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Microorganisms
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Bacteria and Fungi Probiotics: 2nd Edition
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Bacteria and Fungi Probiotics: 2nd Edition

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

Deadline for manuscript submissions: closed (28 February 2025) | Viewed by 7156

Special Issue Editor

Dr. Françoise Coucheney

E-Mail Website
Guest Editor
UMR Transfrontalière BioEcoAgro 1158, Université de Lille, Lille, France
Interests: bacteria and yeasts probiotics; antimicrobial peptides; cheese ecosystem; food biopreservation; animal health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our 2023 Special Issue, "Bacteria and Fungi Probiotics”.

Antibiotic resistance is a global health problem. The increase in the number of microbial strains that have become resistant to antibiotics worldwide and the lack, in some cases, of new therapeutics is worrisome. To this day, the World Health Organization continually warns of this threat and encourages the development of new strategies and alternatives to antibiotics to combat drug resistance.

In general, probiotics are presented as a potential alternative to antibiotics to control and prevent the spread of pathogenic bacteria. Strains belonging to lactic acid bacteria such as Lactobacillus and Bifidobacterium are commonly used as probiotics. These bacteria can produce various antimicrobial agents, such as Bacteriocins, that exert strong antagonistic activity against different pathogenic microbes including Listeria monocytogenes, Escherichia coli, etc. Saccharomyces boulardii is the only commercially available probiotic yeast and is often used as a probiotic for countering intestinal inflammatory processes.

This Special Issue aims to collect research or review articles related to bacteria and fungi probiotics of different origin with a focus on the antimicrobial peptides (AMP) of probiotics.

We look forward to receiving your contributions.

Related International Congress:

OHID 2024 and Antimic 2024: Two congresses for a week dedicated to the One Health approach with applications in several areas (environmental health, plant health, animal health, human health) and the Bioproduction of Natural Antimicrobials, 24–28 June 2024, Lille, France

Dr. Françoise Coucheney
Guest Editor

Manuscript Submission Information

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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.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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

  • bacteria
  • fungi
  • probiotics
  • antimicrobials
  • antioxidant
  • gut microbiota
  • gut immunomodulation
  • animal health
  • human health

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Published Papers (4 papers)

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Research

9 pages, 957 KiB  
Communication
Evaluation of In Vitro Production Capabilities of Indole Derivatives by Lactic Acid Bacteria
by Bingyang Ma, Yan Zhao, Liping Liu, Jianguo Xu, Qingping Hu, Saisai Feng and Liangliang Zhang
Microorganisms 2025, 13(1), 150; https://doi.org/10.3390/microorganisms13010150 - 13 Jan 2025
Viewed by 1046
Abstract
Lactic acid Bacteria (LAB) convert tryptophan to indole derivatives and induce protective IL-22 production in vivo. However, differences in metabolizing capabilities among LAB species have not been widely investigated. In the present study, we compared the capabilities of 186 LAB strains to produce [...] Read more.
Lactic acid Bacteria (LAB) convert tryptophan to indole derivatives and induce protective IL-22 production in vivo. However, differences in metabolizing capabilities among LAB species have not been widely investigated. In the present study, we compared the capabilities of 186 LAB strains to produce four kinds of indole derivatives, including indole-3-carboxaldehyde (IAId), indole-3-lactic acid (ILA), indole-3-propanoic acid (IPA), and indole-3-acetic acid (IAA). These strains were isolated from fermented foods, dairy products, and the feces of healthy individuals, as well as from fish and shrimp from Shanxi and Jiangsu provinces. They represent 15 genera, including Bifidobacterium, Enterococcus, Lacticaseibacillus, Lactiplantibacillus, Lactobacillus, Lactococcus, Limosilactobacillus, Pediococcus, Streptococcus, Weissella, Latilactobacillus, Levilactobacillus, Ligilactobacillus, and Loigolactobacillus. The results indicate widespread IAId-producing capabilities in LAB strains, with positive rates of approximately 90% (106/117) and 100% (69/69) among strains from Shanxi and Jiangsu provinces, respectively. The concentrations of IAId ranged from 72.42 ng/mL to 423.14 ng/mL in all positive strains from Shanxi Province and from 169.39 ng/mL to 503.51 ng/mL in strains from Jiangsu Province. Intriguingly, we also observed specific ILA-producing capabilities in Lactiplantibacillus strains, with positive rates of 55.17% (16/29) and 80.95% (17/21) among strains isolated from Shanxi and Jiangsu provinces, respectively. The overall detection rates of ILA among all tested strains (including both Lactiplantibacillus and other genus strains) were 17.9% (21/117) and 26.1% (18/69). The concentrations of ILA in positive strains ranged from 12.22 ng/mL to 101.86 ng/mL and from 5.75 ng/mL to 62.96 ng/mL from Shanxi and Jiangsu provinces, respectively. IPA and IAA were not detected in any strains. Finally, these indole derivative-producing capabilities were not related to their geographical origins or isolation sources. The current study provides insights into the species- or genus-dependent capabilities for metabolizing indole derivatives. Defining the specific roles of LAB in indole derivative metabolism will uncover the exact physiological mechanisms and be helpful for functional strain screening. Full article
(This article belongs to the Special Issue Bacteria and Fungi Probiotics: 2nd Edition)
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15 pages, 4051 KiB  
Article
Enhanced Tolerance to Antifungals as a General Feature of Rho− Mutants in Yeast Species: Implications to Positive Selection of Respiratory Deficiency
by Zachary Johnson, Farhan Nadim and Mikhajlo K. Zubko
Microorganisms 2025, 13(1), 99; https://doi.org/10.3390/microorganisms13010099 - 7 Jan 2025
Viewed by 1187
Abstract
Although the mitochondrial genome is an attribute of all eukaryotes, some yeast species (called petite-positive) can replicate without mitochondrial DNA (mtDNA). Strains without mtDNA (known as rho− mutants or petite mutants) are respiration-deficient and require fermentable carbon sources (such as glucose) for [...] Read more.
Although the mitochondrial genome is an attribute of all eukaryotes, some yeast species (called petite-positive) can replicate without mitochondrial DNA (mtDNA). Strains without mtDNA (known as rho− mutants or petite mutants) are respiration-deficient and require fermentable carbon sources (such as glucose) for their metabolism. However, they are compromised in many aspects of fitness and competitiveness. Nevertheless, a few research groups have reported that some petite mutants of Candida glabrata and Saccharomyces cerevisiae manifested higher levels of tolerance to the antifungal fluconazole than their wild-type (WT) counterparts. In this study, we show that elevated tolerance to two or three out of four tested antifungals is a generic feature of at least five petite-positive species of yeasts including C. glabrata (higher tolerance of petites to clotrimazole and miconazole), S. bayanus (tolerance to clotrimazole, fluconazole, and miconazole), S. cerevisiae (tolerance to clotrimazole and fluconazole), S. paradoxus (tolerance to clotrimazole, fluconazole, and miconazole), and S. pastorianus (tolerance to clotrimazole and fluconazole). Comparing the levels of tolerance to the antifungals in WT and petite mutants was based on measuring the diameters of the zones of inhibition (ZOIs) using disc diffusion assays. The mode of inhibition in the majority of WT strains by all antifungals was fungicidal; most of the rho− mutants manifested fungistatic inhibition. We observed partial (not complete) inhibition in WT, with four different types of ZOI patterns that were species- and antifungal-specific. The partial inhibition was characterised by the presence of antifungal-tolerant colonies within ZOI areas. The inability of these colonies selected from ZOIs to grow on glycerol, as a single source of carbon, proved that they were rho− mutants spontaneously generated in the WT populations. The results on the elevated tolerance of petite strains to antifungals are discussed in terms of the prospective positive selection of respiratory-deficient mutants and the various implications of such selection. Full article
(This article belongs to the Special Issue Bacteria and Fungi Probiotics: 2nd Edition)
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15 pages, 2495 KiB  
Article
Characterization and Assessment of Native Lactic Acid Bacteria from Broiler Intestines for Potential Probiotic Properties
by Xiaoxia Li, Wang Li, Longmei Zhao, Yuanxiao Li, Wanling He, Ke Ding and Pinghua Cao
Microorganisms 2024, 12(4), 749; https://doi.org/10.3390/microorganisms12040749 - 7 Apr 2024
Cited by 4 | Viewed by 2824
Abstract
Probiotics are the most promising alternative to antibiotics for improving animal production and controlling pathogenic infections, while strains derived from natural hosts are considered highly desirable due to their good adaptation to the gastrointestinal tract. The aim of this study was to screen [...] Read more.
Probiotics are the most promising alternative to antibiotics for improving animal production and controlling pathogenic infections, while strains derived from natural hosts are considered highly desirable due to their good adaptation to the gastrointestinal tract. The aim of this study was to screen Lactobacillus with broad-spectrum antibacterial activity from broilers fed an antibiotic-free diet and evaluate their potential as poultry probiotics. A total of 44 lactic acid bacteria (LAB) strains were isolated from the intestines of healthy broilers, among which 3 strains exhibited outstanding antimicrobial activity and were subsequently identified through 16S rRNA sequencing as Enterococcus faecium L8, Lactiplantibacillus plantarum L10, and Limosilactobacillus reuteri H11. These three isolates demonstrated potent bacteriostatic activity against Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, and Salmonella cholerae, with inhibition zones ranging from 15.67 ± 1.53 to 21.33 ± 0.58 mm. The selected LAB strains exhibited high tolerance to acid and bile salts, with L. reuteri H11 displaying the highest survival rate (ranging from 34.68% to 110.28%) after exposure to 0.3% (w/v) bile salts for 6 h or a low pH environment (pH 2, 2.5, and 3) for 3 h. Notably, L. reuteri H11 outperformed other strains in terms of hydrophobicity (84.31%), auto-aggregation (53.12%), and co−aggregation with E. coli ATCC 25922 (36.81%) and S. aureus ATCC 6538 (40.20%). In addition, the three LAB isolates were either fully or moderately susceptible to the tested antibiotics, except for strain L8, which resisted gentamycin and vancomycin. Consequently, these three LAB strains, especially L. reuteri H11, isolated from the intestines of broiler chickens, represent promising probiotic candidates that can be employed as feed additives to enhance production performance and control poultry pathogens. Full article
(This article belongs to the Special Issue Bacteria and Fungi Probiotics: 2nd Edition)
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14 pages, 1950 KiB  
Article
Impact of Dietary Regime and Seasonality on Hindgut’s Mycobiota Diversity in Dairy Cows
by Ali Sadek, Bernard Taminiau, Georges Daube, Panagiotis Sapountzis, Frédérique Chaucheyras-Durand, Mathieu Castex, Françoise Coucheney and Djamel Drider
Microorganisms 2024, 12(1), 84; https://doi.org/10.3390/microorganisms12010084 - 31 Dec 2023
Cited by 1 | Viewed by 1471
Abstract
We describe and discuss the intestinal mycobiota of dairy cows reared in France following variations in dietary regimes and two seasons. Two groups of 21 animals were followed over a summer and winter period, and another group of 28 animals was followed only [...] Read more.
We describe and discuss the intestinal mycobiota of dairy cows reared in France following variations in dietary regimes and two seasons. Two groups of 21 animals were followed over a summer and winter period, and another group of 28 animals was followed only during the same summer season. The summer diet was based on grazing supplemented with 3–5 kg/d of maize, grass silage and hay, while the winter diet consisted of 30% maize silage, 25% grass silage, 15% hay and 30% concentrate. A total of 69 DNA samples were extracted from the feces of these cows. Amplification and sequencing of the ITS2 region were used to assess mycobiota diversity. Analyses of alpha and beta diversity were performed and compared statistically. The mycobiota changed significantly from summer to winter conditions with a decrease in its diversity, richness and evenness parameters, while beta diversity analysis showed different mycobiota profiles. Of note, the Geotrichum operational taxonomic unit (OTU) was prevalent in the winter group, with a mean relative abundance (RA) of 65% of the total mycobiota. This Geotrichum OTU was also found in the summer group, but to a lesser extent (5%). In conclusion, a summer grazing diet allowed a higher fecal fungal diversity. These data show, for the first time, that a change in diet associated with seasonality plays a central role in shaping hindgut fungal diversity. Full article
(This article belongs to the Special Issue Bacteria and Fungi Probiotics: 2nd Edition)
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