Genomic and Proteomic Analysis of Food Microorganisms

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 304

Special Issue Editors


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Guest Editor
School of Food Science and Technology, State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116000, China
Interests: high-throughput sequencing; application potential; probiotic properties; safety; metabolites; functional mining; interaction networks; targets of action
School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
Interests: natural product chemistry; chemical database construction; extraction and isolation; structure elucidation and bioactivity evaluation; food analysis and quality control
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Special Issue Information

Dear Colleagues,

There is a close relationship between probiotic microorganisms and human health, and these microorganisms are widely used in food. Therefore, it is particularly important to keep exploring safe microorganisms with probiotic potential. These probiotic microorganisms must be tolerant to environmental factors such as pH and bile salts and display osmolality in the human digestive tract. Traditionally, physiological and biochemical indicators have been used to determine the safety and possible biological activity of probiotic microorganisms. However, the lack of predictive tools remains a limiting factor in their screening and application. With the popularization of high-throughput sequencing technology, the approach to this research has shifted from more chemical means to molecular mechanisms and genetic characterization based on histological techniques. Genomic analysis can be used to assess the safety and tolerability of probiotics by detecting genes associated with virulence factors. In addition, a large number of biosynthetic gene clusters (BDCs) encoding natural products may be present in the genes, providing an effective approach for discovering targeted natural products (e.g., polyketides, peptides, terpenoids, etc.). The potential efficacy of beneficial microorganisms can be analyzed by combined genomic and proteomic analyses, such as the ability to survive in the gastrointestinal tract, regulatory efficacy, and the ability to produce beneficial metabolites. All of these provide valuable genetic and functional information for the further research and application of probiotics, contributing to the development of more effective and safe products containing probiotic microorganisms.

The aim of this Special Issue of Food is to collect and present analyses of the functional characterization and metabolite prediction of probiotic microorganisms by multi-omics means in order to widen the range of beneficial probiotic microorganisms used in food products. In this Special Issue, original research articles and reviews are welcome.

Prof. Dr. Shuhong Ye
Dr. Yan Ding
Guest Editors

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Keywords

  • probiogenomics
  • proteomic analysis
  • screening of probiotic microorganisms
  • mining of probiotic functions
  • bioactive metabolites
  • metabolic network modeling
  • target prediction
  • gut microecology regulation
  • health-promoting effect

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Published Papers (1 paper)

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Research

18 pages, 2829 KB  
Article
Unveiling the Potential of Endophytic Bacillus amyloliquefaciens LJ1 from Nanguo Pear: A Genomic and Functional Study for Biocontrol of Post-Harvest Rot
by Zilong Li, Jiamin Jiang, Keyu Sun and Shuhong Ye
Foods 2025, 14(17), 3020; https://doi.org/10.3390/foods14173020 - 28 Aug 2025
Viewed by 166
Abstract
Bacillus amyloliquefaciens is a well-recognized biocontrol agent and plant growth promoter. This study characterized the endophytic B. amyloliquefaciens LJ1, isolated from Nanguo pear fruit, through whole-genome sequencing and functional analyses. The B. amyloliquefaciens LJ1 genome (3,947,365 bp, 46.48% GC content) encodes 3757 protein-coding [...] Read more.
Bacillus amyloliquefaciens is a well-recognized biocontrol agent and plant growth promoter. This study characterized the endophytic B. amyloliquefaciens LJ1, isolated from Nanguo pear fruit, through whole-genome sequencing and functional analyses. The B. amyloliquefaciens LJ1 genome (3,947,365 bp, 46.48% GC content) encodes 3757 protein-coding sequences. Genomic analysis revealed diverse carbohydrate-active enzymes (CAZymes) and 12 secondary metabolite biosynthetic gene clusters, including those potentially producing surfactin, fengycin, bacillibactin, and bacilysin. Safety assessments, including hemolysis, indole production, biogenic amine production, and a 21 day mice-feeding trial, indicated no adverse effects, suggesting B. amyloliquefaciens LJ1 is non-pathogenic. In vitro assays demonstrated significant inhibitory activity against Penicillium expansum, a major post-harvest pathogen, by suppressing spore germination and germ-tube elongation. These results suggest that B. amyloliquefaciens LJ1 possesses significant biocontrol potential and could be a promising agent for sustainable disease management in Nanguo pear and potentially other crops. Full article
(This article belongs to the Special Issue Genomic and Proteomic Analysis of Food Microorganisms)
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