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Theobald S, Vesth TC, Geib E, Nybo JL, Frisvad JC, Larsen TO, Kuo A, LaButti K, Lyhne EK, Kjærbølling I, Ledsgaard L, Barry K, Clum A, Chen C, Nolan M, Sandor L, Lipzen A, Mondo S, Pangilinan J, Salamov A, Riley R, Wiebenga A, Müller A, Kun RS, dos Santos Gomes AC, Henrissat B, Magnuson JK, Simmons BA, Mäkelä MR, Mortensen UH, Grigoriev IV, Brock M, Baker SE, de Vries RP, Andersen MR. Genomic Analysis of Aspergillus Section Terrei Reveals a High Potential in Secondary Metabolite Production and Plant Biomass Degradation. J Fungi (Basel) 2024; 10:507. [PMID: 39057392 PMCID: PMC11278011 DOI: 10.3390/jof10070507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Aspergillus terreus has attracted interest due to its application in industrial biotechnology, particularly for the production of itaconic acid and bioactive secondary metabolites. As related species also seem to possess a prosperous secondary metabolism, they are of high interest for genome mining and exploitation. Here, we present draft genome sequences for six species from Aspergillus section Terrei and one species from Aspergillus section Nidulantes. Whole-genome phylogeny confirmed that section Terrei is monophyletic. Genome analyses identified between 70 and 108 key secondary metabolism genes in each of the genomes of section Terrei, the highest rate found in the genus Aspergillus so far. The respective enzymes fall into 167 distinct families with most of them corresponding to potentially unique compounds or compound families. Moreover, 53% of the families were only found in a single species, which supports the suitability of species from section Terrei for further genome mining. Intriguingly, this analysis, combined with heterologous gene expression and metabolite identification, suggested that species from section Terrei use a strategy for UV protection different to other species from the genus Aspergillus. Section Terrei contains a complete plant polysaccharide degrading potential and an even higher cellulolytic potential than other Aspergilli, possibly facilitating additional applications for these species in biotechnology.
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Affiliation(s)
- Sebastian Theobald
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Tammi C. Vesth
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Elena Geib
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (E.G.); (M.B.)
| | - Jane L. Nybo
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Jens C. Frisvad
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Thomas O. Larsen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Ellen K. Lyhne
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Inge Kjærbølling
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Line Ledsgaard
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Cindy Chen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Matt Nolan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Stephen Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Astrid Müller
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Roland S. Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Ana Carolina dos Santos Gomes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Bernard Henrissat
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jon K. Magnuson
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (J.K.M.); (B.A.S.)
- US Department of Energy Joint Bioenergy Institute, 5885 Hollis St., Emeryville, CA 94608, USA
| | - Blake A. Simmons
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (J.K.M.); (B.A.S.)
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miia R. Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland;
| | - Uffe H. Mortensen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.K.); (K.L.); (K.B.); (A.C.); (C.C.); (M.N.); (L.S.); (A.L.); (S.M.); (J.P.); (A.S.); (R.R.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Matthias Brock
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK; (E.G.); (M.B.)
| | - Scott E. Baker
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (J.K.M.); (B.A.S.)
- US Department of Energy Joint Bioenergy Institute, 5885 Hollis St., Emeryville, CA 94608, USA
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, 3584 Utrecht, The Netherlands; (A.W.); (A.M.); (R.S.K.); (A.C.d.S.G.)
| | - Mikael R. Andersen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.T.); (T.C.V.); (J.L.N.); (J.C.F.); (T.O.L.); (E.K.L.); (I.K.); (L.L.); (B.H.); (U.H.M.)
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Bertlich M, Freytag S, Huber P, Dombrowski T, Oppel E, Gröger M. Serological Cross-Reactivity of Various Aspergillus spp. with Aspergillus fumigatus: A Diagnostic Blind Spot. Int Arch Allergy Immunol 2024; 185:767-774. [PMID: 38537619 DOI: 10.1159/000538082] [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: 12/21/2023] [Accepted: 02/23/2024] [Indexed: 08/09/2024] Open
Abstract
INTRODUCTION Aspergillus fumigatus is the most common airborne allergen of the Aspergillus family. However, allergies to Aspergillus spp. are increasing, and subsequently, allergies to Aspergillus species other than fumigatus are also on the rise. Commercial diagnostic tools are still limited to Aspergillus fumigatus. Hence, there is a need for improved tests. We decided to investigate the correlation between serological sensitization to A. fumigatus and other Aspergillus species. METHODS Hundred and seven patients with positive skin prick tests to A. fumigatus were included in this study. Immunoglobulin E (IgE) concentrations against A. fumigatus, A. terreus, A. niger, A. flavus, and A. versicolor were measured from specimens by fluorescent enzyme-linked immunoassays. RESULTS Patients showed considerably higher IgE concentrations against A. fumigatus (6.00 ± 15.05 kUA/L) than A. versicolor (0.30 ± 1.01 kUA/L), A. niger (0.62 ± 1.59 kUA/L), A. terreus (0.45 ± 1.12 kUA/L), or A. flavus (0.41 ± 0.97 kUA/L). Regression analysis yielded weak positive correlations for all Aspergillus spp., but low r2 values and heteroscedastic distribution indicate an overall poor fit of the calculated models. CONCLUSION Serological sensitization against A. fumigatus does not correlate with sensitization against other Aspergillus spp. To detect sensitization against these, other diagnostic tools like a skin prick test solution of different Aspergillus spp. are needed.
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Affiliation(s)
- Mattis Bertlich
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital, Ludwig-Maximilians University of Munich, Munich, Germany
- Department of Dermatology and Allergy, LMU University Hospital, LMU Munich, Munich, Germany
| | - Saskia Freytag
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Patrick Huber
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Tobias Dombrowski
- Department of Otorhinolarnygology, Head and Neck Surgery, University Medical Center, Göttingen, Germany
| | - Eva Oppel
- Department of Dermatology and Allergy, LMU University Hospital, LMU Munich, Munich, Germany
| | - Moritz Gröger
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital, Ludwig-Maximilians University of Munich, Munich, Germany
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Jiang Y, Du X, Xu Q, Yin C, Zhang H, Liu Y, Liu X, Yan H. Biodegradation of Gossypol by Aspergillus terreus-YJ01. Microorganisms 2023; 11:2148. [PMID: 37763992 PMCID: PMC10535836 DOI: 10.3390/microorganisms11092148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Gossypol, generally found in the roots, stems, leaves, and, especially, the seeds of cotton plants, is highly toxic to animals and humans, which inhibits the use of cotton stalks as a feed resource. Here, a promising fungal strain for biodegrading gossypol was successfully isolated from the soil of cotton stalk piles in Xinjiang Province, China, and identified as Aspergillus terreus-YJ01 with the analysis of ITS. Initial gossypol of 250 mg·L-1 could be removed by 97% within 96 h by YJ01, and initial gossypol of 150 mg·L-1 could also be catalyzed by 98% or 99% within 36 h by the intracellular or extracellular crude enzymes of YJ01. Sucrose and sodium nitrate were found to be the optimal carbon and nitrogen sources for the growth of YJ01, and the optimal initial pH and inoculum size for the growth of YJ01 were 6.0 and 1%, respectively. To further elucidate the mechanisms underlying gossypol biodegradation by YJ01, the draft genome of YJ01 was sequenced using Illumina HiSeq, which is 31,566,870 bp in length with a GC content of 52.27% and a total of 9737 genes. Eight genes and enzymes were predicted to be involved in gossypol biodegradation. Among them, phosphoglycerate kinase, citrate synthase, and other enzymes are related to the energy supply process. With sufficient energy, β-1, 4-endo-xylanase may achieve the purpose of biodegrading gossypol. The findings of this study provide valuable insights into both the basic research and the application of A. terreus-YJ01 in the biodegradation of gossypol in cotton stalks.
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Affiliation(s)
| | | | | | | | | | | | | | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Y.J.)
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Whole genome sequence characterization of Aspergillus terreus ATCC 20541 and genome comparison of the fungi A. terreus. Sci Rep 2023; 13:194. [PMID: 36604572 PMCID: PMC9814666 DOI: 10.1038/s41598-022-27311-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Aspergillus terreus is well-known for lovastatin and itaconic acid production with biomedical and commercial importance. The mechanisms of metabolite formation have been extensively studied to improve their yield through genetic engineering. However, the combined repertoire of carbohydrate-active enzymes (CAZymes), cytochrome P450s (CYP) enzymes, and secondary metabolites (SMs) in the different A. terreus strains has not been well studied yet, especially with respect to the presence of biosynthetic gene clusters (BGCs). Here we present a 30 Mb whole genome sequence of A. terreus ATCC 20541 in which we predicted 10,410 protein-coding genes. We compared the CAZymes, CYPs enzyme, and SMs across eleven A. terreus strains, and the results indicate that all strains have rich pectin degradation enzyme and CYP52 families. The lovastatin BGC of lovI was linked with lovF in A. terreus ATCC 20541, and the phenomenon was not found in the other strains. A. terreus ATCC 20541 lacked a non-ribosomal peptide synthetase (AnaPS) participating in acetylaszonalenin production, which was a conserved protein in the ten other strains. Our results present a comprehensive analysis of CAZymes, CYPs enzyme, and SM diversities in A. terreus strains and will facilitate further research in the function of BGCs associated with valuable SMs.
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Tiew PY, Thng KX, Chotirmall SH. Clinical Aspergillus Signatures in COPD and Bronchiectasis. J Fungi (Basel) 2022; 8:jof8050480. [PMID: 35628736 PMCID: PMC9146266 DOI: 10.3390/jof8050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Pulmonary mycoses remain a global threat, causing significant morbidity and mortality. Patients with airways disease, including COPD and bronchiectasis, are at increased risks of pulmonary mycoses and its associated complications. Frequent use of antibiotics and corticosteroids coupled with impaired host defenses predispose patients to fungal colonization and airway persistence, which are associated with negative clinical consequences. Notably, Aspergillus species remain the best-studied fungal pathogen and induce a broad spectrum of clinical manifestations in COPD and bronchiectasis ranging from colonization and sensitization to more invasive disease. Next-generation sequencing (NGS) has gained prominence in the field of respiratory infection, and in some cases is beginning to act as a viable alternative to traditional culture. NGS has revolutionized our understanding of airway microbiota and in particular fungi. In this context, it permits the identification of the previously unculturable, fungal composition, and dynamic change within microbial communities of the airway, including potential roles in chronic respiratory disease. Furthermore, inter-kingdom microbial interactions, including fungi, in conjunction with host immunity have recently been shown to have important clinical roles in COPD and bronchiectasis. In this review, we provide an overview of clinical Aspergillus signatures in COPD and bronchiectasis and cover the current advances in the understanding of the mycobiome in these disease states. The challenges and limitations of NGS will be addressed.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 168753, Singapore;
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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Abstract
Infections due to Aspergillus species are an acute threat to human health; members of the Aspergillus section Fumigati are the most frequently occurring agents, but depending on the local epidemiology, representatives of section Terrei or section Flavi are the second or third most important. Aspergillus terreus species complex is of great interest, as it is usually amphotericin B resistant and displays notable differences in immune interactions in comparison to Aspergillus fumigatus. The latest epidemiological surveys show an increased incidence of A. terreus as well as an expanding clinical spectrum (chronic infections) and new groups of at-risk patients being affected. Hallmarks of these non-Aspergillus fumigatus invasive mold infections are high potential for tissue invasion, dissemination, and possible morbidity due to mycotoxin production. We seek to review the microbiology, epidemiology, and pathogenesis of A. terreus species complex, address clinical characteristics, and highlight the underlying mechanisms of amphotericin B resistance. Selected topics will contrast key elements of A. terreus with A. fumigatus. We provide a comprehensive resource for clinicians dealing with fungal infections and researchers working on A. terreus pathogenesis, aiming to bridge the emerging translational knowledge and future therapeutic challenges on this opportunistic pathogen.
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Respiratory Mycoses in COPD and Bronchiectasis. Mycopathologia 2021; 186:623-638. [PMID: 33709335 DOI: 10.1007/s11046-021-00539-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and bronchiectasis represent chronic airway diseases associated with significant morbidity and mortality. Bacteria and viruses are commonly implicated in acute exacerbations; however the significance of fungi in these airways remains poorly defined. While COPD and bronchiectasis remain recognized risk factors for the occurrence of Aspergillus-associated disease including chronic and invasive aspergillosis, underlying mechanisms that lead to the progression from colonization to invasive disease remain uncertain. Nonetheless, advances in molecular technologies have improved our detection, identification and understanding of resident fungi characterizing these airways. Mycobiome sequencing has revealed the complex varied and myriad profile of airway fungi in COPD and bronchiectasis, including their association with disease presentation, progression, and mortality. In this review, we outline the emerging evidence for the clinical importance of fungi in COPD and bronchiectasis, available diagnostic modalities, mycobiome sequencing approaches and association with clinical outcomes.
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Ryngajłło M, Boruta T, Bizukojć M. Complete genome sequence of lovastatin producer Aspergillus terreus ATCC 20542 and evaluation of genomic diversity among A. terreus strains. Appl Microbiol Biotechnol 2021; 105:1615-1627. [PMID: 33515286 PMCID: PMC7880949 DOI: 10.1007/s00253-021-11133-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/30/2020] [Accepted: 01/20/2021] [Indexed: 12/02/2022]
Abstract
In the present study, the complete genome of a filamentous fungus Aspergillus terreus ATCC 20542 was sequenced, assembled, and annotated. This strain is mainly recognized for being a model wild-type lovastatin producer and a parental strain of high-yielding industrial mutants. It is also a microorganism with a rich repertoire of secondary metabolites that has been a subject of numerous bioprocess-related studies. In terms of continuity, the genomic sequence provided in this work is of the highest quality among all the publicly available genomes of A. terreus strains. The comparative analysis revealed considerable diversity with regard to the catalog of biosynthetic gene clusters found in A. terreus. Even though the cluster of lovastatin biosynthesis was found to be well-conserved at the species level, several unique genes putatively associated with metabolic functions were detected in A. terreus ATCC 20542 that were not detected in other investigated genomes. The analysis was conducted also in the context of the primary metabolic pathways (sugar catabolism, biomass degradation potential, organic acid production), where the visible differences in gene copy numbers were detected. However, the species-level genomic diversity of A. terreus was more evident for secondary metabolism than for the well-conserved primary metabolic pathways. The newly sequenced genome of A. terreus ATCC 20542 was found to harbor several unique sequences, which can be regarded as interesting subjects for future experimental efforts on A. terreus metabolism and fungal biosynthetic capabilities. KEY POINTS: • The high-quality genome of Aspergillus terreus ATCC 20542 has been assembled and annotated. • Comparative analysis with other sequenced Aspergillus terreus strains has revealed considerable diversity in biosynthetic gene repertoire, especially related to secondary metabolism. • The unique genomic features of A. terreus ATCC 20542 are discussed.
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Affiliation(s)
- Małgorzata Ryngajłło
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, B. Stefanowskiego 4/10, 90-924, Lodz, Poland.
| | - Tomasz Boruta
- Faculty of Process and Environmental Engineering, Department of Bioprocess Engineering, Lodz University of Technology, ul. Wolczanska 213, 90-924, Lodz, Poland
| | - Marcin Bizukojć
- Faculty of Process and Environmental Engineering, Department of Bioprocess Engineering, Lodz University of Technology, ul. Wolczanska 213, 90-924, Lodz, Poland
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Larkin PMK, Multani A, Beaird OE, Dayo AJ, Fishbein GA, Yang S. A Collaborative Tale of Diagnosing and Treating Chronic Pulmonary Aspergillosis, from the Perspectives of Clinical Microbiologists, Surgical Pathologists, and Infectious Disease Clinicians. J Fungi (Basel) 2020; 6:E106. [PMID: 32664547 PMCID: PMC7558816 DOI: 10.3390/jof6030106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic pulmonary aspergillosis (CPA) refers to a spectrum of Aspergillus-mediated disease that is associated with high morbidity and mortality, with its true prevalence vastly underestimated. The diagnosis of CPA includes characteristic radiographical findings in conjunction with persistent and systemic symptoms present for at least three months, and evidence of Aspergillus infection. Traditionally, Aspergillus infection has been confirmed through histopathology and microbiological studies, including fungal culture and serology, but these methodologies have limitations that are discussed in this review. The treatment of CPA requires an individualized approach and consideration of both medical and surgical options. Most Aspergillus species are considered susceptible to mold-active triazoles, echinocandins, and amphotericin B; however, antifungal resistance is emerging and well documented, demonstrating the need for novel therapies and antifungal susceptibility testing that correlates with clinical response. Here, we describe the clinical presentation, diagnosis, and treatment of CPA, with an emphasis on the strengths and pitfalls of diagnostic and treatment approaches, as well as future directions, including whole genome sequencing and metagenomic sequencing. The advancement of molecular technology enables rapid and precise species level identification, and the determination of molecular mechanisms of resistance, bridging the clinical infectious disease, anatomical pathology, microbiology, and molecular biology disciplines.
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Affiliation(s)
- Paige M. K. Larkin
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
- Department of Pathology, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Ashrit Multani
- Department of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.M.); (O.E.B.)
| | - Omer E. Beaird
- Department of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, CA 90095, USA; (A.M.); (O.E.B.)
| | - Ayrton J. Dayo
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
| | - Gregory A. Fishbein
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; (P.M.K.L.); (A.J.D.); (G.A.F.)
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