and storage methods for field-based skin microbiome research. Am J Hum Biol 2021; 34:e23584. [PMID: 33644952 DOI: 10.1002/ajhb.23584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES The skin, as well as its microbial communities, serves as the primary interface between the human body and the surrounding environment. In order to implement the skin microbiome into human biology research, there is a need to explore the effects of different sample collection and storage methodologies, including the feasibility of conducting skin microbiome studies in field settings. METHODS We collected 99 skin microbiome samples from nine infants living in Veracruz, Mexico using a dual-tipped "dry" swab on the right armpit, palm, and forehead and a "wet" swab (0.15 M NaCl and 0.1% Tween 20) on the same body parts on the left side of the body. One swab from each collection method was stored in 95% ethanol while the other was frozen at -20°C. 16S rRNA amplicon sequencing generated data on bacterial diversity and community composition, which were analyzed using PERMANOVA, linear mixed effects models, and an algorithm-based classifier. RESULTS Treatment (wet_ethanol, wet_freezer, dry_ethanol, and dry_freezer) had an effect (~10% explanatory power) on the bacterial community diversity and composition of skin samples, although body site exhibited a stronger effect (~20% explanatory power). Within treatments, the collection method (wet vs. dry) affected measures of bacterial diversity to a greater degree than did the storage method (ethanol vs. freezer). CONCLUSIONS Our study provides novel information on skin microbiome sample collection and storage methods, suggesting that ethanol storage is suitable for research in resource-limited settings. Our results highlight the need for future study design to account for interbody site microbial variation.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Sahana Kuthyar
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | | | | | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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Stewart JD, Kremer P, Shakya KM, Conway M, Saad A. Outdoor Atmospheric Microbial Diversity Is Associated With Urban Landscape Structure and Differs From Indoor-Transit Systems as Revealed by Mobile Monitoring and Three-Dimensional Spatial Analysis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.620461] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Microbes are abundant inhabitants of the near-surface atmosphere in urban areas. The distribution of microbial communities may benefit or hinder human wellbeing and ecosystem function. Surveys of airborne microbial diversity are uncommon in both natural and built environments and those that investigate diversity are stationary in the city, thus missing continuous exposure to microbes that covary with three-dimensional urban structure. Individuals in cities are generally mobile and would be exposed to diverse urban structures outdoors and within indoor-transit systems in a day. We used mobile monitoring of microbial diversity and geographic information system spatial analysis, across Philadelphia, Pennsylvania, USA in outdoor and indoor-transit (subways and train cars) environments. This study identifies to the role of the three-dimensional urban landscape in structuring atmospheric microbiomes and employs mobile monitoring over ~1,920 kilometers to measure continuous biodiversity. We found more diverse communities outdoors that significantly differ from indoor-transit air in microbial community structure, function, likely source environment, and potentially pathogenic fraction of the community. Variation in the structure of the urban landscape was associated with diversity and function of the near-surface atmospheric microbiome in outdoor samples.
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Rai S, Singh DK, Kumar A. Microbial, environmental and anthropogenic factors influencing the indoor microbiome of the built environment. J Basic Microbiol 2021; 61:267-292. [PMID: 33522603 DOI: 10.1002/jobm.202000575] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/03/2021] [Accepted: 01/10/2021] [Indexed: 12/25/2022]
Abstract
A built environment is a human-made environment providing surroundings for human occupancy, activities, and settlement. It is supposed to safeguard humans from all undesirable and harmful pollutants; however, indoor concentrations of some pollutants are much greater than that of the outdoors. Bioaerosols infiltrate from the outdoors in addition to many indoor sources of bioaerosols including the use of various chemicals as well as activities like cooking, smoking, cleaning, or even normal movement. They are also associated with a number of serious health concerns. Various ecological factors associated with the generation, the persistence as well as the dispersal of these microbial components of indoor bioaerosols, are discussed in this review, that have not been considered all together till now. The factors like microbial taxa, environmental factors, and anthropogenic activities (human occupancy, activities, and impact of urbanization) are addressed in the review. Effects of both indoor environmental factors like architectural design, lighting, ventilation, temperature, humidity, indoor/outdoor ratio, particulate matter, indoor chemistry as well as outdoor environmental factors like geography, seasons, and meteorology on the microbial concentrations have been discussed. Efforts are underway to design selective pressures for microbes to create a healthy symbiotic built microbiome as the "right" indoor microbiome is a "healthy" indoor microbiome.
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Affiliation(s)
- Sandhya Rai
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Dileep K Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Amod Kumar
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi, India
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Environmental Impact of Sulfate-Reducing Bacteria, Their Role in Intestinal Bowel Diseases, and Possible Control by Bacteriophages. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11020735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sulfate-reducing bacteria (SRB) represent a group of prokaryotic microorganisms that are widely spread in the anoxic environment (seabed, riverbed and lakebed sediments, mud, intestinal tract of humans and animals, metal surfaces). SRB species also have an impact on processes occurring in the intestinal tract of humans and animals, including the connections between their presence and inflammatory bowel disease (IBD). Since these SRB can develop antimicrobial resistance toward the drugs, including antibiotics and antimicrobial agents, bacteriophages could represent an additional potential effective treatment. The main objectives of the review were as follows: (a) to review SRB (both from intestinal and environmental sources) regarding their role in intestinal diseases as well as their influence in environmental processes; and (b) to review, according to literature data, the influence of bacteriophages on SRB and their possible applications. Since SRB can have a significant adverse influence on industry as well as on humans and animals health, phage treatment of SRB can be seen as a possible effective method of SRB inhibition. However, there are relatively few studies concerning the influence of phages on SRB strains. Siphoviridae and Myoviridae families represent the main sulfide-producing bacteria phages. The most recent studies induced, by UV light, bacteriophages from Desulfovibrio vulgaris NCIMB 8303 and Desulfovibrio desulfuricans ATCC 13541. Notwithstanding costly and medically significant negative impacts of phages on SRB, they have been the subject of relatively few studies. The current search for alternatives to chemical biocides and antibiotics has led to the renewed interest in phages as antibacterial biocontrol and therapeutic agents, including their use against SRB. Hence, phages might represent a promising treatment against SRB in the future.
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Viegas C, Dias M, Monteiro A, Faria T, Lage J, Carolino E, Caetano LA, Gomes AQ, Almeida SM, Verde SC, Belo J, Canha N. Bioburden in sleeping environments from Portuguese dwellings. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 273:116417. [PMID: 33465652 DOI: 10.1016/j.envpol.2020.116417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/20/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
A wider characterization of indoor air quality during sleep is still lacking in the literature. This study intends to assess bioburden before and after sleeping periods in Portuguese dwellings through active methods (air sampling) coupled with passive methods, such as electrostatic dust cloths (EDC); and investigate associations between before and after sleeping and bioburden. In addition, and driven by the lack of information regarding fungi azole-resistance in Portuguese dwellings, a screening with supplemented media was also performed. The most prevalent genera of airborne bacteria identified in the indoor air of the bedrooms were Micrococcus (41%), Staphylococcus (15%) and Neisseria (9%). The major indoor bacterial species isolated in all ten studied bedrooms were Micrococcus luteus (30%), Staphylococcus aureus (13%) and Micrococcus varians (11%). Our results highlight that our bodies are the source of the majority of the bacteria found in the indoor air of our homes. Regarding air fungal contamination, Chrysosporium spp. presented the highest prevalence both in after the sleeping period (40.8%) and before the sleeping period (28.8%) followed by Penicillium spp. (23.47% morning; 23.6% night) and Chrysonilia spp. (12.4% morning; 20.3% night). Several Aspergillus sections were identified in air and EDC samples. However, none of the fungal species/strains (Aspergillus sections Fumigati, Flavi, Nidulantes and Circumdati) were amplified by qPCR in the analyzed EDC. The correlations observed suggest reduced susceptibility to antifungal drugs of some fungal species found in sleeping environments. Toxigenic fungal species and indicators of harmful fungal contamination were observed in sleeping environments.
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Affiliation(s)
- Carla Viegas
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal; NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de, Lisboa, Portugal; Comprehensive Health Research Center (CHRC), Portugal.
| | - Marta Dias
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal
| | - Ana Monteiro
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal
| | - Tiago Faria
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal
| | - Joana Lage
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal
| | - Elisabete Carolino
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal
| | - Liliana Aranha Caetano
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal; Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Anita Quintal Gomes
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal; University of Lisbon Institute of Molecular Medicine, Faculty of Medicine, Lisbon, Portugal
| | - Susana Marta Almeida
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal
| | - Sandra Cabo Verde
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal
| | - Joana Belo
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de, Lisboa, Portugal; Integrated Pathophysiological Mechanisms Research Group (CEDOC) - NMS-UNL, Lisboa, Portugal
| | - Nuno Canha
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066, Bobadela-LRS, Portugal; Centre for Environmental and Marine Studies, Department of Environment and Planning, University of Aveiro, 3810-193, Aveiro, Portugal
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Fuhrmeister ER, Ercumen A, Grembi JA, Islam M, Pickering AJ, Nelson KL. Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households. WATER RESEARCH X 2020; 9:100056. [PMID: 32529181 PMCID: PMC7276488 DOI: 10.1016/j.wroa.2020.100056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 05/24/2023]
Abstract
Understanding household-level transmission pathways of fecal pathogens can provide insight for developing effective strategies to reduce diarrheal illness in low- and middle-income countries. We applied whole bacterial community analysis to investigate pathways of bacterial transmission in 50 rural Bangladeshi households. SourceTracker was used to quantify the shared microbial community in household reservoirs (stored drinking water, soil, and hands) and estimate the percentage of fecal-associated bacteria from child and mothers' feces in these reservoirs. Among the reservoirs studied, most bacterial transfer occurred between mothers' and children's hands and between mothers' hands and stored water. The relative percentage of human fecal-associated bacteria in all household reservoirs was low. We also quantified the number of identical amplicon sequence variants within and between individual households to assess bacterial community exchange in the domestic environment. Intra-household sharing of bacteria between mothers' and children's hands and between hands and soil was significantly greater than inter-household sharing.
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Affiliation(s)
- Erica R. Fuhrmeister
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720, United States
| | - Ayse Ercumen
- School of Public Health, University of California, Berkeley, CA, 94720, United States
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27607, United States
| | - Jessica A. Grembi
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, 94305, United States
| | - Mahfuza Islam
- Environmental Intervention Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Amy J. Pickering
- Civil and Environmental Engineering, Tufts University, Medford, MA, 02153, United States
| | - Kara L. Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720, United States
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Kakumanu ML, DeVries ZC, Barbarin AM, Santangelo RG, Schal C. Bed bugs shape the indoor microbial community composition of infested homes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140704. [PMID: 32927527 DOI: 10.1016/j.scitotenv.2020.140704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 05/12/2023]
Abstract
Indoor pests, and the allergens they produce, adversely affect human health. Surprisingly, however, their effects on indoor microbial communities have not been assessed. Bed bug (Cimex lectularius) infestations pose severe challenges in elderly and low-income housing. They void large amounts of liquid feces into the home environment, which might alter the indoor microbial community composition. In this study, using bed bug-infested and uninfested homes, we showed a strong impact of bed bug infestations on the indoor microbial diversity. Floor dust samples were collected from uninfested and bed bug-infested homes and their microbiomes were analyzed before and after heat interventions that eliminated bed bugs. The microbial communities of bed bug-infested homes were radically different from those of uninfested homes, and the bed bug endosymbiont Wolbachia was the major driver of this difference. After bed bugs were eliminated, the microbial community gradually shifted toward the community composition of uninfested homes, strongly implicating bed bugs in shaping the dust-associated environmental microbiome. Further studies are needed to understand the viability of these microbial communities and the potential risks that bed bug-associated microbes and their metabolites pose to human health.
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Affiliation(s)
- Madhavi L Kakumanu
- Department of Entomology and Plant Pathology and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States.
| | - Zachary C DeVries
- Department of Entomology and Plant Pathology and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States; Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Alexis M Barbarin
- Department of Entomology and Plant Pathology and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States; Division of Public Health, Communicable Disease Branch, Raleigh, NC, United States
| | - Richard G Santangelo
- Department of Entomology and Plant Pathology and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Coby Schal
- Department of Entomology and Plant Pathology and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States.
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Botta C, Ferrocino I, Pessione A, Cocolin L, Rantsiou K. Spatiotemporal Distribution of the Environmental Microbiota in Food Processing Plants as Impacted by Cleaning and Sanitizing Procedures: the Case of Slaughterhouses and Gaseous Ozone. Appl Environ Microbiol 2020; 86:e01861-20. [PMID: 32978124 PMCID: PMC7657643 DOI: 10.1128/aem.01861-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Microbial complexity and contamination levels in food processing plants heavily impact the final product fate and are mainly controlled by proper environmental cleaning and sanitizing. Among the emerging disinfection technologies, ozonation is considered an effective strategy to improve the ordinary cleaning and sanitizing of slaughterhouses. However, its effects on contamination levels and environmental microbiota still need to be understood. For this purpose, we monitored the changes in microbiota composition in different slaughterhouse environments during the phases of cleaning/sanitizing and ozonation at 40, 20, or 4 ppm. Overall, the meat processing plant microbiota differed significantly between secondary processing rooms and deboning rooms, with a greater presence of psychrotrophic taxa in secondary processing rooms because of their lower temperatures. Cleaning/sanitizing procedures significantly reduced the contamination levels and in parallel increased the number of detectable operational taxonomic units (OTUs), by removing the masking effect of the most abundant human/animal-derived OTUs, which belonged to the phylum Firmicutes Subsequently, ozonation at 40 or 20 ppm effectively decreased the remaining viable bacterial populations. However, we could observe selective ozone-mediated inactivation of psychrotrophic bacteria only in the secondary processing rooms. There, the Brochothrix and Pseudomonas abundances and their viable counts were significantly affected by 40 or 20 ppm of ozone, while more ubiquitous genera like Staphylococcus showed a remarkable resistance to the same treatments. This study showed the effectiveness of highly concentrated gaseous ozone as an adjunct sanitizing method that can minimize cross-contamination and so extend the meat shelf life.IMPORTANCE Our in situ survey demonstrates that RNA-based sequencing of 16S rRNA amplicons is a reliable approach to qualitatively probe, at high taxonomic resolution, the changes triggered by new and existing cleaning/sanitizing strategies in the environmental microbiota in human-built environments. This approach could soon represent a fast tool to clearly define which routine sanitizing interventions are more suitable for a specific food processing environment, thus limiting the costs of special cleaning interventions and potential product loss.
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Affiliation(s)
- Cristian Botta
- Department of Agriculture, Forestry, and Food Sciences, University of Turin, Turin, Italy
| | - Ilario Ferrocino
- Department of Agriculture, Forestry, and Food Sciences, University of Turin, Turin, Italy
| | | | - Luca Cocolin
- Department of Agriculture, Forestry, and Food Sciences, University of Turin, Turin, Italy
| | - Kalliopi Rantsiou
- Department of Agriculture, Forestry, and Food Sciences, University of Turin, Turin, Italy
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Mhatre S, Wood JM, Sielaff AC, Mora M, Duller S, Singh NK, Karouia F, Moissl-Eichinger C, Venkateswaran K. Assessing the Risk of Transfer of Microorganisms at the International Space Station Due to Cargo Delivery by Commercial Resupply Vehicles. Front Microbiol 2020; 11:566412. [PMID: 33240227 PMCID: PMC7677455 DOI: 10.3389/fmicb.2020.566412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND With increasing numbers of interplanetary missions, there is a need to establish robust protocols to ensure the protection of extraterrestrial planets being visited from contamination by terrestrial life forms. The current study is the first report comparing the commercial resupply vehicle (CRV) microbiome with the International Space Station (ISS) microbiome to understand the risks of contamination, thus serving as a model system for future planetary missions. RESULTS Samples obtained from the internal surfaces and ground support equipment of three CRV missions were subjected to various molecular techniques for microbial diversity analysis. In total, 25 samples were collected with eight defined locations from each CRV mission prior to launch. In general, the internal surfaces of vehicles were clean, with an order of magnitude fewer microbes compared to ground support equipment. The first CRV mission had a larger microbial population than subsequent CRV missions, which were clean as compared to the initial CRV locations sampled. Cultivation assays showed the presence of Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes and members of Ascomycota and Basidiomycota. As expected, shotgun metagenome analyses revealed the presence of more microbial taxa compared to cultivation-based assays. The internal locations of the CRV microbiome reportedly showed the presence of microorganisms capable of tolerating ultraviolet radiation (e.g., Bacillus firmus) and clustered separately from the ISS microbiome. CONCLUSIONS The metagenome sequence comparison of the CRV microbiome with the ISS microbiome revealed significant differences showing that CRV microbiomes were a negligible part of the ISS environmental microbiome. These findings suggest that the maintenance protocols in cleaning CRV surfaces are highly effective in controlling the contaminating microbial population during cargo transfer to the ISS via the CRV route.
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Affiliation(s)
- Snehit Mhatre
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Jason M. Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Aleksandra Checinska Sielaff
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Maximilian Mora
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Stefanie Duller
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Nitin Kumar Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Fathi Karouia
- Space Bioscience Division, NASA Ames Research Center, Moffett Field, CA, United States
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Li S, Yang Z, Hu D, Cao L, He Q. Understanding building-occupant-microbiome interactions toward healthy built environments: A review. FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING 2020; 15:65. [PMID: 33145119 PMCID: PMC7596174 DOI: 10.1007/s11783-020-1357-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/30/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Built environments, occupants, and microbiomes constitute a system of ecosystems with extensive interactions that impact one another. Understanding the interactions between these systems is essential to develop strategies for effective management of the built environment and its inhabitants to enhance public health and well-being. Numerous studies have been conducted to characterize the microbiomes of the built environment. This review summarizes current progress in understanding the interactions between attributes of built environments and occupant behaviors that shape the structure and dynamics of indoor microbial communities. In addition, this review also discusses the challenges and future research needs in the field of microbiomes of the built environment that necessitate research beyond the basic characterization of microbiomes in order to gain an understanding of the causal mechanisms between the built environment, occupants, and microbiomes, which will provide a knowledge base for the development of transformative intervention strategies toward healthy built environments. The pressing need to control the transmission of SARS-CoV-2 in indoor environments highlights the urgency and significance of understanding the complex interactions between the built environment, occupants, and microbiomes, which is the focus of this review.
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Affiliation(s)
- Shuai Li
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Zhiyao Yang
- Lyles School of Civil Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Da Hu
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Liu Cao
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Institute for a Secure & Sustainable Environment, University of Tennessee, Knoxville, TN 37996 USA
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Caraballo Guzmán A, González Hurtado MI, Cuesta-Astroz Y, Torres G. Metagenomic characterization of bacterial biofilm in four food processing plants in Colombia. Braz J Microbiol 2020; 51:1259-1267. [PMID: 32221908 PMCID: PMC7455661 DOI: 10.1007/s42770-020-00260-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/09/2020] [Indexed: 12/26/2022] Open
Abstract
Bacteria inside biofilms are more persistent and resistant to stress conditions found in the production environment of food processing plants, thus representing a constant risk for product safety and quality. Therefore, the aim of this study was to characterize, using 16S rRNA sequencing, the bacterial communities from biofilms found in four food processing plants (P1, P2, P3, and P4). In total, 50 samples from these four processing plants were taken after cleaning and disinfection processes. Four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroides represented over 94% of the operational taxonomic units found across these four plants. A total of 102 families and 189 genera were identified. Two genera, Pseudomonas spp. and Acinetobacter spp., were the most frequently found (93.47%) across the four plants. In P1, Pseudomonas spp. and Lactobacillus spp. were the dominant genera, whereas Lactobacillus spp. and Streptococcus spp. were identified in P2. On the other hand, biofilms found in P3 and P4 mainly consisted of Pseudomonas spp. and Acinetobacter spp. Our results indicate that different bacterial genera of interest to the food industry due to their ability to form biofilm and affect food quality can coexist inside biofilms, and as such, persist in production environments, representing a constant risk for manufactured foods. In addition, the core microbiota identified across processing plants evaluated was probably influenced by type of food produced and cleaning and disinfection processes performed in each one of these.
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Affiliation(s)
- Arley Caraballo Guzmán
- Colombian Institute of Tropical Medicine, CES University, Carrera 43A # 52 Sur 99, Sabaneta, Colombia
| | | | - Yesid Cuesta-Astroz
- Colombian Institute of Tropical Medicine, CES University, Carrera 43A # 52 Sur 99, Sabaneta, Colombia
| | - Giovanny Torres
- Colombian Institute of Tropical Medicine, CES University, Carrera 43A # 52 Sur 99, Sabaneta, Colombia
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Gupta S, Hjelmsø MH, Lehtimäki J, Li X, Mortensen MS, Russel J, Trivedi U, Rasmussen MA, Stokholm J, Bisgaard H, Sørensen SJ. Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota. MICROBIOME 2020; 8:115. [PMID: 32767985 PMCID: PMC7414761 DOI: 10.1186/s40168-020-00895-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/17/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amount of time indoors, we hypothesize that the indoor bed dust microbiota might be an important factor for the child and for the early colonization of the airway microbiome. To explore this hypothesis, we analyzed the influence of environmental exposures on 577 dust samples from the beds of infants together with 542 airway samples from the Copenhagen Prospective Studies on Asthma in Childhood2010 cohort. RESULTS Both bacterial and fungal community was profiled from the bed dust. Bacterial and fungal diversity in the bed dust was positively correlated with each other. Bacterial bed dust microbiota was influenced by multiple environmental factors, such as type of home (house or apartment), living environment (rural or urban), sex of siblings, and presence of pets (cat and/or dog), whereas fungal bed dust microbiota was majorly influenced by the type of home (house or apartment) and sampling season. We further observed minor correlation between bed dust and airway microbiota compositions among infants. We also analyzed the transfer of microbiota from bed dust to the airway, but we did not find evidence of transfer of individual taxa. CONCLUSIONS Current study explores the influence of environmental factors on bed dust microbiota (both bacterial and fungal) and its correlation with airway microbiota (bacterial) in early life using high-throughput sequencing. Our findings demonstrate that bed dust microbiota is influenced by multiple environmental exposures and could represent an interface between environment and child. Video Abstract.
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Affiliation(s)
- Shashank Gupta
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
| | - Mathis H Hjelmsø
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, Copenhagen University Hospital Gentofte, University of Copenhagen, Gentofte, Denmark
| | - Jenni Lehtimäki
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, Copenhagen University Hospital Gentofte, University of Copenhagen, Gentofte, Denmark
| | - Xuanji Li
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
| | - Martin S Mortensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
| | - Urvish Trivedi
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
| | - Morten A Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, Copenhagen University Hospital Gentofte, University of Copenhagen, Gentofte, Denmark
- Section of Chemometrics and Analytical Technologies, Department of Food Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, Copenhagen University Hospital Gentofte, University of Copenhagen, Gentofte, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, Copenhagen University Hospital Gentofte, University of Copenhagen, Gentofte, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark.
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Novak Babič M, Gostinčar C, Gunde-Cimerman N. Microorganisms populating the water-related indoor biome. Appl Microbiol Biotechnol 2020; 104:6443-6462. [PMID: 32533304 PMCID: PMC7347518 DOI: 10.1007/s00253-020-10719-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/22/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022]
Abstract
Modernisation of our households created novel opportunities for microbial growth and thus changed the array of microorganisms we come in contact with. While many studies have investigated microorganisms in the air and dust, tap water, another major input of microbial propagules, has received far less attention. The quality of drinking water in developed world is strictly regulated to prevent immediate danger to human health. However, fungi, algae, protists and bacteria of less immediate concern are usually not screened for. These organisms can thus use water as a vector of transmission into the households, especially if they are resistant to various water treatment procedures. Good tolerance of unfavourable abiotic conditions is also important for survival once microbes enter the household. Limitation of water availability, high or low temperatures, application of antimicrobial chemicals and other measures are taken to prevent indoor microbial overgrowth. These conditions, together with a large number of novel chemicals in our homes, shape the diversity and abundance of indoor microbiota through constant selection of the most resilient species, resulting in a substantial overlap in diversity of indoor and natural extreme environments. At least in fungi, extremotolerance has been linked to human pathogenicity, explaining why many species found in novel indoor habitats (such as dishwasher) are notable opportunistic pathogens. As a result, microorganisms that often enter our households with water and are then enriched in novel indoor habitats might have a hitherto underestimated impact on the well-being of the increasingly indoor-bound human population. KEY POINTS: Domestic environment harbours a large diversity of microorganisms. Microbiota of water-related indoor habitats mainly originates from tap water. Bathrooms, kitchens and household appliances select for polyextremotolerant species. Many household-related microorganisms are human opportunistic pathogens.
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Affiliation(s)
- Monika Novak Babič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, 266555, China
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
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Surface sampling within a pediatric ward-how multiple factors affect cleaning efficacy. Am J Infect Control 2020; 48:740-745. [PMID: 31818511 DOI: 10.1016/j.ajic.2019.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND The objectives of this study were to assess the number of organisms present on different surfaces within a clinical environment before and after cleaning took place, and to identify the impact of cleaning. The study involved extensive 2-week microbiological environmental monitoring of an entire ward before and after cleaning; the ward was located within a pediatric hematology-oncology ward comprised of a day unit and outpatient ward. METHODS Tryptone soya agar contact plates were used to take a total of 1,160 surface samples before and after cleaning from 55 predetermined sites. Samples were taken from representative surfaces throughout the ward representing a variety of materials, surface heights, functions, and distances from patients, as well as both high-touch and infrequently touched surfaces. RESULTS After surface cleaning was undertaken within the ward, there was a significant difference between the amount of colony-forming units (CFUs) recovered before and after cleaning (P < .0001). Cleaning produced an average CFU reduction of 68% throughout the ward environment. The corridor was the most contaminated area within the ward. There were differences in the CFUs among the various areas within the ward, which were cleaned with varying efficiency. The surface material, who interacted with the surface, levels of initial contamination, perceived risk, and perceived cleanability were all found to have a varying impact on the cleaning effectiveness. CONCLUSIONS To the authors' current knowledge, this is the only study to assess cleaning within a pediatric ward by taking samples directly before and after cleaning. The standard of cleaning undertaken within the ward is open for discussion, and these data highlight the need for an improved cleaning intervention and can provide insight into the multitude of factors that must be considered when designing an effective training protocol.
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Tozzo P, D’Angiolella G, Brun P, Castagliuolo I, Gino S, Caenazzo L. Skin Microbiome Analysis for Forensic Human Identification: What Do We Know So Far? Microorganisms 2020; 8:microorganisms8060873. [PMID: 32527009 PMCID: PMC7356928 DOI: 10.3390/microorganisms8060873] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 01/15/2023] Open
Abstract
Microbiome research is a highly transdisciplinary field with a wide range of applications and methods for studying it, involving different computational approaches and models. The fact that different people host radically different microbiota highlights forensic perspectives in understanding what leads to this variation and what regulates it, in order to effectively use microbes as forensic evidence. This narrative review provides an overview of some of the main scientific works so far produced, focusing on the potentiality of using skin microbiome profiling for human identification in forensics. This review was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The examined literature clearly ascertains that skin microbial communities, although personalized, vary systematically across body sites and time, with intrapersonal differences over time smaller than interpersonal ones, showing such a high degree of spatial and temporal variability that the degree and nature of this variability can constitute in itself an important parameter useful in distinguishing individuals from one another. Even making the effort to organically synthesize all results achieved until now, it is quite evident that these results are still the pieces of a puzzle, which is not yet complete.
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Affiliation(s)
- Pamela Tozzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy;
- Correspondence: ; Tel.: +39-0498272234
| | - Gabriella D’Angiolella
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35121 Padova, Italy;
| | - Paola Brun
- Department of Molecular Medicine, Section of Microbiology, University of Padova, 35121 Padova, Italy; (P.B.); (I.C.)
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, Section of Microbiology, University of Padova, 35121 Padova, Italy; (P.B.); (I.C.)
| | - Sarah Gino
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy;
| | - Luciana Caenazzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy;
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Ding LJ, Zhou XY, Zhu YG. Microbiome and antibiotic resistome in household dust from Beijing, China. ENVIRONMENT INTERNATIONAL 2020; 139:105702. [PMID: 32248025 DOI: 10.1016/j.envint.2020.105702] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/26/2020] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
We spend ever-increasing time indoors along with urbanization; however, the geographical distribution patterns of microbiome and antibiotic resistome, and their driving forces in household environment remains poorly characterized. Here, we surveyed the bacterial and fungal communities, and the resistome in settled dust gathered from 82 homes located across Beijing, China, employing Illumina sequencing and high-throughput quantitative PCR techniques. There was no clear geographical distribution pattern in dust-related bacterial communities although a slight but significant (P < 0.05) distance-decay relationship occurred in its community similarity; by contrast, a relatively distinct geographical clustering and a stronger distance-decay relationship were observed in fungal communities at the local scale. The cross-domain (bacteria versus fungi) relationships in the microbiome of the dust samples were mostly observed as robust co-occurrence correlations. The bacterial communities were dominated by Proteobacteria and Actinobacteria phyla, with human skin, soil and plants being potential major sources. The fungal communities largely comprised potential allergens (a median 61% of the fungal sequences), with Alternaria genus within Ascomycota phylum being the most predominant taxa. The profile of dust-related bacterial communities was mainly affected by housing factors related to occupants and houseplants, while that of fungal communities was determined by georeferenced environmental factors, particularly vascular plant diversity. Additionally, a great diversity (1.96 on average for Shannon index) and normalized abundance (2.22 copies per bacterial cell on average) of antibiotic resistance genes were detected across the dust samples, with the dominance of genes resistant to vancomycin and Macrolide-Lincosamide-Streptogramin B. The resistome profile exhibited no distinct geographical pattern, and was primarily driven by certain bacterial phyla and occupancy-related factors. Overall, we underline the significance of anthropogenic impacts and house location in structuring bacterial and fungal communities inside homes, respectively, and suggest that household dust is an overlooked reservoir for antibiotic resistance.
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Affiliation(s)
- Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xin-Yuan Zhou
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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El‐Liethy MA, Hemdan BA, El‐Taweel GE. Prevalence of
E. coli
,
Salmonella
, and
Listeria
spp. as potential pathogens: A comparative study for biofilm of sink drain environment. J Food Saf 2020. [DOI: 10.1111/jfs.12816] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mohamed Azab El‐Liethy
- Environmental Microbiology Laboratory, Water Pollution Research DepartmentNational Research Centre Giza Egypt
| | - Bahaa A. Hemdan
- Environmental Microbiology Laboratory, Water Pollution Research DepartmentNational Research Centre Giza Egypt
| | - Gamila E. El‐Taweel
- Environmental Microbiology Laboratory, Water Pollution Research DepartmentNational Research Centre Giza Egypt
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Jacksch S, Thota J, Shetty S, Smidt H, Schnell S, Egert M. Metagenomic Analysis of Regularly Microwave-Treated and Untreated Domestic Kitchen Sponges. Microorganisms 2020; 8:microorganisms8050736. [PMID: 32423128 PMCID: PMC7284620 DOI: 10.3390/microorganisms8050736] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/08/2020] [Accepted: 05/08/2020] [Indexed: 01/04/2023] Open
Abstract
Kitchen sponges massively absorb and spread microorganisms, leading to contamination of kitchen appliances, surfaces, and food. Microwaving as an effective and widespread technique can rapidly reduce the microbial load of kitchen sponges. However, long-term effects of such treatments are largely unknown. Notably, it has been speculated that regularly applied domestic cleaning and disinfection may select for microbial communities with a higher pathogenic potential and/or malodorous properties. In this study, we distributed newly purchased polyurethane kitchen sponges to 20 participants, with the instruction to use them under normal household conditions for four weeks. Ten of the participants sanitized their sponges regularly by a standardized microwaving protocol, while the remaining ten sponges remained untreated. Metagenomic sequence data evaluation indicated that, in addition to bacteria, viruses, eukaryotes, and archaea were also part of the kitchen sponge microbiome. Comparisons of sanitized and untreated kitchen sponges indicated a trend towards a reduced structural microbial diversity while functional diversity increased. Microwave sanitization appeared to alter composition and metabolic properties of the microbial communities. Follow-up studies will have to show whether these changes are more positive or negative in terms of domestic hygiene, human health, and well-being.
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Affiliation(s)
- Susanne Jacksch
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (S.J.); (J.T.)
| | - Jyothi Thota
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (S.J.); (J.T.)
| | - Sudarshan Shetty
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (S.S.); (H.S.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (S.S.); (H.S.)
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Centre for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, 35392 Giessen, Germany;
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, 78054 Villingen-Schwenningen, Germany; (S.J.); (J.T.)
- Correspondence: ; Tel.: +49-0-7720-307-4554
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Gupta V, Kumar R, Sood U, Singhvi N. Reconciling Hygiene and Cleanliness: A New Perspective from Human Microbiome. Indian J Microbiol 2020; 60:37-44. [PMID: 32089572 PMCID: PMC7000587 DOI: 10.1007/s12088-019-00839-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/03/2019] [Indexed: 12/12/2022] Open
Abstract
The term hygiene is deeply rooted with the concept of maintaining sound health and alertness towards cleanliness, while "hygiene hypothesis" depicts the protective role of microbial community exposure in development of early immunity and initial allergic and aesthetic reactions. The tug-of-war has now been pushed toward the literal term "hygiene" over the "hygiene hypothesis" and has continued with disinfection of all microbial loads from the related environments to avoid infections in humans. With the advancement in the microbiome studies, it became clear that humans possess warm, and significant relationships with diverse microbial community. With this opinion article, we have emphasized on the importance of hygiene hypothesis in immunological responses. We also propose the individual/targeted hygiene instead of application of unanimous hygiene hypothesis. This review also elaborates the common practices that should be employed to maintain hygiene along with the balanced microbiome.
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Affiliation(s)
- Vipin Gupta
- PhiXGen Private Limited, Gurugram, Haryana 122001 India
- Department of Zoology, University of Delhi, Delhi, Delhi 110007 India
| | - Roshan Kumar
- P.G. Department of Zoology, Magadh University, Bodh-Gaya, Bihar 824231 India
| | - Utkarsh Sood
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003 India
| | - Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, Delhi 110007 India
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Zupančič J, Turk M, Črnigoj M, Ambrožič Avguštin J, Gunde-Cimerman N. The dishwasher rubber seal acts as a reservoir of bacteria in the home environment. BMC Microbiol 2019; 19:300. [PMID: 31856722 PMCID: PMC6924085 DOI: 10.1186/s12866-019-1674-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/04/2019] [Indexed: 11/10/2022] Open
Abstract
Background In modern lifestyles, people make their everyday tasks easier by using household appliances, for example dishwashers. Previous studies showed massive contamination of dishwasher rubber seals with fungi, thus bacterial community, able to survive under harsh conditions, remain undetermined. Methods Bacteria that colonise the extreme environment of household dishwasher rubber seals were investigated using cultivation-dependent and metagenomic approaches. All bacterial isolates were tested for resistance to seven selected antibiotics. Same time bacterial diversity of tap water, connected to the dishwashers was investigated. Results All 30 dishwashers investigated were colonised by various bacteria. Cultivation approaches resulted in 632 bacterial isolates in total, belonging to four phyla, eight classes, 40 genera and 74 species. The majority were Gram-positive, as solely Firmicutes (dominated by the Bacillus cereus group) and Actinobacteria. Gammaproteobacteria were primarily represented by Stenotrophomonas maltophilia, Pseudomonas aeruginosa and Escherichia coli. Metagenomic assessment of the bacterial biodiversity of the dishwasher rubber seals confirmed the predominance of Gram-positive bacteria, as primarily Actinobacteria, followed by Proteobacteria dominated by Gammaproteobacteria, and by pathogenic species such as Escherichia sp., Acinetobacter baumannii, Pseudomonas sp., Stenotrophomonas maltophilia, and Enterobacter sp.. Metagenomic assessment of bacterial biodiversity in the tap water connected to dishwashers revealed predominance of Gram-negative bacteria, in particular Proteobacteria, mainly represented by Tepidimonas sp.. Actinobacteria showed low numbers while no Firmicutes were detected in the tap water. The bacterial diversity of tap water was also lower, 23 genera compared to 39 genera on dishwasher rubber seals. Only 13 out of 49 genera identified by metagenomics approach was found in both environments, of those Gordonia was enriched while half of 13 genera were depleted in dishwashers compared to tap water. Conclusions These data indicate that colonisation of dishwasher rubber seals probably depends primarily on the bacterial input from the dirty vessels, and much less on the bacteria in the tap water. Based on the antibiotic resistance data, the dishwasher rubber seal bacterial isolates do not represent a serious threat for the spread of antibiotic resistance into the household environment. Nevertheless dishwashers cannot be ignored as potential sources of human infections, in particular for immuno-compromised individuals.
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Affiliation(s)
- Jerneja Zupančič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Martina Turk
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Črnigoj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Ljubljana, Slovenia
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