1
|
Nastasi N, Bope A, Meyer ME, Horack JM, Dannemiller KC. Predicting how varying moisture conditions impact the microbiome of dust collected from the International Space Station. MICROBIOME 2024; 12:171. [PMID: 39256883 PMCID: PMC11386075 DOI: 10.1186/s40168-024-01864-3] [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: 02/23/2024] [Accepted: 06/25/2024] [Indexed: 09/12/2024]
Abstract
BACKGROUND The commercialization of space travel will soon lead to many more people living and working in unique built environments similar to the International Space Station, which is a specialized closed environment that contains its own indoor microbiome. Unintended microbial growth can occur in these environments as in buildings on Earth from elevated moisture, such as from a temporary ventilation system failure. This growth can drive negative health outcomes and degrade building materials. We need a predictive approach for modeling microbial growth in these critical indoor spaces. RESULTS Here, we demonstrate that even short exposures to varying elevated relative humidity can facilitate rapid microbial growth and microbial community composition changes in dust from spacecraft. We modeled fungal growth in dust from the International Space Station using the time-of-wetness framework with activation and deactivation limited growth occurring at 85% and 100% relative humidity, respectively. Fungal concentrations ranged from an average of 4.4 × 106 spore equivalents per milligram of dust in original dust with no exposure to relative humidity to up to 2.1 × 1010 when exposed to 100% relative humidity for 2 weeks. As relative humidity and time-elevated increased, fungal diversity was significantly reduced for both alpha (Q < 0.05) and beta (R2 = 0.307, P = 0.001) diversity metrics. Bacteria were unable to be modeled using the time-of-wetness framework. However, bacterial communities did change based on constant relative humidity incubations for both beta (R2 = 0.22, P = 0.001) and alpha diversity decreasing with increasing moisture starting at 85% relative humidity (Q < 0.05). CONCLUSION Our results demonstrate that moisture conditions can be used to develop and predict changes in fungal growth and composition onboard human-occupied spacecraft. This predictive model can be expanded upon to include other spacecraft environmental factors such as microgravity, elevated carbon dioxide conditions, and radiation exposure. Understanding microbial growth in spacecraft can help better protect astronaut health, fortify spacecraft integrity, and promote planetary protection as human activity increases in low-Earth orbit, the moon, Mars, and beyond. Video Abstract.
Collapse
Affiliation(s)
- Nicholas Nastasi
- Environmental Science Graduate Program, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, College of Engineering, Environmental, and Geodetic Engineering, Ohio State University, 470 Hitchcock Hall, 2050 Neil Ave, Columbus, OH, 43210, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA
| | - Ashleigh Bope
- Environmental Science Graduate Program, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, College of Engineering, Environmental, and Geodetic Engineering, Ohio State University, 470 Hitchcock Hall, 2050 Neil Ave, Columbus, OH, 43210, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA
| | - Marit E Meyer
- NASA Glenn Research Center, Cleveland, OH, 44135, USA
| | - John M Horack
- Department of Mechanical and Aerospace Engineering, College of Engineering and John Glenn College of Public Affairs, Ohio State University, Columbus, OH, 43210, USA
| | - Karen C Dannemiller
- Department of Civil, College of Engineering, Environmental, and Geodetic Engineering, Ohio State University, 470 Hitchcock Hall, 2050 Neil Ave, Columbus, OH, 43210, USA.
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA.
- Sustainability Institute, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
2
|
Nastasi N, Haines SR, Bope A, Meyer ME, Horack JM, Dannemiller KC. Fungal diversity differences in the indoor dust microbiome from built environments on earth and in space. Sci Rep 2024; 14:11858. [PMID: 38789478 PMCID: PMC11126634 DOI: 10.1038/s41598-024-62191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Human occupied built environments are no longer confined to Earth. In fact, there have been humans living and working in low-Earth orbit on the International Space Station (ISS) since November 2000. With NASA's Artemis missions and the age of commercial space stations set to begin, more human-occupied spacecraft than ever will be in Earth's orbit and beyond. On Earth and in the ISS, microbes, especially fungi, can be found in dust and grow when unexpected, elevated moisture conditions occur. However, we do not yet know how indoor microbiomes in Earth-based homes and in the ISS differ due to their unique set of environmental conditions. Here we show that bacterial and fungal communities are different in dust collected from vacuum bags on Earth and the ISS, with Earth-based homes being more diverse (465 fungal OTUs and 237 bacterial ASVs) compared to the ISS (102 fungal OTUs and 102 bacterial ASVs). When dust from these locations were exposed to varying equilibrium relative humidity conditions (ERH), there were also significant fungal community composition changes as ERH and time elevated increased (Bray Curtis: R2 = 0.35, P = 0.001). These findings can inform future spacecraft design to promote healthy indoor microbiomes that support crew health, spacecraft integrity, and planetary protection.
Collapse
Affiliation(s)
- Nicholas Nastasi
- Environmental Science Graduate Program, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, College of Engineering, Environmental Health Sciences, The Ohio State University, 470 Hitchcock Hall, 2050 Neil Ave, Columbus, OH, 43210, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA
| | - Sarah R Haines
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, ON, Canada
| | - Ashleigh Bope
- Environmental Science Graduate Program, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, College of Engineering, Environmental Health Sciences, The Ohio State University, 470 Hitchcock Hall, 2050 Neil Ave, Columbus, OH, 43210, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA
| | - Marit E Meyer
- NASA Glenn Research Center, Cleveland, OH, 44135, USA
| | - John M Horack
- Department of Mechanical and Aerospace Engineering, College of Engineering and John Glenn College of Public Affairs, Ohio State University, Columbus, OH, 43210, USA
| | - Karen C Dannemiller
- Department of Civil, Environmental and Geodetic Engineering, College of Engineering, Environmental Health Sciences, The Ohio State University, 470 Hitchcock Hall, 2050 Neil Ave, Columbus, OH, 43210, USA.
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, 43210, USA.
- Sustainability Institute, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
3
|
Roth MG, Westrick NM, Baldwin TT. Fungal biotechnology: From yesterday to tomorrow. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1135263. [PMID: 37746125 PMCID: PMC10512358 DOI: 10.3389/ffunb.2023.1135263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 09/26/2023]
Abstract
Fungi have been used to better the lives of everyday people and unravel the mysteries of higher eukaryotic organisms for decades. However, comparing progress and development stemming from fungal research to that of human, plant, and bacterial research, fungi remain largely understudied and underutilized. Recent commercial ventures have begun to gain popularity in society, providing a new surge of interest in fungi, mycelia, and potential new applications of these organisms to various aspects of research. Biotechnological advancements in fungal research cannot occur without intensive amounts of time, investments, and research tool development. In this review, we highlight past breakthroughs in fungal biotechnology, discuss requirements to advance fungal biotechnology even further, and touch on the horizon of new breakthroughs with the highest potential to positively impact both research and society.
Collapse
Affiliation(s)
- Mitchell G. Roth
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
| | - Nathaniel M. Westrick
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas T. Baldwin
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| |
Collapse
|
4
|
Woo C, Bhuiyan MIU, Kim D, Kumari P, Lee SK, Park JY, Dong K, Lee K, Yamamoto N. DNA metabarcoding-based study on bacteria and fungi associated with house dust mites (Dermatophagoides spp.) in settled house dust. EXPERIMENTAL & APPLIED ACAROLOGY 2022; 88:329-347. [PMID: 36301451 DOI: 10.1007/s10493-022-00755-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
House dust mites (HDMs) including Dermatophagoides spp. are an important cause of respiratory allergies. However, their relationship with microorganisms in house dust has not been fully elucidated. Here, we characterized bacteria and fungi associated with HDMs in house dust samples collected in 107 homes in Korea by using DNA barcode sequencing of bacterial 16S rRNA gene, fungal internal transcribed spacer 2 (ITS2) region, and arthropod cytochrome c oxidase I (COI) gene. Our inter-kingdom co-occurrence network analysis and/or indicator species analysis identified that HDMs were positively related with a xerophilic fungus Wallemia, mycoparasitic fungi such as Cystobasidium, and some human skin-related bacterial and fungal genera, and they were negatively related with the hygrophilous fungus Cephalotrichum. Overall, our study has succeeded in adding novel insights into HDM-related bacteria and fungi in the house dust ecosystem, and in confirming the historically recognized fact that HDMs are associated with xerophilic fungi such as Wallemia. Understanding the microbial ecology in house dust is thought to be important for elucidating the etiology of human diseases including allergies, and our study revealed baseline information of house dust ecology in relation to HDMs. The findings could be useful from a perspective of human health.
Collapse
Affiliation(s)
- Cheolwoon Woo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Mohammad Imtiaj Uddin Bhuiyan
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Donghyun Kim
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Priyanka Kumari
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung-Kyung Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ji Young Park
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ke Dong
- Major of Life Science, College of Natural Sciences, Kyonggi University, Suwon, 16227, Republic of Korea
| | - Kiyoung Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea.
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
5
|
Ding F, Krasilnikova AA, Leontieva MR, Stoyanova LG, Netrusov AI. Analysis of Kefir Grains from Different Regions of the Planet Using High-Throughput Sequencing. MOSCOW UNIVERSITY BIOLOGICAL SCIENCES BULLETIN 2022; 77:286-291. [PMID: 36843649 PMCID: PMC9940072 DOI: 10.3103/s0096392522040010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/23/2022] [Accepted: 11/10/2022] [Indexed: 02/22/2023]
Abstract
The taxonomic composition and spatial localization of yeast and bacteria in kefir grains (KG) obtained for study from different regions of the planet were investigated. The diversity of their microbiome has been demonstrated by high-throughput sequencing of bacterial 16S rRNA genes and the ITS1 region of the 18S-ITS1-5.8S-ITS2-28S complex of yeast rRNA. It has been established that the main representatives of the complex community of KG from different regions are lactic acid bacteria (LAB; lactobacilli, lactococci, and Leuconostoc spp. in different ratios) and different types of yeast of the genus Kazachstania (family Saccharomycetaceae). Acetic acid bacteria and a small percentage of yeast Kluyveromyces marxianus were detected in the KG from Tibet, and yeast Pichia kluyveri was detected in the KG from Ossetia.
Collapse
Affiliation(s)
- F. Ding
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia ,Shenzhen MSU-BIT University, 518172 Shenzhen, China
| | - A. A. Krasilnikova
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - M. R. Leontieva
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - L. G. Stoyanova
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - A. I. Netrusov
- grid.14476.300000 0001 2342 9668Microbiology Department, Biological Faculty, Moscow State University, 119234 Moscow, Russia ,Faculty of Biology and Biotechnology, High School of Economics, 101000 Moscow, Russia
| |
Collapse
|
6
|
Associations between dog keeping and indoor dust microbiota. Sci Rep 2021; 11:5341. [PMID: 33674692 PMCID: PMC7935950 DOI: 10.1038/s41598-021-84790-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/09/2021] [Indexed: 12/27/2022] Open
Abstract
Living with dogs appears to protect against allergic diseases and airway infections, an effect possibly linked with immunomodulation by microbial exposures associated with dogs. The aim of this study was to characterize the influence of dog ownership on house dust microbiota composition. The bacterial and fungal microbiota was characterized with Illumina MiSeq sequencing from floor dust samples collected from homes in a Finnish rural-suburban (LUKAS2, N = 182) birth cohort, and the results were replicated in a German urban (LISA, N = 284) birth cohort. Human associated bacteria variable was created by summing up the relative abundances of five bacterial taxa. Bacterial richness, Shannon index and the relative abundances of seven bacterial genera, mostly within the phyla Proteobacteria and Firmicutes, were significantly higher in the dog than in the non-dog homes, whereas the relative abundance of human associated bacteria was lower. The results were largely replicated in LISA. Fungal microbiota richness and abundance of Leucosporidiella genus were higher in dog homes in LUKAS2 and the latter association replicated in LISA. Our study confirms that dog ownership is reproducibly associated with increased bacterial richness and diversity in house dust and identifies specific dog ownership-associated genera. Dogs appeared to have more limited influence on the fungal than bacterial indoor microbiota.
Collapse
|
7
|
Shinohara N, Woo C, Yamamoto N, Hashimoto K, Yoshida-Ohuchi H, Kawakami Y. Comparison of DNA sequencing and morphological identification techniques to characterize environmental fungal communities. Sci Rep 2021; 11:2633. [PMID: 33514828 PMCID: PMC7846767 DOI: 10.1038/s41598-021-81996-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/11/2021] [Indexed: 11/09/2022] Open
Abstract
Culture-independent DNA sequencing of fungal internal transcribed spacer 2 (ITS2) region was compared to a culture-dependent morphological identification technique to characterize house dust-borne fungal communities. The abundant genera were Aspergillus, Wallemia, Cladosporium, and Penicillium. Statistically significant between-method correlations were observed for Wallemia and Cladosporium (Spearman's ρ = 0.75 and 0.72, respectively; p < 0.001). Penicillium tended to be detected with much higher (averaged 26-times) relative abundances by the culture-based method than by the DNA-based method, although statistically significant inter-method correlation was observed with Spearman's ρ = 0.61 (p = 0.002). Large DNA sequencing-based relative abundances observed for Alternaria and Aureobasidium were likely due to multicellularity of their spores with large number of per-spore ITS2 copies. The failure of the culture-based method in detectiing Toxicocladosporium, Verrucocladosporium, and Sterigmatomyces was likely due to their fastidiousness growth on our nutrient medium. Comparing between the two different techniques clarified the causes of biases in identifying environmental fungal communities, which should be amended and/or taken into consideration when the methods are used for future fungal ecological studies.
Collapse
Affiliation(s)
- Naohide Shinohara
- Research Institute of Science for Safety and Sustainability (RISS), National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Cheolwoon Woo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kazuhiro Hashimoto
- Laboratory of Integrated Pest Management, FCG Research Institute Inc., 1-1-20Koto-ku, Aomi, 135-0064, Japan
| | - Hiroko Yoshida-Ohuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Yuji Kawakami
- Laboratory of Integrated Pest Management, FCG Research Institute Inc., 1-1-20Koto-ku, Aomi, 135-0064, Japan
| |
Collapse
|
8
|
Hegarty B, Pan A, Haverinen-Shaughnessy U, Shaughnessy R, Peccia J. DNA Sequence-Based Approach for Classifying the Mold Status of Buildings. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15968-15975. [PMID: 33258367 DOI: 10.1021/acs.est.0c03904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dampness or water damage in buildings and human exposure to the resultant mold growth is an ever-present public health concern. This study provides quantitative evidence that the airborne fungal ecology of homes with known mold growth ("moldy") differs from the normal airborne fungal ecology of homes with no history of dampness, water damage, or visible mold ("no mold"). Settled dust from indoor air and outdoor air and direct samples from building materials with mold growth were examined in homes from 11 cities across dry, temperate, and continental climate regions within the United States. Community analysis based on the sequence of the internal transcribed spacer region of fungal ribosomal RNA encoding genes demonstrated consistent and quantifiable differences between the fungal ecology of settled dust in homes with inspector-verified water damage and visible mold versus the settled dust of homes with no history of dampness, water damage, or visible mold. These differences include lower community richness (padj = 0.01) in the settled dust of moldy homes versus no mold homes, as well as distinct community taxonomic structures between moldy and no mold homes (ANOSIM, R = 0.15, p = 0.001). We identified 11 Ascomycota taxa that were more highly enriched in moldy homes and 14 taxa from Ascomycota, Basidiomycota, and Zygomycota that were more highly enriched in no mold homes. The indoor air differences between moldy versus no mold homes were significant for all three climate regions considered. These distinct but complex differences between settled dust samples from moldy and no homes were used to train a machine learning-based model to classify the mold status of a home. The model was able to accurately classify 100% of moldy homes and 90% of no mold homes. The integration of DNA-based fungal ecology with advanced computational approaches can be used to accurately classify the presence of mold growth in homes, assist with inspection and remediation decisions, and potentially lead to reduced exposure to hazardous microbes indoors.
Collapse
Affiliation(s)
- Bridget Hegarty
- Department of Chemical and Environmental Engineering, Yale University, P.O. Box 208263 New Haven, Connecticut 06520-8286, United States
| | - Annabelle Pan
- Department of Chemical and Environmental Engineering, Yale University, P.O. Box 208263 New Haven, Connecticut 06520-8286, United States
| | - Ulla Haverinen-Shaughnessy
- Indoor Air Program, The University of Tulsa, 800 South Tucker Drive, Henneke 212, Tulsa, Oklahoma 74101-9700, United States
| | - Richard Shaughnessy
- Indoor Air Program, The University of Tulsa, 800 South Tucker Drive, Henneke 212, Tulsa, Oklahoma 74101-9700, United States
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, P.O. Box 208263 New Haven, Connecticut 06520-8286, United States
| |
Collapse
|
9
|
Haines SR, Siegel JA, Dannemiller KC. Modeling microbial growth in carpet dust exposed to diurnal variations in relative humidity using the "Time-of-Wetness" framework. INDOOR AIR 2020; 30:978-992. [PMID: 32403157 PMCID: PMC7496831 DOI: 10.1111/ina.12686] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/24/2020] [Accepted: 05/02/2020] [Indexed: 06/11/2023]
Abstract
Resuspension of microbes in floor dust and subsequent inhalation by human occupants is an important source of human microbial exposure. Microbes in carpet dust grow at elevated levels of relative humidity, but rates of this growth are not well established, especially under changing conditions. The goal of this study was to model fungal growth in carpet dust based on indoor diurnal variations in relative humidity utilizing the time-of-wetness framework. A chamber study was conducted on carpet and dust collected from 19 homes in Ohio, USA and exposed to varying moisture conditions of 50%, 85%, and 100% relative humidity. Fungal growth followed the two activation regime model, while bacterial growth could not be evaluated using the framework. Collection site was a stronger driver of species composition (P = 0.001, R2 = 0.461) than moisture conditions (P = 0.001, R2 = 0.021). Maximum moisture condition was associated with species composition within some individual sites (P = 0.001-0.02, R2 = 0.1-0.33). Aspergillus, Penicillium, and Wallemia were common fungal genera found among samples at elevated moisture conditions. These findings can inform future studies of associations between dampness/mold in homes and health outcomes and allow for prediction of microbial growth in the indoor environment.
Collapse
Affiliation(s)
- Sarah R. Haines
- Environmental Science Graduate ProgramOhio State UniversityColumbusOhioUSA
- Department of Civil, Environmental & Geodetic EngineeringCollege of EngineeringOhio State UniversityColumbusOhioUSA
- Division of Environmental Health SciencesCollege of Public HealthOhio State UniversityColumbusOhioUSA
| | - Jeffrey A. Siegel
- Department of Civil and Mineral EngineeringUniversity of TorontoTorontoONCanada
| | - Karen C. Dannemiller
- Department of Civil, Environmental & Geodetic EngineeringCollege of EngineeringOhio State UniversityColumbusOhioUSA
- Division of Environmental Health SciencesCollege of Public HealthOhio State UniversityColumbusOhioUSA
- Sustainability InstituteOhio State UniversityColumbusOhioUSA
| |
Collapse
|
10
|
Viegas C, Caetano LA, Cox J, Korkalainen M, Haines SR, Dannemiller KC, Viegas S, Reponen T. The effects of waste sorting in environmental microbiome, THP-1 cell viability and inflammatory responses. ENVIRONMENTAL RESEARCH 2020; 185:109450. [PMID: 32244107 DOI: 10.1016/j.envres.2020.109450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/28/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Workers in the waste sorting industry are exposed to diverse bioaerosols. Characterization of these bioaerosols is necessary to more accurately assess the health risks of exposure. The use of high-throughput DNA sequencing for improved analysis of microbial composition of bioaerosols, in combination with their in vitro study in relevant cell cultures, represents an important opportunity to find answers on the biological effects of bioaerosols. This study aimed to characterize by high-throughput sequencing the biodiversity present in complex aerosol mixtures retained in forklift air conditioning filters of a waste-sorting industry and its effects on cytotoxicity and secretion of proinflammatory cytokines in vitro using human macrophages derived from monocytic THP-1 cells. Seventeen filters from the filtration system from forklifts operating in one waste sorting facility and one control filter (similar filter without prior use) were analyzed using high-throughput sequencing and toxicological tests in vitro. A trend of positive correlation was seen between the number of bacterial and fungal OTUs (r = 0.47, p = 0.06). Seven filters (39%) exhibited low or moderate cytotoxicity (p < 0.05). The highest cytotoxic responses had a reduction in cell viability between 17 and 22%. Filter samples evoked proinflammatory responses, especially the production of TNFα. No significant correlation was found between fungal richness and inflammatory responses in vitro. The data obtained stress the need of thorough exposure assessment in waste-sorting industry and to take immunomodulatory properties into consideration for bioaerosols hazard characterization. The broad spectrum of microbial contamination detected in this study demonstrates that adequate monitoring of bioaerosol exposure is necessary to evaluate and minimize risks. The combined techniques can support the implementation of effective environmental monitoring programs of public and occupational health importance.
Collapse
Affiliation(s)
- C Viegas
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Portugal; NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal; Comprehensive Health Research Center (CHRC), Portugal.
| | - L A Caetano
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Portugal; Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 649-003, Lisbon, Portugal
| | - J Cox
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH, 45242, USA
| | - M Korkalainen
- Finnish Institute for Health and Welfare (THL), Environmental Health, P.O. Box 95, FIN-70701, Kuopio, Finland
| | - S R Haines
- Department of Civil, Environmental, and Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, OH, USA; Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Environmental Science Graduate Program, The Ohio State University, Columbus, OH, USA
| | - K C Dannemiller
- Department of Civil, Environmental, and Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, OH, USA; Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - S Viegas
- H&TRC- Health & Technology Research Center, ESTeSL- Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Portugal; NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal; Comprehensive Health Research Center (CHRC), Portugal
| | - T Reponen
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH, 45242, USA
| |
Collapse
|
11
|
Nastasi N, Haines SR, Xu L, da Silva H, Divjan A, Barnes MA, Rappleye CA, Perzanowski MS, Green BJ, Dannemiller KC. Morphology and quantification of fungal growth in residential dust and carpets. BUILDING AND ENVIRONMENT 2020; 174:10.1016/j.buildenv.2020.106774. [PMID: 33897093 PMCID: PMC8064739 DOI: 10.1016/j.buildenv.2020.106774] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Mold growth indoors is associated with negative human health effects, and this growth is limited by moisture availability. Dust deposited in carpet is an important source of human exposure due to potential elevated resuspension compared to hard floors. However, we need an improved understanding of fungal growth in dust and carpet to better estimate human exposure. The goal of this study was to compare fungal growth quantity and morphology in residential carpet under different environmental conditions, including equilibrium relative humidity (ERH) (50%, 85%, 90%, 95%, 100%), carpet fiber material (nylon, olefin, wool) and presence/absence of dust. We analyzed incubated carpet and dust samples from three Ohio homes for total fungal DNA, fungal allergen Alt a 1, and fungal morphology. Dust presence and elevated ERH (≥85%) were the most important variables that increased fungal growth. Elevated ERH increased mean fungal DNA concentration (P < 0.0001), for instance by approximately 1000 times at 100% compared to 50% ERH after two weeks. Microscopy also revealed more fungal growth at higher ERH. Fungal concentrations were up to 100 times higher in samples containing house dust compared to no dust. For fiber type, olefin had the least total fungal growth, and nylon had the most total fungi and A. alternata growth in unaltered dust. Increased ERH conditions were associated with increased Alt a 1 allergen concentration. The results of this study demonstrate that ERH, presence/absence of house dust, and carpet fiber type influence fungal growth and allergen production in residential carpet, which has implications for human exposure.
Collapse
Affiliation(s)
- Nicholas Nastasi
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, USA
- Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, USA
- Environmental Science Graduate Program, Ohio State University, Columbus, OH, USA
| | - Sarah R. Haines
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, USA
- Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, USA
- Environmental Science Graduate Program, Ohio State University, Columbus, OH, USA
| | - Lingyi Xu
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Hadler da Silva
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Adnan Divjan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Mark A. Barnes
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Chad A. Rappleye
- Department of Microbiology, College of Arts and Sciences, Ohio State University, Columbus, OH, USA
| | - Matthew S. Perzanowski
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Brett J. Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Karen C. Dannemiller
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, USA
- Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, USA
| |
Collapse
|
12
|
Bakker A, Siegel JA, Mendell MJ, Prussin AJ, Marr LC, Peccia J. Bacterial and fungal ecology on air conditioning cooling coils is influenced by climate and building factors. INDOOR AIR 2020; 30:326-334. [PMID: 31845419 DOI: 10.1111/ina.12632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/06/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
The presence of biofilms on the cooling coils of commercial air conditioning (AC) units can significantly reduce the heat transfer efficiency of the coils and may lead to the aerosolization of microbes into occupied spaces of a building. We investigated how climate and AC operation influence the ecology of microbial communities on AC coils. Forty large-scale commercial ACs were considered with representation from warm-humid and hot-dry climates. Both bacterial and fungal ecologies, including richness and taxa, on the cooling coil surfaces were significantly impacted by outdoor climate, through differences in dew point that result in increased moisture (condensate) on coils, and by the minimum efficiency reporting value (MERV 8 vs MERV 14) of building air filters. Based on targeted qPCR and sequence analysis, low efficiency upstream filters (MERV 8) were associated with a greater abundance of pathogenic bacteria and medically relevant fungi. As the implementation of air conditioning continues to grow worldwide, better understanding of the factors impacting microbial growth and ecology on cooling coils should enable more rational approaches for biofilm control and ultimately result in reduced energy consumption and healthier buildings.
Collapse
Affiliation(s)
- Alexa Bakker
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Jeffrey A Siegel
- Department of Civil & Mineral Engineering, The University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, The University of Toronto, Toronto, ON, Canada
| | - Mark J Mendell
- California Department of Public Health, Environmental Health Laboratory Branch, Richmond, CA, USA
| | - Aaron J Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| |
Collapse
|
13
|
Quantitative evaluation of bioaerosols in different particle size fractions in dust collected on the International Space Station (ISS). Appl Microbiol Biotechnol 2019; 103:7767-7782. [PMID: 31388730 DOI: 10.1007/s00253-019-10053-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/17/2019] [Accepted: 07/26/2019] [Indexed: 12/20/2022]
Abstract
Exposure to bioaerosols can adversely influence human health through respiratory tract, eye, and skin irritation. Bioaerosol composition is unique on the International Space Station (ISS), where the size distribution of particles in the air differs from those on Earth. This is due to the lack of gravitational settling and sources of biological particles. However, we do not understand how microbes are influenced by particle size in this environment. We analyzed two types of samples from the ISS: (1) vacuum bag debris which had been sieved into five different size fractions and (2) passively collected particles on a tape substrate with a passive aerosol sampler. Using quantitative polymerase chain reaction (qPCR), the highest concentration of fungal spores was found in the 106-150 μm-sized sieved dust particles, while the highest concentration of bacterial cells was found in the 150-250 μm-sized sieved dust particles. Illumina MiSeq DNA sequencing revealed that particle size was associated with bacterial and fungal communities and statistically significant (p = 0.035, p = 0.036 respectively). Similar fungal and bacterial species were found within the passive aerosol sample and the sieved dust samples. The most abundant fungal species identified in the aerosol and sieved samples are commonly found in food and plant material. Abundant bacterial species were most associated with the oral microbiome and human upper respiratory tract. One limitation to this study was the suboptimal storage conditions of the sieved samples prior to analysis. Overall, our results indicate that microbial exposure in space may depend on particle size. This has implications for ventilation and filtration system design for future space vehicles and habitats.
Collapse
|
14
|
McTaggart LR, Copeland JK, Surendra A, Wang PW, Husain S, Coburn B, Guttman DS, Kus JV. Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis. Front Microbiol 2019; 10:512. [PMID: 30930884 PMCID: PMC6428700 DOI: 10.3389/fmicb.2019.00512] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Invasive fungal infections are an increasingly important cause of human morbidity and mortality. We generated a next-generation sequencing (NGS)-based method designed to detect a wide range of fungi and applied it to analysis of the fungal microbiome (mycobiome) of the lung during fungal infection. Internal transcribed spacer 1 (ITS1) amplicon sequencing and a custom analysis pipeline detected 96% of species from three mock communities comprised of potential fungal lung pathogens with good recapitulation of the expected species distributions (Pearson correlation coefficients r = 0.63, p = 0.004; r = 0.71, p < 0.001; r = 0.62, p = 0.002). We used this pipeline to analyze mycobiomes of bronchoalveolar lavage (BAL) specimens classified as culture-negative (n = 50) or culture-positive (n = 39) for Blastomyces dermatitidis/gilchristii, the causative agent of North America blastomycosis. Detected in 91.4% of the culture-positive samples, Blastomyces dominated (>50% relative abundance) the mycobiome in 68.6% of these culture-positive samples but was absent in culture-negative samples. To overcome any bias in relative abundance due to between-sample variation in fungal biomass, an abundance-weighting calculation was used to normalize the data by accounting for sample-specific PCR cycle number and PCR product concentration data utilized during sample preparation. After normalization, there was a statistically significant greater overall abundance of ITS1 amplicon in the Blastomyces-culture-positive samples versus culture-negative samples. Moreover, the normalization revealed a greater biomass of yeast and environmental fungi in several Blastomyces-culture-positive samples than in the culture-negative samples. Successful detection of Coccidioides, Scedosporium, Phaeoacremonium, and Aspergillus in 6 additional culture-positive BALs by ITS1 amplicon sequencing demonstrates the ability of this method to detect a broad range of fungi from clinical specimens, suggesting that it may be a potentially useful adjunct to traditional fungal microbiological testing for the diagnosis of respiratory mycoses.
Collapse
Affiliation(s)
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | | | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Shahid Husain
- Division of Infectious Diseases, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julianne V Kus
- Public Health Ontario, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
15
|
Abstract
PURPOSE OF REVIEW The evolution of molecular-based methods over the last two decades has provided new approaches to identify and characterize fungal communities or "mycobiomes" at resolutions previously not possible using traditional hazard identification methods. The recent focus on fungal community assemblages within indoor environments has provided renewed insight into overlooked sources of fungal exposure. In occupational studies, internal transcribed spacer (ITS) region sequencing has recently been utilized in a variety of environments ranging from indoor office buildings to agricultural commodity and harvesting operations. RECENT FINDINGS Fungal communities identified in occupational environments have been primarily placed in the phylum Ascomycota and included classes typically identified using traditional fungal exposure methods such as the Eurotiomycetes, Dothideomycetes, Sordariomycetes, and Saccharomycetes. The phylum Basidiomycota has also been reported to be more prevalent than previously estimated and ITS region sequences have been primarily derived from the classes Agaricomycetes and Ustilaginomycetes. These studies have also resolved sequences placed in the Basidiomycota classes Tremellomycetes and Exobasidiomycetes that include environmental and endogenous yeast species. These collective datasets have shown that occupational fungal exposures include a much broader diversity of fungi than once thought. Although the clinical implications for occupational allergy are an emerging field of research, establishing the mycobiome in occupational environments will be critical for future studies to determine the complete spectrum of worker exposures to fungal bioaerosols and their impact on worker health.
Collapse
|
16
|
Luhung I, Wu Y, Xu S, Yamamoto N, Wei-Chung Chang V, Nazaroff WW. Exploring temporal patterns of bacterial and fungal DNA accumulation on a ventilation system filter for a Singapore university library. PLoS One 2018; 13:e0200820. [PMID: 30020972 PMCID: PMC6051664 DOI: 10.1371/journal.pone.0200820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 07/03/2018] [Indexed: 11/20/2022] Open
Abstract
Introduction Ventilation system filters process recirculated indoor air along with outdoor air. This function inspires the idea of using the filter as an indoor bioaerosol sampler. While promising, there remains a need to investigate several factors that could limit the accuracy of such a sampling approach. Among the important factors are the dynamics of microbial assemblages on filter surfaces over time and the differential influence of outdoor versus recirculated indoor air. Methods This study collected ventilation system filter samples from an air handling unit on a regular schedule over a 21-week period and analyzed the accumulation patterns of biological particles on the filter both quantitatively (using fluorometry and qPCR) and in terms of microbial diversity (using 16S rDNA and ITS sequencing). Results The quantitative result showed that total and bacterial DNA accumulated monotonically, rising to 41 ng/cm2 for total DNA and to 2.8 ng/cm2 for bacterial DNA over the 21-week period. The accumulation rate of bacterial DNA correlated with indoor occupancy level. Fungal DNA first rose to 4.0 ng/cm2 before showing a dip to 1.4 ng/cm2 between weeks 6 and 10. The dip indicated a possible artifact of this sampling approach for quantitative analysis as DNA may not be conserved on the filter over the months-long service period. The sequencing results indicate major contributions from outdoor air for fungi and from recirculated indoor air for bacteria. Despite the quantitative changes, the community structure of the microbial assemblages was stable throughout the 21-week sampling period, highlighting the robustness of this sampling method for microbial profiling. Conclusion This study supports the use of ventilation system filters as indoor bioaerosol samplers, but with caveats: 1) an outdoor reference is required to properly understand the contribution of outdoor bioaerosols; and 2) there is a need to better understand the persistence and durability of the targeted organisms on ventilation system filters.
Collapse
Affiliation(s)
- Irvan Luhung
- SinBerBEST Program, Berkeley Education Alliance for Research in Singapore (BEARS), Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, Singapore
- * E-mail:
| | - Yan Wu
- SinBerBEST Program, Berkeley Education Alliance for Research in Singapore (BEARS), Singapore, Singapore
- School of Environmental Science and Engineering, Shandong University, Jinan, China
| | - Siyu Xu
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - Victor Wei-Chung Chang
- SinBerBEST Program, Berkeley Education Alliance for Research in Singapore (BEARS), Singapore, Singapore
- Department of Civil Engineering, Monash University, Victoria, Clayton, Australia
| | - William W. Nazaroff
- SinBerBEST Program, Berkeley Education Alliance for Research in Singapore (BEARS), Singapore, Singapore
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| |
Collapse
|
17
|
Kwan S, Shaughnessy R, Hegarty B, Haverinen‐Shaughnessy U, Peccia J. The reestablishment of microbial communities after surface cleaning in schools. J Appl Microbiol 2018; 125:897-906. [DOI: 10.1111/jam.13898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/13/2018] [Accepted: 04/21/2018] [Indexed: 12/24/2022]
Affiliation(s)
- S.E. Kwan
- Department of Chemical and Environmental Engineering Yale University New Haven CT 06520‐8286 USA
| | - R.J. Shaughnessy
- Department of Chemical Engineering Indoor Air Program The University of Tulsa Tulsa OK 74101‐9700 USA
| | - B. Hegarty
- Department of Chemical and Environmental Engineering Yale University New Haven CT 06520‐8286 USA
| | - U. Haverinen‐Shaughnessy
- Department of Chemical Engineering Indoor Air Program The University of Tulsa Tulsa OK 74101‐9700 USA
| | - J. Peccia
- Department of Chemical and Environmental Engineering Yale University New Haven CT 06520‐8286 USA
| |
Collapse
|
18
|
Tipton L, Cuenco KT, Huang L, Greenblatt RM, Kleerup E, Sciurba F, Duncan SR, Donahoe MP, Morris A, Ghedin E. Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model. BioData Min 2018; 11:12. [PMID: 29983746 PMCID: PMC6003033 DOI: 10.1186/s13040-018-0173-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/27/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Human microbiome studies in clinical settings generally focus on distinguishing the microbiota in health from that in disease at a specific point in time. However, microbiome samples may be associated with disease severity or continuous clinical health indicators that are often assessed at multiple time points. While the temporal data from clinical and microbiome samples may be informative, analysis of this type of data can be problematic for standard statistical methods. RESULTS To identify associations between microbiota and continuous clinical variables measured repeatedly in two studies of the respiratory tract, we adapted a statistical method, the lasso-penalized generalized linear mixed model (LassoGLMM). LassoGLMM can screen for associated clinical variables, incorporate repeated measures of individuals, and address the large number of species found in the microbiome. As is common in microbiome studies, when the number of variables is an order of magnitude larger than the number of samples LassoGLMM can be imperfect in its variable selection. We overcome this limitation by adding a pre-screening step to reduce the number of variables evaluated in the model. We assessed the use of this adapted two-stage LassoGLMM for its ability to determine which microbes are associated with continuous repeated clinical measures.We found associations (retaining a non-zero coefficient in the LassoGLMM) between 10 laboratory measurements and 43 bacterial genera in the oral microbiota, and between 2 cytokines and 3 bacterial genera in the lung. We compared our associations with those identified by the Wilcoxon test after dichotomizing our outcomes and identified a non-significant trend towards differential abundance between high and low outcomes. Our two-step LassoGLMM explained more of the variance seen in the outcome of interest than other variants of the LassoGLMM method. CONCLUSIONS We demonstrated a method that can account for the large number of genera detected in microbiome studies and repeated measures of clinical or longitudinal studies, allowing for the detection of strong associations between microbes and clinical measures. By incorporating the design strengths of repeated measurements and a prescreening step to aid variable selection, our two-step LassoGLMM will be a useful analytic method for investigating relationships between microbes and repeatedly measured continuous outcomes.
Collapse
Affiliation(s)
- Laura Tipton
- Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 USA
- Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003 USA
| | - Karen T. Cuenco
- Genentech, 1 DNA Way, MS-231C, South San Francisco, CA 94080 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Laurence Huang
- Department of Medicine, School of Medicine, University of California, San Francisco, CA 94143 USA
| | - Ruth M. Greenblatt
- Department of Medicine, School of Medicine, University of California, San Francisco, CA 94143 USA
- Departments of Clinical Pharmacy, Epidemiology and Biostatistics, Schools of Pharmacy and Medicine, University of California, San Francisco, CA 94143 USA
| | - Eric Kleerup
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Frank Sciurba
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Steven R. Duncan
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Michael P. Donahoe
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Alison Morris
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Elodie Ghedin
- Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 USA
- Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003 USA
- College of Global Public Health, New York University, New York, NY 10003 USA
| |
Collapse
|
19
|
Woo C, An C, Xu S, Yi SM, Yamamoto N. Taxonomic diversity of fungi deposited from the atmosphere. ISME JOURNAL 2018; 12:2051-2060. [PMID: 29849168 PMCID: PMC6051994 DOI: 10.1038/s41396-018-0160-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/02/2018] [Accepted: 05/07/2018] [Indexed: 11/17/2022]
Abstract
Fungi release spores into the global atmosphere. The emitted spores are deposited to the surface of the Earth by sedimentation (dry deposition) and precipitation (wet deposition), and therefore contribute to the global cycling of substances. However, knowledge is scarce regarding the diversities of fungi deposited from the atmosphere. Here, an automatic dry and wet deposition sampler and high-throughput sequencing plus quantitative PCR were used to observe taxonomic diversities and flux densities of atmospheric fungal deposition. Taxon-specific fungal deposition velocities and aerodynamic diameters (da) were determined using a collocated cascade impactor for volumetric, particle-size-resolved air sampling. Large multicellular spore-producing dothideomycetes (da ≥ 10.0 μm) were predominant in dry deposition, with a mean velocity of 0.80 cm s–1 for all fungal taxa combined. Higher taxonomic richness was observed in fungal assemblages in wet deposition than in dry deposition, suggesting the presence of fungal taxa that are deposited only in wet form. In wet deposition, agaricomycetes, including mushroom-forming fungi, and sordariomycetes, including plant pathogenic species, were enriched, indicating that such fungal spores serve as nuclei in clouds, and/or are discharged preferentially during precipitation. Moreover, this study confirmed that fungal assemblage memberships and structures were significantly different between dry and wet deposition (P-test, p < 0.001). Overall, these findings suggest taxon-specific involvement of fungi in precipitation, and provide important insights into potential links between environmental changes that can disturb regional microbial communities (e.g., deforestation) and changes in precipitation patterns that might be mediated by changes in microbial communities in the atmosphere.
Collapse
Affiliation(s)
- Cheolwoon Woo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Choa An
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Siyu Xu
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung-Muk Yi
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea.,Institute of Health and Environment, Seoul National University, Seoul, 08826, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea. .,Institute of Health and Environment, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
20
|
Maestre JP, Jennings W, Wylie D, Horner SD, Siegel J, Kinney KA. Filter forensics: microbiota recovery from residential HVAC filters. MICROBIOME 2018; 6:22. [PMID: 29382378 PMCID: PMC5791358 DOI: 10.1186/s40168-018-0407-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 01/18/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust samples provides valuable insights into the microbiome present in human-occupied spaces. However, the effect that different sampling methods have on the microbial community recovered from dust samples is not well understood across sample types. Heating, ventilation, and air conditioning (HVAC) filters hold promise as long-term, spatially integrated, high volume samplers to characterize the airborne microbiome in homes and other climate-controlled spaces. In this study, the effect that dust recovery method (i.e., cut and elution, swabbing, or vacuuming) has on the microbial community structure, membership, and repeatability inferred by Illumina sequencing was evaluated. RESULTS The results indicate that vacuum samples captured higher quantities of total, bacterial, and fungal DNA than swab or cut samples. Repeated swab and vacuum samples collected from the same filter were less variable than cut samples with respect to both quantitative DNA recovery and bacterial community structure. Vacuum samples captured substantially greater bacterial diversity than the other methods, whereas fungal diversity was similar across all three methods. Vacuum and swab samples of HVAC filter dust were repeatable and generally superior to cut samples. Nevertheless, the contribution of environmental and human sources to the bacterial and fungal communities recovered via each sampling method was generally consistent across the methods investigated. CONCLUSIONS Dust recovery methodologies have been shown to affect the recovery, repeatability, structure, and membership of microbial communities recovered from dust samples in the built environment. The results of this study are directly applicable to indoor microbiota studies utilizing the filter forensics approach. More broadly, this study provides a better understanding of the microbial community variability attributable to sampling methodology and helps inform interpretation of data collected from other types of dust samples collected from indoor environments.
Collapse
Affiliation(s)
- Juan P. Maestre
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX USA
| | - Wiley Jennings
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX USA
| | - Dennis Wylie
- Genome Sequencing and Analysis Facility, The University of Texas at Austin Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX USA
| | - Sharon D. Horner
- School of Nursing, The University of Texas at Austin, Austin, TX USA
| | - Jeffrey Siegel
- Department of Civil Engineering, University of Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
| | - Kerry A. Kinney
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX USA
| |
Collapse
|
21
|
Tipton L, Müller CL, Kurtz ZD, Huang L, Kleerup E, Morris A, Bonneau R, Ghedin E. Fungi stabilize connectivity in the lung and skin microbial ecosystems. MICROBIOME 2018; 6:12. [PMID: 29335027 PMCID: PMC5769346 DOI: 10.1186/s40168-017-0393-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/19/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND No microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes than in cataloging which microbes are present, the variety of microbes in the community should be considered. However, the majority of ecological interaction networks for microbiomes built to date have included only bacteria. Joint association inference across multiple domains of life, e.g., fungal communities (the mycobiome) and bacterial communities, has remained largely elusive. RESULTS Here, we present a novel extension of the SParse InversE Covariance estimation for Ecological ASsociation Inference (SPIEC-EASI) framework that allows statistical inference of cross-domain associations from targeted amplicon sequencing data. For human lung and skin micro- and mycobiomes, we show that cross-domain networks exhibit higher connectivity, increased network stability, and similar topological re-organization patterns compared to single-domain networks. We also validate in vitro a small number of cross-domain interactions predicted by the skin association network. CONCLUSIONS For the human lung and skin micro- and mycobiomes, our findings suggest that fungi play a stabilizing role in ecological network organization. Our study suggests that computational efforts to infer association networks that include all forms of microbial life, paired with large-scale culture-based association validation experiments, will help formulate concrete hypotheses about the underlying biological mechanisms of species interactions and, ultimately, help understand microbial communities as a whole.
Collapse
Affiliation(s)
- Laura Tipton
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, 15260 PA USA
- Center for Genomics and Systems Biology, New York University, New York, 10003 NY USA
| | - Christian L. Müller
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, 10010 NY USA
| | - Zachary D. Kurtz
- Department of Microbiology, New York University School of Medicine, New York, 10016 NY USA
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine and HIV/AIDS Division, University of California San Francisco, San Francisco, 94110 CA USA
| | - Eric Kleerup
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Richard Bonneau
- Center for Genomics and Systems Biology, New York University, New York, 10003 NY USA
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, 10010 NY USA
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, New York University, New York, 10003 NY USA
- Department of Epidemiology, College of Global Public Health, New York University, New York, NY USA
| |
Collapse
|
22
|
Valkonen M, Täubel M, Pekkanen J, Tischer C, Rintala H, Zock JP, Casas L, Probst-Hensch N, Forsberg B, Holm M, Janson C, Pin I, Gislason T, Jarvis D, Heinrich J, Hyvärinen A. Microbial characteristics in homes of asthmatic and non-asthmatic adults in the ECRHS cohort. INDOOR AIR 2018; 28:16-27. [PMID: 28960492 DOI: 10.1111/ina.12427] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
Microbial exposures in homes of asthmatic adults have been rarely investigated; specificities and implications for respiratory health are not well understood. The objectives of this study were to investigate associations of microbial levels with asthma status, asthma symptoms, bronchial hyperresponsiveness (BHR), and atopy. Mattress dust samples of 199 asthmatics and 198 control subjects from 7 European countries participating in the European Community Respiratory Health Survey II study were analyzed for fungal and bacterial cell wall components and individual taxa. We observed trends for protective associations of higher levels of mostly bacterial markers. Increased levels of muramic acid, a cell wall component predominant in Gram-positive bacteria, tended to be inversely associated with asthma (OR's for different quartiles: II 0.71 [0.39-1.30], III 0.44 [0.23-0.82], and IV 0.60 [0.31-1.18] P for trend .07) and with asthma score (P for trend .06) and with atopy (P for trend .02). These associations were more pronounced in northern Europe. This study among adults across Europe supports a potential protective effect of Gram-positive bacteria in mattress dust and points out that this may be more pronounced in areas where microbial exposure levels are generally lower.
Collapse
Affiliation(s)
- M Valkonen
- Living Environment and Health Unit, National Institute for Health and Welfare, Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - M Täubel
- Living Environment and Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - J Pekkanen
- Living Environment and Health Unit, National Institute for Health and Welfare, Kuopio, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - C Tischer
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - H Rintala
- Living Environment and Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - J-P Zock
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - L Casas
- Centre for Environment and Health - Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
- Research Foundation Flanders (FWO), Brussels, Belgium
| | - N Probst-Hensch
- Head Department Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Department of Public Health, University of Basel, Basel, Switzerland
| | - B Forsberg
- Department of Public Health and Clinical Medicine, Occupational and Environmental Medicine, Umeå University, Umeå, Sweden
| | - M Holm
- Department of Occupational and Environmental Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - C Janson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - I Pin
- CHU de Grenoble Alpes, INSERM U 1209, Université Grenoble Alpes, Grenoble, France
| | - T Gislason
- Department of Respiratory Medicine and Sleep, Landspitali University Hospital (E7), Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - D Jarvis
- Population Health and Occupational Disease, Imperial College, National Heart and Lung Institute, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College, London, UK
| | - J Heinrich
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital Munich, Ludwig Maximillians University Munich, Member of German Center for Lung Research (DZL), Munich, Germany
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - A Hyvärinen
- Living Environment and Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| |
Collapse
|
23
|
Jayaprakash B, Adams RI, Kirjavainen P, Karvonen A, Vepsäläinen A, Valkonen M, Järvi K, Sulyok M, Pekkanen J, Hyvärinen A, Täubel M. Indoor microbiota in severely moisture damaged homes and the impact of interventions. MICROBIOME 2017; 5:138. [PMID: 29029638 PMCID: PMC5640920 DOI: 10.1186/s40168-017-0356-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/27/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND The limited understanding of microbial characteristics in moisture-damaged buildings impedes efforts to clarify which adverse health effects in the occupants are associated with the damage and to develop effective building intervention strategies. The objectives of this current study were (i) to characterize fungal and bacterial microbiota in house dust of severely moisture-damaged residences, (ii) to identify microbial taxa associated with moisture damage renovations, and (iii) to test whether the associations between the identified taxa and moisture damage are replicable in another cohort of homes. We applied bacterial 16S rRNA gene and fungal ITS amplicon sequencing complemented with quantitative PCR and chemical-analytical approaches to samples of house dust, and also performed traditional cultivation of bacteria and fungi from building material samples. RESULTS Active microbial growth on building materials had significant though small influence on the house dust bacterial and fungal communities. Moisture damage interventions-including actual renovation of damaged homes and cases where families moved to another home-had only a subtle effect on bacterial community structure, seen as shifts in abundance weighted bacterial profiles after intervention. While bacterial and fungal species richness were reduced in homes that were renovated, they were not reduced for families that moved houses. Using different discriminant analysis tools, we were able identify taxa that were significantly reduced in relative abundance during renovation of moisture damage. For bacteria, the majority of candidates belonged to different families within the Actinomycetales order. Results for fungi were overall less consistent. A replication study in approximately 400 homes highlighted some of the identified taxa, confirming associations with observations of moisture damage and mold. CONCLUSIONS The present study is one of the first studies to analyze changes in microbiota due to moisture damage interventions using high-throughput sequencing. Our results suggest that effects of moisture damage and moisture damage interventions may appear as changes in the abundance of individual, less common, and especially bacterial taxa, rather than in overall community structure.
Collapse
Affiliation(s)
| | - Rachel I. Adams
- Plant and Microbial Biology, University of California, Berkeley, California USA
- California Department of Public Health, Richmond, California USA
| | - Pirkka Kirjavainen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Anne Karvonen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Asko Vepsäläinen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Maria Valkonen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Kati Järvi
- School of Engineering, Aalto University, Espoo, Finland
| | - Michael Sulyok
- Department for Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, (BOKU), Vienna, Tulln Austria
| | - Juha Pekkanen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
- Department of Public Health, Helsinki University, Helsinki, Finland
| | - Anne Hyvärinen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Martin Täubel
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| |
Collapse
|
24
|
Luhung I, Wu Y, Xu S, Yamamoto N, Chang VWC, Nazaroff WW. DNA accumulation on ventilation system filters in university buildings in Singapore. PLoS One 2017; 12:e0186295. [PMID: 29023520 PMCID: PMC5638523 DOI: 10.1371/journal.pone.0186295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 09/28/2017] [Indexed: 11/26/2022] Open
Abstract
Introduction Biological particles deposit on air handling system filters as they process air. This study reports and interprets abundance and diversity information regarding biomass accumulation on ordinarily used filters acquired from several locations in a university environment. Methods DNA-based analysis was applied both to quantify (via DNA fluorometry and qPCR) and to characterize (via high-throughput sequencing) the microbial material on filters, which mainly processed recirculated indoor air. Results were interpreted in relation to building occupancy and ventilation system operational parameters. Results Based on accumulated biomass, average DNA concentrations per AHU filter surface area across nine indoor locations after twelve weeks of filter use were in the respective ranges 1.1 to 41 ng per cm2 for total DNA, 0.02 to 3.3 ng per cm2 for bacterial DNA and 0.2 to 2.0 ng DNA per cm2 for fungal DNA. The most abundant genera detected on the AHU filter samples were Clostridium, Streptophyta, Bacillus, Acinetobacter and Ktedonobacter for bacteria and Aspergillus, Cladosporium, Nigrospora, Rigidoporus and Lentinus for fungi. Conditional indoor airborne DNA concentrations (median (range)) were estimated to be 13 (2.6–107) pg/m3 for total DNA, 0.4 (0.05–8.4) pg/m3 for bacterial DNA and 2.3 (1.0–5.1) pg/m3 for fungal DNA. Conclusion Conditional airborne concentrations and the relative abundances of selected groups of genera correlate well with occupancy level. Bacterial DNA was found to be more responsive than fungal DNA to differences in occupancy level and indoor environmental conditions.
Collapse
Affiliation(s)
- Irvan Luhung
- Berkeley Education Alliance for Research in Singapore, Singapore, Singapore
- Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yan Wu
- Berkeley Education Alliance for Research in Singapore, Singapore, Singapore
- Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
- School of Environmental Science and Engineering, Shandong University, Jinan, China
| | - Siyu Xu
- Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - Naomichi Yamamoto
- Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - Victor Wei-Chung Chang
- Berkeley Education Alliance for Research in Singapore, Singapore, Singapore
- Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
| | - William W. Nazaroff
- Berkeley Education Alliance for Research in Singapore, Singapore, Singapore
- Civil and Environmental Engineering, University of California, Berkeley, California, United States of America
| |
Collapse
|
25
|
Lee WD, Fong JJ, Eimes JA, Lim YW. Diversity and abundance of human-pathogenic fungi associated with pigeon faeces in urban environments. Mol Ecol 2017. [DOI: 10.1111/mec.14216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Won Dong Lee
- School of Biological Sciences; Seoul National University; Seoul Korea
- Faculty of Biology; Technion-Israel Institute of Technology; Haifa Israel
| | | | - John A. Eimes
- School of Biological Sciences; Seoul National University; Seoul Korea
- University College; Sungkyunkwan University; Suwon Korea
| | - Young Woon Lim
- School of Biological Sciences; Seoul National University; Seoul Korea
| |
Collapse
|
26
|
Ma X, Vikram A, Casson L, Bibby K. Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7648-7657. [PMID: 28562026 DOI: 10.1021/acs.est.7b00768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.
Collapse
Affiliation(s)
- Xiao Ma
- Department of Civil and Environmental Engineering, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
| | - Amit Vikram
- Department of Civil and Environmental Engineering, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
| | - Leonard Casson
- Department of Civil and Environmental Engineering, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
- Graduate School of Public Health, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
| | - Kyle Bibby
- Department of Civil and Environmental Engineering, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
- Department of Computational and Systems Biology, University of Pittsburgh Medical School , Pittsburgh, Pennsylvania 15261, United States
| |
Collapse
|
27
|
Dannemiller KC, Weschler CJ, Peccia J. Fungal and bacterial growth in floor dust at elevated relative humidity levels. INDOOR AIR 2017; 27:354-363. [PMID: 27272645 DOI: 10.1111/ina.12313] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/31/2016] [Indexed: 05/22/2023]
Abstract
Under sustained, elevated building moisture conditions, bacterial and fungal growth occurs. The goal of this study was to characterize microbial growth in floor dust at variable equilibrium relative humidity (ERH) levels. Floor dust from one home was embedded in coupons cut from a worn medium-pile nylon carpet and incubated at 50%, 80%, 85%, 90%, 95%, and 100% ERH levels. Quantitative PCR and DNA sequencing of ribosomal DNA for bacteria and fungi were used to quantify growth and community shifts. Over a 1-wk period, fungal growth occurred above 80% ERH. Growth rates at 85% and 100% ERH were 1.1 × 104 and 1.5 × 105 spore equivalents d-1 mg dust-1 , respectively. Bacterial growth occurred only at 100% ERH after 1 wk (9.0 × 104 genomes d-1 mg dust-1 ). Growth resulted in significant changes in fungal (P<.00001) and bacterial community structure (P<.00001) at varying ERH levels. Comparisons between fungal taxa incubated at different ERH levels revealed more than 100 fungal and bacterial species that were attributable to elevated ERH. Resuspension modeling indicated that more than 50% of airborne microbes could originate from the resuspension of fungi grown at ERH levels of 85% and above.
Collapse
Affiliation(s)
- K C Dannemiller
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, Ohio State University, Columbus, OH, USA
- Division of Environmental Health Sciences, College of Public Health, Ohio State University, Columbus, OH, USA
| | - C J Weschler
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA
| | - J Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| |
Collapse
|
28
|
Kumari P, Woo C, Yamamoto N, Choi HL. Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons. Sci Rep 2016; 6:37929. [PMID: 27892507 PMCID: PMC5124938 DOI: 10.1038/srep37929] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/02/2016] [Indexed: 01/23/2023] Open
Abstract
We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.
Collapse
Affiliation(s)
- Priyanka Kumari
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea
| | - Cheolwoon Woo
- Department of Environmental Health, Graduate School of Public Health, Seoul National University, Seoul 151-742, South Korea
| | - Naomichi Yamamoto
- Department of Environmental Health, Graduate School of Public Health, Seoul National University, Seoul 151-742, South Korea
| | - Hong-Lim Choi
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea
| |
Collapse
|
29
|
An C, Yamamoto N. Fungal compositions and diversities on indoor surfaces with visible mold growths in residential buildings in the Seoul Capital Area of South Korea. INDOOR AIR 2016; 26:714-723. [PMID: 26509799 DOI: 10.1111/ina.12261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
Indoor visible mold growths are known to be associated with allergies and respiratory illnesses. However, a question remains of their compositions and diversities. Using swab sampling and high-throughput DNA sequencing, this study analyzed taxonomic compositions and diversities of fungi on indoor surfaces laden with visible mold growths in residential apartments in South Korea. The sequencing results showed low species diversities with Shannon indices ranging from 0.14 to 2.29 (mean = 1.11). Several allergy-related genera were detected on the same surface, where the most abundant Cladosporium with a mean relative abundance of 41% co-occurred with less abundant Aspergillus (0.094%), Rhodotorula (6.3%), Cryptococcus (3.7%), Alternaria (4.1%), and Crivellia (17%). β diversity analyses showed significant differences in the fungal communities between enclosed balconies and other indoor areas (P < 0.05, ANOSIM), emphasizing a need to sample at multiple indoor locations when assessments are made for indoor visible mold growths. High-throughput sequencing is powerful in characterizing compositions and diversities of fungal communities. Future studies should examine the relationships between taxonomic compositions and diversities of indoor visible molds and health outcomes of allergies and respiratory illnesses in residential buildings.
Collapse
Affiliation(s)
- C An
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - N Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea.
| |
Collapse
|
30
|
Lee S, An C, Xu S, Lee S, Yamamoto N. High-throughput sequencing reveals unprecedented diversities of Aspergillus species in outdoor air. Lett Appl Microbiol 2016; 63:165-71. [PMID: 27333577 DOI: 10.1111/lam.12608] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/04/2016] [Accepted: 06/20/2016] [Indexed: 11/30/2022]
Abstract
UNLABELLED This study used the Illumina MiSeq to analyse compositions and diversities of Aspergillus species in outdoor air. The seasonal air samplings were performed at two locations in Seoul, South Korea. The results showed the relative abundances of all Aspergillus species combined ranging from 0·20 to 18% and from 0·19 to 21% based on the number of the internal transcribed spacer 1 (ITS1) and β-tubulin (BenA) gene sequences respectively. Aspergillus fumigatus was the most dominant species with the mean relative abundances of 1·2 and 5·5% based on the number of the ITS1 and BenA sequences respectively. A total of 29 Aspergillus species were detected and identified down to the species rank, among which nine species were known opportunistic pathogens. Remarkably, eight of the nine pathogenic species were detected by either one of the two markers, suggesting the need of using multiple markers and/or primer pairs when the assessments are made based on the high-throughput sequencing. Due to diversity of species within the genus Aspergillus, the high-throughput sequencing was useful to characterize their compositions and diversities in outdoor air, which are thought to be difficult to be accurately characterized by conventional culture and/or Sanger sequencing-based techniques. SIGNIFICANCE AND IMPACT OF THE STUDY Aspergillus is a diverse genus of fungi with more than 300 species reported in literature. Aspergillus is important since some species are known allergens and opportunistic human pathogens. Traditionally, growth-dependent methods have been used to detect Aspergillus species in air. However, these methods are limited in the number of isolates that can be analysed for their identities, resulting in inaccurate characterizations of Aspergillus diversities. This study used the high-throughput sequencing to explore Aspergillus diversities in outdoor, which are thought to be difficult to be accurately characterized by traditional growth-dependent techniques.
Collapse
Affiliation(s)
- S Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - C An
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - S Xu
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - S Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - N Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
| |
Collapse
|
31
|
Higgins SA, Welsh A, Orellana LH, Konstantinidis KT, Chee-Sanford JC, Sanford RA, Schadt CW, Löffler FE. Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils. Appl Environ Microbiol 2016; 82:2919-2928. [PMID: 26969694 PMCID: PMC4959062 DOI: 10.1128/aem.00243-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Members of the Fungi convert nitrate (NO3 (-)) and nitrite (NO2 (-)) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3 (-) or NO2 (-) in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N2O from NO2 (-) Novel PCR primers targeting the p450nor gene, which encodes the nitric oxide (NO) reductase responsible for N2O production in fungi, yielded 26 novel p450nor amplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylum Ascomycota and expand the known fungal P450nor sequence diversity. p450nor was detected in all fungal isolates that produced N2O from NO2 (-), whereas nirK (encoding the NO-forming NO2 (-) reductase) was amplified in only 13 to 74% of the N2O-forming isolates using two separate nirK primer sets. Collectively, our findings demonstrate the value of p450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation. IMPORTANCE A comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N2O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungal p450nor, a biomarker for fungal N2O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N2O emissions.
Collapse
Affiliation(s)
- Steven A Higgins
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Allana Welsh
- Department of Geology, University of Illinois, Urbana, Illinois, USA
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Robert A Sanford
- Department of Geology, University of Illinois, Urbana, Illinois, USA
| | - Christopher W Schadt
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| |
Collapse
|
32
|
Dannemiller KC, Gent JF, Leaderer BP, Peccia J. Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children. INDOOR AIR 2016; 26:179-92. [PMID: 25833176 PMCID: PMC4591094 DOI: 10.1111/ina.12205] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/27/2015] [Indexed: 05/03/2023]
Abstract
Variations in home characteristics, such as moisture and occupancy, affect indoor microbial ecology as well as human exposure to microorganisms. Our objective was to determine how indoor bacterial and fungal community structure and diversity are associated with the broader home environment and its occupants. Next-generation DNA sequencing was used to describe fungal and bacterial communities in house dust sampled from 198 homes of asthmatic children in southern New England. Housing characteristics included number of people/children, level of urbanization, single/multifamily home, reported mold, reported water leaks, air conditioning (AC) use, and presence of pets. Both fungal and bacterial community structures were non-random and demonstrated species segregation (C-score, P < 0.00001). Increased microbial richness was associated with the presence of pets, water leaks, longer AC use, suburban (vs. urban) homes, and dust composition measures (P < 0.05). The most significant differences in community composition were observed for AC use and occupancy (people, children, and pets) characteristics. Occupant density measures were associated with beneficial bacterial taxa, including Lactobacillus johnsonii as measured by qPCR. A more complete knowledge of indoor microbial communities is useful for linking housing characteristics to human health outcomes. Microbial assemblies in house dust result, in part, from the building's physical and occupant characteristics.
Collapse
Affiliation(s)
- Karen C. Dannemiller
- Department of Chemical and Environmental Engineering, Yale University, 9 Hillhouse Ave, PO Box 208286, New Haven, CT 06520, USA
| | - Janneane F. Gent
- Yale Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, One Church Street, 6 Floor, New Haven, CT 06510, USA
| | - Brian P. Leaderer
- Yale Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, One Church Street, 6 Floor, New Haven, CT 06510, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, 9 Hillhouse Ave, PO Box 208286, New Haven, CT 06520, USA
- Corresponding author: Jordan Peccia, Department of Chemical and Environmental Engineering, Yale University, Mason Laboratory, 9 Hillhouse Avenue, New Haven, CT, 06520-8286, USA, , 203-432-4385
| |
Collapse
|
33
|
Abstract
New state-of-the-art techniques in sequencing offer valuable tools in both detection of mycobiota and in understanding of the molecular mechanisms of resistance against antifungal compounds and virulence. Introduction of new sequencing platform with enhanced capacity and a reduction in costs for sequence analysis provides a potential powerful tool in mycological diagnosis and research. In this review, we summarize the applications of next-generation sequencing techniques in mycology.
Collapse
|
34
|
Dannemiller KC, Gent JF, Leaderer BP, Peccia J. Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children. J Allergy Clin Immunol 2016; 138:76-83.e1. [PMID: 26851966 DOI: 10.1016/j.jaci.2015.11.027] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 11/12/2015] [Accepted: 11/25/2015] [Indexed: 11/29/2022]
Abstract
BACKGROUND Allergic and nonallergic asthma severity in children can be affected by microbial exposures. OBJECTIVE We sought to examine associations between exposures to household microbes and childhood asthma severity stratified by atopic status. METHODS Participants (n = 196) were selected from a cohort of asthmatic children in Connecticut and Massachusetts. Children were grouped according to asthma severity (mild with no or minimal symptoms and medication or moderate to severe persistent) and atopic status (determined by serum IgE levels). Microbial community structure and concentrations in house dust were determined by using next-generation DNA sequencing and quantitative PCR. Logistic regression was used to explore associations between asthma severity and exposure metrics, including richness, taxa identification and quantification, community composition, and concentration of total fungi and bacteria. RESULTS Among all children, increased asthma severity was significantly associated with an increased concentration of summed allergenic fungal species, high total fungal concentrations, and high bacterial richness by using logistic regression in addition to microbial community composition by using the distance comparison t test. Asthma severity in atopic children was associated with fungal community composition (P = .001). By using logistic regression, asthma severity in nonatopic children was associated with total fungal concentration (odds ratio, 2.40; 95% CI, 1.06-5.44). The fungal genus Volutella was associated with increased asthma severity in atopic children (P = .0001, q = 0.04). The yeast genera Kondoa might be protective; Cryptococcus species might also affect asthma severity. CONCLUSION Asthma severity among this cohort of children was associated with microbial exposure, and associations differed based on atopic status.
Collapse
Affiliation(s)
- Karen C Dannemiller
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Conn
| | - Janneane F Gent
- Yale Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, Conn
| | - Brian P Leaderer
- Yale Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, Conn
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Conn.
| |
Collapse
|
35
|
Latest Developments in the Research of Rust Fungi and Their Allies (Pucciniomycotina). ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-29137-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
|
36
|
Kim SH, Clark ST, Surendra A, Copeland JK, Wang PW, Ammar R, Collins C, Tullis DE, Nislow C, Hwang DM, Guttman DS, Cowen LE. Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation. PLoS Pathog 2015; 11:e1005308. [PMID: 26588216 PMCID: PMC4654494 DOI: 10.1371/journal.ppat.1005308] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/03/2015] [Indexed: 01/10/2023] Open
Abstract
The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1) with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from different patients, providing a poignant example of parallel evolution. Together, this combined clinical-genomic approach provides a high-resolution portrait of the fungal microbiome of cystic fibrosis patient lungs and identifies a genetic basis of pathogen adaptation. Microbial cells vastly outnumber human cells in our bodies, yet we are only beginning to understand how these microbes influence human health and disease. One disease for which microbial communities are especially important is cystic fibrosis, where persistent lung infections can be lethal. Fungi are associated with poor respiratory function, but how fungal communities change with disease progression or treatment remains enigmatic. Here, we assess the dynamics of fungal communities by combining high-throughput sequencing of sputum samples from 28 patients with detailed analysis of phenotypes and genotypes of 1,603 fungal isolates. We found stable communities dominated by Candida and Aspergillus, and diversity in traits important for host adaptation. Antifungal drug resistance varied largely between species, while morphogenesis varied within species. For Candida species, the capacity to transition between yeast and filaments is a key virulence trait that is normally regulated by inducing cues, however, 28 isolates grew as filaments without such cues. Filamentation was due to loss-of-function mutations in the transcriptional regulator NRG1 in most isolates, which conferred resistance to the filament-repressive effects of a common bacterial pathogen. This work provides a portrait of the fungal microbiome associated with a lethal disease, and illuminates a genetic basis of pathogen adaptation.
Collapse
Affiliation(s)
- Sang Hu Kim
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shawn T. Clark
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Anuradha Surendra
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Julia K. Copeland
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ron Ammar
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Cathy Collins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Corey Nislow
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - David M. Hwang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - David S. Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
37
|
Lee S, Yamamoto N. Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus. Fungal Biol 2015; 119:1311-1321. [PMID: 26615752 DOI: 10.1016/j.funbio.2015.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/24/2015] [Accepted: 10/07/2015] [Indexed: 11/28/2022]
Abstract
This study characterized the accuracy of high-throughput amplicon sequencing to identify species within the genus Aspergillus. To this end, we sequenced the internal transcribed spacer 1 (ITS1), β-tubulin (BenA), and calmodulin (CaM) gene encoding sequences as DNA markers from eight reference Aspergillus strains with known identities using 300-bp sequencing on the Illumina MiSeq platform, and compared them with the BLASTn outputs. The identifications with the sequences longer than 250 bp were accurate at the section rank, with some ambiguities observed at the species rank due to mostly cross detection of sibling species. Additionally, in silico analysis was performed to predict the identification accuracy for all species in the genus Aspergillus, where 107, 210, and 187 species were predicted to be identifiable down to the species rank based on ITS1, BenA, and CaM, respectively. Finally, air filter samples were analysed to quantify the relative abundances of Aspergillus species in outdoor air. The results were reproducible across biological duplicates both at the species and section ranks, but not strongly correlated between ITS1 and BenA, suggesting the Aspergillus detection can be taxonomically biased depending on the selection of the DNA markers and/or primers.
Collapse
Affiliation(s)
- Seungeun Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 151-742, South Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 151-742, South Korea.
| |
Collapse
|
38
|
Gweon HS, Oliver A, Taylor J, Booth T, Gibbs M, Read DS, Griffiths RI, Schonrogge K. PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods Ecol Evol 2015; 6:973-980. [PMID: 27570615 PMCID: PMC4981123 DOI: 10.1111/2041-210x.12399] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/16/2015] [Indexed: 11/28/2022]
Abstract
Studying fungal biodiversity using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to generating identified operational taxonomic unit (OTU) abundance tables.Here, we introduce PIPITS, an open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables.We provide detailed descriptions of the pipeline and show its utility in the analysis of 9 396 092 sequences generated on the MiSeq platform from Illumina MiSeq. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curated UNITE fungal data set.
Collapse
Affiliation(s)
- Hyun S Gweon
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Anna Oliver
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Joanne Taylor
- Royal Botanic Garden Edinburgh 20A Inverleith Row Edinburgh EH3 5LR UK
| | - Tim Booth
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Melanie Gibbs
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Daniel S Read
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Robert I Griffiths
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Karsten Schonrogge
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| |
Collapse
|
39
|
Yamamoto N, Hospodsky D, Dannemiller KC, Nazaroff WW, Peccia J. Indoor emissions as a primary source of airborne allergenic fungal particles in classrooms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:5098-106. [PMID: 25794178 DOI: 10.1021/es506165z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
This study quantifies the influence of ventilation and indoor emissions on concentrations and particle sizes of airborne indoor allergenic fungal taxa and further examines geographical variability, each of which may affect personal exposures to allergenic fungi. Quantitative PCR and multiplexed DNA sequencing were employed to count and identify allergenic fungal aerosol particles indoors and outdoors in seven school classrooms in four different countries. Quantitative diversity analysis was combined with building characterization and mass balance modeling to apportion source contributions of indoor allergenic airborne fungal particles. Mass balance calculations indicate that 70% of indoor fungal aerosol particles and 80% of airborne allergenic fungal taxa were associated with indoor emissions; on average, 81% of allergenic fungi from indoor sources originated from occupant-generated emissions. Principal coordinate analysis revealed geographical variations in fungal communities among sites in China, Europe, and North America (p < 0.05, analysis of similarity), demonstrating that geography may also affect personal exposures to allergenic fungi. Indoor emissions including those released with occupancy contribute more substantially to allergenic fungal exposures in classrooms sampled than do outdoor contributions from ventilation. The results suggest that design and maintenance of buildings to control indoor emissions may enable reduced indoor inhalation exposures to fungal allergens.
Collapse
Affiliation(s)
- Naomichi Yamamoto
- †Department of Environmental Health, Graduate School of Public Health, Seoul National University, Seoul 151-742, Korea
| | - Denina Hospodsky
- ‡Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Karen C Dannemiller
- ‡Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - William W Nazaroff
- §Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jordan Peccia
- ‡Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| |
Collapse
|
40
|
Ma X, Baron JL, Vikram A, Stout JE, Bibby K. Fungal diversity and presence of potentially pathogenic fungi in a hospital hot water system treated with on-site monochloramine. WATER RESEARCH 2015; 71:197-206. [PMID: 25618520 DOI: 10.1016/j.watres.2014.12.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/09/2014] [Accepted: 12/30/2014] [Indexed: 06/04/2023]
Abstract
Currently, our knowledge of fungal ecology in engineered drinking water systems is limited, despite the potential for these systems to serve as a reservoir for opportunistic pathogens. In this study, hot water samples were collected both prior to and following the addition of monochloramine as an on-site disinfectant in a hospital hot water system. Fungal ecology was then analyzed by high throughput sequencing of the fungal ITS1 region. The results demonstrate that the genera Penicillium, Aspergillus, Peniophora, Cladosporium and Rhodosporidium comprised the core fungal biome of the hospital hot water system. Penicillium dominated the fungal community with an average relative abundance of 88.89% (±6.37%). ITS1 sequences of fungal genera containing potential pathogens such as Aspergillus, Candida, and Fusarium were also detected in this study. No significant change in fungal community structure was observed before and after the initiation of on-site monochloramine water treatment. This work represents the first report of the effects of on-site secondary water disinfection on fungal ecology in premise plumbing system, and demonstrates the necessity of considering opportunistic fungal pathogens during the evaluation of secondary premise plumbing disinfection systems.
Collapse
Affiliation(s)
- Xiao Ma
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Julianne L Baron
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA 15261, USA; Special Pathogens Laboratory, Pittsburgh, PA 15219, USA
| | - Amit Vikram
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Janet E Stout
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; Special Pathogens Laboratory, Pittsburgh, PA 15219, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Computational and Systems Biology, University of Pittsburgh Medical School, Pittsburgh, PA 15261, USA.
| |
Collapse
|
41
|
Ferro M, Antonio EA, Souza W, Bacci M. ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences. BMC Res Notes 2014; 7:857. [PMID: 25430816 PMCID: PMC4258023 DOI: 10.1186/1756-0500-7-857] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 11/19/2014] [Indexed: 11/17/2022] Open
Abstract
Background Studies on fungal diversity and ecology aim to identify fungi and to investigate their interactions with each other and with the environment. DNA sequence-based tools are essential for these studies because they can speed up the identification process and access greater fungal diversity than traditional methods. The nucleotide sequence encoding for the internal transcribed spacer (ITS) of the nuclear ribosomal RNA has recently been proposed as a standard marker for molecular identification of fungi and evaluation of fungal diversity. However, the analysis of large sets of ITS sequences involves many programs and steps, which makes this task intensive and laborious. Findings We developed the web-based pipeline ITScan, which automates the analysis of fungal ITS sequences generated either by Sanger or Next Generation Sequencing (NGS) platforms. Validation was performed using datasets containing ca. 2,000 to 40,000 sequences each. Conclusions ITScan is an online and user-friendly automated pipeline for fungal diversity analysis and identification based on ITS sequences. It speeds up a process which would otherwise be repetitive and time-consuming for users. The ITScan tool and documentation are available at http://evol.rc.unesp.br:8083/itscan.
Collapse
Affiliation(s)
- Milene Ferro
- Centro de Estudos de Insetos Sociais, Instituto de Biociências, UNESP - Univ Estadual Paulista, Rio Claro SP 13506-900, Brazil.
| | | | | | | |
Collapse
|
42
|
Dannemiller KC, Mendell MJ, Macher JM, Kumagai K, Bradman A, Holland N, Harley K, Eskenazi B, Peccia J. Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development. INDOOR AIR 2014; 24:236-47. [PMID: 24883433 PMCID: PMC4048861 DOI: 10.1111/ina.12072] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
UNLABELLED Dampness and visible mold in homes are associated with asthma development, but causal mechanisms remain unclear. The goal of this research was to explore associations among measured dampness, fungal exposure, and childhood asthma development without the bias of culture-based microbial analysis. In the low-income, Latino CHAMACOS birth cohort, house dust was collected at age 12 months, and asthma status was determined at age 7 years.The current analysis included 13 asthma cases and 28 controls. Next-generation DNA sequencing methods quantified fungal taxa and diversity. Lower fungal diversity (number of fungal operational taxonomic units) was significantly associated with increased risk of asthma development: unadjusted odds ratio(OR) 4.80 (95% confidence interval (CI) 1.04–22.1). Control for potential confounders strengthened this relationship. Decreased diversity within the genus Cryptococcus was significantly associated with increased asthma risk (OR 21.0, 95% CI 2.16–204). No fungal taxon (species, genus, class) was significantly positively associated with asthma development, and one was significantly negatively associated. Elevated moisture was associated with increased fungal diversity, and moisture/mold indicators were associated with four fungal taxa. Next-generation DNA sequencing provided comprehensive estimates of fungal identity and diversity, demonstrating significant associations between low fungal diversity and childhood asthma development in this community. PRACTICAL IMPLICATIONS Early life exposure to low fungal diversity in house dust was associated with increased risk for later asthma developmen tin this low-income, immigrant community. No individual fungal taxon (species, genus, or class) was associated with asthma development, although exposure to low diversity within the genus Cryptococcus was associated with asthma development. Future asthma development studies should incorporate fungal diversity measurements, in addition to measuring individual fungal taxa. These results represent a step toward identifying the aspect(s) of indoor microbial populations that are associated with asthma development and suggest that understanding the factors that control diversity in the indoor environment may lead to public health recommendations for asthma prevention in the future.
Collapse
Affiliation(s)
- Karen C. Dannemiller
- Department of Chemical and Environmental Engineering, Yale University, 9 Hillhouse Ave, PO Box 208286, New Haven, CT 06520, USA
| | - Mark J. Mendell
- Indoor Air Quality Section, Environmental Health Laboratory Branch, 850 Marina Bay Parkway, MS G365/EHLB, California Department of Public Health, Richmond, CA 94804, USA
| | - Janet M. Macher
- Indoor Air Quality Section, Environmental Health Laboratory Branch, 850 Marina Bay Parkway, MS G365/EHLB, California Department of Public Health, Richmond, CA 94804, USA
| | - Kazukiyo Kumagai
- Indoor Air Quality Section, Environmental Health Laboratory Branch, 850 Marina Bay Parkway, MS G365/EHLB, California Department of Public Health, Richmond, CA 94804, USA
| | - Asa Bradman
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, UC Berkeley, 1995 University Ave., Suite 265, Berkeley, CA 94720, USA
| | - Nina Holland
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, UC Berkeley, 1995 University Ave., Suite 265, Berkeley, CA 94720, USA
| | - Kim Harley
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, UC Berkeley, 1995 University Ave., Suite 265, Berkeley, CA 94720, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, UC Berkeley, 1995 University Ave., Suite 265, Berkeley, CA 94720, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, 9 Hillhouse Ave, PO Box 208286, New Haven, CT 06520, USA
| |
Collapse
|
43
|
Adams RI, Miletto M, Taylor JW, Bruns TD. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME JOURNAL 2013; 7:1262-73. [PMID: 23426013 PMCID: PMC3695294 DOI: 10.1038/ismej.2013.28] [Citation(s) in RCA: 419] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The indoor microbiome is a complex system that is thought to depend on dispersal from the outdoor biome and the occupants' microbiome combined with selective pressures imposed by the occupants' behaviors and the building itself. We set out to determine the pattern of fungal diversity and composition in indoor air on a local scale and to identify processes behind that pattern. We surveyed airborne fungal assemblages within 1-month time periods at two seasons, with high replication, indoors and outdoors, within and across standardized residences at a university housing facility. Fungal assemblages indoors were diverse and strongly determined by dispersal from outdoors, and no fungal taxa were found as indicators of indoor air. There was a seasonal effect on the fungi found in both indoor and outdoor air, and quantitatively more fungal biomass was detected outdoors than indoors. A strong signal of isolation by distance existed in both outdoor and indoor airborne fungal assemblages, despite the small geographic scale in which this study was undertaken (<500 m). Moreover, room and occupant behavior had no detectable effect on the fungi found in indoor air. These results show that at the local level, outdoor air fungi dominate the patterning of indoor air. More broadly, they provide additional support for the growing evidence that dispersal limitation, even on small geographic scales, is a key process in structuring the often-observed distance–decay biogeographic pattern in microbial communities.
Collapse
Affiliation(s)
- Rachel I Adams
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
| | | | | | | |
Collapse
|