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Popovic D, Kulas J, Tucovic D, Popov Aleksandrov A, Glamoclija J, Sokovic Bajic S, Tolinacki M, Golic N, Mirkov I. Lung microbiota changes during pulmonary Aspergillus fumigatus infection in rats. Microbes Infect 2023; 25:105186. [PMID: 37479024 DOI: 10.1016/j.micinf.2023.105186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Since the realization that the lungs are not sterile but are normally inhabited by various bacterial species, studies have been conducted to define healthy lung microbiota and to investigate whether it changes during lung diseases, infections, and inflammation. Using next-generation sequencing, we investigated bacterial microbiota from whole lungs in two rat strains (previously shown to differ in gut microbiota composition) in a healthy state and during pulmonary infection caused by the opportunistic fungus Aspergillus fumigatus. No differences in alpha diversity indices and microbial composition between DA and AO rats before infection were noted. Fungal infection caused dysbiosis in both rat strains, characterized by increased alpha diversity indices and unchanged beta diversity. The relative abundance of genera and species was increased in DA but decreased in AO rats during infection. Changes in lung microbiota coincided with inflammation (in both rat strains) and oxidative stress (in DA rats). Disparate response of lung microbiota in DA and AO rats to pulmonary fungal infection might render these two rat strains differentially susceptible to a subsequent inflammatory insult.
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Affiliation(s)
- Dusanka Popovic
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia
| | - Jelena Kulas
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia
| | - Dina Tucovic
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia
| | - Aleksandra Popov Aleksandrov
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia
| | - Jasmina Glamoclija
- Mycology Laboratory, Department Plant Physiology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000 Belgrade, Serbia
| | - Svetlana Sokovic Bajic
- Group for Probiotics and Microbiota-host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Maja Tolinacki
- Group for Probiotics and Microbiota-host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Natasa Golic
- Group for Probiotics and Microbiota-host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 444a Vojvode Stepe, Belgrade, Serbia
| | - Ivana Mirkov
- Immunotoxicology Group, Department of Ecology, Institute for Biological Research "Sinisa Stankovic", National Institute of the Republic of Serbia, University of Belgrade, 142 Bulevar Despota Stefana, 11000, Belgrade, Serbia.
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Zhang Y, Ning H, Zheng W, Liu J, Li F, Chen J. Lung microbiome in children with hematological malignancies and lower respiratory tract infections. Front Oncol 2022; 12:932709. [PMID: 36212487 PMCID: PMC9533145 DOI: 10.3389/fonc.2022.932709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/25/2022] [Indexed: 11/22/2022] Open
Abstract
Background Respiratory infectious complications remain a major cause of morbidity and mortality in children with hematological malignancies. Knowledge regarding the lung microbiome in aforementioned children is limited. Methods A prospective cohort was conducted, enrolling 16 children with hematological malignancies complicated with moderate-to-severe lower respiratory tract infections (LRTIs) versus 21 LRTI children with age, gender, weight, and infection severity matched, with no underlying malignancies, to evaluate the lung microbiome from bronchoalveolar lavage fluid samples in different groups. Results The lung microbiome from children with hematological malignancies and LRTIs showed obviously decreased α and β diversity; increased microbial function in infectious disease:bacteria/parasite; drug resistance:antimicrobial and human pathogenesis than the control group; a significantly reduced proportion of Firmicutes, Bacteroidota, Actinobacteriota; increased Proteobacteria at the phylum level; and distinctly elevated Parabacteroides, Klebsiella, Grimontia, Escherichia_Shigella, unclassified_Enterobacteriaceae at the genus level than the control group. Furthermore, it was revealed that α diversity (Shannon), β diversity (Bray-Curtis dissimilarity), Proteobacteria at the phylum level, and unclassified_Enterobacteriaceae and Escherichia_Shigella at the genus level were significantly negatively associated with hospitalization course whereas Firmicutes at the phylum level was established positively correlated with the hospitalization course. Conclusions Children with hematological malignancies and LRTIs showed obviously decreased α and β diversity, significantly increased function in infectious disease pathogenesis, antimicrobial drug resistance, and unfavorable environment tolerance. Moreover, α diversity (Shannon), β diversity (Bray-Curtis dissimilarity), and Proteobacteria may be used as negative correlated predictors for hospitalization course in these children whereas Firmicutes may be utilized as a positive correlated predictor.
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Affiliation(s)
- Yun Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Haonan Ning
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Wenyu Zheng
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Jing Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fuhai Li
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Junfei Chen
- Department of Pediatric Surgery, Qilu Hospital of Shandong University, Jinan, China
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Asai N, Motojima S, Ohkuni Y, Matsunuma R, Nakashita T, Kaneko N, Mikamo H. Pathophysiological mechanism of non-HIV Pneumocystis jirovecii pneumonia. Respir Investig 2022; 60:522-530. [PMID: 35501264 DOI: 10.1016/j.resinv.2022.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/18/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
While Pneumocystis jirovecii pneumonia (PCP) can occur in immunocompromised patients with HIV infection, the prognosis of non-HIV PCP is still poor, showing a high mortality rate of 30%-75%. The pathophysiological mechanism of non-HIV PCP is quite different from that of HIV-PCP. Aging, underlying disease, dysbiotic gut microbiome, and Th1 predominance, leads to macrophagic polarization shifting from M2 to M1. These cause dysregulation in the host immunity against P. jirovecii, resulting in severe lung injury and a high mortality rate among non-HIV PCP patients. This review describes poor prognostic factors, an issue of predictive values used for general pneumonia practice, and new aspects, including the dysbiosis of the gut microbiome and macrophagic polarization in the treatment of non-HIV PCP.
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Affiliation(s)
- Nobuhiro Asai
- Department of Clinical Infectious Diseases, Aichi Medical University, Nagakute, Aichi, Japan; Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shinji Motojima
- Department of Rheumatology & Allergy, Shonan Fujisawa Tokushukai Hospital, Fujisawa, Kanagawa, Japan
| | - Yoshihiro Ohkuni
- Department of Pulmonology, Kameda Medical Center, Kamogawa, Chiba, Japan
| | - Ryo Matsunuma
- Department of Pulmonology, Kameda Medical Center, Kamogawa, Chiba, Japan
| | - Tamao Nakashita
- Department of Rheumatology & Allergy, Shonan Fujisawa Tokushukai Hospital, Fujisawa, Kanagawa, Japan
| | - Norihiro Kaneko
- Department of Pulmonology, Kameda Medical Center, Kamogawa, Chiba, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University, Nagakute, Aichi, Japan.
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d'Enfert C, Kaune AK, Alaban LR, Chakraborty S, Cole N, Delavy M, Kosmala D, Marsaux B, Fróis-Martins R, Morelli M, Rosati D, Valentine M, Xie Z, Emritloll Y, Warn PA, Bequet F, Bougnoux ME, Bornes S, Gresnigt MS, Hube B, Jacobsen ID, Legrand M, Leibundgut-Landmann S, Manichanh C, Munro CA, Netea MG, Queiroz K, Roget K, Thomas V, Thoral C, Van den Abbeele P, Walker AW, Brown AJP. The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives. FEMS Microbiol Rev 2021; 45:fuaa060. [PMID: 33232448 PMCID: PMC8100220 DOI: 10.1093/femsre/fuaa060] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.
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Affiliation(s)
- Christophe d'Enfert
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Ann-Kristin Kaune
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Leovigildo-Rey Alaban
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Sayoni Chakraborty
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany
| | - Nathaniel Cole
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Margot Delavy
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Daria Kosmala
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Benoît Marsaux
- ProDigest BV, Technologiepark 94, B-9052 Gent, Belgium
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links, 9000 Ghent, Belgium
| | - Ricardo Fróis-Martins
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Moran Morelli
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Diletta Rosati
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Marisa Valentine
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Zixuan Xie
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Yoan Emritloll
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Peter A Warn
- Magic Bullet Consulting, Biddlecombe House, Ugbrook, Chudleigh Devon, TQ130AD, UK
| | - Frédéric Bequet
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Marie-Elisabeth Bougnoux
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Stephanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF0545, 20 Côte de Reyne, 15000 Aurillac, France
| | - Mark S Gresnigt
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Bernhard Hube
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Ilse D Jacobsen
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Mélanie Legrand
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Salomé Leibundgut-Landmann
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Chaysavanh Manichanh
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Carol A Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Karla Queiroz
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Karine Roget
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | - Vincent Thomas
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Claudia Thoral
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | | | - Alan W Walker
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Alistair J P Brown
- MRC Centre for Medical Mycology, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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Danesi P, Corrò M, Falcaro C, Carminato A, Furlanello T, Cocchi M, Krockenberger MB, Meyer W, Capelli G, Malik R. Molecular detection of Pneumocystis in the lungs of cats. Med Mycol 2020; 57:813-824. [PMID: 30566653 PMCID: PMC7107658 DOI: 10.1093/mmy/myy139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/09/2018] [Accepted: 11/16/2018] [Indexed: 12/23/2022] Open
Abstract
The genus Pneumocystis comprises potential pathogens that reside normally in the lungs of a wide range of mammals. Although they generally behave as transient or permanent commensals, they can occasionally cause life-threatening pneumonia (Pneumocystis pneumonia; PCP) in immunosuppressed individuals. Several decades ago, the presence of Pneumocystis morphotypes (trophic forms and cysts) was described in the lungs of normal cats and cats with experimentally induced symptomatic PCP (after immunosuppression by corticosteroids); yet to date spontaneous or drug-induced PCP has not been described in the clinical feline literature, despite immunosuppression of cats by long-standing retrovirus infections or after kidney transplantation. In this study, we describe the presence of Pneumocystis DNA in the lungs of normal cats (that died of various unrelated causes; n = 84) using polymerase chain reactions (PCRs) targeting the mitochondrial small and large subunit ribosomal RNA gene (mtSSU rRNA and mtLSU rRNA). The presence of Pneumocystis DNA was confirmed by sequencing in 24/84 (29%) cats, with evidence of two different sequence types (or lineages). Phylogenetically, lineage1 (L1; 19 cats) and lineage 2 (L2; 5 cats) formed separate clades, clustering with Pneumocystis from domestic pigs (L1) and carnivores (L2), respectively. Results of the present study support the notion that cats can be colonized or subclinically infected by Pneumocystis, without histological evidence of damage to the pulmonary parenchyma referable to pneumocystosis. Pneumocystis seems most likely an innocuous pathogen of cats’ lungs, but its possible role in the exacerbation of chronic pulmonary disorders or viral/bacterial coinfections should be considered further in a clinical setting.
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Affiliation(s)
- Patrizia Danesi
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Michela Corrò
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Christian Falcaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Antonio Carminato
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | | | - Monia Cocchi
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Mark B Krockenberger
- Veterinary Pathology Diagnostic Services, Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School, Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, University of Sydney, Westmead Hospital, Westmead Institute for Medical Research, Sydney, Australia
| | - Gioia Capelli
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Richard Malik
- Centre for Veterinary Education, B22, University of Sydney, Sydney, New South Wales, Australia
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Abstract
Aspergillus fumigatus is a saprotrophic fungus; its primary habitat is the soil. In its ecological niche, the fungus has learned how to adapt and proliferate in hostile environments. This capacity has helped the fungus to resist and survive against human host defenses and, further, to be responsible for one of the most devastating lung infections in terms of morbidity and mortality. In this review, we will provide (i) a description of the biological cycle of A. fumigatus; (ii) a historical perspective of the spectrum of aspergillus disease and the current epidemiological status of these infections; (iii) an analysis of the modes of immune response against Aspergillus in immunocompetent and immunocompromised patients; (iv) an understanding of the pathways responsible for fungal virulence and their host molecular targets, with a specific focus on the cell wall; (v) the current status of the diagnosis of different clinical syndromes; and (vi) an overview of the available antifungal armamentarium and the therapeutic strategies in the clinical context. In addition, the emergence of new concepts, such as nutritional immunity and the integration and rewiring of multiple fungal metabolic activities occurring during lung invasion, has helped us to redefine the opportunistic pathogenesis of A. fumigatus.
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Affiliation(s)
- Jean-Paul Latgé
- School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Georgios Chamilos
- School of Medicine, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
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Anaerobic digestion of mixed urban biowaste: The microbial community shift towards stability. N Biotechnol 2019; 55:108-117. [PMID: 31634577 DOI: 10.1016/j.nbt.2019.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 01/26/2023]
Abstract
Anaerobic digestion is applied worldwide to treat food waste (FW) with the aim of obtaining renewable bioenergy by exploiting the methane gas produced. However, there are several problems in practical applications, primarily due to system instability. Although exhaustive knowledge regarding anaerobic microbial community composition has been established, few studies have investigated long-term correlations between microbial consortia, operative conditions and feedstock characteristics. Here, microbial community shifts as a response to feedstock variations were investigated in long-term semi-continuous systems, which were evaluated by an in situ cell detection method and 16S rRNA gene amplicon sequencing. FW digestion showed progressive system instability caused by the inhibition of methanogens, which resulted in volatile fatty acid accumulation and process failure at the low organic loading rate (OLR). Conversely, by co-digesting FW with waste-activated sludge (WAS), a stable process with methane yields of up to 0.27 Nm3 kg-1VSfed for OLR = 1.7 gVS L-1d-1 was achieved. This stabilizing effect was not related to the buffering capacity of WAS, but to its capacity to avoid volatile fatty acid accumulation and falls in pH by overcoming methanogenic activity inhibition. WAS addition promoted the establishment of a stable and active archaeal population in anaerobic co-digestion (AcoD) reactors. The continuous supply of trace elements together with the seeding of microbial functional groups were the main drivers that positively affected process stability.
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Mukherjee C, Beall CJ, Griffen AL, Leys EJ. High-resolution ISR amplicon sequencing reveals personalized oral microbiome. MICROBIOME 2018; 6:153. [PMID: 30185233 PMCID: PMC6126016 DOI: 10.1186/s40168-018-0535-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/17/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Sequencing of the 16S rRNA gene has been the standard for studying the composition of microbial communities. While it allows identification of bacteria at the level of species, this method does not usually provide sufficient information to resolve communities at the sub-species level. Species-level resolution is not adequate for studies of transmission or stability or for exploring subspecies variation in disease association. Strain level analysis using whole metagenome shotgun sequencing has significant limitations that can make it unsuitable for large-scale studies. Achieving sufficient depth of sequencing can be cost-prohibitive, and even with adequate coverage, deconvoluting complex communities such as the oral microbiota is computationally very challenging. Thus, there is a need for high-resolution, yet cost-effective, high-throughput methods for characterizing microbial communities. RESULTS Significant improvement in resolution for amplicon-based bacterial community analysis was achieved by combining amplicon sequencing of a high-diversity marker gene, the ribosomal 16-23S intergenic spacer region (ISR), with a probabilistic error modeling based denoising algorithm, DADA2. The resolving power of this new approach was compared to that of both standard and high-resolution 16S-based approaches using a set of longitudinal subgingival plaque samples. The ISR strategy resulted in a 5.2-fold increase in community resolution compared to reference-based 16S rRNA gene analysis and showed 100% accuracy in predicting the correct source of a clinical sample. Individuals' microbial communities were highly personalized, and although they exhibited some drift in membership and levels over time, that difference was always smaller than the differences between any two subjects, even after 1 year. The construction of an ISR database from publicly available genomic sequences allowed us to explore genomic variation within species, resulting in the identification of multiple variants of the ISR for most species. CONCLUSIONS The ISR approach resulted in significantly improved resolution of communities and revealed a highly personalized human oral microbiota that was stable over 1 year. Multiple ISR types were observed for all species examined, demonstrating a high level of subspecies variation in the oral microbiota. The approach is high-throughput, high-resolution yet cost-effective, allowing subspecies-level community fingerprinting at a cost comparable to that of 16S rRNA gene amplicon sequencing. It will be useful for a range of applications that require high-resolution identification of organisms, including microbial tracking, community fingerprinting, and potentially for identification of virulence-associated strains.
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Affiliation(s)
| | | | - Ann L. Griffen
- College of Dentistry, The Ohio State University, Columbus, OH USA
| | - Eugene J. Leys
- College of Dentistry, The Ohio State University, Columbus, OH USA
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