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Jian P, Liu J, Li L, Song Q, Zhang D, Zhang S, Chai C, Zhao H, Zhao G, Zhu H, Qiao J. AcrR1, a novel TetR/AcrR family repressor, mediates acid and antibiotic resistance and nisin biosynthesis in Lactococcus lactis F44. J Dairy Sci 2024; 107:6576-6591. [PMID: 38762103 DOI: 10.3168/jds.2024-24754] [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: 02/02/2024] [Accepted: 03/31/2024] [Indexed: 05/20/2024]
Abstract
Lactococcus lactis, widely used in the manufacture of dairy products, encounters various environmental stresses both in natural habitats and during industrial processes. It has evolved intricate machinery of stress sensing and defense to survive harsh stress conditions. Here, we identified a novel TetR/AcrR family transcription regulator, designated AcrR1, to be a repressor for acid and antibiotic tolerance that was derepressed in the presence of vancomycin or under acid stress. The survival rates of acrR1 deletion strain ΔAcrR1 under acid and vancomycin stresses were about 28.7-fold (pH 3.0, HCl), 8.57-fold (pH 4.0, lactic acid) and 2.73-fold (300 ng/mL vancomycin) greater than that of original strain F44. We also demonstrated that ΔAcrR1 was better able to maintain intracellular pH homeostasis and had a lower affinity to vancomycin. No evident effects of AcrR1 deletion on the growth and morphology of strain F44 were observed. Subsequently, we characterized that the transcription level of genes associated with amino acids biosynthesis, carbohydrate transport and metabolism, multidrug resistance, and DNA repair proteins significantly upregulated in ΔAcrR1 using transcriptome analysis and quantitative reverse transcription-PCR assays. Additionally, AcrR1 could repress the transcription of the nisin post-translational modification gene, nisC, leading to a 16.3% increase in nisin yield after AcrR1 deletion. Our results not only refined the knowledge of the regulatory mechanism of TetR/AcrR family regulator in L. lactis, but presented a potential strategy to enhance industrial production of nisin.
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Affiliation(s)
- Pingqiu Jian
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Jiaheng Liu
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China.
| | - Li Li
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Qianqian Song
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Di Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Shenyi Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Chaofan Chai
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Hui Zhao
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, 610047 Chengdu, China
| | - Guangrong Zhao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Hongji Zhu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
| | - Jianjun Qiao
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China
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Wang Z, Zhang Z, Shi Q, Liu S, Wu Q, Wang Z, Saiding E, Han J, Zhou J, Wang R, Su X. Comparison of Lactiplantibacillus plantarum isolates from the gut of mice supplemented with different types of nutrients: a genomic and metabolomic study. Front Microbiol 2023; 14:1295058. [PMID: 38033563 PMCID: PMC10684713 DOI: 10.3389/fmicb.2023.1295058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Many studies have focused on the influence of dietary supplements on gut microbiota composition, but limited research have reported their effects on specific bacterial species in the gut. Lactiplantibacillus plantarum is one of the most widely studied probiotics, with a wide range of sources and good environmental adaptability. In this study, in order to elucidate the adaptation strategies of L. plantarum to the gut of mice supplemented with carbohydrates, peptides and minerals, whole genome resequencing and intracellular metabolites detection were performed, and high-frequency mutant genes and differential metabolites were screened. The results suggested different types of dietary supplements do have different effects on L. plantarum from the gut of mice. Additionally, KEGG annotation unveiled that the effects of these dietary supplements on the gene level of L. plantarum primarily pertained to environmental information processing, while the differential metabolites were predominantly associated with metabolism. This study provided new perspectives on the adaptive mechanism of L. plantarum in response to the host's gut environment, suggesting that the diversity of the genome and metabolome of L. plantarum was correlated with dietary supplements. Furthermore, this study offered useful guidance in the effective utilization of dietary supplements.
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Affiliation(s)
- Ziyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhixuan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qiuyue Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Songyi Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qiaoli Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Ze Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Emilaguli Saiding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Rixin Wang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
- School of Marine Sciences, Ningbo University, Ningbo, China
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Wang H, Wang X, Tang Q, Wang L, Mei C, Shao Y, Xu Y, Lu Z, Zhong W. Regulation Mechanism of Nicotine Catabolism in Sphingomonas melonis TY by a Dual Role Transcriptional Regulator NdpR. Appl Environ Microbiol 2023; 89:e0032423. [PMID: 37071026 PMCID: PMC10231238 DOI: 10.1128/aem.00324-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/25/2023] [Indexed: 04/19/2023] Open
Abstract
A gene cluster ndp, responsible for nicotine degradation via a variant of the pyridine and pyrrolidine pathways, was previously identified in Sphingomonas melonis TY, but the regulation mechanism remains unknown. The gene ndpR within the cluster was predicted to encode a TetR family transcriptional regulator. Deletion of ndpR resulted in a notably shorter lag phase, higher maximum turbidity, and faster substrate degradation when cultivated in the presence of nicotine. Real-time quantitative PCR and promoter activity analysis in wild-type TY and TYΔndpR strains revealed that genes in the ndp cluster were negatively regulated by NdpR. However, complementation of ndpR to TYΔndpR did not restore transcription repression, but, instead, the complemented strain showed better growth than TYΔndpR. Promoter activity analysis indicates that NdpR also functions as an activator in the transcription regulation of ndpHFEGD. Further analysis through electrophoretic mobility shift assay and DNase I footprinting assay revealed that NdpR binds five DNA sequences within ndp and that NdpR has no autoregulation. These binding motifs overlap with the -35 or -10 box or are located distal upstream of the corresponding transcriptional start site. Multiple sequence alignment of these five NdpR-binding DNA sequences found a conserved motif, with two of the binding sequences being partially palindromic. 2,5-Dihydroxypyridine acted as a ligand of NdpR, preventing NdpR from binding to the promoter region of ndpASAL, ndpTB, and ndpHFEGD. This study revealed that NdpR binds to three promoters in the ndp cluster and is a dual-role transcriptional regulator in nicotine metabolism. IMPORTANCE Gene regulation is critical for microorganisms in the environment in which they may encounter various kinds of organic pollutants. Our study revealed that transcription of ndpASAL, ndpTB, and ndpHFEGD is negatively regulated by NdpR, and NdpR also exhibits a positive regulatory effect on PndpHFEGD. Furthermore, 2,5-dihydroxypyridine was identified as the effector molecular for NdpR and can both prevent the binding of free NdpR to the promoter and release NdpR from the promoters, which is different from previously reported NicR2. Additionally, NdpR was found to have both negative and positive transcription regulatory effects on the same target, PndpHFEGD, while only one binding site was identified, which is notably different from the previously reported TetR family regulators. Moreover, NdpR was revealed to be a global transcriptional regulator. This study provides new insight into the complex gene expression regulation of the TetR family.
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Affiliation(s)
- Haixia Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiaoyu Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qi Tang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Lvjing Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chengyu Mei
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yunhai Shao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Ying Xu
- Department of Microbial Sciences, State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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Chen S, Yi J, Suo K, Kang Q, Lu L, Lu J. Probiotic properties and proteomics analysis of ethanol-induced Lactococcus lactis subsp. lactis IL1403. World J Microbiol Biotechnol 2023; 39:197. [PMID: 37183191 DOI: 10.1007/s11274-023-03627-y] [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: 02/09/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023]
Abstract
Our previous study indicated that ethanol-induced intracellular extracts (E-IEs) of Lactococcus lactis subsp. Lactis IL1403 (L. lactis IL1403) alleviated hangovers more effectively in mice than untreated intracellular extracts (U-IEs), but the material basis was unclear. Considering that stress-related proteins might play a significant role, the effects of ethanol induction on probiotic properties of L. lactis IL1403 and the associated stress response mechanism were initially explored in this study. E-IEs of L. lactis IL1403 showed better biological activities, significantly increased bacteria survival rates in oxidative stress environments, increased ADH activity, and enhanced proliferation in RAW264.7 and AML-12 cells. Proteomic analyses revealed that 414 proteins were significantly changed in response to ethanol induction. The expression of proteins involved in the universal stress response, DNA repair, oxidative stress response, and ethanol metabolism was rapidly upregulated under ethanol stress, and quantitative real-time PCR (qRT-PCR) results were consistent with proteomic data. KEGG pathway analysis indicated that citrate metabolism, starch and sucrose metabolism, and pyruvate metabolism were significantly enriched during ethanol stress to increase energy requirements and survival rates of stressed cells. Based on this observation, the active induction is an effective strategy for increasing the biological activity of L. lactis IL1403. Exploring the molecular mechanism and material basis of their functions in vivo can help us understand the adaptive regulatory mechanism of microorganisms.
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Affiliation(s)
- Sisi Chen
- Physical Education College, Zhengzhou University, Zhengzhou, 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Food Laboratory of Zhongyuan, Zhengzhou University, Zhengzhou, 450001, China
| | - Juanjuan Yi
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- Food Laboratory of Zhongyuan, Zhengzhou University, Zhengzhou, 450001, China.
| | - Keke Suo
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Food Laboratory of Zhongyuan, Zhengzhou University, Zhengzhou, 450001, China
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Laizheng Lu
- Zhengzhou Mindtek Biotechnology Co. Ltd, Zhengzhou, 450001, Henan, China
| | - Jike Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- Food Laboratory of Zhongyuan, Zhengzhou University, Zhengzhou, 450001, China.
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Formation of biofilm changed the responses of Tetragenococcus halophilus to ethanol stress revealed by transcriptomic and proteomic analyses. Food Res Int 2022; 161:111817. [DOI: 10.1016/j.foodres.2022.111817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/01/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022]
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Hu Y, Zhou Y, Fu S, Zhou M, Xu N, Li D, Wang C, Hu Y. Coordination of characteristic cytomembrane and energy metabolism contributes to ethanol-tolerance of Acetobacter pasteurianus. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chen S, Jia S, Suo K, Kang Q, Hao L, Lu L, Liu X, Huang J, Lu J. Positive effect of ethanol-induced Lactococcus lactis on alcohol metabolism in mice. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2022.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Li Y, Xiong D, Yuan L, Fan P, Xiao Y, Chen J, Feng W. Transcriptome and protein networks to elucidate the mechanism underlying nitrite degradation by Lactiplantibacillus plantarum. Food Res Int 2022; 156:111319. [PMID: 35651074 DOI: 10.1016/j.foodres.2022.111319] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022]
Abstract
Excessive nitrite residue is one of the bottlenecks in the production of many fermented foods. Lactiplantibacillus plantarum PK25 obtained from traditional Chinese pickles exhibited excellent nitrite degradation ability. Here, transcriptome, protein-protein interaction networks, and phenotype were performed to evaluate systematically the mechanism of nitrite degradation of L. plantarum PK25. The results demonstrated that genes expression varied considerably at key time points for nitrite degradation. 553 (upregulated: 366, downregulated: 187) and 767 (upregulated: 425, downregulated: 342) differentially expressed genes were identified at 6 h and 24 h, respectively. The hub genes were mainly enriched in carbohydrate metabolism, energy metabolism, and nucleotide synthesis. PK25 expanded its carbon source utilizing profile and improved glycolysis to produce more ATP to counteract environmental stress. The related enzymes including glycoside hydrolase, sugar ABC transporter protein, and PTS sugar transporter were 5.714, 5.885, and 3.578-fold upregulated at the transcriptional level. For strain to sustain energy levels and acid generation, pyruvate metabolism was critical, with the result that phosphoenolpyruvate synthase and pyruvate oxidase were up-regulated to accelerate the pyruvate transition. To repair DNA lesions induced by nitrite, both base excision repair mechanism and recombinational DNA repair pathway were exploited, such as endodeoxyribonuclease upregulated 5.314 and 19.687-fold at the two moments. The results provided a theoretical reference and practical possibility to reduce nitrite residue and improve safety during food fermented products.
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Affiliation(s)
- Yuanyuan Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Die Xiong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lanyu Yuan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Pengfei Fan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yao Xiao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Wu Feng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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Fan X, Bao T, Yi H, Zhang Z, Zhang K, Liu X, Lin X, Zhang Z, Feng Z. Ribosome Profiling and RNA Sequencing Reveal Genome-Wide Cellular Translation and Transcription Regulation Under Osmotic Stress in Lactobacillus rhamnosus ATCC 53103. Front Microbiol 2021; 12:781454. [PMID: 34899662 PMCID: PMC8656396 DOI: 10.3389/fmicb.2021.781454] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022] Open
Abstract
To determine whether osmotic pressure affects the translation efficiency of Lactobacillus rhamnosus, the ribosome profiling assay was performed to analyze the changes in translation efficiency in L. rhamnosus ATCC 53103. Under osmotic stress, differentially expressed genes (DEGs) involved in fatty acid biosynthesis and metabolism, ribosome, and purine metabolism pathways were co-regulated with consistent expression direction at translation and transcription levels. DEGs involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan, and the phosphotransferase system pathways also were co-regulated at translation and transcription levels, while they showed opposite expression direction at two levels. Moreover, DEGs involved in the two-component system, amino acid metabolism, and pyruvate metabolism pathways were only regulated at the transcription level. And DEGs involved in fructose and mannose metabolism were only regulated at the translation level. The translation efficiency of DEGs involved in the biosynthesis of amino acids was downregulated while in quorum sensing and PTS pathways was upregulated. In addition, the ribosome footprints accumulated in open reading frame regions resulted in impaired translation initiation and elongation under osmotic stress. In summary, L. rhamnosus ATCC 53103 could respond to osmotic stress by translation regulation and control the balance between survival and growth of cells by transcription and translation.
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Affiliation(s)
- Xuejing Fan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Tianyu Bao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Huaxi Yi
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zongcai Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Kenan Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xin Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xue Lin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China.,Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
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