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Liu YY, Hsu CY, Yang YC, Huang CH, Chen CC. ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains. BIOINFORMATICS ADVANCES 2023; 3:vbad153. [PMID: 37928343 PMCID: PMC10625473 DOI: 10.1093/bioadv/vbad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 10/01/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
Motivation ProbioMinServer is a platform designed to help researchers access information on probiotics regarding a wide variety of characteristics, such as safety (e.g. antimicrobial resistance, virulence, pathogenic, plasmid, and prophage genes) and functionality (e.g. functional classes, carbohydrate-active enzyme, and metabolite gene cluster profile). Because probiotics are functional foods, their safety and functionality are a crucial part of health care. Genomics has become a crucial methodology for investigating the safety and functionality of probiotics in food and feed. This shift is primarily attributed to the growing affordability of next-generation sequencing technologies. However, no integrated platform is available for simultaneously evaluating probiotic strain safety, investigating probiotic functionality, and identifying known phylogenetically related strains. Results Thus, we constructed a new platform, ProbioMinServer, which incorporates these functions. ProbioMinServer accepts whole-genome sequence files in the FASTA format. If the query genome belongs to the 25 common probiotic species collected in our database, the server performs a database search and analyzes the core-genome multilocus sequence typing. Front-end applications were implemented in JavaScript with a bootstrap framework, and back-end programs were implemented using PHP, Perl, and Python. ProbioMinServer can help researchers quickly and easily retrieve information on the safety and functionality of various probiotics. Availability and implementation The platform is available at https://probiomindb.imst.nsysu.edu.tw.
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Affiliation(s)
- Yen-Yi Liu
- Department of Biology, National Changhua University of Education, Changhua 500207, Taiwan
| | - Chu-Yi Hsu
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Ya-Chu Yang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300193, Taiwan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
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Zhang Z, Wei Y, Peng Z, Du P, Du X, Zuo G, Wang C, Li P, Wang J, Wang R. Exploration of microbiome diversity of stacked fermented grains by flow cytometry and cell sorting. Front Microbiol 2023; 14:1160552. [PMID: 37051523 PMCID: PMC10083240 DOI: 10.3389/fmicb.2023.1160552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/06/2023] [Indexed: 03/28/2023] Open
Abstract
Sauce-flavor baijiu is one of the twelve flavor types of Chinese distilled fermented product. Microbial composition plays a key role in the stacked fermentation of Baijiu, which uses grains as raw materials and produces flavor compounds, however, the active microbial community and its relationship remain unclear. Here, we investigated the total and active microbial communities of stacked fermented grains of sauce-flavored Baijiu using flow cytometry and high-throughput sequencing technology, respectively. By using traditional high-throughput sequencing technology, a total of 24 bacterial and 14 fungal genera were identified as the core microbiota, the core bacteria were Lactobacillus (0.08–39.05%), Acetobacter (0.25–81.92%), Weissella (0.03–29.61%), etc. The core fungi were Issatchenkia (23.11–98.21%), Monascus (0.02–26.36%), Pichia (0.33–37.56%), etc. In contrast, using flow cytometry combined with high-throughput sequencing, the active dominant bacterial genera after cell sorting were found to be Herbaspirillum, Chitinophaga, Ralstonia, Phenylobacterium, Mucilaginibacter, and Bradyrhizobium, etc., whereas the active dominant fungal genera detected were Aspergillus, Pichia, Exophiala, Candelabrochaete, Italiomyces, and Papiliotrema, etc. These results indicate that although the abundance of Acetobacter, Monascus, and Issatchenkia was high after stacked fermentation, they may have little biological activity. Flow cytometry and cell sorting techniques have been used in the study of beer and wine, but exploring the microbiome in such a complex environment as Chinese baijiu has not been reported. The results also reveal that flow cytometry and cell sorting are convenient methods for rapidly monitoring complex microbial flora and can assist in exploring complex environmental samples.
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Affiliation(s)
- Ziyang Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Yanwei Wei
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Zehao Peng
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Peng Du
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Xinyong Du
- Gubeichun Group Co., Ltd., Jinan, Shandong, China
| | - Guoying Zuo
- Gubeichun Group Co., Ltd., Jinan, Shandong, China
| | | | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
- *Correspondence: Junqing Wang,
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, Shandong, China
- Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong, China
- Ruiming Wang,
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High-Throughput Sequencing as a Tool for the Quality Control of Microbial Bioformulations for Agriculture. Processes (Basel) 2022. [DOI: 10.3390/pr10112243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microbial bioformulations, due to their positive impact on the growth and development of plants, as well as the absence of harmful effects on the environment and humans, have a vast potential for mass introduction into agriculture. Assessing the quality of bioformulations, especially complex ones, is a difficult task. In this study, we show that high-throughput sequencing can be an effective tool for the quality control and safety of microbial bioformulations. By the method of high-throughput sequencing on the MiSeq platform, we studied 20 samples of commercially available microbial bioformulations. In parallel with this, bioformulations were studied by classical microbiological methods. The analysis showed the presence of extraneous undeclared bacterial genera by the manufacturer. Only 10% of the bioformulations fully corresponded to the commercial composition, and another 10% of the bioformulations did not contain the bacteria declared by the manufacturer in their composition at all. The bacterial composition of 80% of the bioformulations partially corresponded to the composition indicated on the package. The most frequent microbial bioformulations contaminants were Enterococcus, Lactobacillaceae, Klebsiella, Escherichia-Shigella and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. Universal methods for the quality control of bioformulations are needed. The advantages of high-throughput sequencing for the evaluation of bioformulations are considered in this work.
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Han J, Kong T, Wang Q, Jiang J, Zhou Q, Li P, Zhu B, Gu Q. Regulation of microbial metabolism on the formation of characteristic flavor and quality formation in the traditional fish sauce during fermentation: a review. Crit Rev Food Sci Nutr 2022; 63:7564-7583. [PMID: 35253552 DOI: 10.1080/10408398.2022.2047884] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fish sauce is a special flavored condiment formed by traditional fermentation of low-value fish in coastal areas, which are consumed and produced in many parts of the world, especially in Southeast Asia. In the process of fish sauce fermentation, the diversity of microbial flora and the complex metabolic reactions of microorganisms, especially lipid oxidation, carbohydrate fermentation and protein degradation, are accompanied by the formation of flavor substances. However, the precise reaction of microorganisms during the fersmentation process is difficult to accurately control in modern industrial production, which leads to the loss of traditional characteristic flavors in fermented fish sauces. This paper reviews the manufacturing processes, core microorganisms, metabolic characteristics and flavor formation mechanisms of fermented fish sauces at home and abroad. Various methods have been utilized to analyze and characterize the composition and function of microorganisms. Additionally, the potential safety issues of fermented fish sauces and their health benefits are also reviewed. Furthermore, some future directions and prospects of fermented fish sauces are also reviewed in this paper. By comprehensive understanding of this review, it is expected to address the challenges in the modern production of fish sauce thereby expanding its application in food or diet.
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Affiliation(s)
- Jiarun Han
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Tao Kong
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Qi Wang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Jialan Jiang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Qingqing Zhou
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Beiwei Zhu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, Liaoning, China
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
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