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Integrating Genomics and Metabolomics to Identify Lactic Acid Bacteria With Broad-Spectrum Antimicrobial Activity and Validation in a Bread System.

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Title: Integrating Genomics and Metabolomics to Identify Lactic Acid Bacteria With Broad-Spectrum Antimicrobial Activity and Validation in a Bread System.
Authors: Zhang X; State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China., Liu L; State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China., Liu D; State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China., Cui M; State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China., Shi C; State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China., Zheng Y; State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China., Su Z; State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China., Shen Y; State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China., Wang M; State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.
Source: Journal of food science [J Food Sci] 2026 Sep; Vol. 91 (9), pp. e71392.
Publication Type: Journal Article
Language: English
Journal Info: Publisher: Wiley on behalf of the Institute of Food Technologists Country of Publication: United States NLM ID: 0014052 Publication Model: Print Cited Medium: Internet ISSN: 1750-3841 (Electronic) Linking ISSN: 00221147 NLM ISO Abbreviation: J Food Sci Subsets: MEDLINE
Imprint Name(s): Publication: Malden, Mass. : Wiley on behalf of the Institute of Food Technologists
Original Publication: Champaign, Ill. Institute of Food Technologists
MeSH Terms: Bread*/microbiology , Lactobacillales*/genetics , Lactobacillales*/metabolism , Anti-Infective Agents*/pharmacology , Lactiplantibacillus plantarum*/genetics , Lactiplantibacillus plantarum*/metabolism, Staphylococcus aureus/drug effects ; Escherichia coli/drug effects ; Aspergillus niger/drug effects ; Penicillium/drug effects ; Metabolomics ; Genomics ; Food Microbiology ; Microbial Sensitivity Tests
Abstract: Foodborne diseases and microbial spoilage remain major threats to food safety and shelf life. This study systematically evaluated Lactiplantibacillus plantarum C-35 for antimicrobial activity, mechanisms, genomic safety, metabolite profile, and application in bread. Among 27 lactic acid bacterial strains, L. plantarum C-35 showed strong broad-spectrum inhibition against Escherichia coli, Staphylococcus aureus, Aspergillus niger, and Penicillium solitum, significantly outperforming L. plantarum ATCC 8014 (p < 0.05). Neutralization reduced residual activity to approximately 35%-55%, whereas protease-treated cell-free supernatant generally retained more than 60% activity, indicating that organic acids were the major antimicrobial contributors and proteinaceous substances played a secondary role. Scanning electron microscopy (SEM) revealed cell shrinkage, membrane disruption, spore collapse, and surface deformation in treated microorganisms. Whole-genome sequencing identified a 2.95 Mb genome with 2803 protein-coding genes and four predicted secondary metabolite biosynthetic gene clusters, whereas no antibiotic resistance or virulence-associated genes meeting the screening criteria were detected. LC-MS metabolomics identified 14 antimicrobial-associated compounds and 416 significantly differential metabolites between L. plantarum C-35 and L. plantarum ATCC 8014, further supporting its enhanced bioactivity. Luteolin, mangiferin, indole-3-lactic acid, glutaric acid, and naringenin were enriched in L. plantarum C-35 and may contribute synergistically to its antimicrobial effects. In bread, visible mold appeared on Days 6, 8, and 10 in the control, L. plantarum ATCC 8014, and L. plantarum C-35 groups, respectively, demonstrating its practical preservation potential. Together, these findings indicate that the strain-specific genomic and metabolomic features of L. plantarum C-35 are associated with its strong antimicrobial performance and support its potential application as a clean-label biopreservative in bread systems.
(© 2026 Institute of Food Technologists.)
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Contributed Indexing: Keywords: Lactiplantibacillus plantarum C‐35; antimicrobial activity; bread preservation; clean label; metabolomics; whole genome
Substance Nomenclature: 0 (Anti-Infective Agents)
Entry Date(s): Date Created: 20260923 Date Completed: 20260923 Latest Revision: 20260923
Update Code: 20260923
DOI: 10.1111/1750-3841.71392
PMID: 42775524
Database: MEDLINE
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  Data: &lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Bread%22&quot;&gt;Bread*&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Bread+microbiology%22&quot;&gt;microbiology&lt;/searchLink&gt; &lt;br /&gt;&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Lactobacillales%22&quot;&gt;Lactobacillales*&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Lactobacillales+genetics%22&quot;&gt;genetics&lt;/searchLink&gt; &lt;br /&gt;&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Lactobacillales%22&quot;&gt;Lactobacillales*&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Lactobacillales+metabolism%22&quot;&gt;metabolism&lt;/searchLink&gt; &lt;br /&gt;&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Anti-Infective+Agents%22&quot;&gt;Anti-Infective Agents*&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Anti-Infective+Agents+pharmacology%22&quot;&gt;pharmacology&lt;/searchLink&gt; &lt;br /&gt;&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Lactiplantibacillus+plantarum%22&quot;&gt;Lactiplantibacillus plantarum*&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Lactiplantibacillus+plantarum+genetics%22&quot;&gt;genetics&lt;/searchLink&gt; &lt;br /&gt;&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Lactiplantibacillus+plantarum%22&quot;&gt;Lactiplantibacillus plantarum*&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MM&quot; term=&quot;%22Lactiplantibacillus+plantarum+metabolism%22&quot;&gt;metabolism&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Staphylococcus+aureus%22&quot;&gt;Staphylococcus aureus&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Staphylococcus+aureus+drug+effects%22&quot;&gt;drug effects&lt;/searchLink&gt; ; &lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Escherichia+coli%22&quot;&gt;Escherichia coli&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Escherichia+coli+drug+effects%22&quot;&gt;drug effects&lt;/searchLink&gt; ; &lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Aspergillus+niger%22&quot;&gt;Aspergillus niger&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Aspergillus+niger+drug+effects%22&quot;&gt;drug effects&lt;/searchLink&gt; ; &lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Penicillium%22&quot;&gt;Penicillium&lt;/searchLink&gt;/&lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Penicillium+drug+effects%22&quot;&gt;drug effects&lt;/searchLink&gt; ; &lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Metabolomics%22&quot;&gt;Metabolomics&lt;/searchLink&gt; ; &lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Genomics%22&quot;&gt;Genomics&lt;/searchLink&gt; ; &lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Food+Microbiology%22&quot;&gt;Food Microbiology&lt;/searchLink&gt; ; &lt;searchLink fieldCode=&quot;MH&quot; term=&quot;%22Microbial+Sensitivity+Tests%22&quot;&gt;Microbial Sensitivity Tests&lt;/searchLink&gt;
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Foodborne diseases and microbial spoilage remain major threats to food safety and shelf life. This study systematically evaluated Lactiplantibacillus plantarum C-35 for antimicrobial activity, mechanisms, genomic safety, metabolite profile, and application in bread. Among 27 lactic acid bacterial strains, L. plantarum C-35 showed strong broad-spectrum inhibition against Escherichia coli, Staphylococcus aureus, Aspergillus niger, and Penicillium solitum, significantly outperforming L. plantarum ATCC 8014 (p&#160;&amp;lt;&#160;0.05). Neutralization reduced residual activity to approximately 35%-55%, whereas protease-treated cell-free supernatant generally retained more than 60% activity, indicating that organic acids were the major antimicrobial contributors and proteinaceous substances played a secondary role. Scanning electron microscopy (SEM) revealed cell shrinkage, membrane disruption, spore collapse, and surface deformation in treated microorganisms. Whole-genome sequencing identified a 2.95&#160;Mb genome with 2803 protein-coding genes and four predicted secondary metabolite biosynthetic gene clusters, whereas no antibiotic resistance or virulence-associated genes meeting the screening criteria were detected. LC-MS metabolomics identified 14 antimicrobial-associated compounds and 416 significantly differential metabolites between L. plantarum C-35 and L. plantarum ATCC 8014, further supporting its enhanced bioactivity. Luteolin, mangiferin, indole-3-lactic acid, glutaric acid, and naringenin were enriched in L. plantarum C-35 and may contribute synergistically to its antimicrobial effects. In bread, visible mold appeared on Days 6, 8, and 10 in the control, L. plantarum ATCC 8014, and L. plantarum C-35 groups, respectively, demonstrating its practical preservation potential. Together, these findings indicate that the strain-specific genomic and metabolomic features of L. plantarum C-35 are associated with its strong antimicrobial performance and support its potential application as a clean-label biopreservative in bread systems.&lt;br /&gt; (&#169; 2026 Institute of Food Technologists.)
– Name: Ref
  Label: References
  Group: RefInfo
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  Data: &lt;i&gt;Keywords: &lt;/i&gt;Lactiplantibacillus plantarum C‐35; antimicrobial activity; bread preservation; clean label; metabolomics; whole genome
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  Data: &lt;i&gt;Date Created: &lt;/i&gt;20260923 &lt;i&gt;Date Completed: &lt;/i&gt;20260923 &lt;i&gt;Latest Revision: &lt;/i&gt;20260923
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  Data: 10.1111/1750-3841.71392
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  Data: 42775524
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        Value: 10.1111/1750-3841.71392
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      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        StartPage: e71392
    Subjects:
      – SubjectFull: Staphylococcus aureus drug effects
        Type: general
      – SubjectFull: Escherichia coli drug effects
        Type: general
      – SubjectFull: Aspergillus niger drug effects
        Type: general
      – SubjectFull: Penicillium drug effects
        Type: general
      – SubjectFull: Metabolomics
        Type: general
      – SubjectFull: Genomics
        Type: general
      – SubjectFull: Food Microbiology
        Type: general
      – SubjectFull: Microbial Sensitivity Tests
        Type: general
      – SubjectFull: Bread microbiology
        Type: general
      – SubjectFull: Lactobacillales genetics
        Type: general
      – SubjectFull: Lactobacillales metabolism
        Type: general
      – SubjectFull: Anti-Infective Agents pharmacology
        Type: general
      – SubjectFull: Lactiplantibacillus plantarum genetics
        Type: general
      – SubjectFull: Lactiplantibacillus plantarum metabolism
        Type: general
    Titles:
      – TitleFull: Integrating Genomics and Metabolomics to Identify Lactic Acid Bacteria With Broad-Spectrum Antimicrobial Activity and Validation in a Bread System.
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          Name:
            NameFull: Shi C
      – PersonEntity:
          Name:
            NameFull: Zheng Y
      – PersonEntity:
          Name:
            NameFull: Su Z
      – PersonEntity:
          Name:
            NameFull: Shen Y
      – PersonEntity:
          Name:
            NameFull: Wang M
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 09
              Text: 2026 Sep
              Type: published
              Y: 2026
          Identifiers:
            – Type: issn-electronic
              Value: 1750-3841
          Numbering:
            – Type: volume
              Value: 91
            – Type: issue
              Value: 9
          Titles:
            – TitleFull: Journal of food science
              Type: main
ResultId 1