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Functional and Fermentative Microbes in Food: Diversity, Ecology, and Applications
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Functional and Fermentative Microbes in Food: Diversity, Ecology, and Applications

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

Deadline for manuscript submissions: 10 August 2026 | Viewed by 1151

Special Issue Editors

Dr. Jing Hou

E-Mail Website
Guest Editor
School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
Interests: enzyme; halophile; safety; fermentaion; archaea
Prof. Dr. Henglin Cui

E-Mail Website
Guest Editor
School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
Interests: diversity; taxonomy; enzyme; halophile; fermentation

Special Issue Information

Dear Colleagues,

Beneficial microbes, such as lactic acid bacteria, yeasts, and other fermentative species, have been used for centuries to improve the flavor, safety, and shelf life of food. Recent advances in microbial ecology, taxonomy, and functional genomics have opened up new avenues for researching food-associated microbes with probiotic potential, bioactive metabolite production, and enzymatic functionalities. This Special Issue aims to explore the diversity, ecological roles, and technological applications of beneficial microbes in food systems, with a particular focus on fermentative and functional microbes that contribute to product quality, nutritional enhancement, and sustainable processing.

We invite contributions in the following topics:

(1) Microbial diversity and taxonomy in fermented or functional foods;

(2) Ecology and succession of microbes during fermentation;

(3) Functional attributes of probiotics and postbiotics and their applications in foods;

(4) Enzymes from food microbes for flavor, safety, texture, or nutrient enhancement;

(5) Omics-based insights into microbial interactions and metabolic functions in fermented foods.

We also welcome original research, reviews, and communications related to the following areas of research:

(1) Traditional or novel fermented food microbiomes;

(2) Lactic acid bacteria and other probiotics in food applications;

(3) Microbial enzymes in food applications;

(4) Starter culture development and optimization;

(5) Microbial community structure and dynamics in food systems;

(6) Molecular taxonomy and phylogeny of food microbes.

Dr. Jing Hou
Prof. Dr. Henglin Cui
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Foods is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • food fermentation
  • probiotics and lactic acid bacteria
  • functional microbes
  • food microbial diversity
  • food microbial ecology
  • food microbial taxonomy
  • enzymes in food

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Published Papers (2 papers)

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Research

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18 pages, 2809 KB  
Article
Impact of Co-Fermentation with Bifidobacterium animalis subsp. lactis IU100 and Type III Resistant Starch on the Aroma Profile of Fermented Milk
by Qingyue Li, Zhi Zhao, Yixuan Li, Zhenghong Wang, Meilun An, Yao Hu, Ran Wang, Hao Zhang, Ke Xu, Qinggang Luan, Siyuan Liu and Xiaoxia Li
Foods 2026, 15(4), 756; https://doi.org/10.3390/foods15040756 - 19 Feb 2026
Viewed by 650
Abstract
The addition of Bifidobacterium animalis subsp. lactis and prebiotics to fermented milk can enhance its flavor and sensory properties; however, research on the effects of their combined supplementation on flavor profiles remains limited. This study investigated the impact of simultaneously adding B. lactis [...] Read more.
The addition of Bifidobacterium animalis subsp. lactis and prebiotics to fermented milk can enhance its flavor and sensory properties; however, research on the effects of their combined supplementation on flavor profiles remains limited. This study investigated the impact of simultaneously adding B. lactis IU100 and resistant starch type III (RS3) to fermented milk on flavor and texture. The results showed that co-supplementation shortened the fermentation time by 1 h. It also increased hardness by 28.8%, springiness by 1.14 mm, and water holding capacity by 12.45%, accompanied by the formation of a more continuous and dense gel network. Headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry (HS-SPME-GC-MS) combined with odor activity value analysis indicated the enrichment of 115 key aromatic compounds, among which ethyl caprylate, ethyl n-butyrate, 1-octanol, and 2,3-heptanedione were identified as representative flavor compounds associated with fruity and creamy notes. KEGG pathway analysis revealed that 24 differential metabolites were predominantly enriched in purine metabolism and amino acid-related pathways. Within these pathways, coordinated enzymatic reactions convert α-keto acids and fatty acid metabolites into key flavor esters and catalyze the formation of volatile alcohols from amino acids and aromatic fatty acid precursors. Overall, this combined strategy effectively optimized fermentation efficiency, texture, and flavor through the targeted reprogramming of microbial metabolic flux. Full article
(This article belongs to the Special Issue Functional and Fermentative Microbes in Food: Diversity, Ecology, and Applications)
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Review

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39 pages, 1187 KB  
Review
Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages
by Dandan Song, Liang Yang and Chunlin Zhang
Foods 2026, 15(10), 1643; https://doi.org/10.3390/foods15101643 - 8 May 2026
Viewed by 160
Abstract
Traditional fermented foods and beverages (TFFB) rely on complex microbial communities that generate distinctive flavors, nutritional attributes, and cultural value, but spontaneous or empirically controlled fermentations often limit reproducibility. Defined microbial consortia (DMCs) provide a promising route for improving fermentation controllability and product [...] Read more.
Traditional fermented foods and beverages (TFFB) rely on complex microbial communities that generate distinctive flavors, nutritional attributes, and cultural value, but spontaneous or empirically controlled fermentations often limit reproducibility. Defined microbial consortia (DMCs) provide a promising route for improving fermentation controllability and product consistency, although overly simplified starters may fail to reproduce the ecological robustness and sensory complexity of traditional systems. This review focuses on how multi-omics and culturomics can support rational DMC design in TFFB. We summarize how metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics reveal community structure, functional potential, active expression, metabolic output, and cultivable strain resources. Particular attention is given to translating multi-omics evidence into strain prioritization through the identification of keystone microorganisms that drive core fermentation functions and helper microorganisms that support ecological or metabolic stability. We further propose an Assembly-Assessment-Redesign (A-A-R) framework for iterative DMC optimization, linking strain selection, functional validation, performance evaluation, and consortium redesign. Finally, we discuss key challenges, including cross-omics integration, experimental verification of microbial functions, standardized validation criteria, and the transfer of laboratory-designed consortia to industrial fermentation systems. Full article
(This article belongs to the Special Issue Functional and Fermentative Microbes in Food: Diversity, Ecology, and Applications)
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