Science AI Journal
Agricultural and Biological Sciences · Research topic

Open research questions in Probiotics and Fermented Foods

46 unresolved questions extracted from the limitations and future-work sections of 918 Probiotics and Fermented Foods papers in our library. Each links back to the study that raised it.

What the literature leaves open

  • Col- lectively, these results suggest that JHB-06 has probiotic- associated properties and warrants further investigation as a potential functional ingredient for oral health-related products.

    Probiotic potential of Bacillus paralicheniformis JHB-06 isolated from traditional doenjang and its antimicrobial activity against oral pathogens · 2026 · DOI

  • This work generates several hypotheses for future study regarding potential early microbial biomarkers and novel interventional targets for AP, which also represents an understudied opportunity for life-threatening IgE-medi- ated food allergy prevention.

    Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis · 2026 · DOI

  • Safety concerns restrict Bacillus spp as probiotics, despite their potential (Sorokulova 2008). Durable spores draw research and commercial interest (Zhang et al. 2020). While Bacillus subtilis benefits animals, further studies are needed for non-lactic bacteria like B. subtilis S1, which shows low bile and acid tolerance, limiting probiotic use. Some bacilli are safe, but individual assessment is needed (Permpoonpat- tana et al. 2012). Bacillus spores are more robust. Vegetative cells grow at pH 8.0, but bacteriocin activity drops at higher pH and is thermolabile. Simpler Subtilosin A purification and in-vivo modelling could improve marketability. Supplementary Information The online version contains supplementary material available at h t t p s : / / d o i . o r g / 1 0 . 1 0 0 7 / s 1 1 2 7 4 - 0 2 6 - 0 5 0 7 0 - 1 . Acknowledgements The authors acknowledge the director of CSIR- CFTRI for providing all the facilities and also are grateful to MoFPI, LSRB and DST for project funding. Author contributions KR and PMJ wrote the main manuscript text PMJ, AK, LVT, NSP, and GK prepared figures. All authors reviewed the manuscript. Funding This work was supported by MoFPI (Ministry of Food Pro- cessing Industries- GAP-536), LSRB-DRDO (The Life Sciences Re- search Board of Defence Research and Development Organisation GAP-537), DST (Department of Science and Technology GAP-590). CSIR (Council of Scientific and Industrial Research) and MoFPI pro- vides funding to researchers. Data availability No datasets were generated or analysed during the current study.

    Characterization of bacteriocin, probiotic attributes and genomic information of Bacillus subtilis S1 · 2026 · DOI

  • Future research should focus on in vivo trials in broiler chickens to address the inherent limitations of in vitro models, specifically regarding bacteriocin stabil- ity and bioavailability within the dynamic gastrointestinal environment. These preliminary results suggest that microcin J25 and pediocin PA-1 are candidates for antibiotic alternatives, though their effi- cacy remains to be established in a complex living sys- tem.

    Uncovering how selected potent bacteriocins reshape the broiler chicken gut microbiome in a PolyFermS continuous in vitro model · 2026 · DOI

  • Additionally, the plantaricin-type bacteriocins and probiotic marker genes identified through genomic analyses have not been experimentally validated, and their functional contributions remain to be confirmed in future studies. A limitation of the present study is that the therapeutic efficacy and safety of L.

    Functional and Genomic Characterization of a Human-Derived Lactiplantibacillus plantarum Strain LP1 with Activity Against Carbapenem-Resistant Enterobacterales · 2026 · DOI

  • Consequently, their clinical relevance remains to be established through future translational studies involving formulation, in vivo models, and human trials. To confirm psychobiotic potential of ATT-06, the efficacy of GABA biosynthesis should be explored under GI conditions and host model systems.

    Pangenomics of Limosilactobacillus fermentum reveals genomic diversity and bacteriocin activity against Staphylococcus aureus and Escherichia coli · 2026 · DOI

  • The present study is primarily limited by its exclusively in vitro the absence of comprehensive metabolomic design and characterisation of the postbiotic compounds. The SCFA detection in this work was of a preliminary nature and not fully validated quantitatively. Additionally, the taxonomic identification based on 16S rRNA gene sequencing may not provide strain-level resolution. The potential influences of age-related variability on the composition of the gut microbiome were not specifically controlled and represent another limitation of this study. Future studies involving whole-genome sequencing, metabolomic profiling, and in vivo validations are therefore necessary to confirm the functional and therapeutic potential of the identified isolates. Notwithstanding these limitations, our study offers important preliminary insights into the functional potential of probiotic isolates derived from a traditionally underexplored population. The integration of culturebased isolation with multi-parameter functional screening provides a useful framework for identifying candidate strains with desirable properties. From a translational perspective, such strains may serve the development of postbiotic-based as a formulations or next-generation probiotics pending rigorous validation.

    Exploring the probiotic landscape in understanding postbiotics from indigenous bacteria isolated from the stool samples of a tribal population at Mulluvadi village, Tamil Nadu, India · 2026 · DOI

  • in the preparation of Additional research efforts should be directed toward extracting and solving the structures of the most important cellular metabolites, such as SCFAs, EPSs, and proteolytic enzymes, along with exploring their effects in appropriate animal models of inflammation, metabolic disorders, and gut microbiota imbalance. At the same time, changes in large-scale fermentation processes are indispensable for promoting their utilisation foods, nutraceuticals, or disease treatments. Moreover, clinical evaluations at identifying new biosynthetic gene clusters will be necessary before such tribal-derived microbial resources can be used as precision these therapeutics. considerations, our study provides a firm basis for the in next-generation efficient use of native microbiomes management of gut health.

    Exploring the probiotic landscape in understanding postbiotics from indigenous bacteria isolated from the stool samples of a tribal population at Mulluvadi village, Tamil Nadu, India · 2026 · DOI

  • Sreevarshini. S1, Saranya N1*, G. Umamageshwari1 1Department of Biotechnology, Nehru Arts and Science College, Coimbatore, Tamil Nadu, India *Corresponding Author E-mail: [email protected] Abstract: Postbiotics represent a paradigm shift in microbiome-based therapeutics, offering the functional benefits of probiotics without the challenges associated with live microorganism administration. Defined by the International Scientific Association for Probiotics and Prebiotics (ISAPP) as "preparations of inanimate microorganisms and/or their components that confer a health benefit on the host," postbiotics encompass a diverse array of bioactive compounds including cell wall components, metabolites, short-chain fatty acids, bacteriocins, and extracellular vesicles. This review synthesizes current evidence on the mechanisms through which postbiotics modulate host physiology, their therapeutic applications across various disease states, and the challenges and opportunities that lie ahead for clinical translation. Emerging evidence supports their efficacy in gastrointestinal disorders, metabolic diseases, immune modulation, and beyond, while their superior stability, safety profile, and standardization potential position them as attractive candidates for next-generation biotherapeutics. Keywords: Postbiotics, Biotherapeutics, Gut Microbiota Received: Jan. 18, 2026 Revised: Feb. 28, 2026 Accepted: March.

    <b>Postbiotics in Human Health: Mechanisms, Therapeutic Applications, and Future Perspectives</b> · 2026 · DOI

  • While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear.

    Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity · 2024 · DOI

  • Since the first study twenty-five years ago, several researchers have used L. casei as a strategy for the control of some parasitosis, bacterial and viral diseases related to veterinary and public health. The results of all these studies have demonstrated the effectiveness of L. casei in regulating the immune response, reducing parasite loads and/or the establishment of adult parasites, reducing tissue damage in various organs, increasing the weight gains and animal survival. Concerning the ability of L. casei to induce immune responses, L. casei stimulates both innate and acquired immunity against parasites, bacteria and viruses. However, the number of investigations for the control of different diseases in production animals is scarce, while they have been evaluated only in animal models or cell cultures. Therefore, it is still necessary to design more studies on the use of L. casei in animal production infected naturally and/or experimentally, but, above all, to increase the parameters to be evaluated and which are related to animal welfare and food quality. REFERENCES Andreu A, AE Stapleton, CL Fennell, SL Hillier and WE Stamm, (1995). Hemagglutination, adherence, and surface properties of vaginal Lactobacillus species. The Journal of Infectious Diseases 171:1237-1243. 361 Complement Altern Med, 2024, xx(x): xxx-xxx. Ashraf M, M Siddique, SU Rahman, M Arshad and HA Khan, (2005). Effect of various microorganisms culture feeding against Salmonella infection in broiler chicks. Journal of Agriculture and Social Sciences 1:29-31. Bajer AA, D García-Tapia, KR Jordan, KM Haas, D Werling, CJ Howard and DM Estes, (2003). Peripheral blood-derived bovine dendritic cells promote IgG1-restricted B cell responses in vitro. Journal of Leukocyte Biology 73:100-106. Bautista-Garfias C, A Fernández-Román, A Posadas-Beltrán and O Ixta-Rodríguez, (2002). Increase of resistance against murine experimental Trichinella spiralis infection using Lactobacillus casei. Veterinaria México 33:173-177. Bautista-Garfias CR, A Posadas-Beltrán and O Ixta, (2004). Immunization of BALB/c mice with antigen from Trichinella spiralis muscle larvae using Lactobacillus casei as adjuvant. Veterinaria México 35:359-368. Bautista Garfias CR, A Rodríguez Lozano, JA Álvarez Martínez, C Rojas Martínez, JV Figueroa Millán, M Díaz López and VG García Rubio, (2016). In vitro Activation of bovine monocytes with Lactobacillus casei: nitric oxide production. Ecosistemas y Recursos Agropecuarios 3:237-242. Bautista-Garfias CR, A Rodríguez Lozano, C Rojas Martínez, JA Álvarez Martínez, JV Figueroa Millán, GR Reyes García, R Castañeda-Arriola and BR Aguilar-Figueroa, (2015).

    Lactobacillus casei: Effects of its use against Pathogens (Parasites, Bacteria and Viruses) of Veterinary and Public Health Importance · 2024 · DOI

  • Conclusion: L1 strain, which have not been reported previously, demonstrated high anti-QS and antibiofilm properties, making EPSs a prospective compound for application in the pharmaceutical and food industries owing to their strong antimicrobial and antioxidant capacities.

    A New Approach to Exopolysaccharides of Post Probiotic Lactobacillus paracasei L1 Strain: Anti-quarum Sensing Activity · 2023 · DOI

  • Having in mind that the sourdough is a difficult matrix for DNA isolation on the one hand, and that there is no standardized DNA extraction protocol for this matrix on the other hand, this pilot study aims to give a small contribution to the future establishment and validation of such a protocol, which will allow accurate assessment of the specific microbiota of sourdough samples.

    Identification of Bulgarian Sourdough Microbiota by Metagenomic Approach Using Three Commercially Available DNA Extraction Protocols · 2023 · DOI

  • Even though the genetic repression was circumvented by the up-regulation of pathway genes using a mutant strain, 3-HP formation was further limited by the substrate and catabolite inhibition.

    A Study on Enhanced Expression of 3-Hydroxypropionic Acid Pathway Genes and Impact on Its Production in Lactobacillus reuteri · 2015 · DOI

  • Several decades ago the results of the studies varied widely: some of them showed that LAB grew better in raw milk and others demonstrated improved growth of the bacteria in heat-treated milk (Foster et al.

    The effect of milk heat treatment on the growth characteristics of lactic acid bacteria. · 2011

  • The exact significance of these preliminary observations with one strain of Fusobacterium nucleatum remains to be deter- mined and deserves further study. For example, analyses of bicarbonate in the saliva samples of different human subjects are known to vary widely (Jenkins, 1978; Kreusser et al.

    La huelga de Río Blanco · 1957 · DOI

  • Furthermore, standardized dose-response thresholds for fermentation inhibition are lacking, and information regarding the long-term effects…

    Technological impacts of antibiotic residues in animal-derived fermented foods: Mechanisms, detection challenges, regulatory gaps, and mitigation strategies · 2026 · DOI

  • Bifidobacteria capable of metabolizing human milk oligosaccharides (HMOs) regulate microbial balance and enhance immune defenses, yet their adhesive properties and pathogen-inhibitory capacity remain understudied.

    Exploring the Adhesion Potential of Bifidobacterium bifidum Strains Isolated from Infant Feces · 2026 · DOI

  • However, their potential is limited by the presence of anti-nutritional factors (ANFs) such as phytic acid, trypsin inhibitors, and chymotrypsin inhibitors (2) .

    Enhancing protein digestibility in red clover and lucerne seeds through lactic acid fermentation · 2026 · DOI

  • However, the nature of the interactions between TV and Lactobacillus is poorly understood.

    Trichomonas vaginalis targets Lactobacillus jensenii via pseudopodia-independent phagocytosis and secreted lysozyme TvGH25 · 2026 · DOI

  • There are few studies on the changes in the oral microbiome caused by drinking Coca-Cola; most of the literature focuses on the effects of long-term consumption of certain beverages…

    The Changes of Microbiome Attached on Clear Aligners after Drinking Coca-Cola · 2026 · DOI

  • Future studies in more diverse geographic settings and across different infant feeding practices are warranted to confirm the broader applicability of these findings.

    Efficacy of Bifidobacterium lactis BLa80 in preventing early childhood eczema and respiratory infections via gut microbiome and immune modulation · 2026 · DOI

  • While there is limited research on the mechanism of biotics in preventing caries, numerous studies have investigated the impacts of probiotics on decreasing caries risk factors.

    The strategic role of biotics in dental caries prevention: A scoping review · 2024 · DOI

  • LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood.

    Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity · 2024 · DOI

  • Future research should focus on personalized probiotic interventions and mechanistic studies to unlock probiotics' full potential in neurodevelopment and neuroprotection.

    Neuroprotection Through Probiotic Intervention: Lessons From Autism Research · 2023 · DOI

Most-cited papers in Probiotics and Fermented Foods

Most recent work

Find a gap in your own Probiotics and Fermented Foods sub-topic

This page shows what the Probiotics and Fermented Foods literature already flags as unresolved. To narrow it to your specific question, run the guided finder — it searches the gap library on demand and checks candidates against 250M+ OpenAlex works.

Open the Research Gap Finder →

Related topics in Agricultural and Biological Sciences

Smart Agriculture and AI
183 open questions
Agricultural Innovations and Practices
135 open questions
Soil Carbon and Nitrogen Dynamics
115 open questions
Diverse Educational Innovations Studies
97 open questions
Agriculture, Land Use, Rural Development
95 open questions
Plant-Microbe Interactions and Immunity
94 open questions
Plant Molecular Biology Research
90 open questions
Animal Nutrition and Physiology
86 open questions
46 open questions have been extracted from the limitations and future-work passages of 918 Probiotics and Fermented Foods papers in our library. Each one below links back to the study that raised it, so you can read the original claim in context.

Tools for your next paper

Gaps & Literature SearchFind open questions in any field — 120,000+ open gaps mined from our own library.Pre-CheckIs your paper ready? A Tier 1–5 acceptance probability in seconds.Journal FinderA ranked shortlist of target journals from a 17,500-venue index.Duplicate Publication CheckerCheck prior-publication & salami-slicing risk across 8 sources.Citation GeneratorFreeA DOI or title → APA, MLA, Vancouver, Chicago, BibTeX, RIS. No signup.Graphical Abstract MakerFreeTurn your findings into a colorblind-safe graphical abstract.

Compare the category — Honest roundups of the AI research tools, ours listed alongside the alternatives.

Command palette

Jump anywhere, run any action.