Probiotics can affect human health, keep the balance between beneficial and pathogenic bacteria, and their colonizing abilities enable the enhancement of the epithelial barrier, preventing the invasion of pathogens. Health benefits of probiotics were related to allergy, depression, eczema, cancer, obesity, inflammatory diseases, viral infections, and immune regulation. Probiotic bacterial cells contain various proteins that function as effector molecules, and explaining their roles in probiotic actions is a key to developing efficient and targeted treatments for various disorders. Systematic proteomic studies of probiotic proteins (probioproteomics) can provide information about the type of proteins involved, their expression levels, and the pathological changes. Advanced proteomic methods with mass spectrometry instrumentation and bioinformatics can point out potential candidates of next-generation probiotics that are regulated under pharmaceutical frameworks. In addition, the application of proteomics with other omics methods creates a powerful tool that can expand our understanding about diverse probiotic functionality. In this review, proteomic strategies for identification/quantitation of the proteins in probiotic bacteria were overviewed. The types of probiotic proteins investigated by proteomics were described, such as intracellular proteins, surface proteins, secreted proteins, and the proteins of extracellular vesicles. Examples of pathological conditions in which probiotic bacteria played crucial roles were discussed.

Institute of Analytical Chemistry of the Czech Academy of Sciences Veveri 97 602 00 Brno Czech Republic

Zobrazit více v PubMed

Hill C., Guarner F., Reid G., Gibson G.R., Merenstein D.J., Pot B., Morelli L., Canani R.B., Flint H.J., Salminen S., et al. Expert consensus document. The Internal Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 2014;11:506–514. doi: 10.1038/nrgastro.2014.66. PubMed DOI

Lebeer S., Bron P.A., Marco M.L., Van Pijkeren J.P., O’Connell Motherway M., Hill C., Pot B., Roos S., Klaenhammer T. Identification of probiotic effector molecules: Present state and future perspectives. Curr. Opin. Biotechnol. 2018;49:217–223. doi: 10.1016/j.copbio.2017.10.007. PubMed DOI

Gupta R.S. Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol. Mol. Biol. Rev. 1998;62:1435–1491. doi: 10.1128/MMBR.62.4.1435-1491.1998. PubMed DOI PMC

Scott J.R., Barnett T.C. Surface proteins of gram-positive bacteria and how they get there. Annu. Rev. Microbiol. 2006;60:397–423. doi: 10.1146/annurev.micro.60.080805.142256. PubMed DOI

Fischetti V.A. Surface proteins on gram-positive bacteria. Microbiol. Spectr. 2019;7:GPP3-0012-2018. doi: 10.1128/microbiolspec.GPP3-0012-2018. PubMed DOI PMC

Flach J., van der Waal M.B., Kardinaal A.F.M., Schloesser J., Ruijschop R.M.A.J., Claasen E. Probiotic research priorities for the healthy adult population: A review on the health benefits of Lactobacillus rhamnosus GG and Bifidobacterium animalis subspecies lactis BB-12. Cogent Food Agric. 2018;66:1452839. doi: 10.1080/23311932.2018.1452839. DOI

Siciliano R.A., Mazzeo M.F. Molecular mechanisms of probiotic action: A proteomic perspective. Curr. Opin. Microbiol. 2012;15:390–396. doi: 10.1016/j.mib.2012.03.006. PubMed DOI

Zhang C., Zhang Y., Li H., Liu X. The potential of proteins, hydrolysates and peptides as growth factors for Lactobacillus and Bifidobacterium: Current research and future perspectives. Food Funct. 2020;11:1946. doi: 10.1039/C9FO02961C. PubMed DOI

Dominguez Rubio A.P.D., D’Antoni C.L., Piuri M., Perez O.E. Probiotics, their extracellular vesicles and infectious diseases. Front. Microbiol. 2022;13:864720. doi: 10.3389/fmicb.2022.864720. PubMed DOI PMC

Escobar-Sancez M., Carrasco-Navarro U., Juarez-Castelan C., Lozano-Aguirre Beltran L., Perez-Chabela M.L., Ponce-Alquicira E. Probiotic properties and proteomic analysis of Pediococcus pentosaceus 1101. Foods. 2022;12:46. doi: 10.3390/foods12010046. PubMed DOI PMC

Szajewska H., Horvath A. Lactobacillus rhamnosus GG in the primary prevention of eczema in children: A systematic review and meta-analysis. Nutrients. 2018;10:1319. doi: 10.3390/nu10091319. PubMed DOI PMC

Liu S., Hu P., Du X., Zhou T., Pei X. Lactobacillus rhamnosus GG supplementation for preventing respiratory infections in children: A meta-analysis of randomized, placebo-controlled trials. Indian Pediatr. 2013;50:377–381. doi: 10.1007/s13312-013-0123-z. PubMed DOI

van Baarlen P., Troost F.J., van Hemert S., Kleerebezem M. Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proc. Natl. Acad. Sci. USA. 2009;106:2371–2376. doi: 10.1073/pnas.0809919106. PubMed DOI PMC

Valdes A.M., Walter J., Segal E., Spector T.D. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179. doi: 10.1136/bmj.k2179. PubMed DOI PMC

Hu S., Wang L., Jiang Z. Dietary additive probiotics modulation of the intestinal microbiota. Protein Pept. Lett. 2017;24:382–387. doi: 10.2174/0929866524666170223143615. PubMed DOI

Chan H.H.Y., Siu P.L.K., Choy C.T., Chan U.K., Zhou J., Wong C.H., Lee Y.W., Chan H.W., Tsui J.C.C., Loo S.K.F., et al. Novel multi-strain E3 probiotic formulation improved mental health symptoms and sleep quality in Hong Kong Chinese. Nutrients. 2023;15:5037. doi: 10.3390/nu15245037. PubMed DOI PMC

Ponda P.P., Mayer L. Mucosal epithelium in health and disease. Curr. Mol. Med. 2005;5:549–556. doi: 10.2174/1566524054863933. PubMed DOI

Turner J.R. Intestinal mucosal barrier function in health and disease. Nat. Rev. Immunol. 2009;9:799–809. doi: 10.1038/nri2653. PubMed DOI

Siciliano R.A., Lippolis R., Mazzeo M.F. Proteomics for the investigation of surface-exposed proteins in probiotics. Front. Nutr. 2019;6:52. doi: 10.3389/fnut.2019.00052. PubMed DOI PMC

Yan F., Polk D.B. Probiotics and immune health. Curr. Opin. Gastroenterol. 2011;27:496–501. doi: 10.1097/MOG.0b013e32834baa4d. PubMed DOI PMC

Gandhi A., Shah N.P. Integrating omics to unravel the stress-response mechanisms in probiotic bacteria: Approaches, challenges, and prospects. Crit. Rev. Food Sci. Nutr. 2017;57:3464–3471. doi: 10.1080/10408398.2015.1136805. PubMed DOI

Remus D.M., Bongers R.S., Meijerink M., Fusetti F., Poolman B., de Vos P., Wells J.M., Kleerebezem M., Bron P.A. Impact of Lactobacillus plantarum sortase on target protein sorting, gastrointestinal persistence, and host immune response modulation. J. Bacteriol. 2013;195:502–509. doi: 10.1128/JB.01321-12. PubMed DOI PMC

Yu X., Wei M., Yang D., Wu X., Wei H., Xu F. Lactiplantibacillus plantarum strain FLPL05 promotes longevity in mice by improving intestinal barrier. Probiotics Antimicrob. Proteins. 2023;15:1193–1205. doi: 10.1007/s12602-022-09933-5. PubMed DOI

Servin A.L. Antagonistic activities of lactobacilli and bifidobacterial against microbial pathogens. FEMS Microbiol. Rev. 2004;28:405–440. doi: 10.1016/j.femsre.2004.01.003. PubMed DOI

Corre S.C., Li Y., Riedel C.U., Gahan C.G.M. Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarus UCC118. Proc. Natl. Acad. Sci. USA. 2007;104:7617–7621. doi: 10.1073/pnas.0700440104. PubMed DOI PMC

Makras L., Triantafyllou V., Fayol-Messaoudi D., Adriany T., Zoumpopoulou G., Tsakalidou E., Servin A., De Vuyst L. Kinetic analysis of the antibacterial activity of probiotic lactobacilli towards Salmonella enterica serovar Typhimurium reveals a role for lactic acid and other inhibitory compounds. Res. Microbiol. 2006;157:241–247. doi: 10.1016/j.resmic.2005.09.002. PubMed DOI

Kazmierczak-Siedlecka K., Skonieczna-Zydecka K., Hupp T., Duchnowska R., Marek-Trzonkowska N., Polom K. Next-generation probiotics—Do they open new therapeutic strategy for cancer patients? Gut Microbes. 2022;14:2035659. doi: 10.1080/19490976.2022.2035659. PubMed DOI PMC

Dudik B., Kinova Sepova H., Greifova G., Bilka F., Bilkova A. Next generation probiotics: An overview of the most promising candidates. Epidemiol. Mikrobiol. Imunol. 2022;71:48–56. PubMed

Das A., Behera R.N., Kapoor A., Ambatipudi K. The potential of meta-proteomics and artificial intelligence to establish the next generation of probiotics for personalized healthcare. J. Agric. Food Chem. 2023;71:17528–17542. doi: 10.1021/acs.jafc.3c03834. PubMed DOI

Louis P., Scott K.P., Duncan S.H., Flint H.J. Understanding the effects of diet on bacterial metabolism in the large intestine. J. Appl. Microbiol. 2007;102:1197–1208. doi: 10.1111/j.1365-2672.2007.03322.x. PubMed DOI

Nie K., Ma K., Luo W., Shen Z., Yang Z., Xiao M., Tong T., Yang Y., Wang X. Roseburia intestinalis: A beneficial gut organism from the discoveries in genus and species. Front. Cell. Infect. Microbiol. 2021;11:757718. doi: 10.3389/fcimb.2021.757718. PubMed DOI PMC

Marco M.L., Pavan S., Kleerebezem M. Towards understanding molecular modes of probiotic action. Curr. Opin. Biotechnol. 2006;17:204–210. doi: 10.1016/j.copbio.2006.02.005. PubMed DOI

Remaut H., Tang C., Henderson N.S., Pinkner J.S., Wang T., Hultgren S.J., Thanassi D.G., Waksman G., Li H. Fiber formation across the bacterial outer membrane by the chaperone/usher pathway. Cell. 2008;133:640–652. doi: 10.1016/j.cell.2008.03.033. PubMed DOI PMC

Sleytr U.B., Beveridge T.J. Bacterial S-layers. Trends Microbiol. 1999;7:253–260. doi: 10.1016/S0966-842X(99)01513-9. PubMed DOI

Yan F., Cao H., Cover T.L., Whitehead R., Washington M.K., Polk D.B. Soluble proteins produced by probiotic bacteria regulate intestinal epithelial cell survival and growth. Gastroenterology. 2007;132:562–575. doi: 10.1053/j.gastro.2006.11.022. PubMed DOI PMC

Tao Y., Grabik K.A., Waypa T.S., Musch M.W., Alverdy J.C., Schneewind O., Chang E.B., Petrof E.O. Soluble factors from Lactobacillus GG activate MAPKS and induce cytoprotective heat shock proteins in intestinal epithelial cells. Am. J. Physiol. Cell. Physiol. 2006;290:C1018-30. doi: 10.1152/ajpcell.00131.2005. PubMed DOI

Yan F., Polk D.B. Characterization of a probiotic-derived soluble protein which reveals a mechanism of preventive and treatment effects of probiotics on intestinal inflammatory diseases. Gut Microbes. 2012;3:25–28. doi: 10.4161/gmic.19245. PubMed DOI PMC

Aires J., Butel M.J. Proteomics, human gut microbiota and probiotics. Expert Rev. Proteom. 2011;8:279–288. doi: 10.1586/epr.11.5. PubMed DOI

Ruiz L., Hidalgo C., Blanco-Miguez A., Lourenco A., Sanchez B., Margolles A. Tackling probiotic and gut microbiota functionality through proteomics. J. Proteom. 2016;147:29–39. doi: 10.1016/j.jprot.2016.03.023. PubMed DOI

De Angelis M., Calasso M., Cavallo N., Di Cagno R., Gobbetti M. Functional proteomics within the genus Lactobacillus. Proteomics. 2016;16:946–962. doi: 10.1002/pmic.201500117. PubMed DOI

Martin R., Langella P. Emerging health concepts in the probiotics field: Streamlining the definitions. Front. Microbiol. 2019;10:1047. doi: 10.3389/fmicb.2019.01047. PubMed DOI PMC

Sauer S., Kliem M. Mass spectrometry tools for the classification and identification of bacteria. Nat. Rev. Microbiol. 2010;8:74–82. doi: 10.1038/nrmicro2243. PubMed DOI

Welker M. Proteomics for routine identification of microorganisms. Proteomics. 2011;11:3143–3152. doi: 10.1002/pmic.201100049. PubMed DOI

Welker M., Van Belkum A., Girard V., Charrier J.P., Pincus D. An update on the routine application of MALDI-TOF MS in clinical microbiology. Expert Rev. Proteom. 2019;16:695–710. doi: 10.1080/14789450.2019.1645603. PubMed DOI

Izquierdo E., Horvatovich P., Marchioni E., Aoude-Werner D., Sanz Y., Ennahar S. 2-DE and MS analysis of key proteins in the adhesion of Lactobacillus plantarum, a first step toward early selection of probiotics based on bacterial biomarkers. Electrophoresis. 2009;30:949–956. doi: 10.1002/elps.200800399. PubMed DOI

Maffei B., Francetic O., Subtil A. Tracking proteins secreted by bacteria: What’s in the toolbox? Front. Cell. Infect. Microbiol. 2017;7:221. doi: 10.3389/fcimb.2017.00221. PubMed DOI PMC

Abele M., Doll E., Bayer F.P., Meng C., Lomp N., Neuhaus K., Scherer S., Kuster B., Ludwig C. Unified workflow for the rapid and in-depth characterization of bacterial proteomes. Mol. Cell. Proteom. 2023;22:100612. doi: 10.1016/j.mcpro.2023.100612. PubMed DOI PMC

Solis N., Cordwell S.J. Current methodologies for proteomics of bacterial surface-exposed and cell envelope proteins. Proteomics. 2011;11:3169–3189. doi: 10.1002/pmic.201000808. PubMed DOI

Bonn F., Maaß S., van Dijl J.M. Enrichment of cell surface-associated proteins in Gram-positive bacteria by biotinylation or trypsin shaving for mass spectrometry analysis. Methods Mol. Biol. 2018;1841:35–43. doi: 10.1007/978-1-4939-8695-8_4. PubMed DOI

Solis N., Larsen M.R., Cordwell S.J. Improved accuracy of cell surface shaving proteomics in Staphylococcus aureus using a false-positive control. Proteomics. 2010;10:2037–2049. doi: 10.1002/pmic.200900564. PubMed DOI

Ong S., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteom. 2002;1:376–386. doi: 10.1074/mcp.M200025-MCP200. PubMed DOI

Dieterich D.C., Link A.J., Graumann J., Tirrell D.A., Schuman E.M. Selective identification of newly synthesized proteins in mammalian cells using biorthogonal noncanonical amino acid tagging (BONCAT) Proc. Natl. Acad. Sci. USA. 2006;103:9482–9487. doi: 10.1073/pnas.0601637103. PubMed DOI PMC

Ma Y., McClatchy D.B., Barkallah S., Wood W.W., Yates J.R., 3rd Quantitative analysis of newly synthesized proteins. Nat. Protoc. 2018;13:1744–1762. doi: 10.1038/s41596-018-0012-y. PubMed DOI PMC

Lange V., Picotti P., Domon B., Aebersold R. Selected reaction monitoring for quantitative proteomics: A tutorial. Mol. Syst. Biol. 2008;4:222. doi: 10.1038/msb.2008.61. PubMed DOI PMC

Hamon E., Horvatovich P., Izquierdo E., Bringel F., Marchioni E., Aoude-Werner D., Ennahar S. Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance. BMC Microbiol. 2011;11:63. doi: 10.1186/1471-2180-11-63. PubMed DOI PMC

Silva W.M., Sousa C.S., Oliveira L.C., Soares S.C., Souza G.F.M.H., Tavares G.C., Resende C.P., Folador E.L., Pereira F.L., Figueiredo H., et al. Comparative proteomic analysis of four biotechnological strains Lactococcus lactis through label-free quantitative proteomics. Microb. Biotechnol. 2019;12:265–274. doi: 10.1111/1751-7915.13305. PubMed DOI PMC

Chen S., Yi J., Suo K., Kang Q., Lu L., Lu J. Probiotic properties and proteomic analysis of ethanol-induced Lactococcus lactis subsp. lactis IL1403. World J. Microbiol. Biotechnol. 2023;39:197. doi: 10.1007/s11274-023-03627-y. PubMed DOI

Chen S., Yi J., Kang Q., Song M., Raubenheimer D., Lu J. Identification of a novel peptide with alcohol dehydrogenase activating ability from ethanol-induced Lactococcus lactis: A combined in silico prediction and in vivo validation. J. Agric. Food Chem. 2024;72:5746–5756. doi: 10.1021/acs.jafc.3c07632. PubMed DOI

Mbye M., Baig M.A., AbuQamar S.F., El-Tarabily K.A., Obaid R.S., Osaili T.M., Al-Nabulsi A.A., Turner M.S., Shah N.P., Ayyash M.M. Updates on understanding of probiotic lactic acid bacteria responses to environmental stresses and highlights on proteomic analyses. Compr. Rev. Food Sci. Food Saf. 2020;19:1110–1124. doi: 10.1111/1541-4337.12554. PubMed DOI

Beck H.C., Madsen S.M., Glenting J., Petersen J., Israelsen H., Norrelykke M.R., Antonsson M., Hansen A.M. Proteomic analysis of cell surface-associated proteins from probiotic Lactobacillus plantarum. FEMS Microbiol. Lett. 2009;297:61–66. doi: 10.1111/j.1574-6968.2009.01662.x. PubMed DOI

Desvaux M., Dumas E., Chafsey I., Hebraud M. Protein cell surface display in Gram-positive bacteria: From single protein to macromolecular protein structure. FEMS Microbiol. Lett. 2006;256:1–15. doi: 10.1111/j.1574-6968.2006.00122.x. PubMed DOI

Kwoji I.D., Aiyegoro O.A., Okpeku M., Adeleke M.A. Elucidating the mechanisms of cell-to-cell crosstalk in probiotics co-culture: A proteomics study of Limosilactobacillus reuteri ZJ625 and Ligilactobacillus salivarius ZJ614. Probiotics Antimicrob. Proteins. 2023 doi: 10.1007/s12602-023-10133-y. PubMed DOI

Wang G., Xia Y., Cui J., Gu Z., Song Y., Chen Y.Q., Chen H., Zhang H., Chen W. The roles of moonlighting proteins in bacteria. Curr. Issues Mol. Biol. 2014;16:15–22. doi: 10.21775/cimb.016.015. PubMed DOI

Jeffery C.J. Intracellular/surface moonlighting proteins that aid in the attachment of gut microbiota to the host. AIMS Microbiol. 2019;5:77–86. doi: 10.3934/microbiol.2019.1.77. PubMed DOI PMC

Dramsi S., Bierne H. Spatial organization of cell wall-anchored proteins at the surface of Gram-positive bacteria. In: Bagnoli F., Rappuoli R., editors. Protein and Sugar Export and Assembly in Gram-Positive Bacteria. Volume 404. Springer; Cham, Switzerland: 2016. Current Topics in Microbiology and Immunology. DOI

Fagan R.P., Fairweather N.F. Biogenesis and functions of bacterial S-layers. Nat. Rev. Microbiol. 2014;12:211–222. doi: 10.1038/nrmicro3213. PubMed DOI

Mazzeo M.F., Reale A., Di Renzo T., Siciliano R.A. Surface layer protein pattern of Levilactobacillus brevis strains investigated by proteomics. Nutrients. 2022;14:3679. doi: 10.3390/nu14183679. PubMed DOI PMC

Klotz C., O’Flaherty S., Goh Y.J., Barrangou R. Investigating the effect of growth phase on the surface-layer associated proteome of Lactobacillus acidophilus using quantitative proteomics. Front. Microbiol. 2017;8:2174. doi: 10.3389/fmicb.2017.02174. PubMed DOI PMC

Proft T., Baker E.N. Pili in Gram-negative and Gram-positive bacteria—Structure, assembly and their role in disease. Cell. Mol. Life Sci. 2009;66:613–635. doi: 10.1007/s00018-008-8477-4. PubMed DOI PMC

Lebeer S., Claes I., Tytgat H.L.P., Verhoeven T.L.A., Marien E., von Ossowski I., Reunanen J., Palva A., de Vos W.M., De Keersmaecker S.C.J., et al. Functional analysis of Lactobacillus rhamnosus GG pili in relation to adhesion and immunomodulatory interactions with intestinal epithelial cells. Appl. Environ. Microbiol. 2012;78:185–193. doi: 10.1128/AEM.06192-11. PubMed DOI PMC

Lightfoot Y.L., Selle K., Yang T., Goh Y.J., Sahay B., Zadeh M., Owen J.L., Colliou N., Li E., Johannssen T., et al. SIGNR3-dependent immune regulation by Lactobacillus acidophilus surface layer protein A in colitis. EMBO J. 2015;34:881–895. doi: 10.15252/embj.201490296. PubMed DOI PMC

Calvo E., Pucciarelli M.G., Bierne H., Cossart P., Albar J.P., Garcia-Del Portillo F. Analysis of the Listeria cell wall proteome by two-dimensional nanoliquid chromatography coupled to mass spectrometry. Proteomics. 2005;5:433–443. doi: 10.1002/pmic.200400936. PubMed DOI

Tjalsma H., van Dijl J.M. Proteomic-based consensus prediction of protein retention in a bacterial membrane. Proteomics. 2005;5:4472–4482. doi: 10.1002/pmic.200402080. PubMed DOI

Candela M., Bergmann S., Vici M., Vitali B., Turroni S., Eikmanns B.J., Hammerschmidt S., Brigidi P. Binding of human plasminogen to Bifidobacterium. J. Bacteriol. 2007;189:5929–5936. doi: 10.1128/JB.00159-07. PubMed DOI PMC

Martin C., Escobedo S., Suarez J.E., Quiros L.M. Widespread use of Lactobacillus OppA, a surface located protein, as an adhesin that recognizes epithelial cell surface glycosaminoglycans. Benef. Microbes. 2019;10:463–472. doi: 10.3920/BM2018.0128. PubMed DOI

Dubey V., Mishra A.K., Ghosh A.R. Cell adherence efficacy of probiotic Pediococcus pentosaceus GS4 (MTCC 12683) and demonstrable role of its surface layer protein (Slp) J. Proteom. 2020;226:103894. doi: 10.1016/j.jprot.2020.103894. PubMed DOI

Zhai Z., Xiong Y., Gu Y., Lei Y., An H., Yi H., Zhao L., Ren F., Hao Y. Up-regulation of sortase-dependent pili in Bifidobacterium longum BBMN68 in response to bile stress enhances its adhesion to HT-29 cells. Pt 2Int. J. Biol. Macromol. 2024;257:127527. doi: 10.1016/j.ijbiomac.2023.127527. PubMed DOI

Qiao L., Dou X., Song X., Chang J., Zeng X., Zhu L., Xu C. Selenite bioremediation by food-grade probiotic Lactobacillus casei ATCC 393: Insights from proteomics analysis. Microbiol. Spectr. 2023;11:e0065923. doi: 10.1128/spectrum.00659-23. PubMed DOI PMC

Yang Y., Song X., Wang G., Xia Y., Xiong Z., Ai L. Understanding Ligilactobacillus salivarius from probiotic properties to omics technology: A review. Foods. 2024;13:895. doi: 10.3390/foods13060895. PubMed DOI PMC

Gilad O., Svensson B., Viborg A.H., Stuer-Lauridsen B., Jacobsen S. The extracellular proteome of Bifidobacterium animalis subsp. lactis BB-12 reveals proteins with putative roles in probiotic effects. Proteomics. 2011;11:2503–2514. doi: 10.1002/pmic.201000716. PubMed DOI

Bagon B.B., Oh J.K., Valeriano V.D.V., Pajarillo E.A.B., Kang D.K. Exploring the bile stress response of Lactobacillus mucosae LM1 through exoproteome analysis. Molecules. 2021;26:5695. doi: 10.3390/molecules26185695. PubMed DOI PMC

Sanchez B., Urdaci M.C., Margolles A. Extracellular proteins secreted by probiotic bacteria as mediators of effects that promote mucosa-bacteria interactions. Microbiology. 2010;156:3232–3242. doi: 10.1099/mic.0.044057-0. PubMed DOI

Krzyzek P., Marinacci B., Vitele I., Grande R. Extracellular vesicles of probiotics: Shedding light on the biological activity and future applications. Pharmaceutics. 2023;15:522. doi: 10.3390/pharmaceutics15020522. PubMed DOI PMC

Shah R., Patel T., Freedman J.E. Circulating extracellular vesicles in human disease. N. Engl. J. Med. 2018;379:958–966. doi: 10.1056/NEJMra1704286. PubMed DOI

Nah G., Park S.C., Kim K., Kim S., Park J., Lee S., Won S. Type-2 diabetics reduces spatial variation of microbiome based on extracellular vesicles from gut microbes across human body. Sci. Rep. 2019;9:20136. doi: 10.1038/s41598-019-56662-x. PubMed DOI PMC

Kalra H., Drummen G.P.C., Mathivanan S. Focus on extracellular vesicles: Introducing the next small big thing. Int. J. Mol. Sci. 2016;17:170. doi: 10.3390/ijms17020170. PubMed DOI PMC

Stastna M. Advances in separation and identification of biologically important milk proteins and peptides. Electrophoresis. 2023;45:101–119. doi: 10.1002/elps.202300084. PubMed DOI

Wegh C.A.M., Geerlings S.Y., Knol J., Roeselers G., Belzer C. Postbiotics and their potential applications in early life nutrition and beyond. Int. J. Mol. Sci. 2019;20:4673. doi: 10.3390/ijms20194673. PubMed DOI PMC

Vindertola G., Sanders M.E., Salminen S. The concept of postbiotics. Foods. 2022;11:1077. doi: 10.3390/foods11081077. PubMed DOI PMC

Kulig K., Kowalik K., Surowiec M., Karnas E., Barczyk-Woznicka O., Zuba-Surma E., Pyza E., Kozik A., Rapala-Kozik M., Karkowska-Kuleta J. Isolation and characteristics of extracellular vesicles produced by probiotics: Yeast Saccharomyces boulardii CNCM I-745 and Bacterium streptococcus salivarius K12. Probiotics Antimicrob. Proteins. 2023;16:936–948. doi: 10.1007/s12602-023-10085-3. PubMed DOI PMC

Lee B.H., Chen Y.Z., Shen T.L., Pan T.M., Hsu W.H. Proteomic characterization of extracellular vesicles derived from lactic acid bacteria. Food Chem. 2023;427:136685. doi: 10.1016/j.foodchem.2023.136685. PubMed DOI

Huang J., Zhao A., He D., Wu X., Yan H., Zhu L. Isolation and proteomic analysis of extracellular vesicles from Lactobacillus salivarius SNK-6. J. Microbiol. Biotechnol. 2024;34:224–231. doi: 10.4014/jmb.2308.08017. PubMed DOI PMC

Rodovalho V.R., da Luz B.S.R., Nicolas A., Jardin J., Briard-Bion V., Folador E.L., Santos A.R., Jan G., Loir Y.L., Azevedo V.A.C., et al. Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles. Microlife. 2023;4:uqad029. doi: 10.1093/femsml/uqad029. PubMed DOI PMC

de Rezende Rodovalho V., da Luz B.S.R., Nicolas A., do Carmo F.L.R., Jardin J., Briard-Bion V., Jan G., Le Loir Y., de Carvalho Azevedo V.A., Guedon E. Environmental conditions modulate the protein content and immunomodulatory activity of extracellular vesicles produced by the probiotic Propionibacterium freudenreichii. Appl. Environ. Microbiol. 2021;87:e02263-20. doi: 10.1128/AEM.02263-20. PubMed DOI PMC

Hill D., Sugrue I., Tobin C., Hill C., Stanton C., Ross R.P. The Lactobacillus casei group: History and health related applications. Front. Microbiol. 2018;9:2107. doi: 10.3389/fmicb.2018.02107. PubMed DOI PMC

Huang R., Wang K., Hu J. Effect of probiotics on depression: A systematic review and meta-analysis of randomized controlled trials. Nutrients. 2016;8:483. doi: 10.3390/nu8080483. PubMed DOI PMC

Borgeraas H., Johnson L.K., Skattebu J., Hertel J.K., Hjemesaeth J. Effects of probiotics on body weight, body mass index, fat mass and fat percentage in subjects with overweight or obesity: A systematic review and meta-analysis of randomized controlled trials. Obes. Rev. 2018;19:219–232. doi: 10.1111/obr.12626. PubMed DOI

Cuello-Garcia C.A., Brozek J.L., Fiocchi A., Pawankar R., Yepes-Nunez J.J., Terracciano L., Gandhi S., Agarwal A., Zhang Y., Schunemann H.J. Probiotics for the prevention of allergy: A systematic review and meta-analysis of randomized controlled trials. J. Allergy Clin. Immunol. 2015;136:952–961. doi: 10.1016/j.jaci.2015.04.031. PubMed DOI

So S.S.Y., Wan M.L.Y., El-Nezami H. Probiotics-mediated suppression of cancer. Curr. Opin. Oncol. 2017;29:62–72. doi: 10.1097/CCO.0000000000000342. PubMed DOI

Raslan M.A., Raslan S.A., Shehata E.M., Mahmoud A.S., Viana M.V.C., Barh D., Sabri N.A., Azevedo V. Applications of proteomics in probiotics having anticancer and chemopreventive properties. Adv. Exp. Med. Biol. 2024;1443:243–256. doi: 10.1007/978-3-031-50624-6_13. PubMed DOI

Beltran-Velasco A.I., Reiriz M., Uceda S., Echeverry-Alzate V. Lactiplantibacillus (Lactobacillus) plantarum as a complementary treatment to improve symptomatology in neurodegenerative disease: A systematic review of open access literature. Int. J. Mol. Sci. 2024;25:3010. doi: 10.3390/ijms25053010. PubMed DOI PMC

Cafaro G., Cruciani G., Bruno L., Dal Pozzolo R., Colangelo A., Tromby F., Nicchi M., Pianese B., Perricone C., Gerli R., et al. Microbiota and arthritis: Cause or consequence? Clin. Exp. Rheumatol. 2024;42:1097–1103. doi: 10.55563/clinexprheumatol/f6q4dc. PubMed DOI

Jarosz L.S., Socala K., Michalak K., Wiater A., Ciszewski A., Majewska M., Marek A., Gradzki Z., Wlaz P. The effect of psychoactive bacteria, Bifidobacterium longum Rosell®-175 and Lactobacillus rgamnosus JB-1, on brain proteome profiles in mice. Psychopharmacology. 2024;241:925–945. doi: 10.1007/s00213-023-06519-z. PubMed DOI PMC

Cufaro M.C., Prete R., Di Marco F., Sabatini G., Corsetti A., Gonzalez N.G., Del Boccio P., Battista N. A proteomic insight reveals the role of food-associated Lactiplantibacillus plantarum C9O4 in reverting intestinal inflammation. iScience. 2023;26:108481. doi: 10.1016/j.isci.2023.108481. PubMed DOI PMC

Averina O.A., Kovtun A.S., Mavletova D.A., Ziganshin R.H., Danilenko V.N., Mihaylova D., Blazheva D., Slavchev A., Brazkova M., Ibrahim S.A., et al. Oxidative stress response of probiotic strain Bifidobacterium longum subsp. longum GT15. Foods. 2023;12:3356. doi: 10.3390/foods12183356. PubMed DOI PMC

Suez J., Zmora N., Segal E., Elinav E. The pros, cons, and many unknowns of probiotics. Nat. Med. 2019;25:716–729. doi: 10.1038/s41591-019-0439-x. PubMed DOI

Siciliano R.A., Reale A., Mazzeo M.F., Morandi S., Silvetti T., Brasca M. Paraprobiotics: A new perspective for functional foods and nutraceuticals. Nutrients. 2021;13:1225. doi: 10.3390/nu13041225. PubMed DOI PMC

Haranahalli Nataraj B., Behare P.V., Yadav H., Srivastava A.K. Emerging pre-clinical safety assessment for potential probiotic strains: A review. Crit. Rev. Food Sci. Nutr. 2023:1–29. doi: 10.1080/10408398.2023.2197066. PubMed DOI

Zucko J., Starcevic A., Diminic J., Oros D., Mortazavian A.M., Putnik P. Probiotic—Friend or foe? Curr. Opin. Food Sci. 2020;32:45–49. doi: 10.1016/j.cofs.2020.01.007. DOI

Wu F., Xie X., Du T., Jiang X., Miao W., Wang T. Lactococcus lactis, a bacterium with probiotic functions and pathogenicity. World J. Microbiol. Biotechnol. 2023;39:325. doi: 10.1007/s11274-023-03771-5. PubMed DOI

Pasala S., Singer L., Arshad T., Roach K. Lactobacillus endocarditis in a healthy patient with probiotic use. IDCases. 2020;22:e00915. doi: 10.1016/j.idcr.2020.e00915. PubMed DOI PMC

Rahman A., Alqaisi S., Nath J. A case of Lactobacillus casei endocarditis associated with probiotic intake in an immunocompromised patient. Cureus. 2023;15:e38049. doi: 10.7759/cureus.38049. PubMed DOI PMC

Stastna M. Post-translational modifications of proteins in cardiovascular diseases examined by proteomic approaches. FEBS J. 2024 doi: 10.1111/febs.17108. Early View . PubMed DOI

Kwoji I.D., Aiyegoro O.A., Okpeku M., Adeleke M.A. ‘Multi-omics’ data integration: Application in probiotics studies. npj Sci. Food. 2023;7:25. doi: 10.1038/s41538-023-00199-x. PubMed DOI PMC

Ferrocino I., Rentsiou K., McClure R., Kostic T., de Souza R.S.C., Lange L., FitzGerald J., Kriaa A., Cotter P., Maguin E., et al. Microbiome Support Consortium. Compr. Rev. Food Sci. Food Saf. 2023;22:1082–1103. doi: 10.1111/1541-4337.13103. PubMed DOI

Rajczewski A.T., Jagtap P.D., Griffin T.J. An overview of technologies for MS-based proteomics-centric multiomics. Expert Rev. Proteomics. 2022;19:165–181. doi: 10.1080/14789450.2022.2070476. PubMed DOI PMC

Bianchi L., Laghi L., Correani V., Schifano E., Landi C., Uccelletti D., Mattei B. A combined proteomics, metabolomics and in vivo analysis approach for the characterization of probiotics in large-scale production. Biomolecules. 2020;10:157. doi: 10.3390/biom10010157. PubMed DOI PMC

Preidis G.A., Weizman A.V., Kashyap P.C., Morgan R.L. AGA technical review on the role of probiotics in the management of gastrointestinal disorders. Gastroenterology. 2020;159:708–738. doi: 10.1053/j.gastro.2020.05.060. PubMed DOI PMC

Al-Fakhrany O., Elekhnawy E. Next-generation probiotics: The upcoming biotherapeutics. Mol. Biol. Rep. 2024;51:505. doi: 10.1007/s11033-024-09398-5. PubMed DOI PMC

Abouelela M.E., Helmy Y.A. Next-generation probiotics as novel therapeutics for improving human health: Current trends and future perspectives. Microorganisms. 2024;12:430. doi: 10.3390/microorganisms12030430. PubMed DOI PMC