Research into beneficial microorganisms and the development of effective formulations are important objectives for modern microbiology, as well as biotechnology, food, and pharmaceutical industries. Finding the relationship between the metabolic specificity of microorganisms and their health-promoting properties has been the goal of many years of research since the establishment of microbiology as a branch of biological science. Pioneers in applied microbiology have paved the way for new discoveries and understanding of the benefits of probiotics. More than a century ago in Europe, Stamen Grigorov, and Elie Metchnikoff pointed out the importance of dairy products for human health and linked these benefits to lactic acid bacteria. Nearly a century ago in Japan, Dr. Minoru Shirota researched the beneficial properties of a strain of Lactobacillus (reclassified as Lacticaseibacillus) casei he had isolated and laid the foundation for the Yakult company we know today. All pioneers of research on health-promoting microorganisms were driven by the idea of helping humanity by fighting diseases with the assistance of beneficial microbes. Over the past century, evidence of the beneficial role of specific microbial strains has shaped the modern understanding of probiotics. The Yakult Symposia 2025, held in São Paulo on March 27 and 28, 2025, focused on beneficial microorganisms with the aim to continue work of the pioneers. The event brought together researchers from Brazil, Japan, Russia, Belgium, the USA, France, Indonesia, Ukraine, Iran, South Korea, Costa Rica, and India to present and discuss the latest discoveries in the study of the benefits of health-promoting microorganisms for humans and other animals. All of this fell under the general concept of the one health initiative. Recognizing the intimate relation between human, animal, and environmental health, this initiative promotes collaboration across disciplines and helps prevent and control cross-species diseases such as zoonotic infections. This approach strengthens public health systems, improves food safety, and supports sustainable ecosystems development. In the face of growing global challenges such as climate change, deforestation and urban expansion, the one health initiative offers a framework for holistically addressing complex health threats. Ultimately, this helps build resilience to various diseases, reduces the risk of pandemics and ensures the well-being of current and future generations. The results of the papers presented at the conference formed the basis for a special issue of the journal Molecular Nutrition and Food Research, published by Wiley. This special issue includes 14 full-length research and review articles reflecting the objectives of the Yakult Symposia 2025 and prepared by international teams of scientists from Algeria, Brazil, China, India, Iran, Ireland, New Zealand, Hong Kong, Pakistan, Portugal, Russia, the Netherlands, and the USA. The articles in this special issue evaluate prebiotics and probiotics, present research on next-generation probiotics (NGPs) and their benefits, and discuss auto probiotics and postbiotics. Also noteworthy are the papers included in the special issue devoted to antimicrobial agents produced by beneficial crops, with an emphasis on bacteriocins, as well as advanced areas of bioinformatics. Jadhav et al. 1 presented a paper on the development of NGPs, discussing the contribution of strains already used as probiotics as well as strains with scientifically proven beneficial effects; in addition, the authors noted the need for new research on personalized therapeutic properties. In some application scenarios, in addition to traditional probiotics such as those of the genera Lactobacillus (in the context of the meaning of this term before the reclassification proposed by Zhang et al. 2) and Bifidobacterium, microorganisms of the so-called NGPs are used, such as Akkermansia muciniphila and Faecalibacterium prausnitzii. Notably, NGP could be a real game-changer in the field of probiotic use. The authors highlight that NHPs are associated with more specific functions, including mucin degradation, butyrate production, increased intestinal barrier integrity, immune system regulation, and modulation of host metabolism and inflammation, all contributing to improved health. Jadhav et al. 1 performed a critical comparison of conventional and emerging treatments, focusing on mechanistic differences and functional advances, and also highlighted safety, regulatory, and implementation challenges. Probiotics, while being safe for consumption, must provide consumers with scientifically proven, reproducible, and consistent benefits. The expected benefits must match the stated properties, such as specific assisting digestive health, modulating immunity, etc. Clear labelling, regular scientific validation of product batches, transparency regarding the species and strains used in products, as well as dosages, are essential. Ultimately, probiotics must deliver tangible results that benefit the health of consumers. Some of the benefits of probiotics may be related to their antioxidant properties or the production of specific enzymes. In particular, Prazdnova et al. 3 assessed the benefits of new probiotics, related to their antioxidant and enzymatic activity, in aquaculture. During the preliminary screening, the authors selected several Bacillus strains with beneficial enzymatic and antioxidant activity. Next, the main focus was on Bacillus velezensis strains MT14 and MT42 (group 1) with proteolytic and amylolytic functions, and Bacillus subtilis strains MT48 and MT74 (group 2), which additionally exhibited antioxidant activity. The authors investigated the benefits of the mentioned strains in animal models in vivo, where the strains were introduced into starter feeds for sterlet larvae for 2 months and observed the effect on weight gain compared to control. Notably, both groups showed a reduction in IL-1β gene expression, which was correlated with reduced inflammation. However, Group 2 exhibited decreased expression of igf-1, hsp 70, and gst genes, most probably related to a positive impact of the antioxidant activity of the potential probiotic on alleviating stress. Genomic sequencing for the evaluated Bacillus strains pointed out that only strains with antioxidant activity possessed genes coding pulcherriminic acid, bacillibactin, subtilosin, and fengicin synthetases—a feature absent in other strains. The authors concluded that these metabolites, especially pulcherriminic acid, may contribute to the antioxidant properties of carrier strains. Moreover, the contribution of Maniya et al. 4 focused on antioxidants, antidiabetic, and antimicrobial activities of bioactive peptides derived from milk fermented with a multi-strain probiotic formulation. The multifaceted biological potential of bioactive peptides produced by indigenous beneficial (probiotic) microorganisms during milk fermentation remains largely understudied and unexploited, limiting their therapeutic application. Maniya et al. 4 investigated the role of the combined use of two strains, Bacillus spizizenii BAB 7915 and B. subtilis BAB 7918, in milk fermentation, associated with an increase in the content of bioactive peptides compared to fermentations involving only one of the strains. After appropriate purification and characterization (RP-HPLC, OHR LCMS/MS), the authors compared the bioactive peptides (≤10 kDa) obtained from the fermentation and identified peptides with the ability to inhibit α-amylase, neutralize the ABTS radical and exhibit antimicrobial activity. According to the authors' hypothesis, consortium fermentation significantly increased the biological activity of fermentation products. All these bioactive peptides have beneficial properties and are promising for the treatment of type 2 diabetes, oxidative stress, and infection control. Future studies should isolate and characterize individual peptides to confirm their specific contribution, elucidate structure-function relationships, and examine their in vivo efficacy, bioavailability, and encapsulation potential. Chen et al. 5 investigated the antioxidant mechanisms of Lacticaseibacillus paracasei ZFM847 and the regulation of oxidative stress in various models. The authors studied the potential antioxidant capacity and mechanisms of action of Lbs. paracasei ZFM847 isolated from fresh milk and showed that the studied strain is able to withstand high concentrations (2.0 mM) of H2O2 and has strong antioxidant capacity. These properties are clearly not related to the enzymatic activity of catalase, since lactic acid bacteria are catalase-negative. According to Chen et al. 5, these properties are due to increased expression of genes related to the thioredoxin system (trx1 and trx2), antioxidant enzymes (sod, nox and npx) and the glutathione redox system (gpx, gshAB, gst and gr). The beneficial effects of Lbs. paracasei ZFM847 activity may be directly related to the significant reduction of oxidative stress and inflammation through the increase in antioxidant enzyme activity and modulation of gut microbiota, as shown in mice with Dgal-induced oxidative stress. Moreover, the authors reported that Lbs. paracasei ZFM847 could also act as a protective culture against oxidative damage induced by Helicobacter pylori in GES-1 cells and mice, potentially through activation of the Nrf2 signaling pathway. Zarezadeh et al. 6 reviewed the protective roles of prebiotics and probiotics against the toxic effects of environmental pollutants described in animal model studies. These toxic substances disrupt the composition and function of the intestinal microbiota, which can be counteracted by prebiotics and probiotics. Probiotics may be a solution to the problem of intoxication with heavy metals, organic pollutants, and mycotoxins. Overall, the review of Zarezadeh et al. 6 supports the role of microbiota, probiotics, prebiotics, and synbiotics in mitigating the toxic effects of pollutants, although future studies should address common issues related to biased results. Sabir et al. 7 assessed the relationship between gut microbiota and health markers using an aqueous extract of Moringa oleifera leaves. Scientific information on prebiotics derived from medicinal plants deserves more attention from the scientific community. In the contribution of Sabir et al. 7, M. oleifera leaf extract was studied for its potential antidiabetic properties in an animal model—male albino rats. The authors assessed various biochemical and microbiological markers, including the observed increase in lactobacilli counts in feces. Additionally, antihyperglycemic activity was observed. The authors suggested that M. oleifera has promising prebiotic and antihyperglycemic properties, and further experiments are needed to determine the effective dose of M. oleifera extract 7. Goyal et al. 8 contributed to the special issue by presenting a study on the technological functions and biosafety characteristics of a novel yeast, Meyerozyma guilliermondii YB1, as a starter for fermented functional foods, including its prospects for application as probiotics. The authors reported xylanase and phytase activity in M. guilliermondii YB1. Furthermore, antimicrobial assays revealed inhibitory activity against Escherichia coli MTCC 3222, Salmonella typhimurium MTCC 3224, and Aspergillus sp. CTS1, confirming the potential use in food preservation. From a technological point of view, authors reported that the studied yeast efficiently fermented a broad range of carbohydrates required for food fermentation. Furthermore, the authors found that auto-aggregation increased from 25% at 2 h to 96.04% at 72 h, and hydrophobicity ranged from 38.54% to 66.16%, demonstrating significant adhesive abilities in the gut. The safety of M. guilliermondii YB1 starter culture was confirmed by antifungal susceptibility testing, the absence of gelatinase and DNase activity, and a negative Congo red binding test result. All this confirms the possibility of its use as a safe and reliable functional food starter. Antimicrobial peptide research featured prominently in the symposia's scientific program and the special issue of the journal. Farias et al. 9 presented the results of their study of a new ring-shaped bacteriocin, streptocyclin BTW, produced by Streptococcus devriesei. Circular bacteriocins are perhaps among the most mysterious bacteriocins 10 when it comes to their synthesis and mode of action. Farias et al. 9 reported on streptocyclin BTW, a 64-amino acid circular bacteriocin produced by Str. devriesei DSM 19639, in the context of the diversity of circular-shaped bacteriocins within the genus. The authors reported that streptocyclin BTW, with a molecular weight of 6118.75 Da, exhibits a broad spectrum of inhibitory activity. The gene cluster associated with expression of streptocyclin BTW is composed of five genes: a core peptide (stpA), a membrane protein (stpB), a DUF95 family protein (stpC), an ATP-binding protein (stpD), and a putative immunity protein (stpE). Moreover, the authors reported that genes associated with the production of streptocyclin BTW-like circular bacteriocins were found in Streptococcus orisasini, Streptococcus equi, Streptococcus pneumoniae, Streptococcus pseudopneumoniae, Streptococcus mitis, and Streptococcus bouchesdurhonensis species. The next noteworthy report was by Lipilkinа et al. 11. The authors presented data on Enterococcus faecium strains isolated from bat fecal samples. The main objective of the mentioned studies was to isolate and characterize bacteriocinogenic strains from faecal samples of bats Nyctalus noctula, as well as to evaluate their probiotic potential and antimicrobial properties. Lipilkina et al. 11 reported two bacteriocin-producing strains, E. faecium ST01TL and ST76TL, which were selected based on rep-PCR fingerprinting and 16S rRNA sequencing. In addition to characterizing the bacteriocins produced, the authors investigated the potential beneficial properties and safety of the studied strains. Molecular analysis showed that E. faecium strains ST01TL and ST76TL contain genes encoding the synthesis of bacteriocins and GABA and can be considered as potential candidates for use in the fields of food safety, gastrointestinal health, and environmental applications (e.g., modulation of bat health). The synthetic biology-based heterologous expression and purification of enterocin A was presented for the special issue by Merzoug et al. 12. This study details the design and synthesis of a complex genetic cassette encoding the mature form of enterocin A, a bacteriocin produced by E. faecium. The vector (pJ404-pEntApep), bearing the synthetic entA gene, was constructed entirely de novo and featured essential regulatory elements as well as an N-terminal His6-tag to facilitate efficient purification. Validation of the genetic construct was performed via PCR, followed by sequencing of the resulting amplicon. In the following, expression in E. coli BL21 (DE3) under optimized conditions (28°C, 0.5 mM IPTG) resulted in production of recombinant leaderless enterocin A (EntA), primarily in the form of inclusion bodies. The purified enterocin A demonstrated potent antimicrobial activity against multidrug-resistant pathogens, including Staphylococcus aureus subsp. aureus ATCC25923, Pseudomonas aeruginosa ATCC27853, Acinetobacter lwoffii GPE3002, Micrococcus luteus GPE3001, and Bacillus cereus GPE3003, with minimum inhibitory concentration (MIC) values ranging from 27 to 109 µg/mL. Bioinformatics is gaining increasing acceptance in microbiology and serves as a platform for predicting and evaluating microbiological experiments. Popov et al. 13 contributed to the special issue by presenting a report on KEGGaNOG, a lightweight tool for profiling KEGG modules based on orthology-derived annotations. Understanding the biological functions encoded in bacterial genomes is important for a wide range of applications, from microbial ecology to the development of biotechnologically effective microorganisms with various beneficial properties (e.g., for improving health, producing enzymes, antibiotics, etc.). KEGGaNOG is a Python tool that takes eggNOGmapper annotations as input and enables pathway-level profiling by converting orthology-based annotations into KEGG module completeness scores. Popov et al. 13 validated the functionality of KEGGaNOG using database-available bacterial genomes, including several probiotic strains. KEGGaNOG enabled the identification of key biosynthetic capabilities with an emphasis on the uniqueness of the studied samples, including vitamin production, stress response pathways, and more. Importantly, KEGGaNOG is a convenient and easy-to-use practical tool for functional annotation and comparative metabolic profiling in microbial genome studies. In the context of probiotic research, KEGGaNOG is useful for the selection of potentially beneficial strains as it allows for a reproducible and interpretable linkage of genomic content to functional capacity. Ermolenko et al. 14 brought to our attention an article that puts forward the concept that autoprobiotics may provide more benefits and should be considered as a topic for future probiotic research. In a pilot study, Ermoolenko et al. 14 assessed the impact of autoprobiotics on health restoration while examining the serum and urine metabolome in patients with metabolic syndrome (MetS). The authors investigated the efficacy of oral administration of autoprobiotics (nonpathogenic, indigenous) E. faecium or Enterococcus hirae in a 20-day experimental period in patients with MetS, characterized by obesity and impaired carbohydrate and lipid metabolism. The dynamics of changes in anthropometric and biochemical parameters, as well as metabolism, were monitored 14 and 28 days after the end of therapy. According to Ermolenko et al. (2026), changes in clinical and laboratory parameters after the use of autoprobiotics indicate a decrease in the severity of MetS. According to the results of the serum metabolome analysis using HPLC-MS, all measured long-chain acylcarnitines—palmitoyl-L-carnitine and well as and showed a significant decrease at 14 and 28 days after therapy. 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