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Seike T, Takekata H, Kono K, Sakata N, Kotani H, Furusawa C, Matsuda F. Discovery and identification of a novel yeast species, Hanseniaspora drosophilae sp. nov., from Drosophila in Okinawa, Japan. Int J Syst Evol Microbiol 2025; 75. [PMID: 39903503 DOI: 10.1099/ijsem.0.006661] [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: 02/06/2025] Open
Abstract
Hanseniaspora, a genus of yeasts in which many species reproduce sexually, has attracted the attention of researchers because of its prevalence in diverse ecological niches. Building on our extensive collection efforts since 2020, three previously unknown yeast strains from wild Drosophila species trapped in ripe bananas in Okinawa, Japan, were isolated. Using a multifaceted approach, including physiological assessments and sequence analysis of the D1/D2 domain of the 26S LSU rRNA gene and the internal transcribed spacer (ITS) region, it was revealed that these strains are novel members of the genus Hanseniaspora. The three strains, JCM 36741T, JCM 36742 and JCM 36748, had identical sequences in their respective D1/D2 and ITS regions, justifying their classification as a single species. Moreover, the new species exhibited a remarkable degree of sequence divergence from its closest relatives, differing by 7 nucleotide substitutions (1.28%) in the D1/D2 domain, 29 nucleotide substitutions and 4 gaps (4.08%) in the ITS regions. These substantial sequence differences highlight the distinctiveness of this novel species in the genus Hanseniaspora. Further analysis revealed physiological characteristics that distinguished the new species from its closest relative, Hanseniaspora hatyaiensis (nom. inval.). These findings culminated in the proposed name Hanseniaspora drosophilae sp. nov., which recognizes the unique ecological niche within the Drosophila microbiota. By uncovering this novel species, this study not only adds to the growing body of knowledge on yeast diversity but also sheds light on the intricate ecological relationships that shape microbial communities. The implications of this discovery extend beyond taxonomic boundaries, inviting further exploration of the evolutionary dynamics and ecological significance of yeast-fly interactions. We propose accommodating H. drosophilae sp. nov. in the genus Hanseniaspora with JCM 36741T as the holotype. The MycoBank accession number is MB 853822.
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Affiliation(s)
- Taisuke Seike
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hiroki Takekata
- Organization for Research Promotion, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Keiko Kono
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
| | - Natsue Sakata
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hazuki Kotani
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Bunkyo-ku, Japan
| | - Fumio Matsuda
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Chen X, Qiao YZ, Hui FL. Hanseniaspora menglaensis f.a., sp. nov., a novel apiculate yeast species isolated from rotting wood. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486335 DOI: 10.1099/ijsem.0.005970] [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: 07/25/2023] Open
Abstract
Two apiculate strains (NYNU 181072 and NYNU 181083) of a bipolar budding yeast species were isolated from rotting wood samples collected in Xishuangbanna Tropical Rainforest in Yunnan Province, southwest PR China. On the basis of phenotypic characteristics and the results of phylogenetic analysis of the D1/D2 domain of the large subunit (LSU) rRNA, internal transcribed spacer (ITS) region and the actin (ACT1) gene, the two strains were found to represent a single novel species of the genus Hanseniaspora, for which the name Hanseniaspora menglaensis f.a., sp. nov. (holotype CICC 33364T; MycoBank MB 847437) is proposed. In the phylogenetic tree, H. menglaensis sp. nov. showed a close relationship with Hanseniaspora lindneri, Hanseniaspora mollemarum, Hanseniaspora smithiae and Hanseniaspora valbyensis. H. menglaensis sp. nov. differed from H. lindneri, the most closely related known species, by 1.2 % substitutions in the D1/D2 domain, 2.5 % substitutions in the ITS region and 5.4 % substitutions in the ACT1 gene, respectively. Physiologically, H. menglaensis sp. nov. can also be distinguished from H. lindneri by its ability to assimilate d-gluconate.
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Affiliation(s)
- Xue Chen
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Ya-Zhuo Qiao
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
| | - Feng-Li Hui
- School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, PR China
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Exploring the Core Microbiota of Four Different Traditional Fermented Beverages from the Colombian Andes. FERMENTATION 2022. [DOI: 10.3390/fermentation8120733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Fermentation is an ancient process used to prepare and preserve food. Currently, fermented beverages are part of the culture of people living in the Colombian Andean Region, and they are a vital part of their cosmology and ancestral vision. Chicha, Forcha, Champús, and Masato are some of the most common Colombian Andes region’s traditional fermented beverages. These drinks come from the fermentation of maize (Zea maize), but other cereals such as wheat or rye, could be used. The fermentation is carried out by a set of bacteria and yeasts that provide characteristic organoleptic properties of each beverage. In this work, the information collected from the metagenomics analyses by sequencing ITS 1-4 (Internal Transcriber Spacer) and the 16S ribosomal gene for fungi and the V3-V4 region of the rDNA for bacteria allowed us to identify the diversity present in these autochthonous fermented beverages made with maize. The sequencing analysis showed the presence of 39 bacterial and 20 fungal genera. In addition, we determined that only nine genera of bacteria and two genera of fungi affect the organoleptic properties of smell, colour, and flavour, given the production of compounds such as lactic acid, alcohol, and phenols, highlighting the critical role of these microorganisms. Our findings provide new insights into the core microbiota of these beverages, represented by Lactobacillus fermentum, Acetobacter pasteurianus, and Saccharomyces cerevisiae.
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Fungal dynamic changes in naturally fermented ‘Kyoho’ grape juice. Arch Microbiol 2022; 204:556. [DOI: 10.1007/s00203-022-03166-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 11/02/2022]
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Influence of indigenous Hanseniaspora uvarum and Saccharomyces cerevisiae from sugar-rich substrates on the aromatic composition of loquat beer. Int J Food Microbiol 2022; 379:109868. [DOI: 10.1016/j.ijfoodmicro.2022.109868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/06/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022]
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Kamilari E, Mina M, Karallis C, Tsaltas D. Metataxonomic Analysis of Grape Microbiota During Wine Fermentation Reveals the Distinction of Cyprus Regional terroirs. Front Microbiol 2021; 12:726483. [PMID: 34630353 PMCID: PMC8494061 DOI: 10.3389/fmicb.2021.726483] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/23/2021] [Indexed: 12/25/2022] Open
Abstract
Wine production in Cyprus has strong cultural ties with the island's tradition, influencing local and foreign consumers' preferences and contributing significantly to Cyprus' economy. A key contributor to wine quality and sensorial characteristics development is the microbiota that colonizes grapes and performs alcoholic fermentation. Still, the microbial patterns of wines produced in different geographic regions (terroir) in Cyprus remain unknown. The present study investigated the microbial diversity of five terroirs in Cyprus, two from the PGI Lemesos region [Kyperounta (PDO Pitsilia) and Koilani (PDO Krasochoria)], and three from the PGI Pafos region [Kathikas (PDO Laona Akamas), Panayia, and Statos (PDO Panayia)], of two grape varieties, Xynisteri and Maratheftiko, using high-throughput amplicon sequencing. Through a longitudinal analysis, we examined the evolution of the bacterial and fungal diversity during spontaneous alcoholic fermentation. Both varieties were characterized by a progressive reduction in their fungal alpha diversity (Shannon index) throughout the process of fermentation. Additionally, the study revealed a distinct separation among different terroirs in total fungal community composition (beta-diversity) for the variety Xynisteri. Also, Kyperounta terroir had a distinct total fungal beta-diversity from the other terroirs for Maratheftiko. Similarly, a significant distinction was demonstrated in total bacterial diversity between the PGI Lemesos region and the PGI Pafos terroirs for grape juice of the variety Xynisteri. Pre-fermentation, the fungal diversity for Xynisteri and Maratheftiko was dominated by the genera Hanseniaspora, Aureobasidium, Erysiphe, Aspergillus, Stemphylium, Penicillium, Alternaria, Cladosporium, and Mycosphaerella. During and post-fermentation, the species Hanseniaspora nectarophila, Saccharomyces cerevisiae, Hanseniaspora guilliermondii, and Aureobasidium pullulans, became the predominant in most must samples. Regarding the bacterial diversity, Lactobacillus and Streptococcus were the predominant genera for both grape varieties in all stages of fermentation. During fermentation, an increase was observed in the relative abundance of some bacteria, such as Acetobacter, Gluconobacter, and Oenococcus oeni. Finally, the study revealed microbial biomarkers with statistically significant higher relative representation, associated with each geographic region and each grape variety, during the different stages of fermentation. The present study's findings provide an additional linkage between the grape microbial community and the wine terroir.
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Affiliation(s)
- Eleni Kamilari
- Department of Agricultural Sciences, Biotechnology, and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Minas Mina
- Department of Agricultural Sciences, Biotechnology, and Food Science, Cyprus University of Technology, Lemesos, Cyprus
- Kyperounda Winery, P. Photiades Group, Nicosia, Cyprus
| | | | - Dimitrios Tsaltas
- Department of Agricultural Sciences, Biotechnology, and Food Science, Cyprus University of Technology, Lemesos, Cyprus
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Matraxia M, Alfonzo A, Prestianni R, Francesca N, Gaglio R, Todaro A, Alfeo V, Perretti G, Columba P, Settanni L, Moschetti G. Non-conventional yeasts from fermented honey by-products: Focus on Hanseniaspora uvarum strains for craft beer production. Food Microbiol 2021; 99:103806. [PMID: 34119099 DOI: 10.1016/j.fm.2021.103806] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/24/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
The increasing interest in novel beer productions focused on non-Saccharomyces yeasts in order to pursue their potential in generating groundbreaking sensory profiles. Traditional fermented beverages represent an important source of yeast strains which could express interesting features during brewing. A total of 404 yeasts were isolated from fermented honey by-products and identified as Saccharomyces cerevisiae, Wickerhamomyces anomalus, Zygosaccharomyces bailii, Zygosaccharomyces rouxii and Hanseniaspora uvarum. Five H. uvarum strains were screened for their brewing capability. Interestingly, Hanseniaspora uvarum strains showed growth in presence of ethanol and hop and a more rapid growth than the control strain S. cerevisiae US-05. Even though all strains showed a very low fermentation power, their concentrations ranged between 7 and 8 Log cycles during fermentation. The statistical analyses showed significant differences among the strains and underlined the ability of YGA2 and YGA34 to grow rapidly in presence of ethanol and hop. The strain YGA34 showed the best technological properties and was selected for beer production. Its presence in mixed- and sequential-culture fermentations with US-05 did not influence attenuation and ethanol concentration but had a significant impact on glycerol and acetic acid concentrations, with a higher sensory complexity and intensity, representing promising co-starters during craft beer production.
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Affiliation(s)
- Michele Matraxia
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Antonio Alfonzo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Rosario Prestianni
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Nicola Francesca
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy.
| | - Raimondo Gaglio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Aldo Todaro
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Vincenzo Alfeo
- Italian Brewing Research Centre, Department of Agricultural, Food and Environmental Science, University of Perugia, 06126, Perugia, Italy
| | - Giuseppe Perretti
- Italian Brewing Research Centre, Department of Agricultural, Food and Environmental Science, University of Perugia, 06126, Perugia, Italy
| | - Pietro Columba
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Luca Settanni
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
| | - Giancarlo Moschetti
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze 4, 90128, Palermo, Italy
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Liu Z, Wang MM, Wang GS, Li AH, Wangmu, Wang QM. Hanseniaspora terricola sp. nov., an ascomycetous yeast isolated from Tibet. Int J Syst Evol Microbiol 2021; 71. [PMID: 33720007 DOI: 10.1099/ijsem.0.004741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eight apiculate strains isolated from Tibet, PR China, were identified as Hanseniaspora taiwanica and a novel species of Hanseniaspora based on the sequence analysis of the ITS region, the D1/D2 domains of the LSU rRNA and the translation elongation factor 1-a (TEF1) gene. Among them, four strains with identical sequences of D1/D2 and ITS formed a separate branch from the known Hanseniaspora species in the phylogenetic trees, and differed from the known species by at least 17 (3 %) nucleotide (nt) substitutions in the D1/D2 domains and more than 6 % substitutions and inserts/deletes in the ITS region. The phylogenetic analysis indicated that those four strains represent a novel species of Hanseniaspora, for which the names Hanseniaspora terricola sp. nov. (holotype CGMCC 2.6175T; MycoBank MB 834591) is proposed. The other four strains belonging to H. taiwanica produce spherical, void or fusiform ascospores, which differ from the original description that ascospores are absent.
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Affiliation(s)
- Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, PR China
| | - Man-Man Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, PR China
| | - Gui-Shuang Wang
- Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, Tibet, PR China.,School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, PR China
| | - Ai-Hua Li
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wangmu
- Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, Tibet, PR China
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, PR China
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Čadež N, Bellora N, Ulloa R, Hittinger CT, Libkind D. Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. PLoS One 2019; 14:e0210792. [PMID: 30699175 PMCID: PMC6353571 DOI: 10.1371/journal.pone.0210792] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 01/03/2019] [Indexed: 11/19/2022] Open
Abstract
A novel yeast species was isolated from the sugar-rich stromata of Cyttaria hariotii collected from two different Nothofagus tree species in the Andean forests of Patagonia, Argentina. Phylogenetic analyses of the concatenated sequence of the rRNA gene sequences and the protein-coding genes for actin and translational elongation factor-1α indicated that the novel species belongs to the genus Hanseniaspora. De novo genome assembly of the strain CRUB 1928T yielded a 10.2-Mbp genome assembly predicted to encode 4452 protein-coding genes. The genome sequence data were compared to the genomes of other Hanseniaspora species using three different methods, an alignment-free distance measure, Kr, and two model-based estimations of DNA-DNA homology values, of which all provided indicative values to delineate species of Hanseniaspora. Given its potential role in a rare indigenous alcoholic beverage in which yeasts ferment sugars extracted from the stromata of Cytarria sp., we searched for the genes that may suggest adaptation of novel Hanseniaspora species to fermenting communities. The SSU1-like gene encoding a sulfite efflux pump, which, among Hanseniaspora, is present only in close relatives to the new species, was detected and analyzed, suggesting that this gene might be one factor that characterizes this novel species. We also discuss several candidate genes that likely underlie the physiological traits used for traditional taxonomic identification. Based on these results, a novel yeast species with the name Hanseniaspora gamundiae sp. nov. is proposed with CRUB 1928T (ex-types: ZIM 2545T = NRRL Y-63793T = PYCC 7262T; MycoBank number MB 824091) as the type strain. Furthermore, we propose the transfer of the Kloeckera species, K. hatyaiensis, K. lindneri and K. taiwanica to the genus Hanseniaspora as Hanseniaspora hatyaiensis comb. nov. (MB 828569), Hanseniaspora lindneri comb. nov. (MB 828566) and Hanseniaspora taiwanica comb. nov. (MB 828567).
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Affiliation(s)
- Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Nicolas Bellora
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medio-ambiente, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Ricardo Ulloa
- Laboratorio de Bioprocesos, Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Neuquén, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medio-ambiente, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
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