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Sautour M, Guilloteau A, Valot S, Basmaciyan L, Bailly E, Sixt N, Tetu J, Lafon I, Caillot D, Dalle F. Risk of fungal exposure in the homes of patients with hematologic malignancies. J Mycol Med 2024; 34:101492. [PMID: 38865808 DOI: 10.1016/j.mycmed.2024.101492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 05/23/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND Patients with hematological malignancies are at a high risk of developing invasive fungal infections (IFI) because they undergo several cycles of treatment leading to episodes of neutropenia. In addition, they alternate between hospital stays and periods spent at home. Thus, when an IFI is diagnosed during their hospital stays, it is highly challenging to identify the origin of the fungal contamination. The objective of this study was to analyze at home fungal exposure of 20 patients with leukemia by taking air and water samples in their living residence. METHODS Air was sampled in 3 rooms of each home with a portable air system impactor. Tap water was collected at 3 water distribution points of each home. For positive samples, fungi were identified by mass spectrometry or on the basis of their morphological features. RESULTS 85 % of homes revealed the presence in air of Aspergillus spp. and those belonging to the section Fumigati presented the highest concentrations and the greatest frequency of isolation. Concerning mucorales, Rhizopus spp. and Mucor spp. were isolated in air of 20 % and 5 % of dwellings, respectively. In 4 homes, more than 70 % of the fungal species identified in air were potential opportunists; these were mainly Aspergillus spp. with concentrations greater than 20 cfu/m3. The water samples revealed the presence of Fusarium in 3 dwellings, with concentrations up to 80 cfu/L. Finally, for one patient, fungal species isolated during a period of hospitalization were phenotypically similar to those isolated in samples taken at home. For a second patient, a PCR Mucorale was positive on a sample of bronchoalveolar fluid while air samples taken at his home also revealed also the presence of mucorales. CONCLUSION The presence of opportunistic fungal species in the air of all the explored homes suggests the need for strengthened preventive measures in the home of immunocompromised patients. It would be interesting to compare the fungi isolated (from patients and from their environment) by genotyping studies aimed at specifying the correspondence existing between fungal species present in the patients' homes and those responsible for IFI in the same patients.
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Affiliation(s)
- Marc Sautour
- Parasitology and Mycology Laboratory, University Hospital of Dijon, 21070 BP, Dijon 37013 CEDEX, France; UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, University Bourgogne Franche-Comté, AgroSup, Dijon, France.
| | - Adrien Guilloteau
- Hospital Hygiene and Epidemiology Unit, University Hospital of Dijon, BP, 21070, Dijon 37013 CEDEX, France
| | - Stéphane Valot
- Parasitology and Mycology Laboratory, University Hospital of Dijon, 21070 BP, Dijon 37013 CEDEX, France
| | - Louise Basmaciyan
- Parasitology and Mycology Laboratory, University Hospital of Dijon, 21070 BP, Dijon 37013 CEDEX, France; UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, University Bourgogne Franche-Comté, AgroSup, Dijon, France
| | - Eloise Bailly
- UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, University Bourgogne Franche-Comté, AgroSup, Dijon, France
| | - Nathalie Sixt
- Department of Bacteriology, University Hospital of Dijon, BP, 21070, Dijon 37013 CEDEX, France
| | - Jennifer Tetu
- Department of Bacteriology, University Hospital of Dijon, BP, 21070, Dijon 37013 CEDEX, France
| | - Ingrid Lafon
- Clinical Haematology unit, University Hospital of Dijon, BP, 21070, Dijon 37013 CEDEX, France
| | - Denis Caillot
- Clinical Haematology unit, University Hospital of Dijon, BP, 21070, Dijon 37013 CEDEX, France
| | - Frédéric Dalle
- Parasitology and Mycology Laboratory, University Hospital of Dijon, 21070 BP, Dijon 37013 CEDEX, France; UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, University Bourgogne Franche-Comté, AgroSup, Dijon, France
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2
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Minahan NT, Chen CH, Chuang YC, Tsai KH, Shen WC, Guo YL. Fungal Spore Richness and Abundance of Allergenic Taxa: Comparing a Portable Impactor and Passive Trap Indoors and Outdoors in an Urban Setting. MICROBIAL ECOLOGY 2024; 87:45. [PMID: 38393401 PMCID: PMC10891272 DOI: 10.1007/s00248-024-02358-3] [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: 11/24/2023] [Accepted: 02/02/2024] [Indexed: 02/25/2024]
Abstract
Fungal spores are common airborne allergens, and fungal richness has been implicated in allergic disease. Amplicon sequencing of environmental DNA from air samples is a promising method to estimate fungal spore richness with semi-quantification of hundreds of taxa and can be combined with quantitative PCR to derive abundance estimates. However, it remains unclear how the choice of air sampling method influences these estimates. This study compared active sampling with a portable impactor and passive sampling with a passive trap over different durations to estimate fungal spore richness and the abundance of allergenic taxa. Air sampling was conducted indoors and outdoors at 12 residences, including repeated measurements with a portable impactor and passive traps with 1-day and 7-day durations. ITS2 amplicon sequence data were transformed to spore equivalents estimated by quantitative PCR, repeated active samples were combined, and abundance-based rarefaction was performed to standardize sample coverage for estimation of genus-level richness and spore abundance. Rarefied fungal richness was similar between methods indoors but higher for passive traps with a 7-day duration outdoors. Rarefied abundance of allergenic genera was similar between methods but some genera had lower abundance for passive traps with a 1-day duration, which differed indoors and outdoors indicating stochasticity in the collection of spores on collocated samplers. This study found that similar estimates of fungal spore richness and abundance of allergenic taxa can be obtained using a portable impactor or a passive trap within one day and that increased passive sample duration provides limited additional information.
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Affiliation(s)
- Nicholas T Minahan
- Institute of Environmental and Occupational Health Sciences, National Taiwan University, Taipei, Taiwan
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Chi-Hsien Chen
- Department of Environmental and Occupational Medicine, National Taiwan University (NTU) College of Medicine and NTU Hospital, Taipei, Taiwan
| | - Yu-Chen Chuang
- Department of Environmental and Occupational Medicine, National Taiwan University (NTU) College of Medicine and NTU Hospital, Taipei, Taiwan
| | - Kun-Hsien Tsai
- Institute of Environmental and Occupational Health Sciences, National Taiwan University, Taipei, Taiwan
| | - Wei-Chiang Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Yue Leon Guo
- Institute of Environmental and Occupational Health Sciences, National Taiwan University, Taipei, Taiwan.
- Department of Environmental and Occupational Medicine, National Taiwan University (NTU) College of Medicine and NTU Hospital, Taipei, Taiwan.
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, Taiwan.
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3
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Visagie CM, Boekhout T, Theelen B, Dijksterhuis J, Yilmaz N, Seifert KA. Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov. Yeast 2023; 40:7-31. [PMID: 36168284 PMCID: PMC10108157 DOI: 10.1002/yea.3816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 01/18/2023] Open
Abstract
A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture-dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self-portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H-24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade-old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi.
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Affiliation(s)
- Cobus M Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.,Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Neriman Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.,Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Keith A Seifert
- Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada.,Department of Biology, Carleton University, Ottawa, Ontario, Canada
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Season, Vegetation Proximity and Building Age Shape the Indoor Fungal Communities’ Composition at City-Scale. J Fungi (Basel) 2022; 8:jof8101045. [PMID: 36294610 PMCID: PMC9605656 DOI: 10.3390/jof8101045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 12/04/2022] Open
Abstract
Exposure to particular microbiome compositions in the built environment can affect human health and well-being. Identifying the drivers of these indoor microbial assemblages is key to controlling the microbiota of the built environment. In the present study, we used culture and metabarcoding of the fungal Internal Transcribed Spacer ribosomal RNA region to assess whether small-scale variation in the built environment influences the diversity, composition and structure of indoor air fungal communities between a heating and an unheated season. Passive dust collectors were used to collect airborne fungi from 259 dwellings representative of three major building periods and five building environments in one city—Lausanne (Vaud, Switzerland)—over a heating and an unheated period. A homogenous population (one or two people with an average age of 75 years) inhabited the households. Geographic information systems were used to assess detailed site characteristics (altitude, proximity to forest, fields and parks, proximity to the lake, and density of buildings and roads) for each building. Our analysis indicated that season was the factor that explained most of the variation in colonies forming unit (CFU) concentration and indoor mycobiome composition, followed by the period of building construction. Fungal assemblages were more diverse during the heating season than during the unheated season. Buildings with effective insulation had distinct mycobiome compositions from those built before 1975 — regardless of whether they were constructed with pre-1945 technology and materials or 1945 — 1974 ones. The urban landscape—as a whole—was a significant predictor of cultivable Penicillium load—the closer the building was to the lake, the higher the Penicillium load—but not of fungal community composition. Nevertheless, the relative abundance of eleven fungal taxa detected by metabarcoding decreased significantly with the urbanization gradient. When urban landscape descriptors were analyzed separately, the explanatory power of proximity to vegetation in shaping fungal assemblages become significant, indicating that land cover type had an influence on fungal community structure that was obscured by the effects of building age and sampling season. In conclusion, indoor mycobiomes are strongly modulated by season, and their assemblages are shaped by the effectiveness of building insulation, but are weakly influenced by the urban landscape.
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5
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Hagiuda R, Oda H, Kawakami Y, Hirose D. Species Diversity based on Revised Systematics of Xerophilic Aspergillus section Restricti Isolated from Storage Rooms and Houses in Japan. Biocontrol Sci 2022; 27:65-80. [PMID: 35753795 DOI: 10.4265/bio.27.65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Eighty-seven strains of Aspergillus section Restricti were isolated from five storage rooms (50 strains) and 21 houses (37 strains) between 2014 and 2020. Eleven species were identified based on their morphological characteristics and molecular phylogeny using the rRNA internal transcribed spacer (ITS) region, calmodulin (CaM), β-tubulin (benA), and RNA polymerase II second largest subunit (RPB2) sequences. A. penicillioides, which was known to cause the deterioration of cultural assets, was isolated at high frequency (73%) from the surfaces of 11 cultural assets in the storage rooms; A. clavatophorus and A. magnivesiculatus, which are closely related to A. penicillioides, were also isolated frequently (45 and 64%, respectively). Five species [A. clavatophorus (42.8%), A. penicillioides (42.8%), A. magnivesiculatus (14.3%), A. reticulatus (28.6%), and A. vitricola (28.6%)] were isolated from dust on the carpets in seven houses. Five species [A. clavatophorus (33.3%), A. penicillioides (55.5%), A. magnivesiculatus (44.4%), A. restrictus (44.4%), and A. gracilis (11.1%)] were isolated from dust on the bedding in nine houses. Using the taxonomic system described by Sklenář et al. (2017), five species (A. clavatophorus, A. magnivesiculatus, A. hordei, A. reticulatus, and A. glabripes) previously identified as A. penicillioides were confirmed as new to Japan.
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Affiliation(s)
| | | | - Yuji Kawakami
- Department of Environmental Science and Education, Tokyo Kasei University
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Tello Martín ML, Lavega R, Carrasco JC, Pérez M, Pérez-Pulido AJ, Thon M, Pérez Benito E. Influence of Agaricus bisporus establishment and fungicidal treatments on casing soil metataxonomy during mushroom cultivation. BMC Genomics 2022; 23:442. [PMID: 35701764 PMCID: PMC9199190 DOI: 10.1186/s12864-022-08638-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 05/16/2022] [Indexed: 11/15/2022] Open
Abstract
The cultivation of edible mushroom is an emerging sector with a potential yet to be discovered. Unlike plants, it is a less developed agriculture where many studies are lacking to optimize the cultivation. In this work we have employed high-throughput techniques by next generation sequencing to screen the microbial structure of casing soil employed in mushroom cultivation (Agaricus bisporus) while sequencing V3-V4 of the 16S rRNA gene for bacteria and the ITS2 region of rRNA for. In addition, the microbiota dynamics and evolution (bacterial and fungal communities) in peat-based casing along the process of incubation of A. bisporus have been studied, while comparing the effect of fungicide treatment (chlorothalonil and metrafenone). Statistically significant changes in populations of bacteria and fungi were observed. Microbial composition differed significantly based on incubation day, changing radically from the original communities in the raw material to a specific microbial composition driven by the A. bisporus mycelium growth. Chlorothalonil treatment seems to delay casing colonization by A. bisporus. Proteobacteria and Bacteroidota appeared as the most dominant bacterial phyla. We observed a great change in the structure of the bacteria populations between day 0 and the following days. Fungi populations changed more gradually, with A. bisporus displacing the rest of the species as the cultivation cycle progresses. A better understanding of the microbial communities in the casing will hopefully allow us to increase the biological efficiency of the crop.
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Affiliation(s)
- Maria Luisa Tello Martín
- Mushroom Technological Research Center of La Rioja (CTICH), Ctra. Calahorra km 4, 26560, Autol, La Rioja, Spain.
| | - Rebeca Lavega
- Mushroom Technological Research Center of La Rioja (CTICH), Ctra. Calahorra km 4, 26560, Autol, La Rioja, Spain
| | - Jaime Carrasco Carrasco
- Mushroom Technological Research Center of La Rioja (CTICH), Ctra. Calahorra km 4, 26560, Autol, La Rioja, Spain.,Department of Plant Sciences, University of Oxford, SParks Rd, Oxford, OX1 3RB, UK
| | - Margarita Pérez
- Mushroom Technological Research Center of La Rioja (CTICH), Ctra. Calahorra km 4, 26560, Autol, La Rioja, Spain
| | - Antonio J Pérez-Pulido
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide (Sevilla), 41013, Sevilla, Spain
| | - Michael Thon
- Universidad de Salamanca, Instituto de Investigación en Agrobiotecnología (CIALE), Calle Río Duero 12, 37185, Villamayor, Salamanca, Spain
| | - Ernesto Pérez Benito
- Universidad de Salamanca, Instituto de Investigación en Agrobiotecnología (CIALE), Calle Río Duero 12, 37185, Villamayor, Salamanca, Spain
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7
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Pattaroni C, Macowan M, Chatzis R, Daunt C, Custovic A, Shields MD, Power UF, Grigg J, Roberts G, Ghazal P, Schwarze J, Gore M, Turner S, Bush A, Saglani S, Lloyd CM, Marsland BJ. Early life inter-kingdom interactions shape the immunological environment of the airways. MICROBIOME 2022; 10:34. [PMID: 35189979 PMCID: PMC8862481 DOI: 10.1186/s40168-021-01201-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/12/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND There is increasing evidence that the airway microbiome plays a key role in the establishment of respiratory health by interacting with the developing immune system early in life. While it has become clear that bacteria are involved in this process, there is a knowledge gap concerning the role of fungi. Moreover, the inter-kingdom interactions that influence immune development remain unknown. In this prospective exploratory human study, we aimed to determine early post-natal microbial and immunological features of the upper airways in 121 healthy newborns. RESULTS We found that the oropharynx and nasal cavity represent distinct ecological niches for bacteria and fungi. Breastfeeding correlated with changes in microbiota composition of oropharyngeal samples with the greatest impact upon the relative abundance of Streptococcus species and Candida. Host transcriptome profiling revealed that genes with the highest expression variation were immunological in nature. Multi-omics factor analysis of host and microbial data revealed unique co-variation patterns. CONCLUSION These data provide evidence of a diverse multi-kingdom microbiota linked with local immunological characteristics in the first week of life that could represent distinct trajectories for future respiratory health. TRIAL REGISTRATION NHS Health Research Authority, IRAS ID 199053. Registered 5 Oct 2016. https://www.hra.nhs.uk/planning-and-improving-research/application-summaries/research-summaries/breathing-together/ Video abstract.
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Affiliation(s)
- Céline Pattaroni
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Matthew Macowan
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Roxanne Chatzis
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Carmel Daunt
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Adnan Custovic
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Michael D. Shields
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Ultan F. Power
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Jonathan Grigg
- Centre for Child Health, Blizard Institute, Queen Mary University of London, London, UK
| | - Graham Roberts
- Human Development in Health School, University of Southampton Faculty of Medicine, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight UK
| | - Peter Ghazal
- School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Jürgen Schwarze
- Centre for Inflammation Research, Child Life and Health, The University of Edinburgh, Edinburgh, UK
| | - Mindy Gore
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
- NHS Grampian, Aberdeen, UK
| | - Andrew Bush
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Sejal Saglani
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Clare M. Lloyd
- National Heart & Lung Institute, Imperial College London, London, UK
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Madsen AM, Rasmussen PU, Frederiksen MW. Accumulation of microorganisms on work clothes of workers collecting different types of waste - A feasibility study. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 139:250-257. [PMID: 34979353 DOI: 10.1016/j.wasman.2021.12.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/01/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Electrostatic dust cloths have previously been used to study microorganisms in settled dust by placing the cloths horizontally on surfaces (called Electrostatic Dust Collectors, EDC). In this study, we investigate whether the same cloths, henceforth called 'E-Cloths', can be used to study accumulation of microorganisms and endotoxin on workers' clothes. This was studied as current methods have limitations. It was examined for waste collection workers, as their work environment is associated with elevated exposure to microorganisms and endotoxin. Each worker received a kit with a T-shirt with an attached E-Cloth on the front, a instruction letter, and a questionnaire. Workers wore the T-shirts during the next two workdays. Unaffected by waste type collected, it was possible to measure the accumulation of bacteria, fungi, and endotoxin from the work environment on the E-Cloths. Geometric mean concentration of 9 × 106 CFU bacteria/m2, 1 × 107 CFU fungi/m2, and 4 × 104 endotoxin units/m2 were found. In total, 100 different bacterial and 25 fungal species were found. The genus Bacillus (with 18 species) and Brevibacterium aurantiacum were among the dominating bacteria. For fungi, Penicillium brevicompactum, P. commune, Penicillium italicum, and Aspergillus niger were most often found. Importantly, mainly environmental bacteria and fungi had accumulated on the E-Cloths and only few skin-related bacterial species were present, showing that accumulation had happened from the work exposure and not workers' skin. In conclusion, the T-shirts with an E-Cloth can be used as a self-administered method for measurement of accumulation of microorganisms and endotoxin from the work environment on waste collection workers' clothes.
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Affiliation(s)
- Anne Mette Madsen
- The National Research Centre for the Working Environment Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark.
| | - Pil Uthaug Rasmussen
- The National Research Centre for the Working Environment Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
| | - Margit W Frederiksen
- The National Research Centre for the Working Environment Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
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9
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Santini A, Migliorini D. Invasive Alien Plant Pathogens: The Need of New Detection Methods. Methods Mol Biol 2022; 2536:111-118. [PMID: 35819601 DOI: 10.1007/978-1-0716-2517-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Invasive alien species are a major threat to natural and anthropogenic ecosystems and to the economy. Many invasive fungal species have severely impacted ecology and human lifestyle in the past. Most of them express a pathogenic lifestyle following introduction into a new region and hosts. They are usually cryptic during the introduction phase and hard to be identified, classified, and monitored.The increasing number of new alien pests coincide with the rapid increase in the volume and diversity of intercontinental trade in plants for planting, underlying the need to reduce the risk of their introduction with the development of molecular-based, inexpensive, rapid, accurate, and reliable methods that can identify and intercept plant pathogens even before symptoms occur in the new environment of diffusion. Applicative aerobiology, for instance, represents a challenging research line for the implementation of pest detection protocols during the early stage of fungal introduction, being capable to target aerial dispersed propagules.In addition to this, new metabarcoding protocols based on an innovative multigene approach, although not yet tested on fungi, are able to provide an output with very high taxonomic resolution and are likely to be considered in the next-future biosurveillance of invasive fungal pathogens.
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Affiliation(s)
- Alberto Santini
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Sesto Fiorentino, Florence, Italy
| | - Duccio Migliorini
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Sesto Fiorentino, Florence, Italy.
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10
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Anslan S, Mikryukov V, Armolaitis K, Ankuda J, Lazdina D, Makovskis K, Vesterdal L, Schmidt IK, Tedersoo L. Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms. PeerJ 2021; 9:e12254. [PMID: 34703674 PMCID: PMC8491618 DOI: 10.7717/peerj.12254] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/14/2021] [Indexed: 01/04/2023] Open
Abstract
With the developments in DNA nanoball sequencing technologies and the emergence of new platforms, there is an increasing interest in their performance in comparison with the widely used sequencing-by-synthesis methods. Here, we test the consistency of metabarcoding results from DNBSEQ-G400RS (DNA nanoball sequencing platform by MGI-Tech) and NovaSeq 6000 (sequencing-by-synthesis platform by Illumina) platforms using technical replicates of DNA libraries that consist of COI gene amplicons from 120 soil DNA samples. By subjecting raw sequencing data from both platforms to a uniform bioinformatics processing, we found that the proportion of high-quality reads passing through the filtering steps was similar in both datasets. Per-sample operational taxonomic unit (OTU) and amplicon sequence variant (ASV) richness patterns were highly correlated, but sequencing data from DNBSEQ-G400RS harbored a higher number of OTUs. This may be related to the lower dominance of most common OTUs in DNBSEQ data set (thus revealing higher richness by detecting rare taxa) and/or to a lower effective read quality leading to generation of spurious OTUs. However, there was no statistical difference in the ASV and post-clustered ASV richness between platforms, suggesting that additional denoising step in the ASV workflow had effectively removed the 'noisy' reads. Both OTU-based and ASV-based composition were strongly correlated between the sequencing platforms, with essentially interchangeable results. Therefore, we conclude that DNBSEQ-G400RS and NovaSeq 6000 are both equally efficient high-throughput sequencing platforms to be utilized in studies aiming to apply the metabarcoding approach, but the main benefit of the former is related to lower sequencing cost.
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Affiliation(s)
- Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Tartumaa, Estonia
- Mycology and Microbiology Center, University of Tartu, Tartu, Tartumaa, Estonia
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Tartumaa, Estonia
- Mycology and Microbiology Center, University of Tartu, Tartu, Tartumaa, Estonia
| | - Kęstutis Armolaitis
- Department of Ecology, Institute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Kaunas, Lithuania
| | - Jelena Ankuda
- Department of Ecology, Institute of Forestry of Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Kaunas, Lithuania
| | - Dagnija Lazdina
- Latvian State Forest Research Institute SILAVA, Riga, Latvia
| | | | - Lars Vesterdal
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Inger Kappel Schmidt
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Tartumaa, Estonia
- Mycology and Microbiology Center, University of Tartu, Tartu, Tartumaa, Estonia
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11
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Cox J, Stone T, Ryan P, Burkle J, Jandarov R, Mendell MJ, Adams RI, Niemeier-Walsh C, Reponen T. Associations of observed home dampness and mold with the fungal and bacterial dust microbiomes. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:491-500. [PMID: 33647083 DOI: 10.1039/d0em00505c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The objective of this analysis was to examine and compare quantitative metrics of observed dampness and mold, including visible mold and moisture damage, and fungal and bacterial microbiomes. In-home visits were conducted at age 7 for children enrolled in the Cincinnati Childhood Allergy and Air Pollution Study. Trained study staff evaluated the primary residence and measured total areas of visible moisture and mold damage in the home. Floor dust was collected and archived. Archived dust samples collected from each home (n = 178) were extracted and analyzed using bacterial (16S rRNA gene) and fungal (internal transcribed spacer region) sequencing. Fungi were also divided into moisture requirement categories of xerophiles, mesophiles, and hydrophiles. Data analyses used Spearman's correlation, Kruskal-Wallis, Permanova, DESeq, and negative binomial regression models. Comparing high moisture or mold damage to no damage, five fungal species and two bacterial species had higher concentrations (absolute abundance) and six fungal species and three bacterial species had lower concentrations. Hydrophilic and mesophilic fungi showed significant dose-related increases with increasing moisture damage and mold damage, respectively. When comparing alpha or beta diversity of fungi and bacteria across mold and moisture damage levels, no significant associations or differences were found. Mold and moisture damage did not affect diversity of fungal and bacterial microbiomes. Instead, both kinds of damage were associated with changes in species composition of both bacterial and fungal microbiomes, indicating that fungal and bacterial communities in the home might be influenced by one another as well as by mold or moisture in the home.
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Affiliation(s)
- Jennie Cox
- Department of Environmental Health, University of Cincinnati, P.O. Box 670056, Cincinnati, OH, USA.
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12
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Niemeier-Walsh C, Ryan PH, Meller J, Ollberding NJ, Adhikari A, Indugula R, Reponen T. The mycobiomes and bacteriomes of sputum, saliva, and home dust. INDOOR AIR 2021; 31:357-368. [PMID: 32969526 DOI: 10.1111/ina.12750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Respiratory microbiome is an understudied area of research compared to other microbiomes of the human body. The respiratory tract is exposed to an array of environmental pollutants, including microbes. Yet, we know very little about the relationship between environmental and respiratory microbiome. The primary aim of our study was to compare the mycobiomes and bacteriomes between three sample types from the same participants, including home dust, saliva, and sputum. Samples were collected from 40 adolescents in a longitudinal cohort. We analyzed the samples using 16s bacterial rDNA and ITS fungal rDNA gene sequencing, as well as quantitative PCR with universal fungal and bacterial primers. Results showed that home dust had the greatest alpha diversity between the three sample types for both bacteria and fungi. Dust had the highest total fungal load and the lowest total bacterial load. Sputum had greater bacterial diversity than saliva, but saliva had greater fungal diversity than sputum. The distribution of major bacterial phyla differed between all sample types. However, the distribution of major fungal classes differed only between sputum and saliva. Future research should examine the biological significance of the taxa found in each sample type based on microbial ecology and associations with health effects.
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Affiliation(s)
| | - Patrick H Ryan
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jarek Meller
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Nicholas J Ollberding
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Atin Adhikari
- Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, GA, USA
| | - Reshmi Indugula
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Tiina Reponen
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
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13
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Carrasco J, García‐Delgado C, Lavega R, Tello ML, De Toro M, Barba‐Vicente V, Rodríguez‐Cruz MS, Sánchez‐Martín MJ, Pérez M, Preston GM. Holistic assessment of the microbiome dynamics in the substrates used for commercial champignon (Agaricus bisporus) cultivation. Microb Biotechnol 2020; 13:1933-1947. [PMID: 32716608 PMCID: PMC7533343 DOI: 10.1111/1751-7915.13639] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022] Open
Abstract
Microorganisms strongly influence and are required to generate the selective substrate that provides nutrients and support for fungal growth, and ultimately to induce mushroom fructification under controlled environmental conditions. In this work, the fungal and bacterial microbiota living in the different substrates employed in a commercial crop (compost phase I, II and III, flush 1 and 2, and casing material on day 1, 6 and 8 after compost casing and during flush 1 and 2) have been characterized along the different stages of cultivation by metataxonomic analysis (16S rRNA and ITS2), analysis of phospholipid fatty acid content (PLFAs) and RT-qPCR. Additionally, laccase activity and the content of lignin and complex carbohydrates in compost and casing have been quantified. The bacterial diversity in compost and casing increased throughout the crop cycle boosted by the connection of both substrates. As reflected by the PLFAs, the total living bacterial biomass appears to be negatively correlated with the mycelium of the crop. Agaricus bisporus was the dominant fungal species in colonized substrates, displacing the pre-eminent Ascomycota, accompanied by a sustained increase in laccase activity, which is considered to be a major product of protein synthesis during the mycelial growth of champignon. From phase II onwards, the metabolic machinery of the fungal crop degrades lignin and carbohydrates in compost, while these components are hardly degraded in casing, which reflects the minor role of the casing for nourishing the crop. The techniques employed in this study provide a holistic and detailed characterization of the changing microbial composition in commercial champignon substrates. The knowledge generated will contribute to improve compost formulations (selection of base materials) and accelerate compost production, for instance, through biotechnological interventions in the form of tailored biostimulants and to design environmentally sustainable bio-based casing materials.
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Affiliation(s)
- Jaime Carrasco
- Department of Plant SciencesUniversity of OxfordS Parks RdOxfordOX1 3RBUK
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH)AutolSpain
| | - Carlos García‐Delgado
- Departamento de Geología y GeoquímicaUniversidad Autónoma de MadridMadridSpain
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA‐CSIC)SalamancaSpain
| | - Rebeca Lavega
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH)AutolSpain
| | - María L. Tello
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH)AutolSpain
| | - María De Toro
- Plataforma de Genómica y BioinformáticaCentro de Investigación Biomédica de La Rioja (CIBIR)LogroñoSpain
| | - Víctor Barba‐Vicente
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA‐CSIC)SalamancaSpain
| | | | | | - Margarita Pérez
- Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH)AutolSpain
| | - Gail M. Preston
- Department of Plant SciencesUniversity of OxfordS Parks RdOxfordOX1 3RBUK
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14
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Banchi E, Ametrano CG, Tordoni E, Stanković D, Ongaro S, Tretiach M, Pallavicini A, Muggia L. Environmental DNA assessment of airborne plant and fungal seasonal diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:140249. [PMID: 32806340 DOI: 10.1016/j.scitotenv.2020.140249] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/25/2020] [Accepted: 06/14/2020] [Indexed: 05/06/2023]
Abstract
Environmental DNA (eDNA) metabarcoding and metagenomics analyses can improve taxonomic resolution in biodiversity studies. Only recently, these techniques have been applied in aerobiology, to target bacteria, fungi and plants in airborne samples. Here, we present a nine-month aerobiological study applying eDNA metabarcoding in which we analyzed simultaneously airborne diversity and variation of fungi and plants across five locations in North and Central Italy. We correlated species composition with the ecological characteristics of the sites and the seasons. The most abundant taxa among all sites and seasons were the fungal genera Cladosporium, Alternaria, and Epicoccum and the plant genera Brassica, Corylus, Cupressus and Linum, the latter being much more variable among sites. PERMANOVA and indicator species analyses showed that the plant diversity from air samples is significantly correlated with seasons, while that of fungi varied according to the interaction between seasons and sites. The results consolidate the performance of a new eDNA metabarcoding pipeline for the simultaneous amplification and analysis of airborne plant and fungal particles. They also highlight the promising complementarity of this approach with more traditional biomonitoring frameworks and routine reports of air quality provided by environmental agencies.
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Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy; National Institute of Oceanography and Applied Geophysics - OGS, via Piccard 54, I-34151 Trieste, Italy
| | - Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - Enrico Tordoni
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - David Stanković
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy; Marine Biology Station, National Institute of Biology, Fornače 41, SLO-6330 Piran, Slovenia
| | - Silvia Ongaro
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - Mauro Tretiach
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy; National Institute of Oceanography and Applied Geophysics - OGS, via Piccard 54, I-34151 Trieste, Italy.
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, I-34127 Trieste, Italy.
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15
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Vandenborght LE, Enaud R, Urien C, Coron N, Girodet PO, Ferreira S, Berger P, Delhaes L. Type 2-high asthma is associated with a specific indoor mycobiome and microbiome. J Allergy Clin Immunol 2020; 147:1296-1305.e6. [PMID: 32926879 PMCID: PMC7486598 DOI: 10.1016/j.jaci.2020.08.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022]
Abstract
Background The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters. Objective The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA). Methods A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during “stable” or pulmonary “exacerbation” periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes. Results Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The β-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation. Conclusion These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma.
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Affiliation(s)
- Louise-Eva Vandenborght
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Microbiota Team, Research and Development Department, GenoScreen, Lille, France
| | - Raphaël Enaud
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Charlotte Urien
- Microbiota Team, Research and Development Department, GenoScreen, Lille, France
| | - Noémie Coron
- Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Pierre-Olivier Girodet
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Stéphanie Ferreira
- Microbiota Team, Research and Development Department, GenoScreen, Lille, France
| | - Patrick Berger
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Laurence Delhaes
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France.
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16
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Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France. Microorganisms 2020; 8:microorganisms8030341. [PMID: 32121209 PMCID: PMC7143953 DOI: 10.3390/microorganisms8030341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 02/25/2020] [Indexed: 12/28/2022] Open
Abstract
The indoor microbial community is a mixture of microorganisms resulting from outdoor ecosystems that seed the built environment. However, the biogeography of the indoor microbial community is still inadequately studied. Dust from more than 3000 dwellings across France was analyzed by qPCR using 17 targets: 10 molds, 3 bacteria groups, and 4 mites. Thus, the first spatial description of the main indoor microbial allergens on the French territory, in relation with biogeographical factors influencing the distribution of microorganisms, was realized in this study. Ten microorganisms out of 17 exhibited increasing abundance profiles across the country: Five microorganisms (Dermatophagoïdes pteronyssinus, Dermatophagoïdes spp., Streptomyces spp., Cladosporium sphaerospermum, Epicoccum nigrum) from northeast to southwest, two (Cryptococcus spp., Alternaria alternata) from northwest to southeast, Mycobacteria from east to west, Aspergillus fumigatus from south to north, and Penicillium chrysogenum from south to northeast. These geographical patterns were partly linked to climate and land cover. Multivariate analysis showed that composition of communities seemed to depend on landscapes, with species related to closed and rather cold and humid landscapes (forests, located in the northeast) and others to more open, hot, and dry landscapes (herbaceous and coastal regions, located in the west). This study highlights the importance of geographical location and outdoor factors that shape communities. In order to study the effect of microorganisms on human health (allergic diseases in particular), it is important to identify biogeographic factors that structure microbial communities on large spatial scales and to quantify the exposure with quantitative tools, such as the multi-qPCR approach.
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17
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Simons A, Bertron A, Aubert JE, Roux C, Roques C. Characterization of the microbiome associated with in situ earthen materials. ENVIRONMENTAL MICROBIOME 2020; 15:4. [PMID: 33902730 PMCID: PMC8066951 DOI: 10.1186/s40793-019-0350-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/07/2019] [Indexed: 06/12/2023]
Abstract
BACKGROUND The current increase in public awareness of environmental risks is giving rise to a growth of interest in the microbiological safety of buildings. In particular, microbial proliferation on construction materials can be responsible for the degradation of indoor air quality that can increase health-risk to occupants. Raw earth materials are still widely used throughout the world and, in some cases, are linked to heritage habitats, as in the southwest of France. Moreover, these building materials are currently the subject of renewed interest for ecological and economic reasons. However, the microbial status of earthen materials raises major concerns: could the microbiome associated with such natural materials cause disease in building occupants? Very few analyses have been performed on the microbial communities present on these supports. Characterizing the raw earth material microbiome is also important for a better evaluation and understanding of the susceptibility of such materials to microbial development. This study presents the distribution of in situ bacterial and fungal communities on different raw earth materials used in construction. Various buildings were sampled in France and the microbial communities present were characterized by amplicon high-throughput sequencing (bacterial 16S rRNA gene and fungal ITS1 region). Bacterial culture isolates were identified at the species level by MALDI-TOF mass spectrometry. RESULTS The major fungal and bacterial genera identified were mainly associated with conventional outdoor and indoor environmental communities, and no specific harmful bacterial species were detected on earthen materials. However, contrary to expectations, few human-associated genera were detected in dwellings. We found lower microbial alpha-diversity in earthen material than is usually found in soil, suggesting a loss of diversity during the use of these materials in buildings. Interestingly enough, the main features influencing microbial communities were building history and room use, rather than material composition. CONCLUSIONS These results constitute a first in-depth analysis of microbial communities present on earthen materials in situ and may be considered as a first referential to investigate microbial communities on such materials according to environmental conditions and their potential health impact. The bacterial and fungal flora detected were similar to those found in conventional habitats and are thought to be mainly impacted by specific events in the building's life, such as water damage.
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Affiliation(s)
- Alexis Simons
- Laboratoire de Génie Chimique, Université de Toulouse, UMR 5503 UPS - CNRS - INPT, Toulouse, France.
- Laboratoire Matériaux et Durabilité des Constructions, Université de Toulouse, UPS - INSA, Toulouse, France.
| | - Alexandra Bertron
- Laboratoire Matériaux et Durabilité des Constructions, Université de Toulouse, UPS - INSA, Toulouse, France
| | - Jean-Emmanuel Aubert
- Laboratoire Matériaux et Durabilité des Constructions, Université de Toulouse, UPS - INSA, Toulouse, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UMR 5546 UPS - CNRS, Castanet-Tolosan, France
| | - Christine Roques
- Laboratoire de Génie Chimique, Université de Toulouse, UMR 5503 UPS - CNRS - INPT, Toulouse, France
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18
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Hooks KB, O'Malley MA. Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research. J Eukaryot Microbiol 2019; 67:279-295. [PMID: 31583780 PMCID: PMC7154641 DOI: 10.1111/jeu.12766] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/11/2019] [Accepted: 09/25/2019] [Indexed: 12/25/2022]
Abstract
Most discussions of human microbiome research have focused on bacterial investigations and findings. Our target is to understand how human eukaryotic microbiome research is developing, its potential distinctiveness, and how problems can be addressed. We start with an overview of the entire eukaryotic microbiome literature (578 papers), show tendencies in the human‐based microbiome literature, and then compare the eukaryotic field to more developed human bacterial microbiome research. We are particularly concerned with problems of interpretation that are already apparent in human bacterial microbiome research (e.g. disease causality, probiotic interventions, evolutionary claims). We show where each field converges and diverges, and what this might mean for progress in human eukaryotic microbiome research. Our analysis then makes constructive suggestions for the future of the field.
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Affiliation(s)
- Katarzyna B Hooks
- CBiB, University of Bordeaux, Bordeaux, 33076, France.,CNRS/LaBRI, University of Bordeaux, Talence, 33405, France
| | - Maureen A O'Malley
- School of History and Philosophy of Science, University of Sydney, Sydney, NSW, 2006, Australia
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19
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Carrasco J, Tello ML, de Toro M, Tkacz A, Poole P, Pérez-Clavijo M, Preston G. Casing microbiome dynamics during button mushroom cultivation: implications for dry and wet bubble diseases. MICROBIOLOGY-SGM 2019; 165:611-624. [PMID: 30994437 DOI: 10.1099/mic.0.000792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The casing material required in mushroom cultivation presents a very rich ecological niche, which is inhabited by a diverse population of bacteria and fungi. In this work three different casing materials, blonde peat, black peat and a 50 : 50 mixture of both, were compared for their capacity to show a natural suppressive response against dry bubble, Lecanicillium fungicola (Preuss) Zare and Gams, and wet bubble, Mycogone perniciosa (Magnus) Delacroix. The highest mushroom production was collected from crops cultivated using the mixed casing and black peat, which were not significantly different in yield. However, artificial infection with mycoparasites resulted in similar yield losses irrespective of the material used, indicating that the casing materials do not confer advantages in disease suppression. The composition of the microbiome of the 50 : 50 casing mixture along the crop cycle and the compost and basidiomes was evaluated through next-generation sequencing (NGS) of the V3-V4 region of the bacterial 16S rRNA gene and the fungal ITS2 region. Once colonized by Agaricus bisporus, the bacterial diversity of the casing microbiome increased and the fungal diversity drastically decreased. From then on, the composition of the casing microbiome remained relatively stable. Analysis of the composition of the bacterial microbiome in basidiomes indicated that it is highly influenced by the casing microbiota. Notably, L. fungicola was consistently detected in uninoculated control samples of compost and casing using NGS, even in asymptomatic crops. This suggests that the naturally established casing microbiota was able to help to suppress disease development when inoculum levels were low, but was not effective in suppressing high pressure from artificially introduced fungal inoculum. Determination of the composition of the casing microbiome paves the way for the development of synthetic casing communities that can be used to investigate the role of specific components of the casing microbiota in mushroom production and disease control.
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Affiliation(s)
- Jaime Carrasco
- 2Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH), Autol, Spain.,1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1, UK
| | - Maria Luisa Tello
- 2Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH), Autol, Spain
| | - Maria de Toro
- 3Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - Andrzej Tkacz
- 1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1, UK
| | - Philip Poole
- 1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1, UK
| | | | - Gail Preston
- 1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1, UK
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20
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Bellanger AP, Reboux G, Rouzet A, Barrera C, Rocchi S, Scherer E, Millon L. Hypersensitivity pneumonitis: A new strategy for serodiagnosis and environmental surveys. Respir Med 2019; 150:101-106. [PMID: 30961934 DOI: 10.1016/j.rmed.2019.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 01/08/2023]
Abstract
We propose a strategy for serodiagnosis of hypersensitivity pneumonitis (HP): 1) question patients about their private or occupational activity, or visit him on site; 2) select panels of six somatic specific antigens appropriate for each type of exposure; 3) and use ELISA to test concomitantly two recombinant antigens highly specific to Farmer's lung, Metalworking-fluid HP, and for Bird fancier's lung. The serodiagnosis provides an immunological argument that may complete radiological, functional lung exploration and clinical features; 4) If the serodiagnosis is negative but the suspicion of HP is strong, a microbial analysis of the patient's specific exposure is conducted; 5) "A la carte" antigens are produced from the microorganisms isolated in the patient's environment sample and tested; 6) Finally, the patient may be asked to undergo a specific inhalation challenge with the offending antigens in a safety cabin, or to avoid his usual environment for a few days.
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Affiliation(s)
- Anne-Pauline Bellanger
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Gabriel Reboux
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France.
| | - Adeline Rouzet
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Coralie Barrera
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Steffi Rocchi
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Emeline Scherer
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
| | - Laurence Millon
- Department of Parasitology Mycology, University Hospital of Besançon, UMR/CNRS 6249 Chrono-Environnement Research Team, University of Bourgogne- Franche-Comté, France
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21
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Reboux G, Rocchi S, Laboissière A, Ammari H, Bochaton M, Gardin G, Rame JM, Millon L. Survey of 1012 moldy dwellings by culture fungal analysis: Threshold proposal for asthmatic patient management. INDOOR AIR 2019; 29:5-16. [PMID: 30368912 DOI: 10.1111/ina.12516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 09/12/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
Different countries have tried to define guidelines to quantify what levels of fungi are considered as inappropriate for housing. This retrospective study analyzes indoor fungi by cultures of airborne samples from 1012 dwellings. Altogether, 908 patients suffering from rhinitis, conjunctivitis, and asthma were compared to 104 controls free of allergies. Portuguese decree law no 118/2013 (PDL118), ANSES (a French environmental and health agency) recommendations, and health regulations of Besançon University Hospital were applied to determine the rates of non-conforming dwellings, which were respectively 55.2%, 5.2%, and 19%. Environmental microbiological results and medical data were compared. The whole number of colonies per cubic meter of air was correlated with asthma (P < 0.001) and rhinitis (P = 0.002). Sixty-seven genera and species were detected in bedrooms. Asthma was correlated to Aspergillus versicolor (P = 0.004) and Cladosporium spp. (P = 0.02). Thresholds of 300 cfu/m3 for A. versicolor or 495 cfu/m3 for Cladosporium spp. are able to discriminate 90% of the asthmatic dwellings. We propose a new protocol to obtain an optimal cost for indoor fungi surveys, excluding surface analyses, and a new guideline to interpret the results based on >1000 cfu/m3 of whole colonies and/or above threshold levels for A. versicolor or Cladosporium spp.
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Affiliation(s)
- Gabriel Reboux
- University of Bourgogne-Franche-Comté, Besançon, France
- Jean Minjoz University Hospital, Besançon, France
| | - Steffi Rocchi
- University of Bourgogne-Franche-Comté, Besançon, France
- Jean Minjoz University Hospital, Besançon, France
| | | | - Habiba Ammari
- Réseaux d'Allergologie de Franche-Comté (RAFT), Besançon, France
| | | | | | - Jean-Marc Rame
- Réseaux d'Allergologie de Franche-Comté (RAFT), Besançon, France
| | - Laurence Millon
- University of Bourgogne-Franche-Comté, Besançon, France
- Jean Minjoz University Hospital, Besançon, France
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22
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Lamb PD, Hunter E, Pinnegar JK, Creer S, Davies RG, Taylor MI. How quantitative is metabarcoding: A meta-analytical approach. Mol Ecol 2018; 28:420-430. [PMID: 30408260 PMCID: PMC7379500 DOI: 10.1111/mec.14920] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Abstract
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
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Affiliation(s)
- Philip D Lamb
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ewan Hunter
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - John K Pinnegar
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - Simon Creer
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Richard G Davies
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
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23
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Unterwurzacher V, Pogner C, Berger H, Strauss J, Strauss-Goller S, Gorfer M. Validation of a quantitative PCR based detection system for indoor mold exposure assessment in bioaerosols. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2018; 20:1454-1468. [PMID: 30225499 DOI: 10.1039/c8em00253c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Determination and assessment of airborne fungal particles is complex and results of different sampling and analytical strategies are hard to compare due to limitations of each of the techniques. Here, an indoor mold detection system based on quantitative polymerase chain reaction (qPCR) is described and validated for its reliability and stability to identify airborne fungal particles collected. Data obtained from testing the system with fungal DNA, spore suspensions and bioaerosols indicated a need for spiking and normalization of measurements due to material loss and assay specific bias. Considering the loss of material during sample processing, detection limits defined for suspensions of Tritirachium oryzae spores were roughly 18 spores per sample. Detection of fungal spore mixtures nebulized under controlled conditions in a bioaerosol chamber showed generally 2-3 times higher normalized values measured with the molecular system compared to cultivation. Data obtained from a mold infested indoor sampling site and its corresponding outdoor reference measurement showed good correlations between qPCR and high-throughput sequencing (rho = 0.83, p < 0.01), if Cladosporium species were excluded. Taking necessary data normalization into account, the described qPCR detection system shows great potential to complement commonly used culture based approaches with the aim to improve the precision of indoor mold assessments. In contrast to already available qPCR assays that detect certain molds on a species level, this system covers a broad range of relevant fungal communities, serving as a promising alternative to high-throughput sequencing to identify indoor molds.
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Affiliation(s)
- Verena Unterwurzacher
- Center for Health and Bioresources, Austrian Institute of Technology - AIT, Tulln, Austria.
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24
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Abstract
Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes. Further morphological study and phylogenetic analyses using sequences of ITS, β-tubulin (BenA), calmodulin (CaM), RNA polymerase II second largest subunit (RPB2), DNA topoisomerase 1 (TOP1), and a pre-mRNA processing protein homolog (TSR1) confirmed the isolation of seven species of subgenus Polypaecilum, including five novel species: A. baarnensis, A. keratitidis, A. kalimae sp. nov., A. noonimiae sp. nov., A. thailandensis sp. nov., A. waynelawii sp. nov., and A. whitfieldii sp. nov. Pyrosequencing detected six of the seven species isolated from house dust, as well as one additional species absent from the cultures isolated, and three clades representing potentially undescribed species. Species were typically found in house dust from subtropical and tropical climates, often in close proximity to the ocean or sea. The presence of subgenus Polypaecilum, a recently described clade of xerophilic/xerotolerant, halotolerant/halophilic, and potentially zoopathogenic species, within the built environment is noteworthy.
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Affiliation(s)
- J.B. Tanney
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - C.M. Visagie
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
- Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood, 0121 Pretoria, South Africa
| | - N. Yilmaz
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
| | - K.A. Seifert
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
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