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Singh H, Gibb B, Abdi R. Abundance and diversity of methicillin-resistant bacteria from bathroom surfaces at workplaces using CHROMagar media, 16S, and dnaJ gene sequence typing. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2024; 15:12-21. [PMID: 38736754 PMCID: PMC11087278 DOI: 10.62347/ejqk3362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/18/2024] [Indexed: 05/14/2024]
Abstract
University campus communities consist of dynamic and diverse human populations originated from different regions of the country or the world. Their national/global movement to and from campus may contribute to the spread and buildup of methicillin-resistant (MR) bacteria, including MR Staphylococci (MRS) on high-touch surfaces, sinks, and toilets. However, studies on MR bacteria contamination of surfaces, sinks, and toilets are scarce in workplaces outside of healthcare settings. Hence, little is known whether university communities contaminate campus bathrooms by MR bacteria. This study evaluated the abundance, identity, and phylogenetics of MR bacteria grown on CHROMagar MRSA media from bathrooms at workplaces. We collected 21 sink and 21 toilet swab samples from 10 buildings on campus and cultured them on CHROMagar MRSA media, extracted DNA from MR bacteria colonies, sequenced PCR products of 16S and dnaJ primers, determined the sequence identities by BLAST search, and constructed a phylogenetic tree. Of 42 samples, 57.1% (24/42) harbored MR bacteria. MR bacteria were more prevalent on the sink (61.9%) than in the toilet (52.2%) and in male bathrooms (54.2%) than in female bathrooms (41.7%). The colony count on the bathroom surfaces of 42 samples varied in that 42.9% (18/42), 33.3, 14.3, and 9.5% of samples harbored 0, 100, and > 1000 MR bacteria colonies, respectively. Of MR bacteria sequenced, BLAST search and phylogenetic analysis showed that Staphylococcus accounted for 60% of the MR bacteria and the rest were non-Staphylococci. Of Staphylococcus carrying MR (n = 15), 53.3% were S. hemolyticus followed by S. lugdunensis (26.7%), S. epidermidis (8%), and a newly discovered S. borealis in 2020 (4%). Of non-Staphylococci MR bacteria, 20% accounted for Sphingomonas koreensis. Campus bathrooms serve as a reservoir for diverse bacteria carrying MR, which pose a direct risk of infection and a potential source of horizontal gene transfer. To reduce the health risk posed by MR bacteria in high traffic areas such as bathrooms additional environmental monitoring and improved decontamination practices are needed.
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Affiliation(s)
- Harshul Singh
- Department of Biological and Chemical Sciences, Theobald Science Center, New York Institute of Technology (NYIT)Old Westbury, NY 11568, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Long Island University (LIU)Greenville, NY 11548, USA
| | - Bryan Gibb
- Department of Biological and Chemical Sciences, Theobald Science Center, New York Institute of Technology (NYIT)Old Westbury, NY 11568, USA
| | - Reta Abdi
- Department of Biomedical Sciences, College of Veterinary Medicine, Long Island University (LIU)Greenville, NY 11548, USA
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2
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Gottel NR, Hill MS, Neal MJ, Allard SM, Zengler K, Gilbert JA. Biocontrol in built environments to reduce pathogen exposure and infection risk. THE ISME JOURNAL 2024; 18:wrad024. [PMID: 38365248 PMCID: PMC10848226 DOI: 10.1093/ismejo/wrad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.
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Affiliation(s)
- Neil R Gottel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
| | - Megan S Hill
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Maxwell J Neal
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
| | - Sarah M Allard
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Karsten Zengler
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
| | - Jack A Gilbert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
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3
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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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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [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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Jabri H, Krings S, Fall PA, Baurain D, Daube G, Taminiau B. Microbiota Profiling on Veterinary Faculty Restroom Surfaces and Source Tracking. Microorganisms 2023; 11:2053. [PMID: 37630613 PMCID: PMC10459056 DOI: 10.3390/microorganisms11082053] [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: 07/10/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
In this study, we aimed to develop a comprehensive microbial source amplicon database tailored for source tracking in veterinary settings. We rigorously tested our locally curated source tracking database by selecting a frequently accessed environment by veterinary students and veterinarians. By exploring the composition of resident microbiota and identifying potential sources of contamination, including animals, the environment, and human beings, we aimed to provide valuable insights into the dynamics of microbial transmission within veterinary facilities. The 16S rDNA amplicon sequencing was used to determine the bacterial taxonomic profiles of restroom surfaces. Bacterial sources were identified by linking our metadata-enriched local database to the microbiota profiling analysis using high-quality sequences. Microbiota profiling shows the dominance of four phyla: Actinobacteria, Bacteroidetes, Proteobacteria, and Firmicutes. If the restroom cleaning process did not appear to impact microbiota composition, significant differences regarding bacterial distribution were observed between male and female users in different sampling campaigns. Combining 16S rDNA profiling to our specific sources labeling pipeline, we found aquatic and human sources were the primary environment keywords in our campaigns. The probable presence of known animal sources (bovids, insects, equids, suids…) associated with bacterial genera such as Chryseobacterium, Bergeyella, Fibrobacter, and Syntrophococcus was also involved in restroom surfaces, emphasizing the proximity between these restrooms and the exchange of bacteria between people involved in animals handling. To summarize, we have demonstrated that DNA sequence-based source tracking may be integrated with high-throughput bacterial community analysis to enrich microbial investigation of potential bacterial contamination sources, especially for little known or poorly identified taxa. However, more research is needed to determine the tool's utility in other applications.
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Affiliation(s)
- Hiba Jabri
- Laboratory of Food Microbiology, Fundamental and Applied Research for Animals and Health Center (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallée 2, B42, Avenue de Cureghem 10, 4000 Liège, Belgium; (H.J.); (G.D.)
| | - Simone Krings
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, Univesity of Surrey, Guildford GU2 7XH, UK;
| | - Papa Abdoulaye Fall
- FoodChainID GENOMICS, Laboratory Manager NGS, Rue Hayeneux, 62, 4040 Herstal, Belgium;
| | - Denis Baurain
- Eukaryotic Phylogenomics, InBioS-PhytoSYSTEMS, University of Liège, 4000 Liège, Belgium;
| | - Georges Daube
- Laboratory of Food Microbiology, Fundamental and Applied Research for Animals and Health Center (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallée 2, B42, Avenue de Cureghem 10, 4000 Liège, Belgium; (H.J.); (G.D.)
| | - Bernard Taminiau
- Laboratory of Food Microbiology, Fundamental and Applied Research for Animals and Health Center (FARAH), Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallée 2, B42, Avenue de Cureghem 10, 4000 Liège, Belgium; (H.J.); (G.D.)
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6
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Du S, Tong X, Lai ACK, Chan CK, Mason CE, Lee PKH. Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution. Nat Commun 2023; 14:2676. [PMID: 37160974 PMCID: PMC10169181 DOI: 10.1038/s41467-023-38400-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assesses viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes are found to be habitat dependent. Caudoviricetes species are ubiquitous on surface habitats in the BEs, and some of them are distinct from those present in other environments. Antimicrobial resistance genes are identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants' skin. Diverse CRISPR/Cas immunity systems and anti-CRISPR proteins are found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus-host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner is identified through a unique gene insertion. This work illustrates that virus-host interactions occur frequently in BEs and that viruses are integral members of BE microbiomes.
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Affiliation(s)
- Shicong Du
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, P. R. China
| | - Alvin C K Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Chak K Chan
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
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7
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Santiago-Rodriguez TM, Le François B, Macklaim JM, Doukhanine E, Hollister EB. The Skin Microbiome: Current Techniques, Challenges, and Future Directions. Microorganisms 2023; 11:1222. [PMID: 37317196 DOI: 10.3390/microorganisms11051222] [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: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership and function may differ depending on the various specialized niches or micro-environments of the skin. The group of microorganisms inhabiting the skin, also known as the skin microbiome, offers protection against pathogens while actively interacting with the host's immune system. Some members of the skin microbiome can also act as opportunistic pathogens. The skin microbiome is influenced by factors such as skin site, birth mode, genetics, environment, skin products, and skin conditions. The association(s) of the skin microbiome with health and disease has (have) been identified and characterized via culture-dependent and culture-independent methods. Culture-independent methods (such as high-throughput sequencing), in particular, have expanded our understanding of the skin microbiome's role in maintaining health or promoting disease. However, the intrinsic challenges associated with the low microbial biomass and high host content of skin microbiome samples have hindered advancements in the field. In addition, the limitations of current collection and extraction methods and biases derived from sample preparation and analysis have significantly influenced the results and conclusions of many skin microbiome studies. Therefore, the present review discusses the technical challenges associated with the collection and processing of skin microbiome samples, the advantages and disadvantages of current sequencing approaches, and potential future areas of focus for the field.
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8
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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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Evaluation of the microbial reduction efficacy and perception of use of an ozonized water spray disinfection technology. Sci Rep 2022; 12:13019. [PMID: 35906472 PMCID: PMC9335460 DOI: 10.1038/s41598-022-16953-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/19/2022] [Indexed: 11/25/2022] Open
Abstract
The development of new approaches for the decontamination of surfaces is important to deal with the processes related to exposure to contaminated surfaces. Therefore, was evaluated the efficacy of a disinfection technology using ozonized water (0.7–0.9 ppm of O3) on the surfaces of garments and accessories of volunteers, aiming to reduce the spread of microbial pathogens in the workplace and community. A Log10 microbial reduction of 1.72–2.40 was observed between the surfaces tested. The microbial reductions remained above 60% on most surfaces, and this indicated that the disinfection technology was effective in microbial log reduction regardless of the type of transport used by the volunteers and/or their respective work activities. In association with the evaluation of efficacy, the analysis of the perception of use (approval percentage of 92.45%) was fundamental to consider this technology as an alternative for use as a protective barrier, in conjunction with other preventive measures against microbiological infections, allowing us to contribute to the availability of proven effective devices against the spread of infectious agents in the environment.
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Urbaniak C, Morrison MD, Thissen JB, Karouia F, Smith DJ, Mehta S, Jaing C, Venkateswaran K. Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station. MICROBIOME 2022; 10:100. [PMID: 35765106 PMCID: PMC9241228 DOI: 10.1186/s40168-022-01293-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/19/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months. METHODS Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results. RESULTS Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 105 cfu/m2 CONCLUSIONS: Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity. Video Abstract.
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Affiliation(s)
- Camilla Urbaniak
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Michael D Morrison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - James B Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Fathi Karouia
- KBRwyle, NASA Ames Research Center, Moffett Field, Mountain View, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - David J Smith
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, Mountain View, CA, USA
| | - Satish Mehta
- JesTech, NASA-Johnson Space Center, Houston, TX, USA
| | - Crystal Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA.
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11
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Pausan MR, Blohs M, Mahnert A, Moissl-Eichinger C. The sanitary indoor environment-a potential source for intact human-associated anaerobes. NPJ Biofilms Microbiomes 2022; 8:44. [PMID: 35650275 PMCID: PMC9160270 DOI: 10.1038/s41522-022-00305-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/04/2022] [Indexed: 02/06/2023] Open
Abstract
A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. People in high-income countries spend most of their time indoors and for this reason, the built environment (BE) might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes. We sampled the bathrooms in ten households and used propidium monoazide (PMA) to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. Quantitative and qualitative analysis revealed that most of the microbial taxa in the BE samples are human-associated. Less than 25% of the prokaryotic signatures originate from intact cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. However, we also confirmed the presence of intact, strictly anaerobic taxa on bathroom floors, including methanogenic archaea. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that human-associated methanogens can survive oxic conditions for at least 6 h. We collected strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.
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Affiliation(s)
- Manuela-Raluca Pausan
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Steigerwald Arzneimittelwerk GmbH, Bayer Consumer Health, Darmstadt, Germany
| | - Marcus Blohs
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
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12
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Balkrishna A, Singh K, Haldar S, Varshney A. Germi-X herbal-based spray disinfects smartphone surfaces: implication on fomite-mediated infection spread. AMB Express 2022; 12:30. [PMID: 35244805 PMCID: PMC8894557 DOI: 10.1186/s13568-022-01369-y] [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: 12/03/2021] [Accepted: 02/19/2022] [Indexed: 11/10/2022] Open
Abstract
Inanimate objects/surfaces become fomites upon contacting infectious agents such as disease-causing bacteria, fungi and viruses. Smartphones are one of the most prominent among these fomites. COVID-19 pandemic has raised the awareness on mobile sanitization, as an active measure to curb fomite-mediated viral transmission. Available mobile sanitizers and ultraviolet (UV) ray mediated mobile sanitization have their own sets of pros and cons, often being less user-friendly. This study explored the germicidal efficacy of an herbal-based sanitizer, Germi-X spray, on hands and mobiles, through microbiological techniques of micro-broth dilution and Kirby-Bauer disc diffusion assay, thumb print assay and swab test. Notably, Germi-X spray was found to be 6–67% more effective against surface pathogens, like, Staphylococcus epidermidis, Staphylococcus aureus, Pseudomonas fluorescens and Pseudomonas aeruginosa, as compared to a very popular product in the Indian market, which was taken as a control for this study. The observed anti-bacterial activity of the spray from disc-diffusion assay suggests its greater surface retentivity as compared to the control. Germicidal potency of Germi-X spray, when used to sanitize hands, was found to be greater than 80%. There was ~ 17-fold reduction in microbial counts after sanitizing smartphones with Germi-X spray. The novelty of this study lies in providing experimental evidence for this herbal-based surface sanitizer in efficiently disinfecting one of the super contaminated fomite, the smartphones. In conclusion, having an herbal base with a high germicidal efficacy against surface pathogens, together with longer surface retention, Germi-X spray appears to be an eco-friendly and cost-effective sanitizer for the surfaces of electronic gadgets like smartphones.
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13
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Pavletić B, Runzheimer K, Siems K, Koch S, Cortesão M, Ramos-Nascimento A, Moeller R. Spaceflight Virology: What Do We Know about Viral Threats in the Spaceflight Environment? ASTROBIOLOGY 2022; 22:210-224. [PMID: 34981957 PMCID: PMC8861927 DOI: 10.1089/ast.2021.0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Viruses constitute a significant part of the human microbiome, so wherever humans go, viruses are brought with them, even on space missions. In this mini review, we focus on the International Space Station (ISS) as the only current human habitat in space that has a diverse range of viral genera that infect microorganisms from bacteria to eukaryotes. Thus, we have reviewed the literature on the physical conditions of space habitats that have an impact on both virus transmissibility and interaction with their host, which include UV radiation, ionizing radiation, humidity, and microgravity. Also, we briefly comment on the practices used on space missions that reduce virus spread, that is, use of antimicrobial surfaces, spacecraft sterilization practices, and air filtration. Finally, we turn our attention to the health threats that viruses pose to space travel. Overall, even though efforts are taken to ensure safe conditions during human space travel, for example, preflight quarantines of astronauts, we reflect on the potential risks humans might be exposed to and how those risks might be aggravated in extraterrestrial habitats.
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Affiliation(s)
- Bruno Pavletić
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Aerospace Microbiology Research Group, Linder Hoehe, Cologne (Köln), Germany
| | - Katharina Runzheimer
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Aerospace Microbiology Research Group, Linder Hoehe, Cologne (Köln), Germany
| | - Katharina Siems
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Aerospace Microbiology Research Group, Linder Hoehe, Cologne (Köln), Germany
| | - Stella Koch
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Aerospace Microbiology Research Group, Linder Hoehe, Cologne (Köln), Germany
| | - Marta Cortesão
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Aerospace Microbiology Research Group, Linder Hoehe, Cologne (Köln), Germany
| | - Ana Ramos-Nascimento
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Aerospace Microbiology Research Group, Linder Hoehe, Cologne (Köln), Germany
| | - Ralf Moeller
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Aerospace Microbiology Research Group, Linder Hoehe, Cologne (Köln), Germany
- Address correspondence to: Ralf Moeller, German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Aerospace Microbiology, Linder Hoehe, Building 24, Room 104, D-51147 Köln, Germany
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14
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Delgado Corrales B, Kaiser R, Nerlich P, Agraviador A, Sherry A. BioMateriOME: To understand microbe-material interactions within sustainable, living architectures. ADVANCES IN APPLIED MICROBIOLOGY 2022; 122:77-126. [PMID: 37085194 DOI: 10.1016/bs.aambs.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BioMateriOME evolved from a prototyping process which was informed from discussions between a team of designers, architects and microbiologists, when considering constructing with biomaterials or human cohabitation with novel living materials in the built environment. The prototype has two elements (i) BioMateriOME-Public (BMP), an interactive public materials library, and (ii) BioMateriOME-eXperimental (BMX), a replicated materials library for rigorous microbiome experimentation. The prototype was installed into the OME, a unique experimental living house, in order to (1) gain insights into society's perceptions of living materials, and (2) perform a comparative analysis of indoor surface microbiome development on novel biomaterials in contrast to conventional indoor surfaces, respectively. This review summarizes the BioMateriOME prototype and its use as a tool in combining microbiology, design, architecture and social science. The use of microbiology and biological components in the fabrication of biomaterials is provided, together with an appreciation of the microbial communities common to conventional indoor surfaces, and how these communities may change in response to the implementation of living materials in our homes. Societal perceptions of microbiomes and biomaterials, are considered within the framework of healthy architecture. Finally, features of architectural design with microbes in mind are introduced, with the possibility of codifying microbial surveillance into design and construction benchmarks, standards and regulations toward healthier buildings and their occupants.
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Affiliation(s)
- Beatriz Delgado Corrales
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Romy Kaiser
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Paula Nerlich
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Armand Agraviador
- Hub for Biotechnology in the Built Environment, School of Architecture, Planning and Landscape, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Angela Sherry
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.
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15
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Early development of the skin microbiome: therapeutic opportunities. Pediatr Res 2021; 90:731-737. [PMID: 32919387 PMCID: PMC7952468 DOI: 10.1038/s41390-020-01146-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/23/2020] [Accepted: 08/16/2020] [Indexed: 02/06/2023]
Abstract
As human skin hosts a diverse microbiota in health and disease, there is an emerging consensus that dysregulated interactions between host and microbiome may contribute to chronic inflammatory disease of the skin. Neonatal skin is a unique habitat, structurally similar to the adult but with a different profile of metabolic substrates, environmental stressors, and immune activity. The surface is colonized within moments of birth with a bias toward maternal strains. Initial colonists are outcompeted as environmental exposures increase and host skin matures. Nonetheless, early life microbial acquisitions may have long-lasting effects on health through modulation of host immunity and competitive interactions between bacteria. Microbial ecology and its influence on health have been of interest to dermatologists for >50 years, and an explosion of recent interest in the microbiome has prompted ongoing investigations of several microbial therapeutics for dermatological disease. In this review, we consider how recent insight into the host and microbial factors driving development of the skin microbiome in early life offers new opportunities for therapeutic intervention. IMPACT: Advancement in understanding molecular mechanisms of bacterial competition opens new avenues of investigation into dermatological disease. Primary development of the skin microbiome is determined by immunological features of the cutaneous habitat. Understanding coordinated microbial and immunological development in the pediatric patient requires a multidisciplinary synthesis of primary literature.
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16
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Beaudry MS, Thomas JC, Baptista RP, Sullivan AH, Norfolk W, Devault A, Enk J, Kieran TJ, Rhodes OE, Perry-Dow KA, Rose LJ, Bayona-Vásquez NJ, Oladeinde A, Lipp EK, Sanchez S, Glenn TC. Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture. Environ Microbiol 2021; 23:7523-7537. [PMID: 34519156 DOI: 10.1111/1462-2920.15767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.
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Affiliation(s)
- Megan S Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Jesse C Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Center for Tropical and Emerging Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Amanda H Sullivan
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - William Norfolk
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Alison Devault
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, 5840 Interface Dr., Suite 101, Ann Arbor, MI, 48103, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Olin E Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, 29808, USA.,Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
| | - K Allison Perry-Dow
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura J Rose
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.,Division of Natural Science and Mathematics, Oxford College, Emory University, Oxford, GA, 30054, USA
| | - Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Erin K Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA
| | - Susan Sanchez
- Department of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
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17
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Kayani MUR, Huang W, Feng R, Chen L. Genome-resolved metagenomics using environmental and clinical samples. Brief Bioinform 2021; 22:bbab030. [PMID: 33758906 PMCID: PMC8425419 DOI: 10.1093/bib/bbab030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/29/2020] [Accepted: 01/20/2021] [Indexed: 12/25/2022] Open
Abstract
Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.
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Affiliation(s)
- Masood ur Rehman Kayani
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| | - Wanqiu Huang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 200,000, China
| | - Ru Feng
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| | - Lei Chen
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
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18
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Jurkevitch E, Pasternak Z. A walk on the dirt: soil microbial forensics from ecological theory to the crime lab. FEMS Microbiol Rev 2021; 45:5937428. [PMID: 33098291 DOI: 10.1093/femsre/fuaa053] [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: 04/02/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.
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Affiliation(s)
- Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Division of Identification and Forensic Science, Israel Police
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19
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Klassert TE, Leistner R, Zubiria-Barrera C, Stock M, López M, Neubert R, Driesch D, Gastmeier P, Slevogt H. Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study. MICROBIOME 2021; 9:169. [PMID: 34380550 PMCID: PMC8359561 DOI: 10.1186/s40168-021-01109-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/02/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Humans spend the bulk of their time in indoor environments. This space is shared with an indoor ecosystem of microorganisms, which are in continuous exchange with the human inhabitants. In the particular case of hospitals, the environmental microorganisms may influence patient recovery and outcome. An understanding of the bacterial community structure in the hospital environment is pivotal for the prevention of hospital-acquired infections and the dissemination of antibiotic resistance genes. In this study, we performed a longitudinal metagenetic approach in a newly opened ward at the Charité Hospital (Berlin) to characterize the dynamics of the bacterial colonization process in the hospital environment after first patient occupancy. RESULTS The sequencing data showed a site-specific taxonomic succession, which led to stable community structures after only a few weeks. This data was further supported by network analysis and beta-diversity metrics. Furthermore, the fast colonization process was characterized by a significant increase of the bacterial biomass and its alpha-diversity. The compositional dynamics could be linked to the exchange with the patient microbiota. Over a time course of 30 weeks, we did not detect a rise of pathogenic bacteria in the hospital environment, but a significant increase of antibiotic resistance determinants on the hospital floor. CONCLUSIONS The results presented in this study provide new insights into different aspects of the environmental microbiome in the clinical setting, and will help to adopt infection control strategies in hospitals and health care-related buildings. Video Abstract.
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Affiliation(s)
- Tilman E Klassert
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany.
| | - Rasmus Leistner
- Institute for Hygiene and Environmental Medicine and Department for Medicine (Gastroenterology, Infectious diseases, Rheumatology), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Magdalena Stock
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany
| | - Mercedes López
- University Institute of Tropical Diseases and Public Health of the Canary Islands, University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Robert Neubert
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany
| | | | - Petra Gastmeier
- Institute for Hygiene and Environmental Medicine, Charité-Universitätsmedizin, Berlin, Germany
| | - Hortense Slevogt
- Jena University Hospital, ZIK Septomics, Host Septomics, Jena, Germany
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20
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Ishak S, Dormontt E, Young JM. Microbiomes in forensic botany: a review. Forensic Sci Med Pathol 2021; 17:297-307. [PMID: 33830453 DOI: 10.1007/s12024-021-00362-4] [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] [Accepted: 02/11/2021] [Indexed: 11/24/2022]
Abstract
Fragments of botanical material can often be found at crime scenes (on live and dead bodies, or on incriminating objects) and can provide circumstantial evidence on various aspects of forensic investigations such as determining crime scene locations, times of death or possession of illegal species. Morphological and genetic analysis are the most commonly applied methods to analyze plant fragment evidence but are limited by their low capacity to differentiate between potential source locations, especially at local scales. Here, we review the current applications and limitations of current plant fragment analysis for forensic investigations and introduce the potential of microbiome analysis to complement the existing forensic plant fragment analysis toolkit. The potential for plant fragment provenance identification at geographic scales meaningful to forensic investigations warrants further investigation of the phyllosphere microbiome in this context. To that end we identify three key areas of future research: 1) Retrieval of microbial DNA of sufficient quality and quantity from botanical material; 2) Variability of the phyllosphere microbiome at different taxonomic and spatial scales, with explicit reference to assignment capacity; 3) Impacts on assignment capacity of time, seasonality and movement of fragments between locations. The development of robust microbiome analysis tools for forensic purposes in botanical material could increase the evidentiary value of the botanical evidence commonly encountered in casework, aiding in the identification of crime scene locations.
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Affiliation(s)
- Sarah Ishak
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada.
| | - Eleanor Dormontt
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jennifer M Young
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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21
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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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22
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Stahl-Rommel S, Jain M, Nguyen HN, Arnold RR, Aunon-Chancellor SM, Sharp GM, Castro CL, John KK, Juul S, Turner DJ, Stoddart D, Paten B, Akeson M, Burton AS, Castro-Wallace SL. Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station Using Nanopore Sequencing. Genes (Basel) 2021; 12:genes12010106. [PMID: 33467183 PMCID: PMC7830261 DOI: 10.3390/genes12010106] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Abstract
For the past two decades, microbial monitoring of the International Space Station (ISS) has relied on culture-dependent methods that require return to Earth for analysis. This has a number of limitations, with the most significant being bias towards the detection of culturable organisms and the inherent delay between sample collection and ground-based analysis. In recent years, portable and easy-to-use molecular-based tools, such as Oxford Nanopore Technologies’ MinION™ sequencer and miniPCR bio’s miniPCR™ thermal cycler, have been validated onboard the ISS. Here, we report on the development, validation, and implementation of a swab-to-sequencer method that provides a culture-independent solution to real-time microbial profiling onboard the ISS. Method development focused on analysis of swabs collected in a low-biomass environment with limited facility resources and stringent controls on allowed processes and reagents. ISS-optimized procedures included enzymatic DNA extraction from a swab tip, bead-based purifications, altered buffers, and the use of miniPCR and the MinION. Validation was conducted through extensive ground-based assessments comparing current standard culture-dependent and newly developed culture-independent methods. Similar microbial distributions were observed between the two methods; however, as expected, the culture-independent data revealed microbial profiles with greater diversity. Protocol optimization and verification was established during NASA Extreme Environment Mission Operations (NEEMO) analog missions 21 and 22, respectively. Unique microbial profiles obtained from analog testing validated the swab-to-sequencer method in an extreme environment. Finally, four independent swab-to-sequencer experiments were conducted onboard the ISS by two crewmembers. Microorganisms identified from ISS swabs were consistent with historical culture-based data, and primarily consisted of commonly observed human-associated microbes. This simplified method has been streamlined for high ease-of-use for a non-trained crew to complete in an extreme environment, thereby enabling environmental and human health diagnostics in real-time as future missions take us beyond low-Earth orbit.
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Affiliation(s)
| | - Miten Jain
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA; (M.J.); (B.P.); (M.A.)
| | - Hang N. Nguyen
- JES Tech, Houston, TX 77058, USA; (S.S.-R.); (H.N.N.); (C.L.C.)
| | - Richard R. Arnold
- Astronaut Office, NASA Johnson Space Center, Houston, TX 77058, USA; (R.R.A.); (S.M.A.-C.)
| | | | | | | | - Kristen K. John
- Project Management and Systems Engineering Division, NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Sissel Juul
- Oxford Nanopore Technologies, New York, NY 10013, USA;
| | - Daniel J. Turner
- Oxford Nanopore Technologies, Oxford Science Park, Oxford OX4 4DQ, UK; (D.J.T.); (D.S.)
| | - David Stoddart
- Oxford Nanopore Technologies, Oxford Science Park, Oxford OX4 4DQ, UK; (D.J.T.); (D.S.)
| | - Benedict Paten
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA; (M.J.); (B.P.); (M.A.)
| | - Mark Akeson
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA; (M.J.); (B.P.); (M.A.)
| | - Aaron S. Burton
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Sarah L. Castro-Wallace
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX 77058, USA
- Correspondence: ; Tel.: +1-281-483-7254
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Zhou Y, Leung MHY, Tong X, Lai Y, Tong JCK, Ridley IA, Lee PKH. Profiling Airborne Microbiota in Mechanically Ventilated Buildings Across Seasons in Hong Kong Reveals Higher Metabolic Activity in Low-Abundance Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:249-259. [PMID: 33346641 DOI: 10.1021/acs.est.0c06201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Metabolically active bacteria within built environments are poorly understood. This study aims to investigate the active airborne bacterial microbiota and compare the total and active microbiota in eight mechanically ventilated buildings over four consecutive seasons using the 16S rRNA gene (rDNA) and the 16S rRNA (rRNA), respectively. The relative abundances of the taxa of presumptive occupants and environmental origins were significantly different between the active and total microbiota. The Sloan neutral model suggested that ecological drift and random dispersal played a smaller role in the assembly of the active microbiota than the total microbiota. The seasonal nature of the active microbiota was consistent with that of the total microbiota in both indoor and outdoor environments, while only the indoor environment was significantly affected by geography. The relative abundances of the active and total taxa were positively correlated, suggesting that the high-abundance members were also the greatest contributors to the community-level metabolic activity. Based on the rRNA/rDNA ratio, the low-abundance members consistently had a higher taxon-level metabolic activity than the high-abundance members over seasons, suggesting that the low-abundance members may have the ability to survive and thrive in the indoor environment and their impact on the health of occupants cannot be overlooked.
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Affiliation(s)
- You Zhou
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Yonghang Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Jimmy C K Tong
- Building Sustainability Group, Arup, Hong Kong SAR, China
| | - Ian A Ridley
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
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24
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Ishida Y, Vyas R, Chauhan G, Delgado L, Kourai H. Bacterial Contamination Analysis of Residential Toilet Room Environment and Delivery of Residual Bacterial Growth Prevention Efficacy on Residential Toilet Permeable Surfaces Using Toilet Air Freshener Product. Biocontrol Sci 2021; 26:85-93. [PMID: 34092718 DOI: 10.4265/bio.26.85] [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] [Indexed: 11/01/2022]
Abstract
Toilet malodor is one of the most concerned malodor in residential houses, so that many technologies and products have been developed by which is aiming to remove or reduce such toilet malodor. Toilet malodour is generated from human faecal matters left inside of toilet bowl and from that deposited outside of toilet bowl such as toilet floors. In order to remove or prevent the malodor generated outside of toilet bowl, it is effective to do more frequent cleaning of toilet room surfaces or place a deodorizer which mask the malodour by perfume. We developed a toilet deodorizer which is preventing malodor generation outside of toilet bowl more effectively by delivering antibacterial efficacy on toilet room permeable surfaces. We analyzed microbiological quality of residential toilet rooms and found that toilet floor is the most contaminated location by bacteria, so that we developed a test method using materials frequently used for residential toilet floors such as vinyl cushion and using bacteria commonly found in toilet room environment. As the results, we found the product can provide bacterial growth prevention efficacy on permeable materials and prevent toilet malodor effectively.
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Affiliation(s)
- Yoshiki Ishida
- Procter and Gamble International Operations SA Singapore branch
| | - Rahul Vyas
- Procter and Gamble International Operations SA Singapore branch
| | - Garima Chauhan
- Procter and Gamble International Operations SA Singapore branch
| | - Liliana Delgado
- Procter and Gamble International Operations SA Singapore branch
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25
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Xu Y, Tandon R, Ancheta C, Arroyo P, Gilbert JA, Stephens B, Kelley ST. Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions. INDOOR AIR 2021; 31:188-205. [PMID: 32757488 DOI: 10.1111/ina.12727] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/01/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
Indoor microbial communities vary in composition and diversity depending on material type, moisture levels, and occupancy. In this study, we integrated bacterial cell counting, fungal biomass estimation, and fluorescence-assisted cell sorting (FACS) with amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities to investigate the influence of wetting on medium density fiberboard (MDF) and gypsum wallboard. Surface samples were collected longitudinally from wetted materials maintained at high relative humidity (~95%). Bacterial and fungal growth patterns were strongly time-dependent and material-specific. Fungal growth phenotypes differed between materials: spores dominated MDF surfaces while fungi transitioned from spores to hyphae on gypsum. FACS confirmed that most of the bacterial cells were intact (viable) on both materials over the course of the study. Integrated cell count and biomass data (quantitative profiling) revealed that small changes in relative abundance often resulted from large changes in absolute abundance, while negative correlations in relative abundances were explained by rapid growth of only one group of bacteria or fungi. Comparisons of bacterial-bacterial and fungal-bacterial networks suggested a top-down control of fungi on bacterial growth, possibly via antibiotic production. In conclusion, quantitative profiling provides novel insights into microbial growth dynamics on building materials with potential implications for human health.
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Affiliation(s)
- Ying Xu
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
| | - Ruby Tandon
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Chrislyn Ancheta
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pablo Arroyo
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Brent Stephens
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Scott T Kelley
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
- Department of Biology, San Diego State University, San Diego, CA, USA
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26
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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: 9] [Impact Index Per Article: 2.3] [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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27
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Bacterial communities in the natural and supplemental nests of an endangered ecosystem engineer. Ecosphere 2020. [DOI: 10.1002/ecs2.3239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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28
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Vargas-Robles D, Gonzalez-Cedillo C, Hernandez AM, Alcaraz LD, Peimbert M. Passenger-surface microbiome interactions in the subway of Mexico City. PLoS One 2020; 15:e0237272. [PMID: 32813719 PMCID: PMC7437895 DOI: 10.1371/journal.pone.0237272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/22/2020] [Indexed: 01/02/2023] Open
Abstract
Interaction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces and compare regular and women-only wagons. We also explored the effect of surface cleaning on microbial resettling. Finally, we studied passenger behavior and characterized microbial changes after traveling. Most passengers (99%), showed some type of surface interaction during a wagon trip, mostly with the hands (92%). We found microbiome differences associated with surfaces, probably reflecting diverse surface materials and usage frequency. The platform floor was the most bacterial diverse surface, while the stair handrail and pole were the least diverse ones. After pole cleaning, the resettling of microbial diversity was fast (5–30 minutes); however, it did not resemble the initial composition. After traveling, passengers significantly increased their hand microbial diversity and converged to a similar microbial composition among passengers. Additionally, passenger hand microbiomes resembled subway surfaces in diversity. However, microbial fingerprints were preserved within passengers after traveling.
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Affiliation(s)
- Daniela Vargas-Robles
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Carolina Gonzalez-Cedillo
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Apolinar M. Hernandez
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Luis D. Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
- * E-mail:
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29
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Chessa D, Murgia M, Sias E, Deligios M, Mazzarello V, Fiamma M, Rovina D, Carenti G, Ganau G, Pintore E, Fiori M, Kay GL, Ponzeletti A, Cappuccinelli P, Kelvin DJ, Wain J, Rubino S. Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace. Sci Rep 2020; 10:12656. [PMID: 32728085 PMCID: PMC7391740 DOI: 10.1038/s41598-020-69497-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
This study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.
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Affiliation(s)
- Daniela Chessa
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Manuela Murgia
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy.
| | - Emanuela Sias
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Massimo Deligios
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Vittorio Mazzarello
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Maura Fiamma
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Daniela Rovina
- Superintendence Archaeology of Sardinia, 07100, Sassari, Italy
| | - Gabriele Carenti
- Department of Nature and Environmental Sciences, University of Sassari, 07100, Sassari, Italy
| | - Giulia Ganau
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Elisabetta Pintore
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | | | - Gemma L Kay
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
- The Quadram Institute, Norwich Research Park, Norwich, UK
| | | | - Piero Cappuccinelli
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - John Wain
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
- The Quadram Institute, Norwich Research Park, Norwich, UK
| | - Salvatore Rubino
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
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30
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Qureshi SS, Kedo M, Berthrong ST. Gender-neutral bathroom surfaces recolonized by microbes more quickly than single-gender bathrooms. Lett Appl Microbiol 2020; 71:134-137. [PMID: 32410293 DOI: 10.1111/lam.13316] [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: 02/05/2019] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 11/30/2022]
Abstract
As humans become increasingly urban and spend more time inside the built environment, there will be increased interactions between humans and shared public surface microbiomes. Recent cultural changes in the United States have led to increased numbers of gender-neutral bathrooms. Given that bathroom surfaces are frequently sanitized, we used this increased availability of gender-neutral bathrooms to examine how single-gender or gender-neutral surfaces are recolonized with microbes. Given that male and female microbiomes vary, we hypothesized that rates of recolonization would differ between male, female and gender-neutral bathroom surfaces. We collected swabs from common hand-contacted surfaces in bathrooms and cultured microbes on selective and rich media to determine microbial abundance after cleaning. Recolonization was dominated by Gram-positive bacteria and was slowest on male, intermediate on female and fastest on gender-neutral surfaces. These results imply that gender-neutral surfaces approach normal climax microbial communities more quickly than single-gender bathrooms. SIGNIFICANCE OF IMPACT OF THE STUDY: Humans now spend substantial amount of time within the built environment, and as a consequence the human microbiome interacts frequently with indoor surfaces. Social changes are making gender-neutral public bathrooms more common, so it is important to study how humans and microbiomes interact with these bathroom surfaces. We found that the gender-neutral bathroom surfaces recolonize more quickly than single-gender, which suggests that there are more potential human-surface microbiome connections in these public spaces. These results will potentially add a new layer to our understanding of the interactions of humans, our microbiomes and how we design our built environment.
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Affiliation(s)
- S S Qureshi
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - M Kedo
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA
| | - S T Berthrong
- Department of Biological Sciences, Butler University, Indianapolis, IN, USA.,Center for Urban Ecology and Sustainability, Butler University, Indianapolis, IN, USA
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31
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McGhee JJ, Rawson N, Bailey BA, Fernandez-Guerra A, Sisk-Hackworth L, Kelley ST. Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics. PeerJ 2020; 8:e8783. [PMID: 32231882 PMCID: PMC7100590 DOI: 10.7717/peerj.8783] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/21/2020] [Indexed: 11/20/2022] Open
Abstract
Background Microbial source tracking methods are used to determine the origin of contaminating bacteria and other microorganisms, particularly in contaminated water systems. The Bayesian SourceTracker approach uses deep-sequencing marker gene libraries (16S ribosomal RNA) to determine the proportional contributions of bacteria from many potential source environments to a given sink environment simultaneously. Since its development, SourceTracker has been applied to an extensive diversity of studies, from beach contamination to human behavior. Methods Here, we demonstrate a novel application of SourceTracker to work with metagenomic datasets and tested this approach using sink samples from a study of coastal marine environments. Source environment metagenomes were obtained from metagenomics studies of gut, freshwater, marine, sand and soil environments. As part of this effort, we implemented features for determining the stability of source proportion estimates, including precision visualizations for performance optimization, and performed domain-specific source-tracking analyses (i.e., Bacteria, Archaea, Eukaryota and viruses). We also applied SourceTracker to metagenomic libraries generated from samples collected from the International Space Station (ISS). Results SourceTracker proved highly effective at predicting the composition of known sources using shotgun metagenomic libraries. In addition, we showed that different taxonomic domains sometimes presented highly divergent pictures of environmental source origins for both the coastal marine and ISS samples. These findings indicated that applying SourceTracker to separate domains may provide a deeper understanding of the microbial origins of complex, mixed-source environments, and further suggested that certain domains may be preferable for tracking specific sources of contamination.
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Affiliation(s)
- Jordan J McGhee
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
| | - Nick Rawson
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
| | - Barbara A Bailey
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
| | - Antonio Fernandez-Guerra
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laura Sisk-Hackworth
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, United States of America
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32
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Idris A, Cutler RR. The presence of multidrug-resistant staphylococcal isolates outside of a major hospital in London, United Kingdom. Cent Eur J Public Health 2020; 27:340-344. [PMID: 31951696 DOI: 10.21101/cejph.a5000] [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: 12/07/2016] [Revised: 06/30/2019] [Accepted: 06/30/2019] [Indexed: 11/15/2022]
Abstract
OBJECTIVE Drug-resistant staphylococci have been a growing threat to the community and hospitals due to the misuse of antibiotics by humans, industrialisation and lack of novel antimicrobials currently available. Little is known about the prevalence of drug-resistant staphylococci in non-healthcare environments outside hospitals in the London area. Staphylococci can spread via contact with contaminated objects. Traffic light buttons present a fast and easy transmission route for staphylococci. METHODS Traffic light buttons outside a major hospital in London were swabbed and cultured onto selective media to isolate staphylococci bacteria before performing antimicrobial susceptibility testing on the isolates. The identity of the isolates were determined using MALDI-TOF mass spectrometry (MS). Staphylococci isolates resistant to oxacillin were further tested for minimum inhibitory concentration (MIC). PCR analysis of the mecA gene, a gene that confers resistance to oxacillin, is used to determine the level of resistance to oxacillin. RESULTS Eight different staphylococcal species were identified by MALDI-TOF-MS analysis. Out of the 66 staphylococci isolates, 16 were resistant to multiple antibiotics including six isolates which were oxacillin resistant. CONCLUSION This work provides evidence of the presence of multidrug-resistant staphylococci in the vicinity of the hospital environment in London.
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Affiliation(s)
- Adi Idris
- PAPRSB Institute of Health Sciences, Brunei Darussalam University, Brunei Darussalam.,Menzies Institute of Health Queensland, School of Medical Science, Griffith University, Southport, Australia
| | - Ron R Cutler
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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33
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Prussin AJ, Belser JA, Bischoff W, Kelley ST, Lin K, Lindsley WG, Nshimyimana JP, Schuit M, Wu Z, Bibby K, Marr LC. Viruses in the Built Environment (VIBE) meeting report. MICROBIOME 2020; 8:1. [PMID: 31901242 PMCID: PMC6942371 DOI: 10.1186/s40168-019-0777-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 12/18/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND During a period of rapid growth in our understanding of the microbiology of the built environment in recent years, the majority of research has focused on bacteria and fungi. Viruses, while probably as numerous, have received less attention. In response, the Alfred P. Sloan Foundation supported a workshop entitled "Viruses in the Built Environment (VIBE)," at which experts in environmental engineering, environmental microbiology, epidemiology, infection prevention, fluid dynamics, occupational health, metagenomics, and virology convened to synthesize recent advances and identify key research questions and knowledge gaps regarding viruses in the built environment. RESULTS Four primary research areas and funding priorities were identified. First, a better understanding of viral communities in the built environment is needed, specifically which viruses are present and their sources, spatial and temporal dynamics, and interactions with bacteria. Second, more information is needed about viruses and health, including viral transmission in the built environment, the relationship between virus detection and exposure, and the definition of a healthy virome. The third research priority is to identify and evaluate interventions for controlling viruses and the virome in the built environment. This encompasses interactions among viruses, buildings, and occupants. Finally, to overcome the challenge of working with viruses, workshop participants emphasized that improved sampling methods, laboratory techniques, and bioinformatics approaches are needed to advance understanding of viruses in the built environment. CONCLUSIONS We hope that identifying these key questions and knowledge gaps will engage other investigators and funding agencies to spur future research on the highly interdisciplinary topic of viruses in the built environment. There are numerous opportunities to advance knowledge, as many topics remain underexplored compared to our understanding of bacteria and fungi. Video abstract.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Jessica A. Belser
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA
| | - Werner Bischoff
- Section on Infectious Diseases, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Kaisen Lin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - William G. Lindsley
- Health Effects Laboratory Division (HELD), National Institute for Occupational Safety and Health, Morgantown, WV 26505 USA
| | | | - Michael Schuit
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702 USA
| | - Zhenyu Wu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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34
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The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome. Cell Rep 2019; 24:1190-1202.e5. [PMID: 30067975 DOI: 10.1016/j.celrep.2018.06.109] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/25/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022] Open
Abstract
The skin functions as the primary interface between the human body and the external environment. To understand how the microbiome varies within urban mass transit and influences the skin microbiota, we profiled the human palm microbiome after contact with handrails within the Hong Kong Mass Transit Railway (MTR) system. Intraday sampling time was identified as the primary determinant of the variation and recurrence of the community composition, whereas human-associated species and clinically important antibiotic resistance genes (ARGs) were captured as p.m. signatures. Line-specific signatures were notably correlated with line-specific environmental exposures and city characteristics. The sole cross-border line appeared as an outlier in most analyses and showed high relative abundance and a significant intraday increment of clinically important ARGs (24.1%), suggesting potential cross-border ARG transmission, especially for tetracycline and vancomycin resistance. Our study provides an important reference for future public health strategies to mitigate intracity and cross-border pathogen and ARG transmission.
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Gupta M, Lee S, Bisesi M, Lee J. Indoor Microbiome and Antibiotic Resistance on Floor Surfaces: An Exploratory Study in Three Different Building Types. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16214160. [PMID: 31661921 PMCID: PMC6862025 DOI: 10.3390/ijerph16214160] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/17/2019] [Accepted: 10/25/2019] [Indexed: 12/15/2022]
Abstract
Floor materials in indoor environments are known to be reservoirs of microbes. We focused on examining bacterial community composition, antibiotic resistance (AR) and microbial source tracking (MST) of fecal bacteria on the floor surfaces. Swab samples were collected from carpet and vinyl floors in three different buildings (medical, veterinary, and office buildings) from high and low traffic areas. Bacterial communities were determined with 16S rRNA sequencing, and AR (tetracycline (tetQ), sulfonamide, and carbapenem (KPC)) and MST (human-, canine-, avian-, and ruminant-specific fecal bacteria) were examined with quantitative polymerase chain reaction (PCR). The results show that Proteobacteria and Actinobacteria were the most abundant phyla. Traffic level significantly affected the number of operational taxonomic units. Traffic level was a key factor for distinctive bacterial community in the medical center. Targeted ARGs were detected from all buildings and tetQ concentration was related with traffic level, and KPC was only detected from the medical center. Most of the floor surfaces showed the presence of dog-specific fecal bacteria (83%) followed by bird-specific fecal bacteria (75%). The results suggest that traffic levels affected the bacterial levels and fecal contamination is prevalent on the floor surfaces. This is the first study that reports KPC presence on the floor surfaces.
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Affiliation(s)
- Mridula Gupta
- College of public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
| | - Seungjun Lee
- College of public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
| | - Michael Bisesi
- College of public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
| | - Jiyoung Lee
- College of public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA.
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Microbial and metabolic succession on common building materials under high humidity conditions. Nat Commun 2019; 10:1767. [PMID: 30992445 PMCID: PMC6467912 DOI: 10.1038/s41467-019-09764-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/27/2019] [Indexed: 02/06/2023] Open
Abstract
Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material. Microbes inhabit built environments and could contribute to degradation of surfaces especially in damp conditions. Here the authors explore how communities of microbes and their metabolites affect four types of built surfaces under varying environmental conditions.
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Prussin AJ, Torres PJ, Shimashita J, Head SR, Bibby KJ, Kelley ST, Marr LC. Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center. MICROBIOME 2019; 7:53. [PMID: 30935423 PMCID: PMC6444849 DOI: 10.1186/s40168-019-0672-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiome (virome). Longitudinal microbiome studies provide insight into the stability and dynamics of microbial communities; however, few such studies exist for the microbiome of the BE, and most have focused on bacteria. Here, we present a longitudinal, metagenomic-based analysis of the airborne DNA and RNA virome of a children's daycare center. Specifically, we investigate how the airborne virome varies as a function of season and human occupancy, and we identify possible sources of the viruses and their hosts, mainly humans, animals, plants, and insects. RESULTS Season strongly influenced the airborne viral community composition, and a single sample collected when the daycare center was unoccupied suggested that occupancy also influenced the community. The pattern of influence differed between DNA and RNA viromes. Human-associated viruses were much more diverse and dominant in the winter, while the summertime virome contained a high relative proportion and diversity of plant-associated viruses. CONCLUSIONS This airborne microbiome in this building exhibited seasonality in its viral community but not its bacterial community. Human occupancy influenced both types of communities. By adding new data about the viral microbiome to complement burgeoning information about the bacterial and fungal microbiomes, this study contributes to a more complete understanding of the airborne microbiome.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Pedro J. Torres
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - John Shimashita
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Steven R. Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Kyle J. Bibby
- Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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Merino N, Zhang S, Tomita M, Suzuki H. Comparative genomics of Bacteria commonly identified in the built environment. BMC Genomics 2019; 20:92. [PMID: 30691394 PMCID: PMC6350394 DOI: 10.1186/s12864-018-5389-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/18/2018] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The microbial community of the built environment (BE) can impact the lives of people and has been studied for a variety of indoor, outdoor, underground, and extreme locations. Thus far, these microorganisms have mainly been investigated by culture-based methods or amplicon sequencing. However, both methods have limitations, complicating multi-study comparisons and limiting the knowledge gained regarding in-situ microbial lifestyles. A greater understanding of BE microorganisms can be achieved through basic information derived from the complete genome. Here, we investigate the level of diversity and genomic features (genome size, GC content, replication strand skew, and codon usage bias) from complete genomes of bacteria commonly identified in the BE, providing a first step towards understanding these bacterial lifestyles. RESULTS Here, we selected bacterial genera commonly identified in the BE (or "Common BE genomes") and compared them against other prokaryotic genera ("Other genomes"). The "Common BE genomes" were identified in various climates and in indoor, outdoor, underground, or extreme built environments. The diversity level of the 16S rRNA varied greatly between genera. The genome size, GC content and GC skew strength of the "Common BE genomes" were statistically larger than those of the "Other genomes" but were not practically significant. In contrast, the strength of selected codon usage bias (S value) was statistically higher with a large effect size in the "Common BE genomes" compared to the "Other genomes." CONCLUSION Of the four genomic features tested, the S value could play a more important role in understanding the lifestyles of bacteria living in the BE. This parameter could be indicative of bacterial growth rates, gene expression, and other factors, potentially affected by BE growth conditions (e.g., temperature, humidity, and nutrients). However, further experimental evidence, species-level BE studies, and classification by BE location is needed to define the relationship between genomic features and the lifestyles of BE bacteria more robustly.
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Affiliation(s)
- Nancy Merino
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Department of Earth Sciences, University of Southern California, Stauffer Hall of Science, Los Angeles, CA, 90089, USA
| | - Shu Zhang
- Global Research Center for Environment and Energy based on Nanomaterials Science, National Institute for Material Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.,Section of Infection and Immunity, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, 90089-0641, USA
| | - Masaru Tomita
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, 252-0882, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0035, Japan
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, 252-0882, Japan. .,Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0035, Japan.
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Stephens B, Azimi P, Thoemmes MS, Heidarinejad M, Allen JG, Gilbert JA. Microbial Exchange via Fomites and Implications for Human Health. CURRENT POLLUTION REPORTS 2019; 5:198-213. [PMID: 34171005 PMCID: PMC7149182 DOI: 10.1007/s40726-019-00123-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
PURPOSE OF REVIEW Fomites are inanimate objects that become colonized with microbes and serve as potential intermediaries for transmission to/from humans. This review summarizes recent literature on fomite contamination and microbial survival in the built environment, transmission between fomites and humans, and implications for human health. RECENT FINDINGS Applications of molecular sequencing techniques to analyze microbial samples have increased our understanding of the microbial diversity that exists in the built environment. This growing body of research has established that microbial communities on surfaces include substantial diversity, with considerable dynamics. While many microbial taxa likely die or lay dormant, some organisms survive, including those that are potentially beneficial, benign, or pathogenic. Surface characteristics also influence microbial survival and rates of transfer to and from humans. Recent research has combined experimental data, mechanistic modeling, and epidemiological approaches to shed light on the likely contributors to microbial exchange between fomites and humans and their contributions to adverse (and even potentially beneficial) human health outcomes. SUMMARY In addition to concerns for fomite transmission of potential pathogens, new analytical tools have uncovered other microbial matters that can be transmitted indirectly via fomites, including entire microbial communities and antibiotic-resistant bacteria. Mathematical models and epidemiological approaches can provide insight on human health implications. However, both are subject to limitations associated with study design, and there is a need to better understand appropriate input model parameters. Fomites remain an important mechanism of transmission of many microbes, along with direct contact and short- and long-range aerosols.
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Affiliation(s)
- Brent Stephens
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL 60616 USA
| | - Parham Azimi
- Environmental Health Department, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Megan S. Thoemmes
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA USA
| | - Mohammad Heidarinejad
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL 60616 USA
| | - Joseph G. Allen
- Environmental Health Department, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA USA
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Poh TY, Ali NABM, Mac Aogáin M, Kathawala MH, Setyawati MI, Ng KW, Chotirmall SH. Inhaled nanomaterials and the respiratory microbiome: clinical, immunological and toxicological perspectives. Part Fibre Toxicol 2018; 15:46. [PMID: 30458822 PMCID: PMC6245551 DOI: 10.1186/s12989-018-0282-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/31/2018] [Indexed: 12/17/2022] Open
Abstract
Our development and usage of engineered nanomaterials has grown exponentially despite concerns about their unfavourable cardiorespiratory consequence, one that parallels ambient ultrafine particle exposure from vehicle emissions. Most research in the field has so far focused on airway inflammation in response to nanoparticle inhalation, however, little is known about nanoparticle-microbiome interaction in the human airway and the environment. Emerging evidence illustrates that the airway, even in its healthy state, is not sterile. The resident human airway microbiome is further altered in chronic inflammatory respiratory disease however little is known about the impact of nanoparticle inhalation on this airway microbiome. The composition of the airway microbiome, which is involved in the development and progression of respiratory disease is dynamic, adding further complexity to understanding microbiota-host interaction in the lung, particularly in the context of nanoparticle exposure. This article reviews the size-dependent properties of nanomaterials, their body deposition after inhalation and factors that influence their fate. We evaluate what is currently known about nanoparticle-microbiome interactions in the human airway and summarise the known clinical, immunological and toxicological consequences of this relationship. While associations between inhaled ambient ultrafine particles and host immune-inflammatory response are known, the airway and environmental microbiomes likely act as intermediaries and facilitate individual susceptibility to inhaled nanoparticles and toxicants. Characterising the precise interaction between the environment and airway microbiomes, inhaled nanoparticles and the host immune system is therefore critical and will provide insight into mechanisms promoting nanoparticle induced airway damage.
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Affiliation(s)
- Tuang Yeow Poh
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, Level 12, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Nur A'tikah Binte Mohamed Ali
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, Level 12, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Micheál Mac Aogáin
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, Level 12, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Mustafa Hussain Kathawala
- School of Materials Science and Engineering, Nanyang Technological University, Block N4.1, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Magdiel Inggrid Setyawati
- School of Materials Science and Engineering, Nanyang Technological University, Block N4.1, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Kee Woei Ng
- School of Materials Science and Engineering, Nanyang Technological University, Block N4.1, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Sanjay Haresh Chotirmall
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, Level 12, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore.
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Trinh P, Zaneveld JR, Safranek S, Rabinowitz PM. One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review. Front Public Health 2018; 6:235. [PMID: 30214898 PMCID: PMC6125393 DOI: 10.3389/fpubh.2018.00235] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/08/2018] [Indexed: 12/17/2022] Open
Abstract
The One Health concept stresses the ecological relationships between human, animal, and environmental health. Much of the One Health literature to date has examined the transfer of pathogens from animals (e.g., emerging zoonoses) and the environment to humans. The recent rapid development of technology to perform high throughput DNA sequencing has expanded this view to include the study of entire microbial communities. Applying the One Health approach to the microbiome allows for consideration of both pathogenic and non-pathogenic microbial transfer between humans, animals, and the environment. We review recent research studies of such transmission, the molecular and statistical methods being used, and the implications of such microbiome relationships for human health. Our review identified evidence that the environmental microbiome as well as the microbiome of animals in close contact can affect both the human microbiome and human health outcomes. Such microbiome transfer can take place in the household as well as the workplace setting. Urbanization of built environments leads to changes in the environmental microbiome which could be a factor in human health. While affected by environmental exposures, the human microbiome also can modulate the response to environmental factors through effects on metabolic and immune function. Better understanding of these microbiome interactions between humans, animals, and the shared environment will require continued development of improved statistical and ecological modeling approaches. Such enhanced understanding could lead to innovative interventions to prevent and manage a variety of human health and disease states.
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Affiliation(s)
- Pauline Trinh
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Jesse R Zaneveld
- Division of Biological Sciences, School of Science, Technology, Education, and Mathematics, University of Washington, Bothell, WA, United States
| | - Sarah Safranek
- Health Sciences Library, University of Washington, Seattle, WA, United States
| | - Peter M Rabinowitz
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
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43
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Gilbert JA. Ecological medicine. Environ Microbiol 2018; 20:1917-1919. [PMID: 29614208 DOI: 10.1111/1462-2920.14115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Jack A Gilbert
- Department of Surgery, University of Chicago, Chicago, IL, 60637, USA.,The Microbiome Center, University of Chicago, Chicago, IL, 60637, USA
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44
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Gomez-Silvan C, Leung MHY, Grue KA, Kaur R, Tong X, Lee PKH, Andersen GL. A comparison of methods used to unveil the genetic and metabolic pool in the built environment. MICROBIOME 2018; 6:71. [PMID: 29661230 PMCID: PMC5902888 DOI: 10.1186/s40168-018-0453-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/28/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting. RESULTS We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community. CONCLUSIONS Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.
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Affiliation(s)
- Cinta Gomez-Silvan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Katherine A. Grue
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Current affiliation: Department of Physical Therapy and Rehabilitation Science, University of California, San Francisco, CA USA
| | - Randeep Kaur
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Gary L. Andersen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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Rosario K, Fierer N, Miller S, Luongo J, Breitbart M. Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1014-1027. [PMID: 29298386 DOI: 10.1021/acs.est.7b04203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Diverse bacterial and fungal communities inhabit human-occupied buildings and circulate in indoor air; however, viral diversity in these man-made environments remains largely unknown. Here we investigated DNA and RNA viruses circulating in the air of 12 university dormitory rooms by analyzing dust accumulated over a one-year period on heating, ventilation, and air conditioning (HVAC) filters. A metagenomic sequencing approach was used to determine the identity and diversity of viral particles extracted from the HVAC filters. We detected a broad diversity of viruses associated with a range of hosts, including animals, arthropods, bacteria, fungi, humans, plants, and protists, suggesting that disparate organisms can contribute to indoor airborne viral communities. Viral community composition and the distribution of human-infecting papillomaviruses and polyomaviruses were distinct in the different dormitory rooms, indicating that airborne viral communities are variable in human-occupied spaces and appear to reflect differential rates of viral shedding from room occupants. This work significantly expands the known airborne viral diversity found indoors, enabling the design of sensitive and quantitative assays to further investigate specific viruses of interest and providing new insight into the likely sources of viruses found in indoor air.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida , Saint Petersburg, Florida 33701, United States
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado , Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado , Boulder, Colorado 80309, United States
| | - Shelly Miller
- Department of Mechanical Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Julia Luongo
- Department of Mechanical Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida , Saint Petersburg, Florida 33701, United States
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Shoemaker WR, Lennon JT. Evolution with a seed bank: The population genetic consequences of microbial dormancy. Evol Appl 2018; 11:60-75. [PMID: 29302272 PMCID: PMC5748526 DOI: 10.1111/eva.12557] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 09/08/2017] [Indexed: 12/31/2022] Open
Abstract
Dormancy is a bet‐hedging strategy that allows organisms to persist through conditions that are suboptimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long‐term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence the evolutionary dynamics of microorganisms as well as other taxa.
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Affiliation(s)
| | - Jay T Lennon
- Department of Biology Indiana University Bloomington IN USA
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Dobbler PCT, Laureano ÁM, Sarzi DS, Cañón ERP, Metz GF, de Freitas AS, Takagaki BM, D Oliveira CB, Pylro VS, Copetti AC, Victoria F, Redmile-Gordon M, Morais DK, Roesch LFW. Differences in bacterial composition between men's and women's restrooms and other common areas within a public building. Antonie van Leeuwenhoek 2017; 111:551-561. [PMID: 29127623 DOI: 10.1007/s10482-017-0976-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/31/2017] [Indexed: 12/21/2022]
Abstract
Humans distribute a wide range of microorganisms around building interiors, and some of these are potentially pathogenic. Recent research established that humans are the main drivers of the indoor microbiome and up to now significant literature has been produced about this topic. Here we analyzed differences in bacterial composition between men's and women's restrooms and other common areas within the same public building. Bacterial DNA samples were collected from restrooms and halls of a three-floor building from the Federal University of Pampa, RS, Brazil. The bacterial community was characterized by amplification of the V4 region of the 16S rRNA gene and sequencing. Throughout all samples, the most abundant phylum was Proteobacteria, followed by Actinobacteria, Bacteroidetes and Firmicutes. Beta diversity metrics showed that the structure of the bacterial communities were different among the areas and floors tested, however, only 6-9% of the variation in bacterial communities was explained by the area and floors sampled. A few microorganisms showed significantly differential abundance between men's and women's restrooms, but in general, the bacterial communities from both places were very similar. Finally, significant differences among the microbial community profile from different floors were reported, suggesting that the type of use and occupant demographic within the building may directly influence bacterial dispersion and establishment.
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Affiliation(s)
- Priscila Caroline Thiago Dobbler
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Álvaro Macedo Laureano
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Deise Schroder Sarzi
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Ehidy Rocio Peña Cañón
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Geferson Fernando Metz
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Anderson Santos de Freitas
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Beatriz Midori Takagaki
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Cristiane Barbosa D Oliveira
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Victor Satler Pylro
- Soil Microbiology Laboratory, Department of Soil Science, Luiz de Queiroz" College of Agriculture, University of São Paulo - ESALQ/USP, Av Pádua Dias, 11 CP 09, Piracicaba, São Paulo, 13400-970, Brazil
| | - André Carlos Copetti
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Filipe Victoria
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil
| | - Marc Redmile-Gordon
- Department of Sustainable Soils and Grassland Systems, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Daniel Kumazawa Morais
- Biosystems Informatics and Genomics Group, René Rachou Research Center, Belo Horizonte, Brazil
| | - Luiz Fernando Wurdig Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, São Gabriel, Rio Grande do Sul, 97300-000, Brazil.
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Schwendner P, Mahnert A, Koskinen K, Moissl-Eichinger C, Barczyk S, Wirth R, Berg G, Rettberg P. Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing. MICROBIOME 2017; 5:129. [PMID: 28974259 PMCID: PMC5627443 DOI: 10.1186/s40168-017-0345-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/18/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND The Mars500 project was conceived as the first full duration simulation of a crewed return flight to Mars. For 520 days, six crew members lived confined in a specifically designed spacecraft mock-up. The herein described "MIcrobial ecology of Confined Habitats and humAn health" (MICHA) experiment was implemented to acquire comprehensive microbiota data from this unique, confined manned habitat, to retrieve important information on the occurring microbiota dynamics, the microbial load and diversity in the air and on various surfaces. In total, 360 samples from 20 (9 air, 11 surface) locations were taken at 18 time-points and processed by extensive cultivation, PhyloChip and next generation sequencing (NGS) of 16S rRNA gene amplicons. RESULTS Cultivation assays revealed a Staphylococcus and Bacillus-dominated microbial community on various surfaces, with an average microbial load that did not exceed the allowed limits for ISS in-flight requirements indicating adequate maintenance of the facility. Areas with high human activity were identified as hotspots for microbial accumulation. Despite substantial fluctuation with respect to microbial diversity and abundance throughout the experiment, the location within the facility and the confinement duration were identified as factors significantly shaping the microbial diversity and composition, with the crew representing the main source for microbial dispersal. Opportunistic pathogens, stress-tolerant or potentially mobile element-bearing microorganisms were predicted to be prevalent throughout the confinement, while the overall microbial diversity dropped significantly over time. CONCLUSIONS Our findings clearly indicate that under confined conditions, the community structure remains a highly dynamic system which adapts to the prevailing habitat and micro-conditions. Since a sterile environment is not achievable, these dynamics need to be monitored to avoid spreading of highly resistant or potentially pathogenic microorganisms and a potentially harmful decrease of microbial diversity. If necessary, countermeasures are required, to maintain a healthy, diverse balance of beneficial, neutral and opportunistic pathogenic microorganisms. Our results serve as an important data collection for (i) future risk estimations of crewed space flight, (ii) an optimized design and planning of a spacecraft mission and (iii) for the selection of appropriate microbial monitoring approaches and potential countermeasures, to ensure a microbiologically safe space-flight environment.
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Affiliation(s)
- Petra Schwendner
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center e.V. (DLR), Linder Höhe, 51147 Cologne, Germany
- Institute for Microbiology, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany
- Present address: UK Center for Astrobiology, University of Edinburgh, School of Physics and Astronomy, Peter Guthrie Tait Road, Edinburgh, EH9 3FD UK
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
| | - Kaisa Koskinen
- Medical University of Graz, Department of Internal Medicine, Auenbruggerplatz 15, 8036 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Christine Moissl-Eichinger
- Medical University of Graz, Department of Internal Medicine, Auenbruggerplatz 15, 8036 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Simon Barczyk
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center e.V. (DLR), Linder Höhe, 51147 Cologne, Germany
| | - Reinhard Wirth
- Institute for Microbiology, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
| | - Petra Rettberg
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center e.V. (DLR), Linder Höhe, 51147 Cologne, Germany
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Shamarina D, Stoyantcheva I, Mason CE, Bibby K, Elhaik E. Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research. MICROBIOME 2017; 5:132. [PMID: 28978331 PMCID: PMC5628477 DOI: 10.1186/s40168-017-0349-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/20/2017] [Indexed: 05/07/2023]
Abstract
The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding microorganisms, the general public are apt to think of diseases rather than of the majority of harmless or beneficial species that inhabit our bodies and the built and natural environment. As long as microbiome research was confined to labs, the public's exposure to microbiology was limited. The recent launch of global microbiome surveys, such as the Earth Microbiome Project and MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) project, has raised ethical, financial, feasibility, and sustainability concerns as to the public's level of understanding and potential reaction to the findings, which, done improperly, risk negative implications for ongoing and future investigations, but done correctly, can facilitate a new vision of "smart cities." To facilitate improved future research, we describe here the major concerns that our discussions with ethics committees, community leaders, and government officials have raised, and we expound on how to address them. We further discuss ethical considerations of microbiome surveys and provide practical recommendations for public engagement.
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Affiliation(s)
- Daria Shamarina
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Iana Stoyantcheva
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021 USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY 10021 USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021 USA
| | - Kyle Bibby
- University of Notre Dame Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dameᅟ, IN 46556 USA
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN UK
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