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Acevedo KL, Eaton E, Leite J, Zhao S, Chacon-Vargas K, McCarthy CM, Choi D, O’Donnell S, Gluck-Thaler E, Yu JH, Gibbons JG. Population Genomics of Aspergillus sojae is Shaped by the Food Environment. Genome Biol Evol 2025; 17:evaf067. [PMID: 40195023 PMCID: PMC12014904 DOI: 10.1093/gbe/evaf067] [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: 09/12/2023] [Revised: 02/13/2025] [Accepted: 03/26/2025] [Indexed: 04/09/2025] Open
Abstract
Traditional fermented foods often contain specialized microorganisms adapted to their unique environments. For example, the filamentous mold Aspergillus oryzae, used in saké fermentation, has evolved to thrive in starch-rich conditions compared to its wild ancestor, Aspergillus flavus. Similarly, Aspergillus sojae, used in soybean-based fermentations like miso and shochu, is hypothesized to have been domesticated from Aspergillus parasiticus. Here, we examined the effects of long-term A. sojae use in soybean fermentation on population structure, genome variation, and phenotypic traits. We analyzed 17 A. sojae and 24 A. parasiticus genomes (23 of which were sequenced for this study), alongside phenotypic traits of 9 isolates. Aspergillus sojae formed a distinct, low-diversity population, suggesting a recent clonal expansion. Interestingly, a population of A. parasiticus was more closely related to A. sojae than other A. parasiticus populations. Genome comparisons revealed loss-of-function mutations in A. sojae, notably in biosynthetic gene clusters encoding secondary metabolites, including the aflatoxin cluster. Interestingly though, A. sojae harbored a partial duplication of a siderophore biosynthetic cluster. Phenotypic assays showed A. sojae lacked aflatoxin production, while it was variable in A. parasiticus isolates. Additionally, certain A. sojae strains exhibited larger colony diameters under miso-like salt conditions. These findings support the hypothesis that A. parasiticus is the progenitor of A. sojae and that domestication significantly reduced genetic diversity. Future research should explore how wild and food-associated strains influence sensory attributes and microbial community dynamics in fermented soy products.
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Affiliation(s)
- Kimberly L Acevedo
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
- Organismic & Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Elizabeth Eaton
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Julia Leite
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Shu Zhao
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Katherine Chacon-Vargas
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Colin M McCarthy
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Dasol Choi
- Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samuel O’Donnell
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA
| | - Emile Gluck-Thaler
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA
| | - Jae-Hyuk Yu
- Department of Bacteriology, Food Research Institute, University of Wisconsin, Madison, WI 53706, USA
| | - John G Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
- Organismic & Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
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Wu L, Chen M, Huo X, Xu Q, Yin X, Zhao XH, Zhou Y, Huang J. Development and validation of a DLLME-HPLC-FLD method for determination of aflatoxins in Chrysanthemum morifolium based on quality by design principles. PHYTOCHEMICAL ANALYSIS : PCA 2025; 36:326-338. [PMID: 39261748 DOI: 10.1002/pca.3445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/23/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024]
Abstract
INTRODUCTION Aflatoxins, potent carcinogens produced by Aspergillus species, present significant health risks and commonly contaminate herbal products such as Chrysanthemum morifolium. Detecting these toxins in C. morifolium proves challenging due to the complex nature of the herbal matrix and the fluctuating levels of toxins found in different samples. OBJECTIVES This study aimed to develop and optimize a novel method for the detection of aflatoxins in C. morifolium using dispersive liquid-liquid microextraction combined with high-performance liquid chromatography-fluorescence detection based on quality by design principles. METHODOLOGY The method involved determining critical method attributes and parameters through the Plackett-Burman design, followed by optimization using the Box-Behnken design. Monte Carlo simulation was employed to establish a design space, which was experimentally verified. Method validation was performed to confirm accuracy, precision, and stability. RESULTS The developed method exhibited excellent linearity (R2 > 0.9991) for aflatoxins B1, B2, G1, and G2 across a range of concentrations, with recovery rates between 85.52% and 102.01%. The validated method effectively quantified aflatoxins in C. morifolium under different storage conditions, highlighting the impact of temperature and storage time on aflatoxin production. CONCLUSION This study successfully established a reliable and effective method for the detection of aflatoxins in C. morifolium, highlighting the importance of strict storage conditions to reduce aflatoxin contamination. Using a quality by design framework, the method demonstrated robustness and high analytical performance, making it suitable for routine quality control of herbal products.
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Affiliation(s)
- Linlin Wu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Meixu Chen
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xinyi Huo
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Qilin Xu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xianggang Yin
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xiao Han Zhao
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yifeng Zhou
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
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Luong HQ, Le TN, Lee PH, Hsieh PC. Optimization of nonspecific protease activity fabrication by Bacillus subtilis N30 isolated from Taiwan using different models of response surface methodology. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Wang Y, Zhou Y, Qin Y, Wang L. Effect of environmental factors on the aflatoxin production by Aspergillus flavus during storage in upland rice seed using response surface methodology. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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