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Recent Molecular Tools for the Genetic Manipulation of Highly Industrially Important Mucoromycota Fungi. J Fungi (Basel) 2021; 7:jof7121061. [PMID: 34947043 PMCID: PMC8705501 DOI: 10.3390/jof7121061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/27/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022] Open
Abstract
Mucorales is the largest and most well-studied order of the phylum Mucormycota and is known for its rapid growth rate and various industrial applications. The Mucorales fungi are a fascinating group of filamentous organisms with many uses in research and the industrial and medical fields. They are widely used biotechnological producers of various secondary metabolites and other value-added products. Certain members of Mucorales are extensively used as model organisms for genetic and molecular investigation and have extended our understanding of the metabolisms of other members of this order as well. Compared with other fungal species, our understanding of Mucoralean fungi is still in its infancy, which could be linked to their lack of effective genetic tools. However, recent advancements in molecular tools and approaches, such as the construction of recyclable markers, silencing vectors, and the CRISPR-Cas9-based gene-editing system, have helped us to modify the genomes of these model organisms. Multiple genetic modifications have been shown to generate valuable products on a large scale and helped us to understand the morphogenesis, basic biology, pathogenesis, and host–pathogen interactions of Mucoralean fungi. In this review, we discuss various conventional and modern genetic tools and approaches used for efficient gene modification in industrially important members of Mucorales.
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Where are the basal fungi? Current status on diversity, ecology, evolution, and taxonomy. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00642-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lee JH, Kwon KC, Koo SH. Molecular Analysis of Pathogenic Molds Isolated from Clinical Specimen. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.3.229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jang Ho Lee
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Korea
| | - Kye Chul Kwon
- Department of Laboratory Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Sun Hoe Koo
- Department of Laboratory Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
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Stohs E, Zimmer A. An Approach to Suspected Invasive Fungal Infection in Patients with Hematologic Malignancy and HCT Recipients with Persistent Neutropenic Fever Despite Mold-Active Prophylaxis. CURRENT FUNGAL INFECTION REPORTS 2020. [DOI: 10.1007/s12281-020-00375-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Madani M, Zia M. Isolation of Mucorales from biological environment and identification of Rhizopus among the isolates using PCRRFLP. ACTA ACUST UNITED AC 2019. [DOI: 10.34172/jsums.2019.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background and aims: Mucorales are fungi belonging to the category of Zygomycetes, found much in nature. Culture-based methods for clinical samples are often negative, difficult and time-consuming and mainly identify isolates to the genus level, and sometimes only as Mucorales. Therefore, applying fast and accurate diagnosis methods such as molecular approaches seems necessary. This study aims at isolating Mucorales for determination of Rhizopus genus between the isolates using molecular methods. Methods: In this descriptive observational study, a total of 500 samples were collected from air and different surfaces and inoculated on Sabouraud Dextrose Agar supplemented with chloramphenicol. Then, the fungi belonging to Mucorales were identified and their pure culture was provided. DNA extraction was done using extraction kit and the chloroform method. After amplification, the samples belonging to Mucorales were identified by observing 830 bp bands. For enzymatic digestion, enzyme BmgB1 was applied for identification of Rhizopus species by formation of 593 and 235 bp segments. Results: One hundred pure colonies belonging to Mucorales were identified using molecular methods and after enzymatic digestion, 21 isolates were determined as Rhizopus species. The sequencing of PCR products and macroscopic and microscopic studies confirmed the existence of R. stolonifera, R. oryzae and R. caespitosus in the samples. Conclusion: Generally, developing a reliable method for determining Zygomycete species can be a useful tool for better understanding of the epidemiology of mucoromycosis.
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Affiliation(s)
- Mahboobeh Madani
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Mohammadali Zia
- Department of Basic Science, Khorasgan (Isfahan) Branch, Islamic Azad University, Isfahan, Iran
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Molecular Identification of Causative Agents in 25 Cases with Mucormycosis in Iran. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2019. [DOI: 10.5812/archcid.69100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Diversity of mucoralean fungi in soils of papaya (Carica papaya L.) producing regions in Mexico. Fungal Biol 2018; 122:810-816. [PMID: 30007431 DOI: 10.1016/j.funbio.2018.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/17/2018] [Indexed: 11/22/2022]
Abstract
Mexico is the fifth largest producer of papaya worldwide and has recently reported problems with mucoralean fungi in this crop. These fungi are considered saprophytes in the soil and are ubiquitous in nature. In this work, they were isolated from soil in regions of intensive papaya cultivation in Mexico. Collections were made in the states of Colima, Oaxaca and Veracruz in Apr 2016. A total of 72 mucorales fungal isolates was obtained and morphologically characterized and then molecular characterization (28S ribosomal region) of 25 representative isolates was carried out. Phylogenetic analysis of the sequences confirmed the presence of the species Gilbertella persicaria, Rhizopus oryzae, Rhizopus stolonifer, Mucor circinelloides and Mucor hiemalis, which cause soft rot in papaya fruits, therefore, spores of these fungi found in the orchard soils can be considered as a constant source of contamination that affects healthy fruits. Additionally, Choanephora cucurbitarum, Mucor ellipsoideus, Rhizopus homothallicus, Rhizopus microsporus, Rhizopus schipperae, Lichteimia ramosa, Gongronella butleri, Cunninghamella bertholletiae and Cunninghamella blakesleeana were identified which are considered to have agricultural, biotechnological and medical importance.
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Banerjee S, Peck KN, Feldman MD, Schuster MG, Alwine JC, Robertson ES. Identification of fungal pathogens in a patient with acute myelogenic leukemia using a pathogen detection array technology. Cancer Biol Ther 2017; 17:339-45. [PMID: 26619325 DOI: 10.1080/15384047.2015.1121349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Invasive zygomycosis in immunocompromised patients results in a high mortality rate, and early identification is crucial to optimize therapy and to reduce morbidity. However, diagnosing specific species of zygomycetes fungi possess challenge in the clinical laboratories. A need for a rapid and sensitive diagnostic tool for early recognition of a zygomycetes fungus in clinical samples to the species level will lead to prompt and accurate therapy and the PathoChip provides one such platform. We utilized a pathogen array technology referred to as PathoChip, comprised of oligonucleotide probes that can detect all the sequenced viruses as well as known pathogenic bacteria, fungi and parasites and family-specific conserved probes, thus providing a means for detecting previously uncharacterized members of a family. We rapidly identified a zygomycetous fungus, Rhizomucor pusillus, an otherwise challenge for the clinical laboratories, predominantly in a patient with acute myelogenous leukemia. This report highlights the value of PathoChip as a diagnostic tool to identify micro-organisms to the species level, especially for those difficult to identify in most clinical laboratories. It will also help clinicians to obtain a critical snapshot of the infection profile of a patient to plan treatment strategies.
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Affiliation(s)
- Sagarika Banerjee
- a Department of Microbiology , University of Pennsylvania , Philadelphia , PA , USA
| | - Kristen N Peck
- a Department of Microbiology , University of Pennsylvania , Philadelphia , PA , USA
| | - Michael D Feldman
- b Department of Pathology and Laboratory Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Mindy G Schuster
- c Infectious Diseases Division, University of Pennsylvania , Philadelphia , PA , PA , USA
| | - James C Alwine
- d Department of Cancer Biology , University of Pennsylvania , Philadelphia , PA , USA
| | - Erle S Robertson
- a Department of Microbiology , University of Pennsylvania , Philadelphia , PA , USA
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Yang M, Lee JH, Kim YK, Ki CS, Huh HJ, Lee NY. Identification of mucorales from clinical specimens: a 4-year experience in a single institution. Ann Lab Med 2017; 36:60-3. [PMID: 26522761 PMCID: PMC4697345 DOI: 10.3343/alm.2016.36.1.60] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/28/2015] [Accepted: 09/16/2015] [Indexed: 01/03/2023] Open
Abstract
Mucormycosis, a fatal opportunistic infection in immunocompromised hosts, is caused by fungi belonging to the order Mucorales. Early diagnosis based on exact identification and multidisciplinary treatments is critical. However, identification of Mucorales fungi is difficult and often delayed, resulting in poor prognosis. This study aimed to compare the results of phenotypic and molecular identification of 12 Mucorales isolates collected from 4-yr-accumulated data. All isolates were identified on the basis of phenotypic characteristics such as growth rate, colony morphology, and reproductive structures. PCR and direct sequencing were performed to target internal transcribed spacer (ITS) and/or D1/D2 regions. Target DNA sequencing identified five Lichtheimia isolates, two Rhizopus microsporus isolates, two Rhizomucor pusillus isolates, one Cunninghamella bertholletiae isolate, one Mucor fragilis isolate, and one Syncephalastrum racemosum isolate. Five of the 12 (41.7%) isolates were incorrectly identified on the basis of phenotypic identification. DNA sequencing showed that of these five isolates, two were Lichtheimia isolates, one was Mucor isolate, one was Rhizomucor isolate, and one was Rhizopus microspores. All the isolates were identified at the species level by ITS and/or D1/D2 analyses. Phenotypic differentiation and identification of Mucorales is difficult because different Mucorales share similar morphology. Our results indicate that the molecular methods employed in this study are valuable for identifying Mucorales.
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Affiliation(s)
- Mina Yang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jang Ho Lee
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Korea
| | - Young Kwon Kim
- Department of Biomedical Laboratory Science, Konyang University, Daejeon, Korea
| | - Chang Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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Morin-Sardin S, Nodet P, Coton E, Jany JL. Mucor: A Janus-faced fungal genus with human health impact and industrial applications. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2016.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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