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Beneficial Microorganisms: Metabolites, Strain Selection and Utilization

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 8035

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Special Issue Editor

Prof. Dr. Yunping Zhu

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Guest Editor

School of Food and Health, Beijing Technology and Business University, Beijing, China
Interests: secondary metabolites; microbiology; bioactivity; molecular biology

Special Issue Information

Dear Colleagues,

The unparalleled advantages of microorganisms have been recently highlighted for producing functional ingredients via fermentation. For example, microorganisms are easy to culture; their growth rate is fast; and the cultivation cost is relatively low. Therefore, microbial sources of active substances have attracted increasing attention. However, the low yield of substance is a critical issue. In recent years, the metabolites, strain selection, and utilization of microorganisms have been studied to develop high-productivity strategies to obtain functional ingredients.

We invite authors to contribute their knowledge and expertise to further elucidate the approaches for discovering beneficial strains, parsing metabolites, and ensuring effective utilization.

This Special Issue aims to collect original research and review articles dealing with metabolites, strain selection and the utilization of beneficial microorganisms. In particular, papers focusing on the discovery and selection of various microorganisms on screening probiotics; research on high-productivity strategies and biosynthetic pathways of functional ingredients in microorganisms; and papers presenting novel approaches for the optimization of cultures and efficient utilization are welcome.

Prof. Dr. Yunping Zhu
Guest Editor

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 100 words) can be sent to the Editorial Office for announcement on this website.

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

beneficial microorganisms or probiotics
bioavailability
biosynthetic pathways
fermentation
food safety
functional ingredients
productivity strategy
strain selection
utilization

Published Papers (7 papers)

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Research

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14 pages, 7558 KiB

Open AccessArticle

Weissella cibaria Relieves Gut Inflammation Caused by Escherichia coli through Inflammation Modulation and Gut Microbiota Regulation

by Xiaoyu Liu, Nan Jiang, Xinyue Wang, Haowen Yan, Lili Guan, Lingcong Kong, Jingrui Chen, Haipeng Zhang and Hongxia Ma

Foods 2024, 13(7), 1133; https://doi.org/10.3390/foods13071133 - 08 Apr 2024

Viewed by 553

Abstract

The emergence of multi-drug-resistant (MDR) pathogens has considerably challenged the development of new drugs. Probiotics that inhibit MDR pathogens offer advantages over chemical antibiotics and drugs due to their increased safety and fewer side effects. This study reported that Weissella cibaria P-8 isolated from pickles showed excellent antibacterial activity against intestinal pathogens, particularly the antibacterial activity against MDR Escherichia coli B2 was the highest. This study showed that the survival rates of W. cibaria P-8 at pH 2.0 and 0.3% bile salt concentration were 72% and 71.56%, respectively, and it still had antibacterial activity under pepsin, trypsin, protease K, and catalase hydrolysis. Moreover, W. cibaria P-8 inhibits the expression of inflammatory factors interleukin-1β, tumor necrosis factor-α, and interleukin-6, upregulates the interleukin-10 level, and increases total antioxidant capacity and superoxide dismutase enzyme activity in serum. W. cibaria P-8 also efficiently repairs intestinal damage caused by E. coli infection. The gut microbiota analysis demonstrated that W. cibaria P-8 colonizes the intestine and increases the abundance of some beneficial intestinal microorganisms, particularly Prevotella. In conclusion, W. cibaria P-8 alleviated MDR E. coli-induced intestinal inflammation by regulating inflammatory cytokine and enzyme activity and rebalancing the gut microbiota, which could provide the foundation for subsequent clinical analyses and probiotic product development. Full article

(This article belongs to the Special Issue Beneficial Microorganisms: Metabolites, Strain Selection and Utilization)

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15 pages, 3520 KiB

Open AccessArticle

RNA-Based Anti-Inflammatory Effects of Membrane Vesicles Derived from Lactiplantibacillus plantarum

by Shino Yamasaki-Yashiki, Fumie Kawashima, Azusa Saika, Ryota Hosomi, Jun Kunisawa and Yoshio Katakura

Foods 2024, 13(6), 967; https://doi.org/10.3390/foods13060967 - 21 Mar 2024

Viewed by 691

Abstract

Bacteria generally release extracellular membrane vesicles (MVs), which are nanoparticles that play important roles in bacterial–bacterial and bacterial–host communication. As probiotics, lactic acid bacteria provide diverse health benefits to their hosts. In this study, we found that the Gram-positive lactic acid bacteria Lactiplantibacillus plantarum subsp. plantarum NBRC 15891 produce high amounts of MVs (LpMVs), and that LpMVs inhibit interleukin (IL)-8 production induced by lipopolysaccharide in intestinal epithelial HT29 cells. Heat- or UV-killed bacterial cells did not exhibit anti-inflammatory effects, and there was no uptake of these bacterial cells; contrarily, LpMVs were taken up into the cytoplasm of HT29 cells. Small RNAs extracted from LpMVs also suppressed IL-8 production in HT29 cells, suggesting that RNAs in the cytoplasm of bacterial cells are encapsulated in the MVs and released from the cells, which may be delivered to HT29 cells to exert their anti-inflammatory effects. In addition, administration of LpMVs to mice with dextran sodium sulfate-induced colitis alleviated colitis-induced weight loss and colon length shortening, indicating that LpMV intake is likely to be effective in preventing or ameliorating colitis. Full article

(This article belongs to the Special Issue Beneficial Microorganisms: Metabolites, Strain Selection and Utilization)

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18 pages, 2113 KiB

Open AccessArticle

Evaluation of Safety and Probiotic Traits from a Comprehensive Genome-Based In Silico Analysis of Ligilactobacillus salivarius P1CEA3, Isolated from Pigs and Producer of Nisin S

by Ester Sevillano, Irene Lafuente, Nuria Peña, Luis M. Cintas, Estefanía Muñoz-Atienza, Pablo E. Hernández and Juan Borrero

Foods 2024, 13(1), 107; https://doi.org/10.3390/foods13010107 - 28 Dec 2023

Viewed by 971

Abstract

Ligilactobacillus salivarius is an important member of the porcine gastrointestinal tract (GIT). Some L. salivarius strains are considered to have a beneficial effect on the host by exerting different probiotic properties, including the production of antimicrobial peptides which help maintain a healthy gut microbiota. L. salivarius P1CEA3, a porcine isolated strain, was first selected and identified by its antimicrobial activity against a broad range of pathogenic bacteria due to the production of the novel bacteriocin nisin S. The assembled L. salivarius P1CEA3 genome includes a circular chromosome, a megaplasmid (pMP1CEA3) encoding the nisin S gene cluster, and two small plasmids. A comprehensive genome-based in silico analysis of the L. salivarius P1CEA3 genome reveals the presence of genes related to probiotic features such as bacteriocin synthesis, regulation and production, adhesion and aggregation, the production of lactic acid, amino acids metabolism, vitamin biosynthesis, and tolerance to temperature, acid, bile salts and osmotic and oxidative stress. Furthermore, the strain is absent of risk-related genes for acquired antibiotic resistance traits, virulence factors, toxic metabolites and detrimental metabolic or enzymatic activities. Resistance to common antibiotics and gelatinase and hemolytic activities have been discarded by in vitro experiments. This study identifies several probiotic and safety traits of L. salivarius P1CEA3 and suggests its potential as a promising probiotic in swine production. Full article

(This article belongs to the Special Issue Beneficial Microorganisms: Metabolites, Strain Selection and Utilization)

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17 pages, 4049 KiB

Open AccessArticle

bglG Regulates the Heterogeneity Driven by the Acid Tolerance Response in Lacticaseibacillus paracasei L9

by Zhichao Shen, Li Lin, Zhengyuan Zhai, Jingjing Liang, Long Chen, Yanling Hao and Liang Zhao

Foods 2023, 12(21), 3971; https://doi.org/10.3390/foods12213971 - 30 Oct 2023

Viewed by 1016

Abstract

The acid tolerance of lactic acid bacteria is crucial for their fermentation and probiotic functions. Acid adaption significantly enhances the acid tolerance of strains, and the phenotypic heterogeneity driven by the acid tolerance response (ATR) contributes to this process by providing a selective advantage in harsh environments. The mechanism of heterogeneity under the ATR is not yet clear, but individual gene expression differences are recognized as the cause. In this study, we observed four heterogeneous subpopulations (viable, injured, dead, and unstained) of Lacticaseibacillus paracasei L9 (L9) induced by acid adaption (pH 5.0, 40 min) using flow cytometry. The viable subpopulation represented a significantly superior acid tolerance to the injured subpopulation or total population. Different subpopulations were sorted and transcriptomic analysis was performed. Five genes were found to be upregulated in the viable subpopulation and downregulated in the injured subpopulation, and bglG (LPL9_RS14735) was identified as having a key role in this process. Using salicin (glucoside)-inducing gene expression and gene insertion mutagenesis, we verified that bglG regulated the heterogeneity of the acid stress response and that the relevant mechanisms might be related to activating hsp20. This study provides new evidence for the mechanism of the ATR and may contribute to the theoretical basis of improving the acid tolerance of Lacticaseibacillus paracasei L9. Full article

(This article belongs to the Special Issue Beneficial Microorganisms: Metabolites, Strain Selection and Utilization)

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16 pages, 1816 KiB

Open AccessArticle

Evaluation of Indigenous Yeasts Screened from Chinese Vineyards as Potential Starters for Improving Wine Aroma

by Xiaoxin Ge, Jie Wang, Xiaodi Wang, Yaqiong Liu, Chao Dang, Ran Suo and Jianfeng Sun

Foods 2023, 12(16), 3073; https://doi.org/10.3390/foods12163073 - 16 Aug 2023

Cited by 1 | Viewed by 988

Abstract

Exploitation of the biodiversity of native wine yeast is a means of modifying the sensory characteristics of wine. Samples from different regions in China were analysed to screen native isolates as potential starter cultures. Through morphological and molecular biological analyses, we found six species, belonging to four genera (Hanseniaspora, Saccharomyces, Rhodotorula and Metschnikowia). These species were subjected to stress tolerance assays (ethanol, glucose, SO₂ and pH), enzymatic activity tests (sulphite reductase activity, β-glucosidase activity and protease activity) and fermentation tests. Saccharomyces cerevisiae showed a high tolerance to ethanol and completed fermentation independently. Hanseniaspora demonstrated good enzymatic activity and completed sequential fermentation. The fermentation experiment showed that the PCT4 strain had the best aroma complexity. This study provides a reference for selecting new starters from the perspective of flavour enzymes and tolerance and diversifying the sensory quality of wines from the region. Full article

(This article belongs to the Special Issue Beneficial Microorganisms: Metabolites, Strain Selection and Utilization)

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Graphical abstract

17 pages, 4271 KiB

Open AccessArticle

Phenotypic Traits and Probiotic Functions of Lactiplantibacillus plantarum Y42 in Planktonic and Biofilm Forms

by Jiayi Li, Guangqing Mu and Yanfeng Tuo

Foods 2023, 12(7), 1516; https://doi.org/10.3390/foods12071516 - 03 Apr 2023

Cited by 3 | Viewed by 1424

Abstract

Bacteria in planktonic and biofilm forms exhibit different phenotypic properties. In this study, the phenotypic traits and probiotic functions of Lactiplantibacillus plantarum Y42 in planktonic and biofilm forms were assessed. After 36 h of static culture, scanning electron microscopy and confocal laser scanning microscopy showed that the L. plantarum Y42 bacterial cells contained interconnected adhesive matter on the surface, forming a ~18 μm layer of dense biofilms. The surface properties of L. plantarum Y42 in biofilm form, including autoaggregation ability, hydrophobicity, acid-base charge, and adhesiveness, were all higher than those in the planktonic form. Biofilm L. plantarum Y42 showed a higher tolerance to adverse environmental conditions and a higher survival rate, enzymatic activity, and integrity after vacuum lyophilization. And biofilm L. plantarum Y42 had higher adhesion to human enterocyte HT-29 cell monolayers, inhibited the expressions of proinflammatory factors IL-6 and TNF-α, and promoted the expressions of the anti-inflammatory factor IL-10 and barrier proteins Claudin-1 and Occludin. In addition, L. plantarum Y42 in biofilm form can inhibit the adhesion and invasion of Listeria monocytogenes ATCC 19115 to HT-29 cell monolayers and is more effective in relieving the inflammatory reactions and injuries of HT-29 cells caused by L. monocytogenes ATCC 19115. In conclusion, L. plantarum Y42 in biofilm form exhibited better probiotic functions compared to that in planktonic form. This indicated that L. plantarum Y42 can form biofilms to enhance its probiotic functions, which provided a theoretical basis for better development and utilization of L. plantarum Y42. Full article

(This article belongs to the Special Issue Beneficial Microorganisms: Metabolites, Strain Selection and Utilization)

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Review

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23 pages, 1736 KiB

Open AccessReview

Research Progress of α-Glucosidase Inhibitors Produced by Microorganisms and Their Applications

by Fei Ren, Nairu Ji and Yunping Zhu

Foods 2023, 12(18), 3344; https://doi.org/10.3390/foods12183344 - 06 Sep 2023

Cited by 1 | Viewed by 1816

Abstract

Based on the easy cultivation of microorganisms and their short cycle time, research on α-glucosidase inhibitors (α-GIs) of microbial origin is receiving extensive attention. Raw materials used in food production, such as cereals, dairy products, fruits, and vegetables, contain various bioactive components, like flavonoids, polyphenols, and alkaloids. Fermentation with specific bacterial strains enhances the nutritional value of these raw materials and enables the creation of hypoglycemic products rich in diverse active ingredients. Additionally, conventional food processing often results in significant byproduct generation, causing resource wastage and environmental issues. However, using bacterial strains to ferment these byproducts into α-GIs presents an innovative solution. This review describes the microbial-derived α-GIs that have been identified. Moreover, the production of α-GIs using industrial food raw materials and processing byproducts as a medium in fermentation is summarized. It is worth analyzing the selection of strains and raw materials, the separation and identification of key compounds, and fermentation broth research methods. Notably, the innovative ideas in this field are described as well. This review will provide theoretical guidance for the development of microbial-derived hypoglycemic foods. Full article

(This article belongs to the Special Issue Beneficial Microorganisms: Metabolites, Strain Selection and Utilization)

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