Current Trends in the Applications of Probiotics and Other Beneficial Microbes, Second Edition

Special Issue Editor


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Guest Editor
Faculty of Health Sciences, University of Maribor, Žitna Ulica 15, 2000 Maribor, Slovenia
Interests: probiotics; beneficial microbes; antimicrobial effect; lactobacilli; bifidobacteria; fermented foods
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Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issue, entitled “Current Trends in the Applications of Probiotics and Other Beneficial Microbes”.

Beneficial microbes are abundant and all around us, as they are adaptable to many environments. One important group of beneficial microbes is probiotics, which are defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host”. Probiotics and other beneficial microbes can have many beneficial effects on their hosts via modulation of the gut microbiota. They can also influence other parts of the body via various axes in humans and animals, such as the gut–microbiota–brain axis, gut–microbiota–skin axis, gut–vagina axis, etc. Other beneficial microbes include microbes, which are responsible for the fermentation of foods such as yoghurt, kefir, kombucha, kimchi, and many others. The beneficial effect of these foods is enhanced due to the microbial production of nutrients, antimicrobial and antioxidant substances, as well as bioactive peptides. Last of all, microbes play a dominant role in regulating the biogeochemical cycles on our planet. The potential topics of this Special Issue will focus on the many applications of beneficial microbes, including but not limited to the following: beneficial microbes and host–microbiome modulation; beneficial microbes and fermented foods; novel beneficial microbes; and beneficial microbes and ecology.

Dr. Sabina Fijan
Guest Editor

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Keywords

  • probiotics
  • beneficial microbes
  • host–microbiome modulation
  • fermented foods
  • ecology

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Related Special Issue

Published Papers (3 papers)

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Research

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16 pages, 1350 KB  
Article
An Indigenous Pseudomonas Strain from Maize Rhizosphere Enhances Plant Growth Through Multiple Mechanisms
by Muhammad Usman Nadeem, Najam Naveed, Fatima Murtaza, Maryam Ali and Izzah Shahid
Appl. Microbiol. 2026, 6(3), 41; https://doi.org/10.3390/applmicrobiol6030041 - 6 Mar 2026
Viewed by 244
Abstract
The excessive use of chemical fertilizers has depleted agricultural soils, necessitating a paradigm shift toward eco-friendly alternatives such as plant-beneficial microbes. However, the integration of plant-beneficial bacteria into global agroecosystems requires strategic and comprehensive analyses, as well as the development of optimally designed [...] Read more.
The excessive use of chemical fertilizers has depleted agricultural soils, necessitating a paradigm shift toward eco-friendly alternatives such as plant-beneficial microbes. However, the integration of plant-beneficial bacteria into global agroecosystems requires strategic and comprehensive analyses, as well as the development of optimally designed bioinocula to maximize their benefits. In this study, twenty-one rhizobacteria isolated from the maize rhizosphere were systematically screened for plant-beneficial traits, including phosphate and zinc solubilization, indole-3-acetic acid (IAA) production, and the synthesis of extracellular hydrolytic enzymes, followed by their evaluation for plant growth promotion. Among all bacterial isolates, Pseudomonas sp. NCR2 displayed the most comprehensive plant growth-promoting traits. In a pot-scale experiment, maize plants inoculated with multifaceted Pseudomonas sp. NCR2 showed significantly increased root growth, chlorophyll, soluble proteins, and phenolic contents as compared to untreated plants. This study underscores the significance of systematic screening of host-adaptive rhizobacteria for developing promising and tailored bioinocula. Furthermore, the results of this study also demonstrate the use of multifunctional biofertilizing inoculum for the systematic decrease of chemical inputs while simultaneously maintaining the crop productivity. Full article
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25 pages, 1850 KB  
Article
Recovery, Identification, and Presumptive Agricultural Application of Soil Bacteria
by Guadalupe Steele, Andrew K. Rindsberg and Hung King Tiong
Appl. Microbiol. 2026, 6(1), 11; https://doi.org/10.3390/applmicrobiol6010011 - 9 Jan 2026
Viewed by 592
Abstract
Conventional and organic agriculture can both cause soil microbial community structure (SMCS) destruction, infertility, and abandonment. The application of soil productivity-improving biofertilizers is a sustainable practice that requires holistic knowledge, including complex biointeractions, diverse microbial metabolism, and culture requirements, the last of which [...] Read more.
Conventional and organic agriculture can both cause soil microbial community structure (SMCS) destruction, infertility, and abandonment. The application of soil productivity-improving biofertilizers is a sustainable practice that requires holistic knowledge, including complex biointeractions, diverse microbial metabolism, and culture requirements, the last of which rely on methodology and technology. In this study, a holistic culture-based and meta-analysis approach was employed to explore pristine and domesticated soils for presumptive plant growth-promoting (PGP) bacteria. Various soil samples were logistically acquired and processed using enrichment and heat alternatives. Morphologically diverse isolates were streak-purified and analyzed for 16S rRNA bacterial identification. Meta-analysis of PGP bacteria in domesticated environments was conducted using Google Search and NCBI PubMed. Soil fertility was analyzed for the pH and nitrogen/phosphorus/potassium (NPK) contents using biochemical tests. Notably, 7 genera and 15 species were differentially recovered, with Bacillus being the most prevalent and diverse in species. Conversely, Aeromonas, Lactobacillus, Lelliottia, Pseudomonas, and Staphylococcus were found only in pristine soil. While soil pH was consistent in all pristine soil samples, NPK contents ranged widely across the pristine (i.e., P/K) and domesticated samples (i.e., N/P/K). These findings could enhance biofertilizer SMCS, function, and effectiveness in the agricultural productivity needed to feed the expanding population. Full article
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Review

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22 pages, 815 KB  
Review
Gut Microbiome Modulation by Probiotics: Implications for Livestock Growth Performance and Health—Narrative Review
by Peter Ayodeji Idowu, Lwando Mbambalala, Oluwakamisi Festus Akinmoladun and Adeola Patience Idowu
Appl. Microbiol. 2025, 5(4), 149; https://doi.org/10.3390/applmicrobiol5040149 - 16 Dec 2025
Cited by 1 | Viewed by 1990
Abstract
Probiotics have emerged as gut modulators, capable of restructuring microbial communities to enhance animal health and performance. This review synthesizes peer-reviewed studies published between 2015 and 2025, retrieved from Scopus, Web of Science, and Google Scholar. It encompasses both ruminant and monogastric species [...] Read more.
Probiotics have emerged as gut modulators, capable of restructuring microbial communities to enhance animal health and performance. This review synthesizes peer-reviewed studies published between 2015 and 2025, retrieved from Scopus, Web of Science, and Google Scholar. It encompasses both ruminant and monogastric species to evaluate the effects of probiotic supplementation under diverse production environments. Evidence indicates that diet, age, host genetics, and management practices strongly influence gut microbiome composition and function, explaining the context-dependent nature of probiotic efficacy. These interventions improve growth performance, feed efficiency, gut morphology, pathogen resistance, and systemic immune parameters, supporting their potential as sustainable alternatives to antibiotic growth promoters. However, responses vary and are context-dependent, based on differences in strain specificity, dosage, host physiology, and environmental stress. By explaining how probiotic-mediated modulation translates into improved productivity, reduced antimicrobial dependence, and greater resilience in real-world farming systems, this review highlights their practical value for modern livestock production. Future research should focus on field-based validation, multi-omics approaches to resolve host–microbiota–probiotic interactions, and long-term assessments of animal health, productivity, and environmental impacts. Strategic deployment of probiotics, combined with scalable delivery technologies and regulatory alignment, can enhance resilience, sustainability, and efficiency in livestock production systems. Full article
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