1
|
Bigey F, Menatong Tene X, Wessner M, Pradal M, Aury JM, Cruaud C, Neuvéglise C. Differential adaptation of the yeast Candida anglica to fermented food. Food Microbiol 2024; 123:104584. [PMID: 39038890 DOI: 10.1016/j.fm.2024.104584] [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: 03/03/2024] [Revised: 05/22/2024] [Accepted: 06/07/2024] [Indexed: 07/24/2024]
Abstract
A single strain of Candida anglica, isolated from cider, is available in international yeast collections. We present here seven new strains isolated from French PDO cheeses. For one of the cheese strains, we achieved a high-quality genome assembly of 13.7 Mb with eight near-complete telomere-to-telomere chromosomes. The genomes of two additional cheese strains and of the cider strain were also assembled and annotated, resulting in a core genome of 5966 coding sequences. Phylogenetic analysis showed that the seven cheese strains clustered together, away from the cider strain. Mating-type locus analysis revealed the presence of a MATa locus in the cider strain but a MATalpha locus in all cheese strains. The presence of LINE retrotransposons at identical genome position in the cheese strains, and two different karyotypic profiles resulting from chromosomal rearrangements were observed. Together, these findings are consistent with clonal propagation of the cheese strains. Phenotypic trait variations were observed within the cheese population under stress conditions whereas the cider strain was found to have a much greater capacity for growth in all conditions tested.
Collapse
Affiliation(s)
- Frédéric Bigey
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | - Marc Wessner
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Martine Pradal
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, 91057, France
| | | |
Collapse
|
2
|
Liu F, Hu ZD, Zhao XM, Zhao WN, Feng ZX, Yurkov A, Alwasel S, Boekhout T, Bensch K, Hui FL, Bai FY, Wang QM. Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species. PERSOONIA 2024; 52:22-43. [PMID: 39161632 PMCID: PMC11319837 DOI: 10.3767/persoonia.2024.52.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/12/2024] [Indexed: 08/21/2024]
Abstract
Candida is a polyphyletic genus of asexually reproducing yeasts in the Saccharomycotina with more than 400 species that occur in almost all families of the subclass and its name is strongly connected with the infectious disease candidiasis. During the last two decades, approximately half of the Candida species have been reassigned into more than 36 already existing genera and 14 newly proposed genera, but the polyphyletic feature of the genus largely remained. Candida auris is an important, globally emerging opportunistic pathogen that has caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the Candida auris-Candida haemuli (CAH) clade in the Metschnikowiaceae, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from natural environments. The clade is phylogenetically positioned remotely from the type species of the genus Candida that is Candida vulgaris (currently interpreted as a synonym of Candida tropicalis) and belongs to the family Debaryomycetaceae. Although previous phylogenetic and phylogenomic studies confirmed the position of C. auris in the Metschnikowiaceae, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera Clavispora and Metschnikowia. To resolve the position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of C. auris and related species in the Metschnikowiaceae using several metrics, such as the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). Based on those approaches, 13 new genera are proposed for various Candida and Hyphopichia species, including members of the CAH clade in the Metschnikowiaceae. As a result, C. auris and related species are reassigned to the genus Candidozyma. Fifty-five new combinations and nine new species are introduced and this will reduce the polyphyly of the genus Candida. Citation: Liu F, Hu Z-D, Zhao X-M, et al. 2024. Phylogenomic analysis of the Candida auris-Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species. Persoonia 52: 22-43. https://doi.org/10.3767/persoonia.2024.52.02 .
Collapse
Affiliation(s)
- F. Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - Z.-D. Hu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - X.-M. Zhao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - W.-N. Zhao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - Z.-X. Feng
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - S. Alwasel
- College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - T. Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi Arabia
- The Yeasts Foundation, Amsterdam, The Netherlands
| | - K. Bensch
- Westerdijk Institute of Fungal Biodiversity, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - F.-L. Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, China
| | - F.-Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Q.-M. Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, Hebei, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding 071002, Hebei, China
| |
Collapse
|
3
|
Liu F, Hu ZD, Yurkov A, Chen XH, Bao WJ, Ma Q, Zhao WN, Pan S, Zhao XM, Liu JH, Wang QM, Boekhout T. Saccharomycetaceae: delineation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies. PERSOONIA 2024; 52:1-21. [PMID: 39161631 PMCID: PMC11319838 DOI: 10.3767/persoonia.2024.52.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/08/2024] [Indexed: 08/21/2024]
Abstract
A correct classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses. However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short ribosomal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in Saccharomycetaceae, namely Eremothecium, Grigorovia, Kazachstania, Kluyveromyces, Lachancea, Nakaseomyces, Naumovozyma, Saccharomyces, Tetrapisispora, Torulaspora, Vanderwaltozyma, Zygosaccharomyces and Zygotorulaspora. As a result, most of these genera are supported by the genomics-based metrics, but the genera Kazachstania, Nakaseomyces and Tetrapisispora were shown to be genetically highly diverse based on the above listed analyses. Considering the results obtained for the presently recognized genera, a range of 80-92 % POCP values and a range of 60-70 % AAI values might be valuable thresholds to discriminate genera in Saccharomycetaceae. Furthermore, the genus-specific genes identified in the PAPO analysis and the CSIs were found to be useful as synapomorphies to characterize and define genera in Saccharomycetaceae. Our results indicate that the combined monophyly-based phylogenomic analysis together with genomic relatedness indices and synapomorphies provide promising approaches to delineating yeast genera and likely those of filamentous fungi as well. The genera Kazachstania, Nakaseomyces and Tetrapisispora are revised and we propose eight new genera and 41 new combinations. Citation: Liu F, Hu Z-D, Yurkov A, et al. 2024. Saccharomycetaceae: delinaeation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies. Persoonia 52: 1-21. https://doi.org/10.3767/persoonia.2024.52.01.
Collapse
Affiliation(s)
- F. Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - Z.-D. Hu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - X.-H. Chen
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - W.-J. Bao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - Q. Ma
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - W.-N. Zhao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - S. Pan
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - X.-M. Zhao
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - J.-H. Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
| | - Q.-M. Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, China
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding 071002, Hebei, China
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding 071002, Hebei, China
| | - T. Boekhout
- College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
4
|
Spruijtenburg B, de Souza Lima BJF, Tosar STG, Borman AM, Andersen CT, Nizamuddin S, Ahmad S, de Almeida Junior JN, Vicente VA, Nosanchuk JD, Buil JB, de Hoog S, Meijer EFJ, Meis JF, de Groot T. The yeast genus Tardiomyces gen. nov. with one new species and two new combinations. Infection 2024:10.1007/s15010-024-02229-6. [PMID: 38573472 DOI: 10.1007/s15010-024-02229-6] [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: 12/18/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE Rare yeasts species are increasingly reported as causative agents of invasive human infection. Proper identification and antifungal therapy are essential to manage these infections. Candida blankii is one of these emerging pathogens and is known for its reduced susceptibility to multiple antifungals. METHODS To obtain more insight into the characteristics of this species, 26 isolates reported as C. blankii were investigated using genetic and phenotypical approaches. RESULTS Among the 26 isolates, seven recovered either from blood, sputum, urine, or the oral cavity, displayed substantial genetic and some phenotypical differences compared to the other isolates, which were confirmed as C. blankii. We consider these seven strains to represent a novel species, Tardiomyces depauwii. Phylogenomics assigned C. blankii, C. digboiensis, and the novel species in a distinct branch within the order Dipodascales, for which the novel genus Tardiomyces is erected. The new combinations Tardiomyces blankii and Tardiomyces digboiensis are introduced. Differences with related, strictly environmental genera Sugiyamaella, Crinitomyces, and Diddensiella are enumerated. All three Tardiomyces species share the rare ability to grow up to 42 °C, display slower growth in nutrient-poor media, and show a reduced susceptibility to azoles and echinocandins. Characteristics of T. depauwii include high MIC values with voriconazole and a unique protein pattern. CONCLUSION We propose the novel yeast species Tardiomyces depauwii and the transfer of C. blankii and C. digboiensis to the novel Tardiomyces genus.
Collapse
Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands.
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands.
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands.
| | - Bruna Jacomel Favoreto de Souza Lima
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Sonia T Granadillo Tosar
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands
| | - Andrew M Borman
- UK Health Security Agency National Mycology Reference Laboratory, Southmead Hospital, Bristol, BS10 5NB, UK
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, EX4 4QD, UK
| | | | - Summiya Nizamuddin
- Section of Microbiology, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | | | - Vânia Aparecida Vicente
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, Curitiba, Brazil
- Microbiological Collections of Paraná Network (CMRP/Taxonline), Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Joshua D Nosanchuk
- Department of Medicine (Division of Infectious Diseases) and Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Jochem B Buil
- Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Sybren de Hoog
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Eelco F J Meijer
- Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology, Radboudumc, Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Institute of Translational Research, Cologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Excellence Center for Medical Mycology, University of Cologne, Cologne, Germany
| | - Theun de Groot
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands
| |
Collapse
|
5
|
Liu M, Ding RX, Zhang YX, Li HZ, Wang QM. Wickerhamomyces corioli f.a., sp. nov. , a novel yeast species discovered in two mushroom species. Int J Syst Evol Microbiol 2024; 74. [PMID: 38591772 DOI: 10.1099/ijsem.0.006333] [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: 04/10/2024] Open
Abstract
Two yeast strains, designated as 19-39-3 and 19-40-2, obtained from the fruiting bodies of Trametes versicolor and Marasmius siccus collected in Yunwu Mountain Forest Park, PR China, have been identified as representing a novel asexual ascomycetous yeast species. From the results of phylogenetic analyses of the sequences of the D1/D2 domains of the large subunit (LSU) rRNA, small subunit (SSU) rRNA and translation elongation factor 1-α (TEF1) genes, it was determined that these strains represent a member of the genus Wickerhamomyces, with Wickerhamomyces alni and Candida ulmi as the closest relatives. The novel species exhibited 6.6 and 6.7% differences in the D1/D2 domains compared with W. alni and C. ulmi, respectively. Additionally, distinct biochemical and physiological differences were observed between the novel species and its related counterparts. No sexual reproduction was observed in these strains, leading to the proposal of the name Wickerhamomyces corioli f.a., sp. nov. for this newly discovered species.
Collapse
Affiliation(s)
- Min Liu
- School of Life Sciences, Hebei University, Baoding 071002, Hebei, PR China
- Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding 071002, Hebei, PR China
| | - Ruo-Xin Ding
- School of Life Sciences, Hebei University, Baoding 071002, Hebei, PR China
| | - Yu-Xuan Zhang
- School of Life Sciences, Hebei University, Baoding 071002, Hebei, PR China
| | - Hao-Ze Li
- School of Life Sciences, Hebei University, Baoding 071002, Hebei, PR China
| | - Qi-Ming Wang
- School of Life Sciences, Hebei University, Baoding 071002, Hebei, PR China
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding 071002, Hebei, PR China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding 071002, Hebei, PR China
| |
Collapse
|
6
|
Borman AM, Johnson EM. Changes in fungal taxonomy: mycological rationale and clinical implications. Clin Microbiol Rev 2023; 36:e0009922. [PMID: 37930182 PMCID: PMC10732072 DOI: 10.1128/cmr.00099-22] [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: 05/22/2023] [Accepted: 07/13/2023] [Indexed: 11/07/2023] Open
Abstract
Numerous fungal species of medical importance have been recently subjected to and will likely continue to undergo nomenclatural changes as a result of the application of molecular approaches to fungal classification together with abandonment of dual nomenclature. Here, we summarize those changes affecting key groups of fungi of medical importance, explaining the mycological (taxonomic) rationale that underpinned the changes and the clinical relevance/importance (where such exists) of the key nomenclatural revisions. Potential mechanisms to mitigate unnecessary taxonomic instability are suggested, together with approaches to raise awareness of important changes to minimize potential clinical confusion.
Collapse
Affiliation(s)
- Andrew M. Borman
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
| | - Elizabeth M. Johnson
- UK HSA National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol, United Kingdom
- Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
| |
Collapse
|
7
|
Kreulen IAM, de Jonge WJ, van den Wijngaard RM, van Thiel IAM. Candida spp. in Human Intestinal Health and Disease: More than a Gut Feeling. Mycopathologia 2023; 188:845-862. [PMID: 37294505 PMCID: PMC10687130 DOI: 10.1007/s11046-023-00743-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023]
Abstract
Fungi are an essential part of the normal collection of intestinal microorganisms, even though their collective abundance comprises only 0.1-1% of all fecal microbes. The composition and role of the fungal population is often studied in relation to early-life microbial colonization and development of the (mucosal) immune system. The genus Candida is frequently described as one of the most abundant genera, and altered fungal compositions (including elevated abundance of Candida spp.) have been linked with intestinal diseases such as inflammatory bowel disease and irritable bowel syndrome. These studies are performed using both culture-dependent and genomic (metabarcoding) techniques. In this review, we aimed to summarize existing data on intestinal Candida spp. colonization in relation to intestinal disease and provide a brief overview of the biological and technical challenges in this field, including the recently described role of sub-species strain variation of intestinal Candida albicans. Together, the evidence for a contributing role of Candida spp. in pediatric and adult intestinal disease is quickly expanding, even though technical and biological challenges may limit full understanding of host-microbe interactions.
Collapse
Affiliation(s)
- Irini A M Kreulen
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Department of General, Visceral, Thoracic and Vascular Surgery, University Hospital Bonn, 53127, Bonn, Germany
| | - René M van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Isabelle A M van Thiel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands.
- Royal Netherlands Academy of Arts and Sciences, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands.
| |
Collapse
|
8
|
Čadež N, Boundy-Mills K, Botha A, Kachalkin A, Dlauchy D, Péter G. Taxogenomic placement of Rasporella oleae and Rasporella dianae gen. and spp. nov., two insect associated yeast species. Yeast 2023; 40:594-607. [PMID: 37885298 DOI: 10.1002/yea.3904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
During the course of independent studies in Europe, North America, and Africa, seven yeast strains were isolated from insect frass, decaying wood, tree flux, and olive oil sediment. Phylogenetic analysis of two barcoding DNA regions (internal transcribed spacer and the D1/D2 domain of the LSU rRNA gene) revealed that they belong to two closely related undescribed species distinct from all genera in the family Debaryomycetaceae. For reliable taxonomic placement the genomes of four strains of the two novel species and six type strains of closely related species were sequenced. Orthologous genes from 54 genomes of representatives of the Pichiomycetes and 23 outgroup taxa were concatenated to construct a fully supported phylogenetic tree. Consistent with the assumptions, we found that the two new species belong to a novel genus. In addition, the delimitation of the novel species was supported by genetic distance calculations from average nucleotide identity (ANI) and digital DNA:DNA hybridization (dDDH) values. The physiological characterization of the novel species was generally consistent with their genomic content. All strains had two alleles encoding secretory lipase in either two or three copies depending on the species. However, lipolytic activity was detected only in strains with three copies of the secretory lipase gene. Nevertheless, lipolytic activity might be related to their association with the insect gut. Based on these results, formal descriptions of the new genus Rasporella gen. nov. and of two new species Rasporella dianae sp. nov. (holotype UCDFST 68-643T , MycoBank no.: 850238) and Rasporella oleae sp. nov. (holotype ZIM 2471T , MycoBank no.: 850126) are provided.
Collapse
Affiliation(s)
- Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kyria Boundy-Mills
- Phaff Yeast Culture Collection, Food Science and Technology, University of California Davis, Davis, California, USA
| | - Alfred Botha
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Aleksey Kachalkin
- Soil Biology Department, Faculty of Soil Science, M. V. Lomonosov Moscow State University, Moscow, Russia
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, Russia
| | - Dénes Dlauchy
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| |
Collapse
|
9
|
Ahearn DG. Another perspective: a marine origin and adaptability of the emerging yeast pathogen Candida haemulonii. mBio 2023; 14:e0095423. [PMID: 37310725 PMCID: PMC10510331 DOI: 10.1128/mbio.00954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 06/14/2023] Open
Affiliation(s)
- Donald G. Ahearn
- Professor of Microbiology (Emeritus) Center for Applied & Environmental Microbiology, Georgia State University, Atlanta, Georgia, USA
| |
Collapse
|
10
|
Groenewald M, Hittinger C, Bensch K, Opulente D, Shen XX, Li Y, Liu C, LaBella A, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe K, Rosa C, Boekhout T, Čadež N, éter G, Sampaio J, Lachance MA, Yurkov A, Daniel HM, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Stud Mycol 2023; 105:1-22. [PMID: 38895705 PMCID: PMC11182611 DOI: 10.3114/sim.2023.105.01] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/12/2023] [Indexed: 06/21/2024] Open
Abstract
The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. Taxonomic novelties: New classes: Alloascoideomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Dipodascomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Lipomycetes M. Groenew., Hittinger, Opulente, A. Rokas, Pichiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Sporopachydermiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Trigonopsidomycetes M. Groenew., Hittinger, Opulente & A. Rokas. New orders: Alloascoideomycetes: Alloascoideales M. Groenew., Hittinger, Opulente & A. Rokas; Dipodascomycetes: Dipodascales M. Groenew., Hittinger, Opulente & A. Rokas; Lipomycetes: Lipomycetales M. Groenew., Hittinger, Opulente & A. Rokas; Pichiomycetes: Alaninales M. Groenew., Hittinger, Opulente & A. Rokas, Pichiales M. Groenew., Hittinger, Opulente & A. Rokas, Serinales M. Groenew., Hittinger, Opulente & A. Rokas; Saccharomycetes: Phaffomycetales M. Groenew., Hittinger, Opulente & A. Rokas, Saccharomycodales M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiomycetes: Sporopachydermiales M. Groenew., Hittinger, Opulente & A. Rokas; Trigonopsidomycetes: Trigonopsidales M. Groenew., Hittinger, Opulente & A. Rokas. New families: Alaninales: Pachysolenaceae M. Groenew., Hittinger, Opulente & A. Rokas; Pichiales: Pichiaceae M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiales: Sporopachydermiaceae M. Groenew., Hittinger, Opulente & A. Rokas. Citation: Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen X-X, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Čadež N, Péter G, Sampaio JP, Lachance M-A, Yurkov AM, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A (2023). A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology 105: 1-22. doi: 10.3114/sim.2023.105.01 This study is dedicated to the memory of Cletus P. Kurtzman (1938-2017), a pioneer of yeast taxonomy.
Collapse
Affiliation(s)
- M. Groenewald
- Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The
Netherlands;
| | - C.T. Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic
Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow
Institute for the Study of Evolution, University of Wisconsin-Madison,
Madison, WI 53726, USA;
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The
Netherlands;
| | - D.A. Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic
Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow
Institute for the Study of Evolution, University of Wisconsin-Madison,
Madison, WI 53726, USA;
- Department of Biology, Villanova University, Villanova, PA
19085;
| | - X.-X. Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou
310058, China;
| | - Y. Li
- Institute of Marine Science and Technology, Shandong University, Qingdao
266237, China;
| | - C. Liu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou
310058, China;
| | - A.L. LaBella
- Department of Bioinformatics and Genomics, The University of North
Carolina at Charlotte, Charlotte NC 28223, USA;
| | - X. Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease
Control, Integrative Microbiology Research Center, South China Agricultural
University, Guangzhou 510642, China;
| | - S. Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University,
Bangkok 10900, Thailand;
| | - S. Jindamorakot
- Microbial Diversity and Utilization Research Team, National Center for
Genetic Engineering and Biotechnology, National Science and Technology
Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang,
Pathum Thani 12120, Thailand;
| | - P. Gonçalves
- Associate Laboratory i4HB–Institute for Health and Bioeconomy,
NOVA School of Science and Technology, Universidade NOVA de Lisboa,
Caparica, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life
Sciences, NOVA School of Science and Technology, Universidade NOVA de
Lisboa, Caparica, Portugal;
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The
Netherlands;
| | - K.H. Wolfe
- Conway Institute and School of Medicine, University College Dublin,
Dublin 4, Ireland;
| | - C.A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de
Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil;
| | - T. Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi
Arabia;
| | - N. Čadež
- Food Science and Technology Department, Biotechnical Faculty, University
of Ljubljana, Ljubljana, Slovenia;
| | - G. éter
- National Collection of Agricultural and Industrial Microorganisms,
Institute of Food Science and Technology, Hungarian University of
Agriculture and Life Sciences, H-1118, Budapest, Somlói út
14-16., Hungary;
| | - J.P. Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de
Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516
Caparica, Portugal;
| | - M.-A. Lachance
- Department of Biology, University of Western Ontario, London, ON N6A
5B7, Canada;
| | - A.M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell
Cultures, 38124 Braunschweig, Germany;
| | - H.-M. Daniel
- BCCM/MUCL, Earth and Life Institute, Mycology Laboratory,
Université catholique de Louvain, 1348 Louvain-la-Neuve,
Belgium;
| | - M. Takashima
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI),
Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502,
Japan;
| | - K. Boundy-Mills
- Food Science and Technology, University of California Davis, Davis, CA,
95616, USA;
| | - D. Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera,
Instituto Andino Patagónico de Tecnologías Biológicas y
Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB,
Quintral 1250, San Carlos de Bariloche, 8400, Río Negro,
Argentina;
| | - K. Aoki
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI),
Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502,
Japan;
| | - T. Sugita
- Laboratory of Microbiology, Meiji Pharmaceutical University, Noshio,
Kiyose, Tokyo 204-8588, Japan;
| | - A. Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative,
Vanderbilt University, Nashville, TN 37235, USA
| |
Collapse
|
11
|
Nualthaisong P, Sakolrak B, Panicharoen T, Limtong S, Khunnamwong P. Kodamaea samutsakhonensis f.a., sp. nov., a novel ascomycetous yeast species isolated from wild mushrooms in Thailand. Int J Syst Evol Microbiol 2023; 73. [PMID: 37167093 DOI: 10.1099/ijsem.0.005840] [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: 05/13/2023] Open
Abstract
Two strains of genus Kodamaea, representing a novel anamorphic yeast species, were isolated from two samples of Marasmiellus sp. collected in Thailand. Analysis of the sequences of the internal transcribed spacer (ITS) regions and the D1/D2 domains of the large subunit (LSU) rRNA gene showed that the two strains differed by 27-42 nucleotide substitutions in the D1/D2 domains of the LSU rRNA gene and 7-34 nucleotide substitutions in the ITS region of a group of related species, Kodamaea smagusa CBS 11430T, Kodamaea fungicola JCM 10142T, Kodamaea plutei ATCC MYA-4329T, Kodamaea lidongshanica SD5S01T and Kodamaea jinghongensis NYNU 167162T. Phylogenetic analysis based on the concatenated sequences of the ITS and the D1/D2 domains of the LSU rRNA gene showed that the two strains were placed in the Kodamaea clade and clearly separated from other recognized species of the genus. Therefore, the two strains were assigned as a novel species of the genus Kodamaea, for which we propose the name Kodamaea samutsakhonensis f.a., sp. nov. The holotype is TBRC 16043T (=DMKU-BP19T) and the isotype is PYCC 9354. The MycoBank number of the novel species is MB 846490.
Collapse
Affiliation(s)
- Panadda Nualthaisong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok, 10900, Thailand
| | - Baramee Sakolrak
- Department of National Parks, Wildlife and Plant Conservation, Bangkok, 10900, Thailand
| | - Thitaya Panicharoen
- Division of Microbiology, Department of Science, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok, 10600, Thailand
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok, 10900, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok, 10300, Thailand
| | - Pannida Khunnamwong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok, 10900, Thailand
| |
Collapse
|
12
|
In silico environmental sampling of emerging fungal pathogens via big data analysis. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
13
|
Barros KO, Alvarenga FBM, Magni G, Souza GFL, Abegg MA, Palladino F, da Silva SS, Rodrigues RCLB, Sato TK, Hittinger CT, Rosa CA. The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species. Yeast 2023; 40:84-101. [PMID: 36582015 DOI: 10.1002/yea.3837] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
This study investigated the diversity of yeast species associated with rotting wood in Brazilian Amazonian rainforests. A total of 569 yeast strains were isolated from rotting wood samples collected in three Amazonian areas (Universidade Federal do Amazonas-Universidade Federal do Amazonas [UFAM], Piquiá, and Carú) in the municipality of Itacoatiara, Amazon state. The samples were cultured in yeast nitrogen base (YNB)-d-xylose, YNB-xylan, and sugarcane bagasse and corncob hemicellulosic hydrolysates (undiluted and diluted 1:2 and 1:5). Sugiyamaella was the most prevalent genus identified in this work, followed by Kazachstania. The most frequently isolated yeast species were Schwanniomyces polymorphus, Scheffersomyces amazonensis, and Wickerhamomyces sp., respectively. The alpha diversity analyses showed that the dryland forest of UFAM was the most diverse area, while the floodplain forest of Carú was the least. Additionally, the difference in diversity between UFAM and Carú was the highest among the comparisons. Thirty candidates for new yeast species were obtained, representing 36% of the species identified and totaling 101 isolates. Among them were species belonging to the clades Spathaspora, Scheffersomyces, and Sugiyamaella, which are recognized as genera with natural xylose-fermenting yeasts that are often studied for biotechnological and ecological purposes. The results of this work showed that rotting wood collected from the Amazonian rainforest is a tremendous source of diverse yeasts, including candidates for new species.
Collapse
Affiliation(s)
- Katharina O Barros
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Flávia B M Alvarenga
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Giulia Magni
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gisele F L Souza
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maxwel A Abegg
- Institute of Exact Sciences and Technology (ICET), Federal University of Amazonas (UFAM), Itacoatiara, Brazil
| | - Fernanda Palladino
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sílvio S da Silva
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Rita C L B Rodrigues
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Carlos A Rosa
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
14
|
Kidd SE, Abdolrasouli A, Hagen F. Fungal Nomenclature: Managing Change is the Name of the Game. Open Forum Infect Dis 2023; 10:ofac559. [PMID: 36632423 PMCID: PMC9825814 DOI: 10.1093/ofid/ofac559] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/18/2022] [Indexed: 01/09/2023] Open
Abstract
Fungal species have undergone and continue to undergo significant nomenclatural change, primarily due to the abandonment of dual species nomenclature in 2013 and the widespread application of molecular technologies in taxonomy allowing correction of past classification errors. These have effected numerous name changes concerning medically important species, but by far the group causing most concern are the Candida yeasts. Among common species, Candida krusei, Candida glabrata, Candida guilliermondii, Candida lusitaniae, and Candida rugosa have been changed to Pichia kudriavzevii, Nakaseomyces glabrata, Meyerozyma guilliermondii, Clavispora lusitaniae, and Diutina rugosa, respectively. There are currently no guidelines for microbiology laboratories on implementing changes, and there is ongoing concern that clinicians will dismiss or misinterpret laboratory reports using unfamiliar species names. Here, we have outlined the rationale for name changes across the major groups of clinically important fungi and have provided practical recommendations for managing change.
Collapse
Affiliation(s)
- Sarah E Kidd
- Correspondence: Sarah E. Kidd, BMedSc(Hons), PhD , National Mycology Reference Centre, SA Pathology, Frome Road, Adelaide, South Australia 5000, Australia ()
| | - Alireza Abdolrasouli
- Department of Medical Microbiology, King's College Hospital, London, United Kingdom,Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| |
Collapse
|
15
|
Michalczyk M, Sokół R, Lipczyńska-Ilczuk K, Bancerz-Kisiel A. Phylogenetic analysis of Starmerella apis in honey bees (Apis mellifera). J Eukaryot Microbiol 2023; 70:e12931. [PMID: 35711086 DOI: 10.1111/jeu.12931] [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: 04/03/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 01/13/2023]
Abstract
Honey bees are among the most effective pollinators that promote plant reproduction. Bees are highly active in the pollen collection season, which can lead to the transmission of selected pathogens between colonies. The clade Starmerella comprises yeasts that are isolated mainly from bees and their environment. When visiting plants, bees can come into contact with Starmerella spp. The aim of this study was to determine the prevalence and phylogenetic position of S. apis in bee colonies. Bee colonies were collected from nine apiaries in three regions. Ten colonies were sampled randomly from each apiary, and pooled samples were collected from the central part of the hive in each colony. A total of 90 (100%) bee colonies from nine apiaries were examined. Starmerella apis was detected in 31 (34.44%) samples, but related species were not identified. The 18S rRNA amplicon sequences of S. apis were compatible with the GenBank sequences of Starmerella spp. from India, Japan, Syria, Thailand, and the USA. The amplicon sequences of S. apis were also 99.06% homologous with the sequences deposited in GenBank under accession numbers JX515988 and NG067631.This is the first study to perform a phylogenetic analysis of S. apis in Polish honey bees.
Collapse
Affiliation(s)
- Maria Michalczyk
- Department of Parasitology and Invasive Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Rajmund Sokół
- Department of Parasitology and Invasive Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Karolina Lipczyńska-Ilczuk
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Agata Bancerz-Kisiel
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| |
Collapse
|
16
|
Chai CY, Li Y, Yan ZL, Hui FL. Phylogenetic and genomic analyses of two new species of Clavispora (Metschnikowiaceae, Saccharomycetales) from Central China. Front Microbiol 2022; 13:1019599. [PMID: 36312955 PMCID: PMC9608443 DOI: 10.3389/fmicb.2022.1019599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022] Open
Abstract
Species in the genus Clavispora have previously been reported primarily in the northeast and northwest regions of China; the species diversity of Clavispora in central China is not currently clear. In this study, phylogenetic inferences of Clavispora based on sequences of a single-locus (LSU D1/D2) and a two-locus (LSU D1/D2 and ITS) were conducted. Two new species isolated from rotting wood in central China, namely Clavispora xylosa sp. nov. and Clavispora paralusitaniae sp. nov., were delimited and proposed based on morphological and molecular evidence. Cl. xylosa was closely related to C. thailandica CBS 10610T, but with 11.5% divergence in the LSU D1/D2 domains and 11.5% divergence in the ITS regions. Cl. paralusitaniae was a sister to Cl. lusitaniae CBS 6936T from which it differs with 4.7% divergence in the LSU D1/D2 domains and 5.4% divergence in the ITS regions. Description of Cl. xylosa sp. nov. and Cl. paralusitaniae sp. nov. was also supported by morphological comparisons and genomic analyses between the two new species and their closest relatives, C. thailandica CBS 10610T and Cl. lusitaniae CBS 6936T. These results indicate a potentially great diversity of Clavispora spp. inhabiting rotting wood in central China, ripe for future discovery.
Collapse
Affiliation(s)
- Chun-Yue Chai
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
| | - Ying Li
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Zhen-Li Yan
- State Key Laboratory of Motor Vehicle Biofuel Technology, Henan Tianguan Enterprise Group Co., Ltd, Nanyang, China
| | - Feng-Li Hui
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang Normal University, Nanyang, China
- *Correspondence: Feng-Li Hui,
| |
Collapse
|
17
|
Chai CY, Gao WL, Yan ZL, Hui FL. Four new species of Trichomonascaceae (Saccharomycetales, Saccharomycetes) from Central China. MycoKeys 2022; 90:1-18. [PMID: 36760421 PMCID: PMC9849089 DOI: 10.3897/mycokeys.90.83829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
Trichomonascaceae is the largest family of ascomycetous yeast in the order Saccharomycetales. In spite of the extensive body of research on Trichomonascaceae in China, there remain new species to be discovered. Here, we describe four new species isolated from several rotting wood samples from Henan Province, Central China. Phylogenetic analysis of a combined ITS and nrLSU dataset with morphological studies revealed four new species in the Trichomonascaceae: Diddensiellaluoyangensis, Sugiyamaellacylindrica, Su.robnettiae, and Zygoascusdetingensis. Clustering in the Diddensiella clade, D.luoyangensis' closest neighbour was D.transvaalensis. Meanwhile, Su.cylindrica clustered in the Sugiyamaella clade closest to Su.marilandica and Su.qingdaonensis. Also clustering in the Sugiyamaella clade, Su.robnettiae was most closely related to Su.chuxiongensis. Finally, Z.detingensis occupied a distinct and separated basal branch from the other species of the genus Zygoascus. These results indicate a high species diversity of Trichomonascaceae.
Collapse
Affiliation(s)
- Chun-Yue Chai
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina,Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang 473061, ChinaResearch Center of Henan Provincial Agricultural Biomass Resource Engineering and TechnologyNanyangChina
| | - Wan-Li Gao
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina
| | - Zhen-Li Yan
- State Key Laboratory of Motor Vehicle Biofuel Technology, Henan Tianguan Enterprise Group Co., Ltd., Nanyang 473000, ChinaState Key Laboratory of Motor Vehicle Biofuel Technology, Henan Tianguan Enterprise Group Co., Ltd.NanyangChina
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina,Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang 473061, ChinaResearch Center of Henan Provincial Agricultural Biomass Resource Engineering and TechnologyNanyangChina
| |
Collapse
|
18
|
Helmstetter N, Chybowska AD, Delaney C, Da Silva Dantas A, Gifford H, Wacker T, Munro C, Warris A, Jones B, Cuomo CA, Wilson D, Ramage G, Farrer RA. Population genetics and microevolution of clinical Candida glabrata reveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes, and drug targets. Genetics 2022; 221:iyac031. [PMID: 35199143 PMCID: PMC9071574 DOI: 10.1093/genetics/iyac031] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/16/2022] [Indexed: 12/02/2022] Open
Abstract
Candida glabrata is the second most common etiological cause of worldwide systemic candidiasis in adult patients. Genome analysis of 68 isolates from 8 hospitals across Scotland, together with 83 global isolates, revealed insights into the population genetics and evolution of C. glabrata. Clinical isolates of C. glabrata from across Scotland are highly genetically diverse, including at least 19 separate sequence types that have been recovered previously in globally diverse locations, and 1 newly discovered sequence type. Several sequence types had evidence for ancestral recombination, suggesting transmission between distinct geographical regions has coincided with genetic exchange arising in new clades. Three isolates were missing MATα1, potentially representing a second mating type. Signatures of positive selection were identified in every sequence type including enrichment for epithelial adhesins thought to facilitate fungal adhesin to human epithelial cells. In patent microevolution was identified from 7 sets of recurrent cases of candidiasis, revealing an enrichment for nonsynonymous and frameshift indels in cell surface proteins. Microevolution within patients also affected epithelial adhesins genes, and several genes involved in drug resistance including the ergosterol synthesis gene ERG4 and the echinocandin target FKS1/2, the latter coinciding with a marked drop in fluconazole minimum inhibitory concentration. In addition to nuclear genome diversity, the C. glabrata mitochondrial genome was particularly diverse, with reduced conserved sequence and conserved protein-encoding genes in all nonreference ST15 isolates. Together, this study highlights the genetic diversity within the C. glabrata population that may impact virulence and drug resistance, and 2 major mechanisms generating this diversity: microevolution and genetic exchange/recombination.
Collapse
Affiliation(s)
- Nicolas Helmstetter
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | | | - Christopher Delaney
- School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Hugh Gifford
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Theresa Wacker
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Carol Munro
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Adilia Warris
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Brian Jones
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | | | - Duncan Wilson
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
| | - Gordon Ramage
- School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Rhys A Farrer
- Medical Research Council, Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD UK
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
19
|
Chai CY, Gao WL, Li Y, Yan ZL, Hui FL. Kodamaeahongheensis f.a., sp. nov., Kodamaeaovata f.a., sp. nov. and Kodamaeayamadae f.a., sp. nov., three new yeast species of Kodamaea (Saccharomycetales, Debaryomycetacae) from China. MycoKeys 2022; 89:121-137. [PMID: 36760829 PMCID: PMC9849074 DOI: 10.3897/mycokeys.89.81119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/15/2022] [Indexed: 11/12/2022] Open
Abstract
Kodamaea includes a growing number of interesting yeasts of the family Debaryomycetacae that are widely distributed in temperate, subtropical and tropical regions of different continents. During recent yeast collections in Henan and Yunnan Province in China, several isolates of Kodamaea were obtained from rotting wood, all of which represent undescribed taxa. Based on morphological and phylogenetic analyses (ITS and LSU rDNA), three new species are proposed: K.hongheensis f.a., sp. nov., K.ovata f.a., sp. nov. and K.yamadae f.a., sp. nov. In addition, sixteen Candida species, which are members of the Kodamaea clade based on phylogenetic analysis, are transferred to Kodamaea as new combinations. Our results indicate high species diversity of Kodamaea waiting to be discovered in rotting wood from tropical and subtropical China.
Collapse
Affiliation(s)
- Chun-Yue Chai
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina,Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang 473061, ChinaResearch Center of Henan Provincial Agricultural Biomass Resource Engineering and TechnologyNanyangChina
| | - Wan-Li Gao
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina
| | - Ying Li
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina
| | - Zhen-Li Yan
- State Key Laboratory of Motor Vehicle Biofuel Technology, Henan Tianguan Enterprise Group Co., Ltd., Nanyang 473000, ChinaState Key Laboratory of Motor Vehicle Biofuel TechnologyNanyangChina
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, ChinaNanyang Normal UniversityNanyangChina,Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Nanyang 473061, ChinaResearch Center of Henan Provincial Agricultural Biomass Resource Engineering and TechnologyNanyangChina
| |
Collapse
|
20
|
Irinyi L, Roper M, Malik R, Meyer W. Finding a needle in a haystack – <i>in silico</i> search for environmental traces of <i>Candida auris</i><i> </i>. Jpn J Infect Dis 2022; 75:490-495. [DOI: 10.7883/yoken.jjid.2022.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Australia
| | - Michael Roper
- Division of Biomedical Science and Biochemistry, Australian National University, Australia
| | - Richard Malik
- Centre for Veterinary Education, The University of Sydney, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Australia
| |
Collapse
|
21
|
Sakpuntoon V, Péter G, Groenewald M, Dlauchy D, Limtong S, Srisuk N. Description of Crinitomyces reliqui gen. nov., sp. nov. and Reassignment of Trichosporiella flavificans and Candida ghanaensis to the Genus Crinitomyces. J Fungi (Basel) 2022; 8:224. [PMID: 35330226 PMCID: PMC8953626 DOI: 10.3390/jof8030224] [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: 01/30/2022] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
The systematic position of 16 yeast strains isolated from Thailand, Hungary, The Netherlands, and the Republic of Poland were evaluated using morphological, physiological, and phylogenetic analyses. Based on the similarity of the D1/D2 domain of the LSU rRNA gene, the strains were assigned to two distinct species, Trichosporiella flavificans and representatives of a new yeast species. Phylogenetic analyses revealed that Candida ghanaensis CBS 8798T showed a strong relationship with the aforementioned two species. The more fascinating issue is that Candida and Trichosporiella genera have been placed in different subphyla, Saccharomycotina and Pezizomycotina, respectively. The close relationship between Trichosporiella flavificans, Candida ghanaensis and the undescribed species was unexpected and needed to be clarified. As for morphological and physiological characteristics, the three yeast species shared a hairy colony appearance and an ability to assimilate 18 carbon sources. Based on phylogenetic analyses carried out in the present study, Crinitomyces gen. nov. was proposed to accommodate the new yeast species, Crinitomyces reliqui sp. nov. (Holotype: TBRC 15054, Isotypes: DMKU-FW23-23 and PYCC 9001). In addition, the two species Trichosporiella flavificans and Candida ghanaensis were reassigned to the genus Crinitomyces as, Crinitomyces flavificans (Type: CBS 760.79) comb. nov. and Crinitomyces ghanaensis (Type: CBS 8798) comb. nov., respectively.
Collapse
Affiliation(s)
- Varunya Sakpuntoon
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (V.S.); (S.L.)
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, H-1118 Budapest, Hungary; (G.P.); (D.D.)
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan, 8, 3584CT Utrecht, The Netherlands;
| | - Dénes Dlauchy
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, H-1118 Budapest, Hungary; (G.P.); (D.D.)
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (V.S.); (S.L.)
- Biodiversity Center, Kasetsart University (BDCKU), Bangkok 10900, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
| | - Nantana Srisuk
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (V.S.); (S.L.)
- Biodiversity Center, Kasetsart University (BDCKU), Bangkok 10900, Thailand
| |
Collapse
|
22
|
Franco-Duarte R, Čadež N, Rito T, Drumonde-Neves J, Dominguez YR, Pais C, Sousa MJ, Soares P. Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment. J Fungi (Basel) 2022; 8:jof8010052. [PMID: 35049992 PMCID: PMC8781136 DOI: 10.3390/jof8010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/16/2022] Open
Abstract
Clavispora santaluciae was recently described as a novel non-Saccharomyces yeast species, isolated from grapes of Azores vineyards, a Portuguese archipelago with particular environmental conditions, and from Italian grapes infected with Drosophila suzukii. In the present work, the genome of five Clavispora santaluciae strains was sequenced, assembled, and annotated for the first time, using robust pipelines, and a combination of both long- and short-read sequencing platforms. Genome comparisons revealed specific differences between strains of Clavispora santaluciae reflecting their isolation in two separate ecological niches—Azorean and Italian vineyards—as well as mechanisms of adaptation to the intricate and arduous environmental features of the geographical location from which they were isolated. In particular, relevant differences were detected in the number of coding genes (shared and unique) and transposable elements, the amount and diversity of non-coding RNAs, and the enzymatic potential of each strain through the analysis of their CAZyome. A comparative study was also conducted between the Clavispora santaluciae genome and those of the remaining species of the Metschnikowiaceae family. Our phylogenetic and genomic analysis, comprising 126 yeast strains (alignment of 2362 common proteins) allowed the establishment of a robust phylogram of Metschnikowiaceae and detailed incongruencies to be clarified in the future.
Collapse
Affiliation(s)
- Ricardo Franco-Duarte
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
- Correspondence: or
| | - Neža Čadež
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 101, 1000 Ljubljana, Slovenia;
| | - Teresa Rito
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - João Drumonde-Neves
- IITAA—Institute of Agricultural and Environmental Research and Technology, University of Azores, 9700-042 Angra do Heroísmo, Portugal;
| | | | - Célia Pais
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Maria João Sousa
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Soares
- CBMA, Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.R.); (C.P.); (M.J.S.); (P.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| |
Collapse
|
23
|
Abstract
AbstractYeasts, usually defined as unicellular fungi, occur in various fungal lineages. Hence, they are not a taxonomic unit, but rather represent a fungal lifestyle shared by several unrelated lineages. Although the discovery of new yeast species occurs at an increasing speed, at the current rate it will likely take hundreds of years, if ever, before they will all be documented. Many parts of the earth, including many threatened habitats, remain unsampled for yeasts and many others are only superficially studied. Cold habitats, such as glaciers, are home to a specific community of cold-adapted yeasts, and, hence, there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change. The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion. Many countries of the so-called Global South have not been sampled for yeasts, despite their economic promise. However, extensive research activity in Asia, especially China, has yielded many taxonomic novelties. Comparative genomics studies have demonstrated the presence of yeast species with a hybrid origin, many of them isolated from clinical or industrial environments. DNA-metabarcoding studies have demonstrated the prevalence, and in some cases dominance, of yeast species in soils and marine waters worldwide, including some surprising distributions, such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.
Collapse
|
24
|
Binati RL, Salvetti E, Bzducha-Wróbel A, Bašinskienė L, Čižeikienė D, Bolzonella D, Felis GE. Non-conventional yeasts for food and additives production in a circular economy perspective. FEMS Yeast Res 2021; 21:6380488. [PMID: 34601574 DOI: 10.1093/femsyr/foab052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/27/2021] [Indexed: 12/18/2022] Open
Abstract
Yeast species have been spontaneously participating in food production for millennia, but the scope of applications was greatly expanded since their key role in beer and wine fermentations was clearly acknowledged. The workhorse for industry and scientific research has always been Saccharomyces cerevisiae. It occupies the largest share of the dynamic yeast market, that could further increase thanks to the better exploitation of other yeast species. Food-related 'non-conventional' yeasts (NCY) represent a treasure trove for bioprospecting, with their huge untapped potential related to a great diversity of metabolic capabilities linked to niche adaptations. They are at the crossroad of bioprocesses and biorefineries, characterized by low biosafety risk and produce food and additives, being also able to contribute to production of building blocks and energy recovered from the generated waste and by-products. Considering that the usual pattern for bioprocess development focuses on single strains or species, in this review we suggest that bioprospecting at the genus level could be very promising. Candida, Starmerella, Kluyveromyces and Lachancea were briefly reviewed as case studies, showing that a taxonomy- and genome-based rationale could open multiple possibilities to unlock the biotechnological potential of NCY bioresources.
Collapse
Affiliation(s)
- Renato L Binati
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Elisa Salvetti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Anna Bzducha-Wróbel
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159c St., 02-776 Warsaw, Poland
| | - Loreta Bašinskienė
- Department of Food Science and Technology, Kaunas University of Technology, Radvilėnų St. 19A, 44249 Kaunas, Lithuania
| | - Dalia Čižeikienė
- Department of Food Science and Technology, Kaunas University of Technology, Radvilėnų St. 19A, 44249 Kaunas, Lithuania
| | - David Bolzonella
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134 Verona (VR), Italy
| |
Collapse
|
25
|
Stalpers JA, Redhead SA, May TW, Rossman AY, Crouch JA, Cubeta MA, Dai YC, Kirschner R, Langer GJ, Larsson KH, Mack J, Norvell LL, Oberwinkler F, Papp V, Roberts P, Rajchenberg M, Seifert KA, Thorn RG. Competing sexual-asexual generic names in Agaricomycotina (Basidiomycota) with recommendations for use. IMA Fungus 2021; 12:22. [PMID: 34380577 PMCID: PMC8359032 DOI: 10.1186/s43008-021-00061-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 04/03/2021] [Indexed: 11/10/2022] Open
Abstract
With the change to one scientific name for fungal taxa, generic names typified by species with sexual or asexual morph types are being evaluated to determine which names represent the same genus and thus compete for use. In this paper generic names of the Agaricomycotina (Basidiomycota) were evaluated to determine synonymy based on their type. Forty-seven sets of sexually and asexually typified names were determined to be congeneric and recommendations are made for which generic name to use. In most cases the principle of priority is followed. However, 16 generic names are recommended for use that do not have priority and thus need to be protected: Aleurocystis over Matula; Armillaria over Acurtis and Rhizomorpha; Asterophora over Ugola; Botryobasidium over Acladium, Allescheriella, Alysidium, Haplotrichum, Physospora, and Sporocephalium; Coprinellus over Ozonium; Coprinopsis over Rhacophyllus; Dendrocollybia over Sclerostilbum and Tilachlidiopsis; Diacanthodes over Bornetina; Echinoporia over Echinodia; Neolentinus over Digitellus; Postia over Ptychogaster; Riopa over Sporotrichum; Scytinostroma over Artocreas, Michenera, and Stereofomes; Tulasnella over Hormomyces; Typhula over Sclerotium; and Wolfiporia over Gemmularia and Pachyma. Nine species names are proposed for protection: Botryobasidium aureum, B. conspersum, B. croceum, B. simile, Pellicularia lembosporum (syn. B. lembosporum), Phanerochaete chrysosporium, Polyporus metamorphosus (syn. Riopa metamorphosa), Polyporus mylittae (syn. Laccocephalum mylittae), and Polyporus ptychogaster (syn. Postia ptychogaster). Two families are proposed for protection: Psathyrellaceae and Typhulaceae. Three new species names and 30 new combinations are established, and one lectotype is designated.
Collapse
Affiliation(s)
| | - Scott A Redhead
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, CEF, Ottawa, Ontario, K1A OC6, Canada
| | - Tom W May
- Royal Botanic Gardens Victoria, 100 Birdwood Avenue, Melbourne, Victoria, 3004, Australia
| | - Amy Y Rossman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Jo Anne Crouch
- USDA-ARS, Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD, 20705, USA
| | - Marc A Cubeta
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27606, USA
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Roland Kirschner
- Department of Biomedical Sciences and Engineering, National Central University, Zhongli District, Taoyuan City, 320, Taiwan, Republic of China
| | - Gitta Jutta Langer
- Department of Forest Protection, Northwest German Forest Research Institute (NW-FVA), 37079, Goettingen, Lower Saxony, Germany
| | | | - Jonathan Mack
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, CEF, Ottawa, Ontario, K1A OC6, Canada
| | | | - Franz Oberwinkler
- Lehrstuhl für Spezielle Botanik und Mykologie, Botanisches Institut, Universität, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Viktor Papp
- Department of Botany, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | | | - Mario Rajchenberg
- Centro Forestal CIEFAP, C.C. 14, 9200, Esquel, Chubut, Argentina.,National Research Council of Argentina (CONICET), Buenos Aires, Argentina
| | - Keith A Seifert
- Department of Biology, Carlton University, Ottawa, Ontario, K1S 5B6, Canada
| | - R Greg Thorn
- Department of Biology, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| |
Collapse
|
26
|
The Curious Case of Nonrepetitive Centromeric DNA Sequences in Candida auris and Related Species. mBio 2021; 12:e0147621. [PMID: 34340554 PMCID: PMC8406187 DOI: 10.1128/mbio.01476-21] [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] [Indexed: 11/22/2022] Open
Abstract
2009 saw the first description of Candida auris, a yeast pathogen of humans. C. auris has since grown into a global problem in intensive care settings, where it causes systemic infections in patients with underlying health issues. Recent whole-genome sequencing has discerned five C. auris clades with distinct phenotypic features which display genomic divergence on a DNA sequence and a chromosome structure level. In the absence of sexual reproduction in C. auris, the mechanism(s) behind the rapid genomic evolution of this emerging killer yeast has remained obscure. Yet, one important bit of information about chromosome organization was missing, the identification of the centromeres. In a recent study, Sanyal and coworkers (A. Narayanan, R. N. Vadnala, P. Ganguly, P. Selvakumar, et al., mBio 12:e00905-21, 2021, https://doi.org/10.1128/mBio.00905-21) filled this knowledge gap by mapping the centromeres in C. auris and its close relatives. This represents a major advance in the chromosome biology of the Candida/Clavispora clade.
Collapse
|
27
|
Yurkov A, Alves A, Bai FY, Boundy-Mills K, Buzzini P, Čadež N, Cardinali G, Casaregola S, Chaturvedi V, Collin V, Fell JW, Girard V, Groenewald M, Hagen F, Hittinger CT, Kachalkin AV, Kostrzewa M, Kouvelis V, Libkind D, Liu X, Maier T, Meyer W, Péter G, Piątek M, Robert V, Rosa CA, Sampaio JP, Sipiczki M, Stadler M, Sugita T, Sugiyama J, Takagi H, Takashima M, Turchetti B, Wang QM, Boekhout T. Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes. IMA Fungus 2021; 12:18. [PMID: 34256869 PMCID: PMC8278710 DOI: 10.1186/s43008-021-00067-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/18/2021] [Indexed: 01/25/2023] Open
Abstract
The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.
Collapse
Affiliation(s)
- Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany.
| | - Artur Alves
- Departamento de Biologia, CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, Phaff Yeast Culture Collection, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Neža Čadež
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ul. 101, 1000, Ljubljana, Slovenia
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY, 12208, USA
| | - Valérie Collin
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France
| | - Jack W Fell
- Emeritus Professor, Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Key Biscayne, FL, 33149, USA
| | - Victoria Girard
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | - Aleksey V Kachalkin
- Faculty of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1-12, 119991, Moscow, Russia.,All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms (IBPM RAS), Russian Academy of Sciences, Prospect Nauki 5, 142290, Puschino, Russia
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Vassili Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701, Athens, Greece
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) CONICET - Universidad Nacional del Comahue, Quintral 1250, San Carlos de Bariloche, Rio Negro, Argentina
| | - Xinzhan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China
| | - Thomas Maier
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, 2006, Australia.,Westmead Institute for Medical Research, 176 Hawkesbury Rd, Westmead, NSW, 2145, Australia.,Westmead Hospital (Research and Education Network), Darcy Rd, Westmead, NSW, 2145, Australia
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, Budapest, H-1118, Hungary
| | - Marcin Piątek
- Department of Mycology, W. Szafer Institute of Botany of the Polish Academy of Sciences, Lubicz ul. 46, 31-512, Kraków, Poland
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Carlos A Rosa
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627 Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Jose Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Largo da Torre, 2825-149, Caparica, Portugal.,Departamento de Ciências da Vida, PYCC - Portuguese Yeast Culture Collection, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Largo da Torre, 2825-149, Caparica, Portugal
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Egyetem tér 1, Debrecen, 4010, Hungary
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2 Chome-522-1 Noshio, Kiyose, Tokyo, 204-8588, Japan
| | - Junta Sugiyama
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan.,TechnoSuruga Laboratory Co., Ltd., 388-1, Nagasaki, Shimuzu, Shizuoka, 424-0065, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Masako Takashima
- Laboratory of Yeast Systematics, Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences & Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3-1 Beichen West Road., Chaoyang District, Beijing, 100101, People's Republic of China.,College of Life Sciences, Hebei University, 180 Wusi Dong Road, Lian Chi District, Baoding City, Hebei Province, 071002, People's Republic of China
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 904 Science Park, 1098 XH, Amsterdam, The Netherlands
| |
Collapse
|
28
|
Narayanan A, Vadnala RN, Ganguly P, Selvakumar P, Rudramurthy SM, Prasad R, Chakrabarti A, Siddharthan R, Sanyal K. Functional and Comparative Analysis of Centromeres Reveals Clade-Specific Genome Rearrangements in Candida auris and a Chromosome Number Change in Related Species. mBio 2021; 12:e00905-21. [PMID: 33975937 PMCID: PMC8262905 DOI: 10.1128/mbio.00905-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/22/2022] Open
Abstract
The thermotolerant multidrug-resistant ascomycete Candida auris rapidly emerged since 2009 causing systemic infections worldwide and simultaneously evolved in different geographical zones. The molecular events that orchestrated this sudden emergence of the killer fungus remain mostly elusive. Here, we identify centromeres in C. auris and related species, using a combined approach of chromatin immunoprecipitation and comparative genomic analyses. We find that C. auris and multiple other species in the Clavispora/Candida clade shared a conserved small regional GC-poor centromere landscape lacking pericentromeres or repeats. Further, a centromere inactivation event led to karyotypic alterations in this species complex. Interspecies genome analysis identified several structural chromosomal changes around centromeres. In addition, centromeres are found to be rapidly evolving loci among the different geographical clades of the same species of C. auris Finally, we reveal an evolutionary trajectory of the unique karyotype associated with clade 2 that consists of the drug-susceptible isolates of C. aurisIMPORTANCECandida auris, the killer fungus, emerged as different geographical clades, exhibiting multidrug resistance and high karyotype plasticity. Chromosomal rearrangements are known to play key roles in the emergence of new species, virulence, and drug resistance in pathogenic fungi. Centromeres, the genomic loci where microtubules attach to separate the sister chromatids during cell division, are known to be hot spots of breaks and downstream rearrangements. We identified the centromeres in C. auris and related species to study their involvement in the evolution and karyotype diversity reported in C. auris We report conserved centromere features in 10 related species and trace the events that occurred at the centromeres during evolution. We reveal a centromere inactivation-mediated chromosome number change in these closely related species. We also observe that one of the geographical clades, the East Asian clade, evolved along a unique trajectory, compared to the other clades and related species.
Collapse
Affiliation(s)
- Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Rakesh Netha Vadnala
- Computational Biology, The Institute of Mathematical Sciences/HBNI, Chennai, India
| | - Promit Ganguly
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Pavitra Selvakumar
- Computational Biology, The Institute of Mathematical Sciences/HBNI, Chennai, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rajendra Prasad
- Amity Institute of Biotechnology, Amity University Haryana, Haryana, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rahul Siddharthan
- Computational Biology, The Institute of Mathematical Sciences/HBNI, Chennai, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Osaka University, Suita, Japan
| |
Collapse
|
29
|
Fungal taxonomy and sequence-based nomenclature. Nat Microbiol 2021; 6:540-548. [PMID: 33903746 PMCID: PMC10116568 DOI: 10.1038/s41564-021-00888-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 03/05/2021] [Indexed: 02/02/2023]
Abstract
The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This includes lineages represented only by sequence data. At present, these taxa cannot be formally described under the current nomenclature rules. By considering approaches used in bacterial taxonomy, we propose solutions for the nomenclature of taxa known only from sequences to facilitate consistent reporting and communication in the literature and public sequence repositories.
Collapse
|
30
|
Brysch-Herzberg M, Dlauchy D, Seidel M, Péter G. Cyberlindnera sylvatica sp. nov., a yeast species isolated from forest habitats. Int J Syst Evol Microbiol 2021; 71. [PMID: 33507858 DOI: 10.1099/ijsem.0.004477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five yeast strains isolated from forest habitats in Hungary and Germany were characterized phenotypically and by sequencing of the D1/D2 domain of the large subunit rRNA gene and the ITS1-5.8S-ITS2 (ITS) region of the rRNA gene. The strains have identical D1/D2 domain and ITS region sequences. By sequence comparisons, Candida mycetangii and Candida maritima were identified as the closest relatives among the currently recognized yeast species. The DNA sequences of the investigated strains differ by 1.2 % (six substitutions) in the D1/D2 domain and by 3.5 % (12 substitutions and eight indels) in the ITS region from the type strain of C. mycetangii (CBS 8675T) while by 1.2 % (six substitutions and one indel) in the D1/D2 domain and by 7 % (32 substitutions and seven indels) in the ITS region from the type strain of C. maritima (CBS 5107T). Because the intraspecies heterogeneity seems to be very low and the distance to the most closely related species is above the commonly expected level for intraspecies variability Cyberlindnera sylvatica sp. nov. (holotype, CBS 16335T; isotype, NCAIM Y.02233T; MycoBank no., MB 835268) is proposed to accommodate the above-noted five yeast strains. Phenotypically the novel species can be distinguished from C. mycetangii and C. maritima by the formation of ascospores. Cyberlindnera sylvatica forms one or two hat-shaped ascospores per ascus on many different media as well as well-developed pseudohyphae and true hyphae. Additionally, we propose the transfer of three anamorphic members of the Cyberlindnera americana sub-clade to the genus Cyberlindnera as the following new taxonomic combinations Cyberlindnera maritima f.a., comb. nov., Cyberlindnera mycetangii f.a., comb. nov. and Cyberlindnera nakhonratchasimensis f.a., comb. nov.
Collapse
Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany
| | - Dénes Dlauchy
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Somlói út 14-16, H-1118 Budapest, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Szent István University, Somlói út 14-16, H-1118 Budapest, Hungary
| |
Collapse
|
31
|
Burini JA, Eizaguirre JI, Loviso C, Libkind D. [Non-conventional yeasts as tools for innovation and differentiation in brewing]. Rev Argent Microbiol 2021; 53:359-377. [PMID: 33674169 DOI: 10.1016/j.ram.2021.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 11/18/2020] [Accepted: 01/04/2021] [Indexed: 11/16/2022] Open
Abstract
Yeasts play a crucial role in brewing. During fermentation, besides ethanol and carbon dioxide, yeasts produce a considerable number of organic compounds, which are essential for beer flavor. In particular, Saccharomyces cerevisiae and Saccharomyces pastorianus are traditionally used in the production of ale and lager beers, respectively. Nowadays, the continuous growth of the craft beer market motivates the production of differential and innovative beers; leading specialists and brewers focus on non-conventional yeasts as tools for new product development. In this work, we describe the potential application of non-conventional yeast species such as those of the genera Brettanomyces, Torulaspora, Lachancea, Wickerhamomyces, Pichia and Mrakia in the craft brewing industry, as well as non-traditional brewing yeasts of the Saccharomyces genus. Furthermore, the fermentation conditions of these non-conventional yeasts are discussed, along with their abilities to assimilate and metabolize diverse wort components providing differential characteristics to the final product. In summary, we present a comprehensive review of the state-of-the-art of non-conventional yeasts, which is highly relevant for their application in the production of novel craft beers including flavored beers, non-alcoholic beers, low-calorie beers and functional beers.
Collapse
Affiliation(s)
- Julieta Amalia Burini
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), CONICET - Universidad Nacional del Comahue, San Carlos de Bariloche, Argentina
| | - Juan Ignacio Eizaguirre
- Laboratorio de Biología Celular de Membranas (LBCM), Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE-CONICET), FCEN-UBA, Pabellón IFIByNE, Buenos Aires, Argentina
| | - Claudia Loviso
- Centro para el Estudio de Sistemas Marinos (CESIMAR), CONICET, Puerto Madryn, Argentina
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), CONICET - Universidad Nacional del Comahue, San Carlos de Bariloche, Argentina.
| |
Collapse
|
32
|
SU Y, ZHU JN, LI XR, ZHANG XG, FENG M, WANG N, LIU WJ. Candida tropicalis sp. Nov., a novel, zinc-enriched yeast species found in China. FOOD SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1590/fst.23419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yu SU
- Key Laboratory of Screening and Processing in new Tibetan medicine of Gansu Province, China
| | - Jian-Ning ZHU
- Drug Evaluation and Certification Center of Gansu Drug Administration, China
| | - Xiao-Ru LI
- Key Laboratory of Screening and Processing in new Tibetan medicine of Gansu Province, China
| | - Xin-Guo ZHANG
- Key Laboratory of Screening and Processing in new Tibetan medicine of Gansu Province, China
| | - Ming FENG
- Key Laboratory of Screening and Processing in new Tibetan medicine of Gansu Province, China
| | - Nan WANG
- Key Laboratory of Screening and Processing in new Tibetan medicine of Gansu Province, China
| | - Wen-Jie LIU
- Key Laboratory of Screening and Processing in new Tibetan medicine of Gansu Province, China
| |
Collapse
|
33
|
Abstract
The current article summarizes recent changes in nomenclature for fungi of medical importance published in the years 2018 to 2019, including new species and revised names for existing ones. Many of the revised names have been widely adopted without further discussion. However, those that concern common pathogens of humans may take longer to achieve general usage, with new and current names reported together to engender increasing familiarity with the correct taxonomic classification.
Collapse
|
34
|
Drumonde-Neves J, Čadež N, Reyes-Domínguez Y, Gallmetzer A, Schuller D, Lima T, Pais C, Franco-Duarte R. Clavispora santaluciae f.a., sp. nov., a novel ascomycetous yeast species isolated from grapes. Int J Syst Evol Microbiol 2021; 70:6307-6312. [PMID: 33090949 DOI: 10.1099/ijsem.0.004531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study of yeast diversity in Azorean vineyards, four strains were isolated which were found to represent a novel yeast species based on the sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) and of the D1/D2 domain of the large subunit (LSU) rRNA gene, together with their physiological characteristics. An additional strain isolated from Drosophila suzukii in Italy had identical D1/D2 sequences and very similar ITS regions (five nucleotide substitutions) to the Azorean strains. Phylogenetic analysis using sequences of the ITS region and D1/D2 domain showed that the five strains are closely related to Clavispora lusitaniae, although with 56 nucleotide differences in the D2 domain. Intraspecies variation revealed between two and five nucleotide differences, considering the five strains of Clavispora santaluciae. Some phenotypic discrepancies support the separation of the new species from their closely related ones, such as the inability to grow at temperatures above 35 °C, to produce acetic acid and the capacity to assimilate starch. Neither conjugations nor ascospore formation were observed in any of the strains. The name Clavispora santaluciae f.a., sp. nov., is proposed to accommodate the above noted five strains (holotype, CBS 16465T; MycoBank no., MB 835794).
Collapse
Affiliation(s)
- João Drumonde-Neves
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Portugal
- IITAA - Institute of Agricultural and Environmental Research and Technology, University of Azores, Angra do Heroísmo, Portugal
| | - Neža Čadež
- University of Ljubljana Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana, Ljubljana, Slovenia
| | | | | | - Dorit Schuller
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Portugal
| | - Teresa Lima
- IITAA - Institute of Agricultural and Environmental Research and Technology, University of Azores, Angra do Heroísmo, Portugal
| | - Célia Pais
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Portugal
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Portugal
| | - Ricardo Franco-Duarte
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Portugal
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Portugal
| |
Collapse
|
35
|
Sousa-Silva M, Vieira D, Soares P, Casal M, Soares-Silva I. Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii. J Fungi (Basel) 2021; 7:36. [PMID: 33435379 PMCID: PMC7827542 DOI: 10.3390/jof7010036] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022] Open
Abstract
Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii.
Collapse
Affiliation(s)
- Maria Sousa-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Daniel Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Soares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Margarida Casal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Isabel Soares-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| |
Collapse
|
36
|
Lv SL, Chai CY, Wang Y, Yan ZL, Hui FL. Five new additions to the genus Spathaspora (Saccharomycetales, Debaryomycetaceae) from southwest China. MycoKeys 2020; 75:31-49. [PMID: 33223920 PMCID: PMC7669824 DOI: 10.3897/mycokeys.75.57192] [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: 08/03/2020] [Accepted: 10/25/2020] [Indexed: 12/28/2022] Open
Abstract
Spathaspora is an important genus of d-xylose-fermenting yeasts that are poorly studied in China. During recent yeast collections in Yunnan Province in China, 13 isolates of Spathaspora were obtained from rotting wood and all represent undescribed taxa. Based on morphological and phylogenetic analyses (ITS and nuc 28S), five new species are proposed: Spathaspora elongata, Sp. mengyangensis, Sp. jiuxiensis, Sp. parajiuxiensis and Sp. rosae. Our results indicate a high species diversity of Spathaspora waiting to be discovered in rotting wood from tropical and subtropical southwest China. In addition, the two Candida species, C. jeffriesii and C. materiae, which are members of the Spathaspora clade based on phylogeny, are transferred to Spathaspora as new combinations.
Collapse
Affiliation(s)
- Shi-Long Lv
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China Nanyang Normal University Nanyang China
| | - Chun-Yue Chai
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China Nanyang Normal University Nanyang China
| | - Yun Wang
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China Nanyang Normal University Nanyang China
| | - Zhen-Li Yan
- State Key Laboratory of Motor Vehicle Biofuel Technology, Henan Tianguan Enterprise Group Co. Ltd., Nanyang 473000, China Henan Tianguan Enterprise Group Nanyang China
| | - Feng-Li Hui
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China Nanyang Normal University Nanyang China
| |
Collapse
|
37
|
Takashima M, Suh SO, Bai FY, Sugita T. Takashi Nakase's last tweet: what is the current direction of microbial taxonomy research? FEMS Yeast Res 2020; 19:5670643. [PMID: 31816016 DOI: 10.1093/femsyr/foz066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 12/07/2019] [Indexed: 12/14/2022] Open
Abstract
During the last few decades, type strains of most yeast species have been barcoded using the D1/D2 domain of their LSU rRNA gene and internal transcribed spacer (ITS) region. Species identification using DNA sequences regarding conspecificity in yeasts has also been studied. Most yeast species can be identified according to the sequence divergence of their ITS region or a combination of the D1/D2 and ITS regions. Studies that have examined intraspecific diversity have used multilocus sequence analyses, whereas the marker regions used in this analysis vary depending upon taxa. D1/D2 domain and ITS region sequences have been used as barcodes to develop primers suitable for the detection of the biological diversity of environmental DNA and the microbiome. Using these barcode sequences, it is possible to identify relative lineages and infer their gene products and function, and how they adapt to their environment. If barcode sequence was not variable enough to identify a described species, one could investigate the other biological traits of these yeasts, considering geological distance, environmental circumstances and isolation of reproduction. This article is dedicated to late Dr Takashi Nakase (1939-2018).
Collapse
Affiliation(s)
- Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan.,Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Sung-Oui Suh
- Manufacturing Science and Technology, American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, VA 20110, USA
| | - Feng-Yan Bai
- Institute of Microbiology, State Key Laboratory of Mycology, Chinese Academy of Sciences, Beijing 100101, China
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| |
Collapse
|
38
|
Stavrou AA, Pérez-Hansen A, Lackner M, Lass-Flörl C, Boekhout T. Elevated minimum inhibitory concentrations to antifungal drugs prevail in 14 rare species of candidemia-causing Saccharomycotina yeasts. Med Mycol 2020; 58:987-995. [DOI: 10.1093/mmy/myaa005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/15/2020] [Accepted: 01/23/2020] [Indexed: 12/27/2022] Open
Abstract
AbstractAntifungal susceptibility profiles of rare Saccharomycotina yeasts remain missing, even though an increase in prevalence of such rare Candida species was reported in candidemia. Majority of these rare yeast species carry intrinsic resistances against at least one antifungal compound. Some species are known to be cross-resistant (against multiple drugs of the same drug class) or even multi-drug resistant (against multiple drugs of different drug classes). We performed antifungal susceptibility testing (AFST) according to EUCAST broth microdilution for 14 rare species (Clavispora lusitaniae, Candida intermedia, Candida auris, Diutina rugosa, Wickerhamiella pararugosa, Yarrowia lipolytica, Pichia norvegensis, Candida nivariensis, Kluyveromyces marxianus, Wickerhamomyces anomalus, Candida palmioleophila, Meyerozyma guilliermondii, Meyerozyma caribbica, and Debaryomyces hansenii) known to cause candidemia. In total, 234 isolates were tested for amphotericin B, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, micafungin, and caspofungin. Amphothericin B had the broadest efficiency against the 14 tested rare yeast species, while high minimum inhibitory concentrations (MICs) against azole drugs and echinocandins were common. Voriconazole was the most efficient azole drug. Multidrug resistance was observed for the species C. auris and K. marxianus. Multidrug resistant individual isolates were found for Y. lipolytica and M. caribbica. In conclusion, the observed high MIC values of the rare Saccharomycotina species tested limit antifungal treatment options, complicating the management of such infections.
Collapse
Affiliation(s)
- Aimilia A Stavrou
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098XH Amsterdam, The Netherlands
| | - Antonio Pérez-Hansen
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Michaela Lackner
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schoepfstrasse 41, 6020 Innsbruck, Austria
| | - Teun Boekhout
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098XH Amsterdam, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Shanghai 200003, China
| |
Collapse
|
39
|
Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Scientific Opinion on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA (2017-2019). EFSA J 2020; 18:e05966. [PMID: 32874212 PMCID: PMC7448045 DOI: 10.2903/j.efsa.2020.5966] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The qualified presumption of safety (QPS) was developed to provide a safety pre-assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as 'qualifications'. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS-recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.
Collapse
|
40
|
Zangl I, Pap IJ, Aspöck C, Schüller C. The role of Lactobacillus species in the control of Candida via biotrophic interactions. MICROBIAL CELL 2019; 7:1-14. [PMID: 31921929 PMCID: PMC6946018 DOI: 10.15698/mic2020.01.702] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microbial communities have an important role in health and disease. Candida spp. are ubiquitous commensals and sometimes opportunistic fungal pathogens of humans, colonizing mucosal surfaces of the genital, urinary, respiratory and gastrointestinal tracts and the oral cavity. They mainly cause local mucosal infections in immune competent individuals. However, in the case of an ineffective immune defense, Candida infections may become a serious threat. Lactobacillus spp. are part of the human microbiome and are natural competitors of Candida in the vaginal environment. Lactic acid, low pH and other secreted metabolites are environmental signals sensed by fungal species present in the microbiome. This review briefly discusses the ternary interaction between host, Lactobacillus species and Candida with regard to fungal infections and the potential antifungal and fungistatic effect of Lactobacillus species. Our understanding of these interactions is incomplete due to the variability of the involved species and isolates and the complexity of the human host.
Collapse
Affiliation(s)
- Isabella Zangl
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Applied Genetics and Cell Biology (DAGZ), Tulln, Austria
| | - Ildiko-Julia Pap
- University Hospital of St. Pölten, Institute for Hygiene and Microbiology, St Pölten, Austria
| | - Christoph Aspöck
- University Hospital of St. Pölten, Institute for Hygiene and Microbiology, St Pölten, Austria
| | - Christoph Schüller
- University of Natural Resources and Life Sciences Vienna (BOKU), Department of Applied Genetics and Cell Biology (DAGZ), Tulln, Austria.,Bioactive Microbial Metabolites (BiMM), BOKU, Tulln, Austria
| |
Collapse
|
41
|
Buchta V, Bolehovská R, Hovorková E, Cornely OA, Seidel D, Žák P. Saprochaete clavata Invasive Infections - A New Threat to Hematological-Oncological Patients. Front Microbiol 2019; 10:2196. [PMID: 31736883 PMCID: PMC6830389 DOI: 10.3389/fmicb.2019.02196] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022] Open
Abstract
Background Saprochaete clavata (formerly Geotrichum clavatum, now proposed as Magnusiomyces clavatus) is a filamentous yeast-like fungus that has recently been described as an emerging pathogen mostly in patients with acute leukemia. Methods This is a retrospective study of patients diagnosed with proven and probable S. clavata infection at the University Hospital, Hradec Králové, Czechia between March 2005 and December 2017. Previous cases were identified from the literature and FungiScope® database. Results Six new cases (5 females, 1 male) of blood-stream S. clavata infections at the hemato-oncological department were described including epidemiological data of additional 48 patients colonized with the species. Overall, 116 strains of S. clavata were isolated from different clinical specimens of 54 patients; most of them belonged to the respiratory tract (60.3%). S. clavata was the most frequent species among arthroconidial yeasts (Trichosporon, Galactomyces, Magnusiomyces) recovered from the blood. All our patients with S. clavata infection had profound neutropenia, a central venous catheter, broad-spectrum antibiotics and antifungal prophylaxis; four had a history of a biliary tract system disease. The diagnosis was based on a positive blood culture in all patients. Four patients died of multiorgan failure and sepsis despite treatment with lipid-based amphotericin B and/or voriconazole. From the literature and FungiScope database, 67 previous cases of S. clavata infections were evaluated in context of our cases. Conclusion Saprochaete clavata infection represents a life-threatening mycosis in severely immunocompromised patients. The successful outcome of treatment seems to be critically dependent on the early diagnosis and the recovery of underlying conditions associated with immune dysfunction or deficiency.
Collapse
Affiliation(s)
- Vladimir Buchta
- Department of Clinical Microbiology, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| | - Radka Bolehovská
- Department of Clinical Biochemistry and Diagnostics, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| | - Eva Hovorková
- The Fingerland Department of Pathology, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| | - Oliver A Cornely
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Department I of Internal Medicine, ECMM Diamond Center of Excellence in Medical Mycology, German Centre for Infection Research (DZIF), University of Cologne, Cologne, Germany.,Clinical Trials Centre Cologne (ZKS Köln), University of Cologne, Cologne, Germany
| | - Danila Seidel
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Department of Internal Medicine, ECMM Diamond Center of Excellence in Medical Mycology, University of Cologne, Cologne, Germany
| | - Pavel Žák
- 4th Department of Internal Medicine - Division of Hematology, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| |
Collapse
|
42
|
Zhai YC, Huang LN, Xi ZW, Chai CY, Hui FL. Candida yunnanensis sp. nov. and Candida parablackwelliae sp. nov., two yeast species in the Candida albicans/ Lodderomyces clade. Int J Syst Evol Microbiol 2019; 69:2775-2780. [PMID: 31237537 DOI: 10.1099/ijsem.0.003552] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During studies on the yeast communities associated with rotting wood in the Xishuangbanna Tropical Rainforest in PR China, four novel yeast strains were found. Phylogenetic analysis based on the concatenated sequences of the D1/D2 domains of the large subunit rRNA gene and the ITS regions showed that these strains represented two novel species in the Candida albicans/Lodderomyces clade. The novel species, represented by strains NYNU 17948 and NYNU 17981, formed a clade with Candida maltosa and Candida baotianmanensis, with 1-1.8% sequence divergence in the D1/D2 domains and 8.9-10% sequence divergence in the ITS regions. The other novel species, represented by NYNU 17105 and NYNU 17763, is most closely related to Candida blackwelliae with 0.7 % sequence divergence in the D1/D2 domains and 6.9 % sequence divergence in the ITS regions. The two novel species could be distinguished from their closest described species in terms of physiological traits. The two novel species are described as Candida yunnanensis sp. nov. (holotype NYNU 17948) and Candida parablackwelliae sp. nov. (holotype NYNU 17763).
Collapse
Affiliation(s)
- Yi-Chang Zhai
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Lin-Na Huang
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Zhi-Wen Xi
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Chun-Yue Chai
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| | - Feng-Li Hui
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, PR China
| |
Collapse
|
43
|
Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales. Fungal Genet Biol 2019; 130:31-42. [DOI: 10.1016/j.fgb.2019.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/19/2019] [Accepted: 04/20/2019] [Indexed: 02/03/2023]
|
44
|
Kaewwichian R, Khunnamwong P, Am-In S, Jindamorakot S, Groenewald M, Limtong S. Candida xylosifermentans sp. nov., a d-xylose-fermenting yeast species isolated in Thailand. Int J Syst Evol Microbiol 2019; 69:2674-2680. [DOI: 10.1099/ijsem.0.003505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rungluk Kaewwichian
- Microbiology Program, Department of Science, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok, 10600, Thailand
| | - Pannida Khunnamwong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Somjit Am-In
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Sasitorn Jindamorakot
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 Utrecht, The Netherlands
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, 10300, Thailand
| |
Collapse
|
45
|
deKay K. Clinical Issues—September 2019. AORN J 2019; 110:316-324. [DOI: 10.1002/aorn.12786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
46
|
Johansen PG, Owusu-Kwarteng J, Parkouda C, Padonou SW, Jespersen L. Occurrence and Importance of Yeasts in Indigenous Fermented Food and Beverages Produced in Sub-Saharan Africa. Front Microbiol 2019; 10:1789. [PMID: 31447811 PMCID: PMC6691171 DOI: 10.3389/fmicb.2019.01789] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/19/2019] [Indexed: 12/28/2022] Open
Abstract
Indigenous fermented food and beverages represent a valuable cultural heritage in sub-Saharan Africa, having one of the richest selections of fermented food products in the world. In many of these indigenous spontaneously fermented food and beverages, yeasts are of significant importance. Several factors including raw materials, processing methods, hygienic conditions as well as the interactions between yeasts and other commensal microorganisms have been shown to influence yeast species diversity and successions. Both at species and strain levels, successions take place due to the continuous change in intrinsic and extrinsic growth factors. The selection pressure from the microbial stress factors leads to niche adaptation and both yeast species and strains with traits deviating from those generally acknowledged in current taxonomic keys, have been isolated from indigenous sub-Saharan African fermented food products. Yeasts are important for flavor development, impact shelf life, and nutritional value and do, in some cases, even provide host-beneficial effects. In order to sustain and upgrade these traditional fermented products, it is quite important to obtain detailed knowledge on the microorganisms involved in the fermentations, their growth requirements and interactions. While other publications have reported on the occurrence of prokaryotes in spontaneously fermented sub-Saharan food and beverages, the present review focuses on yeasts considering their current taxonomic position, relative occurrence and successions, interactions with other commensal microorganisms as well as beneficial effects and importance in human diet. Additionally, the risk of opportunistic yeasts is discussed.
Collapse
Affiliation(s)
| | - James Owusu-Kwarteng
- Department of Food Science and Technology, University of Energy and Natural Resources, Sunyani, Ghana
| | - Charles Parkouda
- Département Technologie Alimentaire, IRSAT/CNRST, Ouagadougou, Burkina Faso
| | | | - Lene Jespersen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
47
|
Sutcliffe IC. Valediction: descriptions of novel prokaryotic taxa published in Antonie van Leeuwenhoek—change in editorial policy and a signpost to the future? Antonie van Leeuwenhoek 2019; 112:1281-1282. [DOI: 10.1007/s10482-019-01311-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
48
|
Jackson BR, Chow N, Forsberg K, Litvintseva AP, Lockhart SR, Welsh R, Vallabhaneni S, Chiller T. On the Origins of a Species: What Might Explain the Rise of Candida auris? J Fungi (Basel) 2019; 5:E58. [PMID: 31284576 PMCID: PMC6787658 DOI: 10.3390/jof5030058] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 11/16/2022] Open
Abstract
Candida auris is an emerging multidrug-resistant yeast first described in 2009 that has since caused healthcare-associated outbreaks of severe human infections around the world. In some hospitals, it has become a leading cause of invasive candidiasis. C. auris is markedly different from most other pathogenic Candida species in its genetics, antifungal resistance, and ability to spread between patients. The reasons why this fungus began spreading widely in the last decade remain a mystery. We examine available data on C. auris and related species, including genomic epidemiology, phenotypic characteristics, and sites of detection, to put forth hypotheses on its possible origins. C. auris has not been detected in the natural environment; related species have been detected in in plants, insects, and aquatic environments, as well as from human body sites. It can tolerate hypersaline environments and higher temperatures than most Candida species. We explore hypotheses about the pre-emergence niche of C. auris, whether in the environmental or human microbiome, and speculate on factors that might have led to its spread, including the possible roles of healthcare, antifungal use, and environmental changes, including human activities that might have expanded its presence in the environment or caused increased human contact.
Collapse
Affiliation(s)
- Brendan R Jackson
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne, and Environmental Diseases, Mycotic Diseases Branch, Atlanta, GA 30329, USA.
| | - Nancy Chow
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne, and Environmental Diseases, Mycotic Diseases Branch, Atlanta, GA 30329, USA
| | - Kaitlin Forsberg
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne, and Environmental Diseases, Mycotic Diseases Branch, Atlanta, GA 30329, USA
- IHRC, Inc., Atlanta, GA 30346, USA
| | - Anastasia P Litvintseva
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne, and Environmental Diseases, Mycotic Diseases Branch, Atlanta, GA 30329, USA
| | - Shawn R Lockhart
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne, and Environmental Diseases, Mycotic Diseases Branch, Atlanta, GA 30329, USA
| | - Rory Welsh
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne, and Environmental Diseases, Mycotic Diseases Branch, Atlanta, GA 30329, USA
| | - Snigdha Vallabhaneni
- Centers for Disease Control and Prevention, Division of Healthcare Quality Promotion, Prevention and Response Branch, Atlanta, GA 30329, USA
| | - Tom Chiller
- Centers for Disease Control and Prevention, Division of Foodborne, Waterborne, and Environmental Diseases, Mycotic Diseases Branch, Atlanta, GA 30329, USA
| |
Collapse
|
49
|
Pérez-Hansen A, Lass-Flörl C, Lackner M, Aigner M, Alastruey-Izquierdo A, Arikan-Akdagli S, Bader O, Becker K, Boekhout T, Buzina W, Cornely OA, Hamal P, Kidd SE, Kurzai O, Lagrou K, Lopes Colombo A, Mares M, Masoud H, Meis JF, Oliveri S, Rodloff AC, Orth-Höller D, Guerrero-Lozano I, Sanguinetti M, Segal E, Taj-Aldeen SJ, Tortorano AM, Trovato L, Walther G, Willinger B. Antifungal susceptibility profiles of rare ascomycetous yeasts. J Antimicrob Chemother 2019; 74:2649-2656. [DOI: 10.1093/jac/dkz231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/30/2019] [Accepted: 05/04/2019] [Indexed: 12/21/2022] Open
Abstract
AbstractObjectivesTo generate antifungal susceptibility patterns for Trichomonascus ciferrii (Candida ciferrii), Candida inconspicua (Torulopsis inconspicua) and Diutina rugosa species complex (Candida rugosa species complex), and to provide key parameters such as MIC50, MIC90 and tentative epidemiological cut-off values (TECOFFs).MethodsOur strain set included isolates of clinical origin: C. inconspicua (n = 168), D. rugosa species complex (n = 90) [Candida pararugosa (n = 60), D. rugosa (n = 26) and Candida mesorugosa (n = 4)], Pichia norvegensis (Candida norvegensis) (n = 15) and T. ciferrii (n = 8). Identification was performed by MALDI-TOF MS or internal transcribed spacer sequencing. Antifungal susceptibility patterns were generated for azoles, echinocandins and amphotericin B using commercial Etest and the EUCAST broth microdilution method v7.3.1. Essential agreement (EA) was calculated for Etest and EUCAST.ResultsC. inconspicua, C. pararugosa and P. norvegensis showed elevated azole MICs (MIC50 ≥0.06 mg/L), and D. rugosa and C. pararugosa elevated echinocandin MICs (MIC50 ≥0.06 mg/L). EA between methods was generally low (<90%); EA averaged 77.45%. TECOFFs were suggested for C. inconspicua and D. rugosa species complex.ConclusionsRare yeast species tested shared high fluconazole MICs. D. rugosa species complex displayed high echinocandin MICs, while C. inconspicua and P. norvegensis were found to have high azole MICs. Overall, the agreement between EUCAST and Etest was poor and therefore MIC values generated with Etest cannot be directly compared with EUCAST results.
Collapse
Affiliation(s)
- Antonio Pérez-Hansen
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, Austria
| | - Michaela Lackner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, Austria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Stavrou AA, Lackner M, Lass-Flörl C, Boekhout T. The changing spectrum of Saccharomycotina yeasts causing candidemia: phylogeny mirrors antifungal susceptibility patterns for azole drugs and amphothericin B. FEMS Yeast Res 2019; 19:5510445. [DOI: 10.1093/femsyr/foz037] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/20/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
- Aimilia A Stavrou
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098XH Amsterdam, The Netherlands
| | - Michaela Lackner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria
| | - Teun Boekhout
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098XH Amsterdam, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| |
Collapse
|