Current Trends in the Applications of Probiotics and Other Beneficial Microbes: Expanding Horizons

While pathogenic microbes, such as Yersinia pestis, Mycobacterium tuberculosis, Clostridium tetani, influenza a virus, and many others, have historically been the focus of scientific attention due to their role in causing severe diseases, beneficial microorganisms are being increasingly recognized for their essential contributions to human, animal, and plant health within the One Health framework, as well as their contributions to nutrition and the stability of ecosystems [1,2,3,4]. Beneficial microbes are abundant, omnipresent, and adaptable to a wide variety of environments. Therefore, they are important in supporting the health and well-being of humans, animals, and plants, as well as being essential in relation to maintaining ecological balance.

The most important group of beneficial microbes for human health is the human microbiome. It is composed of diverse microbial communities in the gut, skin, oral cavity, and urogenital tract, which aid in nutrient uptake, immune regulation, and protection against pathogens, thus showing the systemic importance of microbe–host interactions [1]. Through various physiological axes, such as the gut–brain, gut–skin, and gut–vaginal axes, the microbiome can influence neurological function, dermatological health, urogenital balance, etc., demonstrating the systemic importance of microbe–host interactions [5].

Probiotics are one of the most well-known beneficial microbes and are defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host” [6]. The primary positive effect of probiotics is the modulation of the gut microbiota, where they help restore microbial balance, enhance colonization resistance against pathogens, and strengthen host immune responses. The primary mechanisms of action of probiotics include antimicrobial activity, competitive exclusion, immunomodulation, and the strengthening of the intestinal epithelial barrier function, as well as exerting effects on the immune, the central nervous, and the endocrine systems [5,7,8,9]. Their influence, therefore, extends far beyond the gut [5].

In addition to probiotics, many other beneficial microbes contribute to human health through their role in fermentation. Fermented foods are defined as “foods made through desired microbial growth and enzymatic conversions of food components” [10]. Microorganisms such as lactic acid bacteria and yeasts are responsible for the production of traditional and modern fermented foods, including yogurt, kefir, kombucha, kimchi, sauerkraut, tempeh, and many others [11]. Beyond preservation and flavor enhancement, fermentation enriches foods with health-promoting compounds. These include vitamins, bioactive peptides, antimicrobial metabolites, and antioxidant molecules. These enrichments improve the nutritional profile of the food; upon consumption, they may support gut health and offer protection against chronic disease. Beneficial microbes can therefore not only preserve foods but also transform them into functional foods with added health value [12,13].

Beyond the human gut, microbiomes in animals and plants can promote nutrient uptake and improve plant resilience against environmental stresses. Additionally, the soil microbiome plays a crucial role in nutrient cycling, plant health, and ecosystem functioning, acting as a key driver of soil fertility and resilience [14]. The role of beneficial microbes in the broader biosphere is even more fundamental. Microorganisms aid in regulating global biogeochemical cycles, including those of carbon, nitrogen, sulfur, and phosphorus [15]. By driving key processes such as carbon fixation, methane oxidation, and nitrogen fixation, microbes sustain life on Earth and maintain ecosystem resilience. In this sense, beneficial microbes represent the unseen infrastructure of our planet, linking human health, food systems, and planetary homeostasis into one interconnected whole.

Research in the field of microorganisms relies on diverse approaches. In vitro studies provide mechanistic insights into microbes at the cellular and molecular level, where researchers investigate microbial properties, antimicrobial activity, microbe–microbe interactions, etc., under controlled laboratory conditions. In vivo models extend these findings by demonstrating how microbes interact with their animal or plant hosts within complex biological systems, offering essential evidence of safety, colonization, and functional effects. Observational studies contribute valuable information on the associations between microbial exposure, host health, and disease outcomes in real-world settings, although they cannot establish causality on their own. On the other hand, randomized controlled clinical trials (RCTs) remain the gold standard for establishing causal links and confirming the health benefits of specific beneficial microbial strains in humans. Reviews then connect experimental and clinical data to provide critical overviews of emerging findings and novel conceptual advances in relation to microbes. Ultimately, systematic reviews and meta-analyses synthesize results across studies to assess consistency, highlight gaps, and guide translation into practice. Together, these various methodologies enable new biologically plausible and clinically meaningful knowledge about beneficial microbes [16,17,18].

This Special Issue, entitled “Current Trends in the Applications of Probiotics and Other Beneficial Microbes”, contains 14 publications that focus on the diverse effects of beneficial microbes in relation to host–microbiome modulation, fermented foods, and novel and innovative applications. In vitro methods were used in nine publications [19,20,21,22,23,24,25,26,27]; among these publications, three studies also included in vivo models [19,23,27], while another three studies also conducted randomized controlled trials (RCTs) to confirm clinical efficacy [21,24,26]. Complementing these studies, this Special Issue also includes four review articles [28,29,30,31] and one perspective [32]. Across these contributions, multiple methods were often combined within individual studies, reflecting the complexity and applied nature of microbiological research in relation to beneficial microbes. This diversity of approaches shows the importance of combining laboratory, animal, or plant models, as well as clinical studies, with critical reviews and perspectives in order to advance both scientific understanding and practical applications. The main findings are depicted in

Table 1. Main findings of the 14 studies included in the Special Issue, entitled “Current Trends in the Applications of Probiotics and Other Beneficial Microbes.”

Authors (Year)	Study Subject	Focus	Strain/Food/Microorganism	Population/Model
Steen Dobloug et al., 2023 [19]	Animal	Probiotic/ Ecological	Aliivibrio spp.	Atlantic salmon against salmon lice
Stumpf et al., 2024 [20]	Technological—Vitamin B12 production	Fermented food application	Acetobacter malorum HFD 3141; Acetobacter orientalis HFD 3031	Sourdough isolates; application in apple juice
Pérez-González et al., 2024 [21]	Human (Indigenous community)	Fermented food/Oral microbiome	Filamentous fungi (Cladosporium)	37 participants; impact of traditional fermented beverages (pozol)
Balland et al., 2025 [22]	Ecological/ Technological—mercury leaching	Bioremediation	Trichoderma koningiopsis; Talaromyces verruculosus	Fungi from Hg-contaminated soils; mercury immobilization
Senn et al., 2025 [23]	Plant	Ecological/ Transcriptomics	Microbiota (Pedobacter, Filimonas, Cohnella, Sorangium)	Oak (Quercus agrifolia) post-fire
Ehala-Aleksejev et al., 2025 [24]	Human	Fermented food/Dietary fiber	Pectin smoothie (fibers)	28 healthy women; urate levels and gut microbiota
Gocheva et al., 2025 [25]	Technological—sialidase production	Fermentation/ Enzyme production	Oerskovia paurometabola O129	Optimization of sialidase production conditions
Lares-Michel et al., 2025 [26]	Human (Observational)	Diet–Microbiota interaction	Diet EAT-Lancet; Bifidobacterium, Akkermansia, Prevotella, Bilophila	54 young adults in Mexico
Mohamed et al., 2025 [27]	Animal	Probiotic	Microencapsulated probiotics	Rats with induced myocardial infarction
Najjar, 2025 [28]	Plant/ Ecological (Review)	Endophytes/ Sustainable agriculture	Endophytic fungi and bacteria	Plant applications
Bamicha et al., 2024 [29]	Human (Review)	Gut microbiome and Neurotransmitters	Microbiota–brain interactions, neurotransmitters	Autism; diet–microbiota connection
Fijan et al., 2024 [30]	Human (Review)	Fermented food	Kimchi, sauerkraut, Brassica foods	Health benefits
Burlakoti et al., 2024 [31]	Plant (Review)	Beneficial microbes	Rhizobacteria and other beneficial microbes in maize	Interactions for stress tolerance
Yakimova et al., 2025 [32]	Human/ Technological (Perspective)	Microbiota engineering	Genetically modified microbiota	Radioprotection in space

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Human microbiome modulation was a central theme in this Special Issue. Ehala-Aleksejev et al. [24] showed that a high-pectin smoothie modulated gut bacteria, including Bacteroides, Prevotella, and Faecalibacterium, in 28 healthy women, highlighting the need for personalized nutrition. Lares-Michel et al. [26] found that adherence to the EAT-Lancet diet in 54 young adults shifted key gut bacteria such as Bifidobacterium, Akkermansia, and Prevotella, linking sustainable diets to microbiome composition. Pérez-González et al. [21] found that filamentous oral fungi, mainly Cladosporium, were associated with lower dental caries in indigenous Mexican populations consuming traditional fermented maize beverages that modified the oral microbiome. Bamicha et al. [29] explored the gut–brain axis in autism, showing that dietary modulation can influence neurotransmitter dynamics. Fijan et al. [30] reviewed clinical and observational studies on Brassica-based fermented foods, such as kimchi and sauerkraut, demonstrating their benefits for metabolic health, obesity risk, and IBS symptoms via gut microbiome modification. Despite these findings, it should be noted that individual microbiomes are unique [33], akin to a fingerprint, making it very difficult to draw definitive conclusions about health outcomes from microbiome modulation alone.

Two studies focused on the health applications of animal probiotics. Steen Dobloug et al. [19] reported that Aliivibrio strains could reduce salmon lice infestation in farmed Atlantic salmon, pointing to probiotics as sustainable alternatives to chemical treatments in aquaculture. Mohamed et al. [27] showed that microencapsulated probiotics (Bifidobacterium bifidum NRRL B-41410, Lactobacillus helveticus CNRZ32, and Lacticaseibacillus casei FEGY 9973) protected rats against myocardial infarction by improving biochemical and histological parameters and increasing the proportion of beneficial gut bacteria. Both studies highlighted the preventive and protective effects of probiotics, illustrating how microbe–host interactions can improve resilience against stressors, whether parasitic or inflammatory.

The benefits of fermented foods were investigated in three studies contained in this Special Issue. Stumpf et al. [20] isolated Acetobacter strains from sourdough that were capable of synthesizing a human-active form of vitamin B12 (cobalamin) under low-pH conditions, thus offering a promising biosynthesis method within plant-based foods for vegan and vegetarian diets. As mentioned previously, Pérez-González et al. [21] linked traditional maize-based diets and fermented beverages to increased oral fungal diversity, potentially offering protection against dental caries, while Fijan et al. [30] observed the health potential of fermented foods such as kimchi and sauerkraut.

Beneficial microbes also play a critical role in environmental and ecological applications. Three contributions in this Special Issue focused on ecological and plant-associated microbes. Burlakoti et al. [31] reviewed the critical roles of beneficial rhizobacteria and other microbes, highlighting mechanisms that improve the tolerance of maize to drought, salinity, and heat stress. Najjar [28] emphasized the importance of endophytic microbes for sustainable agriculture, reducing dependence on chemical fertilizers and pesticides. In a transcriptomic study, Senn et al. [23] characterized oak responses to fire events and identified microbial taxa in its rhizosphere microbiota that may aid in recovery, offering insights into plant–microbe–environment resilience. Together, these studies show how beneficial microbes aid both plant health and broader ecological balance.

Novel technological approaches also emerged in three studies in this Special Issue. Gocheva et al. [25] optimized fermentation conditions in Oerskovia paurometabola for the efficient production of sialidase, which is a biotechnologically valuable enzyme with medical applications. Balland et al. [22] demonstrated how mercury-resistant fungi such as Trichoderma koningiopsis and Talaromyces verruculosus could remove Hg from cinnabar ore, providing a bioremediation strategy for polluted environments. Yakimova et al. [32] proposed a futuristic perspective, envisioning microbiota-based radioprotection during spaceflight by genetically engineering gut microbes to secrete protective compounds. These contributions emphasize the versatility of microbes as tools not only for human nutrition but also for biomedicine, industrial innovation, and planetary challenges.

In conclusion, the 14 contributions in this Special Issue illustrate that the roles of beneficial microbes extend far beyond traditional probiotics, as they also include important aspects of shaping host health, food, ecosystems, and technology within the One Health framework. From probiotics that protect the heart and gut to fungi that detoxify mercury, as well as fermented foods that deliver essential vitamins to endophytes that support crops, these studies show a common message—beneficial microbes are key allies in shaping a healthier and more sustainable future. Although these findings provided promising insights, several gaps remain, including understanding the mechanisms and long-term outcomes. The long-term health impacts of diet–microbiota interactions will require larger, well-designed controlled clinical trials, while the underlying mechanisms still need to be clarified. Additionally, implementing microbiome engineering concepts, such as radioprotective probiotics, from theory to practice remains a challenge. Future research should address these gaps to utilize the full potential of beneficial microbes in human health, food systems, and ecological sustainability.