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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: 28 February 2025 | Viewed by 21819

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Prof. Dr. Marc G. J. Feuilloley

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Guest Editor

Research Unit Bacterial Communication and Anti-infectious Strategies (UR CBSA), University of Rouen Normandie, 27000 Evreux, France
Interests: bacterial communication; bacterial virulence; skin-bacteria-cosmetics interactions; endocrine microbiology; cutaneous microbiota
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Dr. Mohamed Zommiti

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Research Unit Bacterial Communication and Anti-infectious Strategies (UR CBSA), University of Rouen Normandie, 27000 Evreux, France
Interests: food microbiology; beneficial microbes; gut microbiota; probiotics; bacteriocins; Organ-On-Chip; microfluidics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue, "Beneficial Microbes: Food, Mood and Beyond".

With trillions of microorganisms of all kinds—bacteria, yeasts, fungi, archaea, protozoa, and even viruses—living on our skin and mucosal tissues, the human microbiota, as the most outstanding reservoir for such diversity, has recently been considered a “functional organism”—an unquestionable efficient ecosystem associated with the body. In both animals and humans, gut microbiota is crucially implicated in metabolism, immune tolerance, and nutrient absorption, inside and outside of the gut. However, any type of imbalance of gut microbiota, also known as “dysbiosis”, generated by diet, use of antibiotics, or infections, can be detrimental to host equilibrium, leading to intestinal and extra-intestinal ailments and disorders. To surmount such hurdles and to alleviate these critical burdens, the use of beneficial microbes of all kinds and bioactive ingredients—encompassing pre-, pro-, post-, para- and psycho-biotics, Bacillus sp. species and even several yeasts—seem to be the solution of tomorrow in the face of chemicals, synthetic pharmaceuticals, and antibiotics. The aforementioned prefixes, when directly related to the term ‘biotics’, have led to different definitions of beneficial microbes, ingredients and compounds that have beneficially colonized and affected all fields and facets of life, reflecting a wide range of trends, propensities and applications. The latter have impacted and continue to impact humans as well as animals. In this Special Issue, we aim to shed light on the various faces of beneficial microbes and their positive interference in nutrition, pharmaceuticals, biomedical investigation, and even psychological areas through their probiotic potential and their antimicrobial compounds and bioactive peptides. We will also discuss the safety of such microorganisms, their safety in terms of secure use in food, in modulating mood, their interference with pathogens in the presence of neurotransmitters, and their efficiency at the clinical investigation level or even at commercial scale. Herein, every single feature of the probiotics realm will be examined—encompassing food, mood and beyond—a task that is not yet completed. Involvement

Prof. Dr. Marc G. J. Feuilloley
Dr. Mohamed Zommiti
Guest Editors

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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. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

prebiotics
probiotics
postbiotics
parabiotics
psycho-biotics
food
mood
benefactions
safety
antibiotics
neurotransmitters
humans
animals

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Beneficial Microbes: Food, Mood and Beyond in Microorganisms (7 articles)

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Research

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34 pages, 9635 KiB

Open AccessArticle

Screening and Comparative Genomics of Probiotic Lactic Acid Bacteria from Bee Bread of Apis Cerana: Influence of Stevia and Stevioside on Bacterial Cell Growth and the Potential of Fermented Stevia as an Antidiabetic, Antioxidant, and Antifungal Agent

by Samra Basharat, Lixin Zhai, Fuyao Jiang, Tanzila Asjad, Adil Khan and Xiangru Liao

Microorganisms 2025, 13(2), 216; https://doi.org/10.3390/microorganisms13020216 - 21 Jan 2025

Viewed by 691

Abstract

The purpose of this research is to identify and characterize lactic acid bacteria (LAB) species in bee bread produced by honey bees (Apis Cerana) in the east mountain area of Suzhou, China. We isolated three strains, Apilactobacillus kunkeei (S1), Lactiplantibacillus plantarum (S2), and Lacticaseibacillus pentosus (S3), with S2 producing the highest amount of lactic acid. Phylogenetic analysis indicated that these isolates, along with the type strain, formed a distinct sub-cluster within the LAB group. The strains exhibited non-hemolytic activity, lacked functional virulence factors, demonstrated high acid and bile tolerance, strong adhesion to intestinal cells, and antimicrobial activity against pathogens, collectively indicating their safety and high probiotic potential for therapeutic applications. Our studies demonstrated that S2 and S3 grew well in the presence of stevia leaf powder and steviosides, while S1 showed reduced growth and inhibitory effects. Importantly, the stevia-fermented strains exhibited strong probiotic potential along with significant antidiabetic, antioxidant, and antifungal properties in vitro. These findings highlight their potential applications in the food, feed, and pharmaceutical industries. Future research should focus on in vivo experiments to validate these results and evaluate compatibility among the strains before their application in functional foods. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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16 pages, 3192 KiB

Open AccessArticle

Probiotic Supplementation Alleviates Corticosterone-Induced Fatty Liver Disease by Regulating Hepatic Lipogenesis and Increasing Gut Microbiota Diversity in Broilers

by Yuyan Feng, Wenqing Mei, Qu Chen, Xiaojing Chen, Yingdong Ni, Mingming Lei and Jie Liu

Microorganisms 2025, 13(1), 200; https://doi.org/10.3390/microorganisms13010200 - 17 Jan 2025

Viewed by 478

Abstract

Emerging evidence indicates a close relationship between gut microbiota and fatty liver disease. It has been suggested that gut microbiota modulation with probiotics ameliorates fatty liver disease in rodents and humans, yet it remains unclear whether the same results will also be obtained in poultry. The aim of this study was to investigate whether a mixture of probiotics supplemented after hatching can prevent CORT-induced fatty liver disease in broilers, and to determine how such effects, if any, are associated with hepatic de novo lipogenesis and gut microbiota composition. Ninety-six one-day-old green-legged chickens were divided into a control group (CON) and probiotic group (PB). At 28 days of age, fatty liver was induced in 16 broilers that were randomly selected from the CON or PB group. At the end of the experiment, broilers from four groups, (i) the control group (CON), (ii) corticosterone group (CORT), (iii) probiotic group (PB), and (iv) PB plus CORT group (CORT&PB), were slaughtered for sampling and analysis. The results showed that probiotic administration significantly prevented CORT-induced body weight loss (p < 0.05) but did not alleviate the weight loss of immune organs caused by CORT. Compared to CON, the broilers in the CORT group exhibited a significant increase in triglyceride (TG) levels in plasma and liver (p < 0.01), as well as severe hepatocytic steatosis and hepatocellular ballooning, which was accompanied by the upregulation of hepatic lipogenesis gene expression. However, probiotic supplementation markedly decreased the intrahepatic lipid accumulation and steatosis histological score, which was associated with the downregulation of sterol regulatory element-binding protein-1 (SREBP1) and acetyl-CoA carboxylase (ACC) mRNA (p < 0.05) and the expression of its protein (p = 0.06). The cecal microbiota composition was determined by 16S rRNA high-throughput sequencing. The results showed that CORT treatment induced distinct gut microbiota alterations with a decrease in microbial diversity and an increase in Proteobacteria abundance (p < 0.05). In contrast, probiotic supplementation increased the beta diversity, the community richness, and the diversity index (p > 0.05), as well as the abundance of Intestinimonas (p < 0.05). Our results indicate that CORT treatment induced severe fatty liver disease and altered the gut microbiota composition in broilers. However, post-hatching probiotic supplementation had a beneficial effect on alleviating fatty liver disease by regulating lipogenic gene expression and increasing gut microbiota diversity and the abundance of beneficial bacteria. We demonstrate for the first time that the supplementation of probiotics to chicks had a beneficial effect on preventing fatty liver disease through regulating lipogenic gene expression and improving the gut microbial balance. Thus, our results indicate that probiotics are a potential nutritional agent for preventing fatty liver disease in chickens. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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13 pages, 2119 KiB

Open AccessArticle

Isolation of Bacillus altitudinis 5-DSW with Protease Activity from Deep-Sea Mineral Water and Preparation of Functional Active Peptide Fractions from Chia Seeds

by Hao Jin, Eun-Gyo Lee, Faiza Khalid, Seung-Wha Jo and Sang-Ho Baik

Microorganisms 2024, 12(10), 2048; https://doi.org/10.3390/microorganisms12102048 - 10 Oct 2024

Viewed by 1113

Abstract

In this study, we successfully isolated Bacillus strains with high protease activity from deep-sea mineral water in Korea and used them to obtain functional peptide fractions from chia seeds. The obtained Bacillus strains showed a high similarity of 99% with B. altitude with a long rod type (named B. altitudinis 5-DSW) and high protease activity at 40 °C, and 70% of the activity remained even at 70 °C. The defatted chia seed protein (15–50 kDa) was treated with crude protease from B. altitudinis 5-DSW and digested into small peptides below 20 kDa. The obtained chia seed peptides showed 3 times and 1.5 times higher antioxidant activity in DPPH and ABT radical scavenging assays, respectively. Moreover, chia seed peptides showed enhanced AChE inhibitory activity with an IC₅₀ value of 14.48 ± 0.88 μg/mL and BChE inhibition activity with an IC₅₀ value of 10.90 ± 0.80 μg/mL. Our results indicate that the newly isolated B. altitudinis 5-DSW and chia seed protein hydrolysates have potential applications in biotechnology and functional food development, enhancing the nutritional quality and value-added utilization of chia byproducts. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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21 pages, 2135 KiB

Open AccessArticle

Cell-Free Culture Supernatant of Lactobacillus acidophilus AG01 and Bifidobacterium animalis subsp. lactis AG02 Reduces the Pathogenicity of NetB-Positive Clostridium perfringens in a Chicken Intestinal Epithelial Cell Line

by Darshana Kadekar, Andreea Cornelia Udrea, Steffen Yde Bak, Niels Christensen, Kirsty Gibbs, Chong Shen and Marion Bernardeau

Microorganisms 2024, 12(4), 839; https://doi.org/10.3390/microorganisms12040839 - 22 Apr 2024

Cited by 5 | Viewed by 2109

Abstract

The worldwide reduction in the use of antibiotics in animal feed is fueling the need for alternatives for the prevention and control of poultry intestinal diseases such as necrotic enteritis (NE), which is caused by Clostridium perfringens. This is the first report on the use of an intestinal epithelial chicken cell line (CHIC-8E11) to study the pathogenic traits of C. perfringens and to investigate the mode of action of cell-free supernatants (CFS) from probiotic Lactobacillus acidophilus AG01 and Bifidobacterium animalis subsp. lactis AG02 in reducing the pathogenicity of C. perfringens. The cell adhesion, permeability and cytotoxicity were assessed under challenge with four C. perfringens strains isolated from broiler NE episodes of differing geographical origin (CP1–UK; CP10–Sweden; 25037–CP01 and CP22–USA). All the C. perfringens strains could adhere to the CHIC-8E11 cells, with varying affinity (0.05–0.48% adhesion across the strains). The CFS from one out of two strains (CP22) increased the cell permeability (+4.5-fold vs. the control, p < 0.01), as measured by the fluorescein isothiocyanate-dextran (FD4) content, with NetB toxin implicated in this effect. The CFS from all the strains was cytotoxic against the CHIC-8E11 cells in a dose- and strain-dependent manner (cytotoxicity 23–62% across the strains when dosed at 50 µL/mL, as assessed by the MTT cell viability assay). Pre-treatment of the cells with CFS from B. animalis subsp. lactis AG02 but not L. acidophilus AG01 reduced the cell adhesion of three out of four C. perfringens strains (by 77–85% vs. the control, p < 0.001) and reduced the negative effect of two NetB-positive strains on the cell permeability. The CFS of both probiotics alleviated the cytotoxicity of all the C. perfringens strains, which was dependent on the dose. The results confirm the suitability of the CHIC-8E11 cell line for the study of host–pathogen cell interactions in the context of NE caused by C. perfringens and reveal a beneficial mode of action of B. animalis subsp. lactis AG02 in reducing C. perfringens cell adhesion and, together with L. acidophilus AG01, in reducing C. perfringens cytotoxicity. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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13 pages, 8592 KiB

Open AccessArticle

Inhibitory Effect of Lactococcus and Enterococcus faecalis on Citrobacter Colitis in Mice

by Ullah Naveed, Chenxi Jiang, Qingsong Yan, Yupeng Wu, Jinhui Zhao, Bowen Zhang, Junhong Xing, Tianming Niu, Chunwei Shi and Chunfeng Wang

Microorganisms 2024, 12(4), 730; https://doi.org/10.3390/microorganisms12040730 - 3 Apr 2024

Viewed by 1315

Abstract

Probiotics are beneficial for intestinal diseases. Research shows that probiotics can regulate intestinal microbiota and alleviate inflammation. Little research has been done on the effects of probiotics on colitis in mice. The purpose of this study was to investigate the inhibitory effect of the strains isolated and screened from the feces of healthy piglets on the enteritis of rocitrobacter. The compound ratio of isolated Lactobacillus L9 and Enterococcus faecalis L16 was determined, and the optimal compound ratio was selected according to acid production tests and bacteriostatic tests in vitro. The results showed that when the ratio of Lactobacillus L9 to Enterococcus faecalis L16 was 4:1, the pH value was the lowest, and the antibacterial diameter was the largest. Then, in animal experiments, flow cytometry was used to detect the number of T lymphocytes in the spleen and mesenteric lymph nodes of mice immunized with complex lactic acid bacteria. The results showed that the number of T lymphocytes in the spleen and mesenteric lymph nodes of mice immunized with complex lactic acid bacteria significantly increased, which could improve the cellular immunity of mice. The microbiota in mouse feces were sequenced and analyzed, and the results showed that compound lactic acid bacteria could increase the diversity of mouse microbiota. It stabilized the intestinal microbiota structure of mice and resisted the damage of pathogenic bacteria. The combination of lactic acid bacteria was determined to inhibit the intestinal colitis induced by Citrobacter, improve the cellular immune response of the body, and promote the growth of animals. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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12 pages, 778 KiB

Open AccessArticle

Isolation, Characterization, and Safety Evaluation of the Novel Probiotic Strain Lacticaseibacillus paracasei IDCC 3401 via Genomic and Phenotypic Approaches

by Han Bin Lee, Won Yeong Bang, Gyu Ri Shin, Hyeon Ji Jeon, Young Hoon Jung and Jungwoo Yang

Microorganisms 2024, 12(1), 85; https://doi.org/10.3390/microorganisms12010085 - 31 Dec 2023

Cited by 3 | Viewed by 2111

Abstract

This study aimed to explore the safety and properties of Lacticaseibacillus paracasei IDCC 3401 as a novel probiotic strain via genomic and phenotypic analyses. In whole-genome sequencing, the genes associated with antibiotic resistance and virulence were not detected in this strain. The minimum inhibitory concentration test revealed that L. paracasei IDCC 3401 was susceptible to all the antibiotics tested, except for kanamycin. Furthermore, the strain did not produce toxigenic compounds, such as biogenic amines and D-lactate, nor did it exhibit significant toxicity in a single-dose acute oral toxicity test in rats. Phenotypic characterization of carbohydrate utilization and enzymatic activities indicated that L. paracasei IDCC 3401 can utilize various nutrients, allowing it to grow in deficient conditions and produce health-promoting metabolites. The presence of L. paracasei IDCC 3401 supernatants significantly inhibited the growth of enteric pathogens (p < 0.05). In addition, the adhesion ability of L. paracasei IDCC 3401 to intestinal epithelial cells was found to be as superior as that of Lacticaseibacillus rhamnosus GG. These results suggest that L. paracasei IDCC 3401 is safe for consumption and provides health benefits to the host. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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12 pages, 864 KiB

Open AccessArticle

Characterization of Lactococcus lactis 11/19-B1 Isolated from Kiwi Fruit as a Potential Probiotic and Paraprobiotic

by Ken Ishioka, Nozomu Miyazaki, Kyoko Nishiyama and Tatsuo Suzutani

Microorganisms 2023, 11(12), 2949; https://doi.org/10.3390/microorganisms11122949 - 9 Dec 2023

Viewed by 1619

Abstract

Probiotics are live bacteria used as food additives that are beneficial to human health. Lactococcus lactis 11/19-B1 strain isolated from kiwi fruit stimulates innate immunity in silkworms. Intake of yogurt containing the living 11/19-B1 strain significantly decreases the level of low-density lipoproteins (LDLs) in high-LDL volunteers and improves atopic dermatitis in humans. In this study, the probiotic properties of the 11/19-B1 strain, such as sensitivity to antimicrobial compounds, biogenic amine production, some virulence genes for human health, antimicrobial activity, tolerance to gastric acid and bile acids, and ability to adhere to the intestinal mucosa, were evaluated. The 11/19-B1 strain did not show resistance to the tested antimicrobial compounds except cefoxitin and fosfomycin. In addition, no production of amines that can harm humans, the antimicrobial activity required for probiotics, and the absence of adhesion to Caco-2 cells suggest that it is unlikely to attach to the intestinal epithelium. The 11/19-B1 strain grew in 0.3% but not in 1% bile salt. In the presence of 2% skim milk, the survival rate of the 11/19-B1 strain under simulated gastrointestinal tract conditions was 67% even after 4 h. These results indicate that the 11/19-B1 strain may function as a probiotic or paraprobiotic to be utilized in the food industry. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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13 pages, 1327 KiB

Open AccessArticle

Isolation of Latilactobacillus curvatus with Enhanced Nitric Oxide Synthesis from Korean Traditional Fermented Food and Investigation of Its Probiotic Properties

by Hao Jin, Sang-Kyu Park, Yong-Gun Yun, Nho-Eul Song and Sang-Ho Baik

Microorganisms 2023, 11(9), 2285; https://doi.org/10.3390/microorganisms11092285 - 11 Sep 2023

Cited by 2 | Viewed by 1752

Abstract

Nitric oxide (NO) is a free radical associated with physiological functions such as blood pressure regulation, cardiovascular health, mitochondrial production, calcium transport, oxidative stress, and skeletal muscle repair. This study aimed to isolate Latilactobacillus curvatus strains with enhanced NO production from the traditional Korean fermented food, jangajji, and evaluate their probiotic properties for industrial purposes. When cells were co-cultured with various bacterial stimulants, NO production generally increased, and NO synthesis was observed in the range of 20–40 mg/mL. The selected strains of Lat. curvatus were resistant to acid and bile conditions and with variable effectiveness (1–14%) in adhering to Caco-2 cells. Most bacterial strains can inhibit the growth of various pathogens. In addition, they are capable of reducing cholesterol levels via assimilation of cholesterol at 10–50%. Among the selected NO synthases from Lat. curvatus strains, the strain JBCC38 showed the highest capacity to scavenge ABTS (30.1%) and DPPH radicals (39.4%). Moreover, these strains exhibited immunomodulatory properties. The production of TNF-α and IL-6 in the macrophages treated with various bacterial stimulants was induced in all the selected strains. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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Review

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15 pages, 746 KiB

Open AccessReview

Psychobiotics and the Microbiota–Gut–Brain Axis: Where Do We Go from Here?

by Sylvie Binda, Annie Tremblay, Umar Haris Iqbal, Ola Kassem, Mélanie Le Barz, Vincent Thomas, Stéphane Bronner, Tara Perrot, Nafissa Ismail and J.Alex Parker

Microorganisms 2024, 12(4), 634; https://doi.org/10.3390/microorganisms12040634 - 22 Mar 2024

Cited by 3 | Viewed by 7650

Abstract

The bidirectional relationship between the gut microbiota and the nervous system is known as the microbiota–gut–brain axis (MGBA). The MGBA controls the complex interactions between the brain, the enteric nervous system, the gut-associated immune system, and the enteric neuroendocrine systems, regulating key physiological functions such as the immune response, sleep, emotions and mood, food intake, and intestinal functions. Psychobiotics are considered tools with the potential to modulate the MGBA through preventive, adjunctive, or curative approaches, but their specific mechanisms of action on many aspects of health are yet to be characterized. This narrative review and perspectives article highlights the key paradigms needing attention as the scope of potential probiotics applications in human health increases, with a growing body of evidence supporting their systemic beneficial effects. However, there are many limitations to overcome before establishing the extent to which we can incorporate probiotics in the management of neuropsychiatric disorders. Although this article uses the term probiotics in a general manner, it remains important to study probiotics at the strain level in most cases. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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Other

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13 pages, 897 KiB

Open AccessSystematic Review

Lacticaseibacillus rhamnosus GG Versus Placebo for Eradication of Vancomycin-Resistant Enterococcus faecium in Intestinal Carriers: A Systematic Review and Meta-Analysis

by Ingrid Maria Cecilia Rubin, Maja Johanne Søndergaard Knudsen, Sofie Ingdam Halkjær, Christian Schaadt Ilsby, Mette Pinholt and Andreas Munk Petersen

Microorganisms 2023, 11(11), 2804; https://doi.org/10.3390/microorganisms11112804 - 19 Nov 2023

Cited by 1 | Viewed by 1495

Abstract

The aim of this review was to assess the efficacy and safety of Lacticaseibacillus rhamnosus GG (LGG) (previously known as Lactobacillus rhamnosus GG) for the eradication of vancomycin-resistant Enterococcus faecium (VREfm) in colonized carriers. We searched Cochrane Central, EMBASE, and the PubMed Library from inception to 21 August 2023, for randomized controlled trials (RCTs) investigating the effectiveness of LGG for the eradication of gastrointestinal carriage of VREfm. An initial screening was performed followed by a full-text evaluation of the papers. Out of 4076 articles in the original screening, six RCTs (167 participants) were included in the review. All were placebo-controlled RCTs. The meta-analysis was inconclusive with regard to the effect of LGG for clearing VREfm colonization. The overall quality of the evidence was low due to inconsistency and the small number of patients in the trials. We found insufficient evidence to support the use of LGG for the eradication of VREfm in colonized carriers. There is a need for larger RCTs with a standardized formulation and dosage of LGG in future trials. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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