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Molecular Research in Prebiotics, Probiotics and Postbiotics: 2nd Edition
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Molecular Research in Prebiotics, Probiotics and Postbiotics: 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 20 November 2025 | Viewed by 4216

Special Issue Editors

Dr. Julio Villena

E-Mail Website
Guest Editor
Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Chacabuco 145, San Miguel de Tucuman CP400, Argentina
Interests: probiotics; immunobiotics; mucosal immunology; genomics; lactic acid bacteria; microbiota
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Haruki Kitazawa

E-Mail Website
Guest Editor
Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
Interests: probiotics; immunobiotics; mucosal immunology; lactic acid bacteria; functional foods; animal science
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, titled "Molecular Research in Prebiotics, Probiotics and Postbiotics".

In recent decades, we have witnessed remarkable advances in the study of beneficial microorganisms and their impact on both human and animal health. The field of probiotics has expanded, and thanks to advances in microbiology, immunology, molecular biology, and “omic” tools, the effects and mechanisms of probiotics, prebiotics, and postbiotics are now understood. This Special Issue is supervised by Dr. Julio Villena and Prof. Dr. Haruki Kitazawa, with assistance from our Topical Advisory Panel Member, Dr. Leonardo Albarracín.

This Special Issue provides a platform for the submission of high-quality publications that address recent advances in prebiotics, probiotics, and postbiotics. Studies that address the cellular and molecular interactions between beneficial microorganisms or their effector molecules and the host, as well as the development of new functional foods and feeds, are welcome.

Dr. Julio Villena
Prof. Dr. Haruki Kitazawa
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • probiotics
  • prebiotics
  • postbiotics
  • symbiotics
  • immunobiotics
  • functional foods
  • health improvement
  • mucosal immunology
  • microbiota

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Published Papers (4 papers)

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12 pages, 2390 KiB  
Article
The Probiotic Strain Clostridium butyricum TO-A Produces Butyrate by Utilizing Lactate and Acetate
by Shotaro Honda, Hiromichi Eguchi, Yoichi Okino and Dian-Sheng Wang
Int. J. Mol. Sci. 2025, 26(7), 2951; https://doi.org/10.3390/ijms26072951 - 24 Mar 2025
Viewed by 637
Abstract
Lactate-utilizing bacteria (LUB) are intestinal bacteria that produce butyrate from lactate and acetate, key metabolites in the gut. As LUB help maintain lactate and butyrate concentrations in the intestinal tract, they are promising probiotic candidates. Clostridium butyricum TO-A (CBTOA) has reportedly been effective [...] Read more.
Lactate-utilizing bacteria (LUB) are intestinal bacteria that produce butyrate from lactate and acetate, key metabolites in the gut. As LUB help maintain lactate and butyrate concentrations in the intestinal tract, they are promising probiotic candidates. Clostridium butyricum TO-A (CBTOA) has reportedly been effective in treating various gastrointestinal issues in humans and animals. Although CBTOA is known to increase intestinal butyrate levels, it is unclear how it utilizes lactate and acetate, similar to LUB, to produce butyrate. We investigated lactate utilization-related genes in CBTOA and examined the relationship between lactate and acetate utilization and butyrate production using peptone–yeast medium supplemented with D-lactate, L-lactate, and/or acetate. This study demonstrates for the first time that the probiotic strain CBTOA harbors lactate utilization-related genes and efficiently produces butyrate only in the presence of exogenous lactate and acetate instead of sugars. Furthermore, CBTOA expresses a lactate racemase that enables the bacterium to utilize both lactate enantiomers while regulating the ratio of D-lactate to L-lactate in the intestinal microenvironment via racemization. In conclusion, CBTOA efficiently produces butyrate utilizing lactate and acetate, similar to LUB; therefore, CBTOA could be an efficient butyrate supplier as a probiotic strain in the intestinal tract. Full article
(This article belongs to the Special Issue Molecular Research in Prebiotics, Probiotics and Postbiotics: 2nd Edition)
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26 pages, 4794 KiB  
Article
Modulation of Macrophages TLR4-Mediated Transcriptional Response by Lacticaseibacillus rhamnosus CRL1505 and Lactiplantibacillus plantarum CRL1506
by Masahiko Suzuki, Ayelen Baillo, Leonardo Albarracin, Mariano Elean, Rodrigo Serda, Yoshihito Suda, Fu Namai, Keita Nishiyama, Haruki Kitazawa and Julio Villena
Int. J. Mol. Sci. 2025, 26(6), 2688; https://doi.org/10.3390/ijms26062688 - 17 Mar 2025
Viewed by 508
Abstract
Lacticaseibacillus rhamnosus CRL1505 and Lactiplantibacillus plantarum CRL1506 increase the resistance of mice to Gram-negative pathogens infections. In this work, we advanced the characterization of the CRL1505 and CRL1506 immunomodulatory properties by evaluating their effect on the Toll-like receptor 4 (TLR4)-triggered immune response in [...] Read more.
Lacticaseibacillus rhamnosus CRL1505 and Lactiplantibacillus plantarum CRL1506 increase the resistance of mice to Gram-negative pathogens infections. In this work, we advanced the characterization of the CRL1505 and CRL1506 immunomodulatory properties by evaluating their effect on the Toll-like receptor 4 (TLR4)-triggered immune response in macrophages. We performed experiments in murine RAW 264.7 macrophages stimulated with lipopolysaccharide (LPS) to evaluate the transcriptomic changes induced by lactobacilli. These in vitro experiments were complemented with in vivo studies in mice to determine the effect of CRL1505 and CRL1506 strains on Peyer’s patches and peritoneal macrophages. Microarray transcriptomic studies and qPCR confirmation showed that the CRL1505 and CRL1506 strains modulated the expression of inflammatory cytokines and chemokines as well as adhesion molecules in LPS-challenged RAW macrophages, making the effect of L. rhamnosus CRL1505 more remarkable. Lactobacilli also modulate regulatory factors in macrophages. L. plantarum CRL1506 increased il10 and socs2 while L. rhamnosus CRL1505 upregulated il27, socs1, and socs3 in RAW cells, indicating a strain-specific effect. However, in vivo, both strains induced similar effects. Peyer’s patches and peritoneal macrophages from mice treated with lactobacilli produced higher levels of tumor necrosis factor (TNF)-α, interferon (IFN)-γ, interleukin (IL)-6, and colony stimulating factor (CSF)-3 after LPS stimulation. This effect would allow improved protection against pathogens. In addition, both lactobacilli equally modulated socs1 and socs2 expressions and IL-10 and IL-27 production in Peyer’s patches macrophages and socs3 and IL-10 in peritoneal cells. Furthermore, lactobacilli reduced the production of IL-1β, IL-12, CSF2, C-C motif chemokine ligand (CCL)-2, and CCL8 in LPS-challenged macrophages. This differential modulation of regulatory and inflammatory factors would allow minimal inflammatory-mediated tissue damage during the generation of the innate immune response. This work provides evidence that L. rhamnosus CRL1505 and L. plantarum CRL1506 modulate macrophages’ TLR4-mediated immunotranscriptomic response, helping to improve protection against Gram-negative bacterial infections. Full article
(This article belongs to the Special Issue Molecular Research in Prebiotics, Probiotics and Postbiotics: 2nd Edition)
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13 pages, 1993 KiB  
Article
A Probiotic Mixture of Lactobacillus rhamnosus LR 32, Bifidobacterium lactis BL 04, and Bifidobacterium longum BB 536 Counteracts the Increase in Permeability Induced by the Mucosal Mediators of Irritable Bowel Syndrome by Acting on Zonula Occludens 1
by Maria Raffaella Barbaro, Francesca Bianco, Cesare Cremon, Giovanni Marasco, Vincenzo Stanghellini and Giovanni Barbara
Int. J. Mol. Sci. 2025, 26(6), 2656; https://doi.org/10.3390/ijms26062656 - 15 Mar 2025
Viewed by 1040
Abstract
Irritable Bowel Syndrome (IBS) is a disorder of gut- brain interaction characterized by recurrent abdominal pain associated with altered bowel habits. The therapeutic options for IBS patients include the use of probiotics. The aim of this study was to assess the effect of [...] Read more.
Irritable Bowel Syndrome (IBS) is a disorder of gut- brain interaction characterized by recurrent abdominal pain associated with altered bowel habits. The therapeutic options for IBS patients include the use of probiotics. The aim of this study was to assess the effect of a multi-strain probiotic made up by Lactobacillus rhamnosus LR 32, Bifidobacterium lactis BL 04, and Bifidobacterium longum BB 536 (Serobioma, Bromatech s.r.l., Milano, Italy) on an in vitro model of the intestinal epithelial barrier in the presence of mucosal mediators that are released by IBS patients. IBS (n = 28; IBS with predominant diarrhea, IBS-D = 10; IBS with predominant constipation, IBS-C = 9; and IBS with mixed bowel habits, IBS-M = 9) patients, diagnosed according to the Rome IV criteria, and asymptomatic controls (ACs, n = 7) were enrolled. Mucosal mediators that were spontaneously released by colonic biopsies were collected (supernatants). Two doses of Serobioma were tested with/without IBS/AC mediators. RNA was extracted from Caco-2 cells to evaluate the tight junction (TJ) expression. Serobioma (106 CFU/mL) significantly reinforced the Caco-2 monolayer compared to growth medium alone (p < 0.05). IBS supernatants significantly increased Caco-2 paracellular permeability compared to the AC supernatants. The co-incubation of Caco-2 cells with IBS supernatants and Serobioma (106 CFU/mL) avoided the paracellular permeability alterations that were induced by IBS supernatants alone (p < 0.001), and, in particular, IBS-D and IBS-M ones. The co-incubation of Serobioma (106 CFU/mL) and IBS-D supernatants significantly increased ZO-1 expression compared to Caco-2 cells incubated with supernatants alone (p < 0.05), as confirmed via qPCR analyses. Serobioma (106 CFU/mL) counteracts the paracellular permeability changes that are induced by IBS supernatants, in particular IBS-D and IBS-M supernatants, likely modulating ZO-1 expression. Full article
(This article belongs to the Special Issue Molecular Research in Prebiotics, Probiotics and Postbiotics: 2nd Edition)
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15 pages, 15546 KiB  
Article
Enhancing β-Galactosidase Performance for Galactooligosaccharides Preparation via Strategic Glucose Re-Tunneling
by Jihua Zhao, Dandan Niu, Jiaqi Liu, Zhuolin Jin, Nokuthula Peace Mchunu, Suren Singh and Zhengxiang Wang
Int. J. Mol. Sci. 2024, 25(22), 12316; https://doi.org/10.3390/ijms252212316 - 16 Nov 2024
Viewed by 1456
Abstract
This study focuses on the characterization and re-engineering of glucose transport in β-galactosidase (BglD) to enhance its catalytic efficiency. Computational prediction methods were employed to identify key residues constituting access tunnels for lactose and glucose, revealing distinct pockets for both substrates. In silico [...] Read more.
This study focuses on the characterization and re-engineering of glucose transport in β-galactosidase (BglD) to enhance its catalytic efficiency. Computational prediction methods were employed to identify key residues constituting access tunnels for lactose and glucose, revealing distinct pockets for both substrates. In silico simulated saturation mutagenesis of residues T215 and T473 led to the identification of eight mutant variants exhibiting potential enhancements in glucose transport. Site-directed mutagenesis at T215 and T473 resulted in mutants with consistently enhanced specific activities, turnover rates, and catalytic efficiencies. These mutants also demonstrated improved galactooligosaccharide (GOS) synthesis, yielding an 8.1–10.6% enhancement over wild-type BglD yield. Structural analysis revealed that the mutants exhibited transformed configurations and localizations of glucose conduits, facilitating expedited glucose release. This study’s findings suggest that the re-engineered mutants offer promising avenues for enhancing BglD’s catalytic efficiency and glucose translocation, thereby improving GOS synthesis. By-product (glucose) re-tunneling is a viable approach for enzyme tunnel engineering and holds significant promise for the molecular evolution of enzymes. Full article
(This article belongs to the Special Issue Molecular Research in Prebiotics, Probiotics and Postbiotics: 2nd Edition)
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