Hill, C. et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 11, 506–514 (2014).

Article 
PubMed 

Google Scholar
 

Liu, H. et al. A multicellular self-organized probiotic platform for oral delivery enhances intestinal colonization. Nat. Commun. 16, 7060 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Konstantinov, S. R. et al. S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. Proc. Natl Acad. Sci. USA 105, 19474–19479 (2008).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Asare, P. T. et al. Reuterin demonstrates potent antimicrobial activity against a broad panel of human and poultry meat Campylobacter spp. isolates. Microorganisms 8, 78 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Rutter, J. W. et al. A bacteriocin expression platform for targeting pathogenic bacterial species. Nat. Commun. 15, 6332 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Kamada, N. et al. Nonpathogenic Escherichia coli strain Nissle 1917 inhibits signal transduction in intestinal epithelial cells. Infect. Immun. 76, 214–220 (2008).

Article 
CAS 
PubMed 

Google Scholar
 

Baralić, K., Živančević, K., Bozic, D. & Đukić-Ćosić, D. Probiotic cultures as a potential protective strategy against the toxicity of environmentally relevant chemicals: state-of-the-art knowledge. Food Chem. Toxicol. 172, 113582 (2023).

Article 
PubMed 

Google Scholar
 

O’Toole, P. W., Marchesi, J. R. & Hill, C. Next-generation probiotics: the spectrum from probiotics to live biotherapeutics. Nat. Microbiol. 2, 17057 (2017).

Article 
PubMed 

Google Scholar
 

Suez, J., Zmora, N., Segal, E. & Elinav, E. The pros, cons, and many unknowns of probiotics. Nat. Med. 25, 716–729 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Baião, R. et al. Multispecies probiotic administration reduces emotional salience and improves mood in subjects with moderate depression: a randomised, double-blind, placebo-controlled study. Psychol. Med. 53, 3437–3447 (2023).

Article 
PubMed 

Google Scholar
 

Asghari, K. M. et al. The effect of probiotic supplementation on the clinical and para-clinical findings of multiple sclerosis: a randomized clinical trial. Sci. Rep. 13, 18577 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Gibson, G. R. et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat. Rev. Gastroenterol. Hepatol. 14, 491–502 (2017).

Article 
PubMed 

Google Scholar
 

Hutkins, R. et al. Classifying compounds as prebiotics — scientific perspectives and recommendations. Nat. Rev. Gastroenterol. Hepatol. 22, 54–70 (2025).

Article 
PubMed 

Google Scholar
 

Swanson, K. S. et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics. Nat. Rev. Gastroenterol. Hepatol. 17, 687–701 (2020).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Lewis, Z. T. et al. Validating bifidobacterial species and subspecies identity in commercial probiotic products. Pediatr. Res. 79, 445–452 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

MarketsandMarkets. Probiotics Market Report (Global Forecast to 2029) (MarketsandMarkets, 2025).

McFarland, L. V. Systematic review and meta-analysis of Saccharomyces boulardii in adult patients. World J. Gastroenterol. 16, 2202–2222 (2010).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Li, M. et al. Engineered probiotics with sustained release of interleukin-2 for the treatment of inflammatory bowel disease after oral delivery. Biomaterials 309, 122584 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Allegretti, J. R. et al. Safety and efficacy of fecal microbiota, live-jslm (REBYOTA®), for the prevention of recurrent Clostridioides difficile infection in participants with inflammatory bowel disease in PUNCH CD3-OLS. Inflamm. Bowel Dis. 31, 2112–2122 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Rosenberg, J. & Ritter, T. Practical use of fecal microbiota spores, live-brpk (formerly SER-109): an oral therapeutic for the prevention of recurrent Clostridioides difficile infection. Expert Rev. Antiinfect. Ther. 21, 687–690 (2023).

Article 
CAS 

Google Scholar
 

Feuerstadt, P. et al. SER-109, an oral microbiome therapy for recurrent Clostridioides difficile infection. N. Engl. J. Med. 386, 220–229 (2022).

Article 
CAS 
PubMed 

Google Scholar
 

Khanna, S. et al. Efficacy and safety of RBX2660 in PUNCH CD3, a phase III, randomized, double-blind, placebo-controlled trial with a Bayesian primary analysis for the prevention of recurrent Clostridioides difficile infection. Drugs 82, 1527–1538 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Peled, J. U. et al. Microbiota as predictor of mortality in allogeneic hematopoietic-cell transplantation. N. Engl. J. Med. 382, 822–834 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Rashidi, A. et al. Randomized double-blind phase II trial of fecal microbiota transplantation versus placebo in allogeneic hematopoietic cell transplantation and AML. J. Clin. Oncol. 41, 5306–5319 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Veiga, P., Suez, J., Derrien, M. & Elinav, E. Moving from probiotics to precision probiotics. Nat. Microbiol. 5, 878–880 (2020).

Article 
PubMed 

Google Scholar
 

Zmora, N. et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174, 1388–1405.e21 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Hernández Medina, R. et al. Machine learning and deep learning applications in microbiome research. ISME Commun. 2, 98 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Marcos-Zambrano, L. J. et al. Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment. Front. Microbiol. 12, 634511 (2021).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174–180 (2011).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Li, N. & Guo, X. The gut microbiota and host immunity synergistically orchestrate colonization resistance. Gut Microbes 18, 2611545 (2026).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Merenstein, D. J. et al. Is there evidence to support probiotic use for healthy people? Adv. Nutr. 15, 100265 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

McFarland, L. V., Evans, C. T. & Goldstein, E. J. C. Strain-specificity and disease-specificity of probiotic efficacy: a systematic review and meta-analysis. Front. Med. 5, 124 (2018).

Article 

Google Scholar
 

Kochan, P. et al. Lactobacillus rhamnosus administration causes sepsis in a cardiosurgical patient — is the time right to revise probiotic safety guidelines? Clin. Microbiol. Infect. 17, 1589–1592 (2011).

Article 
CAS 
PubMed 

Google Scholar
 

Land, M. H. et al. Lactobacillus sepsis associated with probiotic therapy. Pediatrics 115, 178–181 (2005).

Article 
PubMed 

Google Scholar
 

Suez, J. et al. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell 174, 1406–1423.e16 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Zhang, W. et al. Bacteroides fragilis protects against antibiotic-associated diarrhea in rats by modulating intestinal defenses. Front. Immunol. 9, 1040 (2018).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Kang, C.-H. et al. Pasteurized Akkermansia muciniphila HB05 (HB05P) improves muscle strength and function: a 12-week, randomized, double-blind, placebo-controlled clinical trial. Nutrients 16, 4037 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, H. et al. Akkermansia muciniphila ONE effectively ameliorates dextran sulfate sodium (DSS)-induced ulcerative colitis in mice. npj Sci. Food 8, 97 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Xiao, X. et al. Akkermansia muciniphila supplementation improves hyperlipidemia, cardiac function, and gut microbiota in high fat fed apolipoprotein E-deficient mice. Prostaglandins Other Lipid Mediat. 175, 106906 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Blacher, E. et al. Potential roles of gut microbiome and metabolites in modulating ALS in mice. Nature 572, 474–480 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Desai, M. S. et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339–1353.e21 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Cox, L. M. et al. Gut microbiome in progressive multiple sclerosis. Ann. Neurol. 89, 1195–1211 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Walter, J., Maldonado-Gómez, M. X. & Martínez, I. To engraft or not to engraft: an ecological framework for gut microbiome modulation with live microbes. Curr. Opin. Biotechnol. 49, 129–139 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Shen, X. et al. Short-term probiotic supplementation affects the diversity, genetics, growth, and interactions of the native gut microbiome. iMeta 3, e253 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Maldonado-Gómez, M. X. et al. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host Microbe 20, 515–526 (2016).

Article 
PubMed 

Google Scholar
 

Chávarri, M. et al. Microencapsulation of a probiotic and prebiotic in alginate-chitosan capsules improves survival in simulated gastro-intestinal conditions. Int. J. Food Microbiol. 142, 185–189 (2010).

Article 
PubMed 

Google Scholar
 

Cook, M. T., Tzortzis, G., Charalampopoulos, D. & Khutoryanskiy, V. V. Microencapsulation of probiotics for gastrointestinal delivery. J. Control. Release 162, 56–67 (2012).

Article 
CAS 
PubMed 

Google Scholar
 

Tremblay, A. et al. Total transit time and probiotic persistence in healthy adults: a pilot study. J. Neurogastroenterol. Motil. 29, 218–228 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Singhal, R. & Shah, Y. M. Oxygen battle in the gut: hypoxia and hypoxia-inducible factors in metabolic and inflammatory responses in the intestine. J. Biol. Chem. 295, 10493–10505 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Kiu, R. et al. Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains. Nat. Microbiol. 8, 1160–1175 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Baishya, J. et al. The impact of intraspecies and interspecies bacterial interactions on disease outcome. Pathogens 10, 96 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Holzapfel, W., Arini, A., Aeschbacher, M., Coppolecchia, R. & Pot, B. Enterococcus faecium SF68 as a model for efficacy and safety evaluation of pharmaceutical probiotics. Benef. Microbes 9, 375–388 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Montealegre, M. C., Singh, K. V. & Murray, B. E. Gastrointestinal tract colonization dynamics by different Enterococcus faecium clades. J. Infect. Dis. 213, 1914–1922 (2016).

Article 
PubMed 

Google Scholar
 

Leendertse, M. et al. Enterococcal surface protein transiently aggravates Enterococcus faecium-induced urinary tract infection in mice. J. Infect. Dis. 200, 1162–1165 (2009).

Article 
CAS 
PubMed 

Google Scholar
 

Leavis, H. L., Willems, R. J. L., Top, J. & Bonten, M. J. M. High-level ciprofloxacin resistance from point mutations in gyrA and parC confined to global hospital-adapted clonal lineage CC17 of Enterococcus faecium. J. Clin. Microbiol. 44, 1059–1064 (2006).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Torres, M. et al. Bacterial fitness for plant colonization is influenced by plant growth substrate. N. Phytol. 248, 3168–3190 (2025).

Article 
CAS 

Google Scholar
 

Han, S. et al. Probiotic gastrointestinal transit and colonization after oral administration: a long journey. Front. Cell. Infect. Microbiol. 11, 609722 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sassone-Corsi, M. et al. Microcins mediate competition among Enterobacteriaceae in the inflamed gut. Nature 540, 280–283 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Osbelt, L. et al. Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production. PLoS Pathog. 16, e1008448 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Strock, R. et al. Archaea produce peptidoglycan hydrolases that kill bacteria. PLoS Biol. 23, e3003235 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Alavi, S. et al. Interpersonal gut microbiome variation drives susceptibility and resistance to cholera infection. Cell 181, 1533–1546.e13 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Long, X. et al. Interindividual variability in gut microbiome mediates the efficacy of resistant starch on MASLD. Cell Metab. 37, 2342–2361.e9 (2025).

Article 
CAS 
PubMed 

Google Scholar
 

Wang, H. et al. Microbial metabolite deoxycholic acid controls Clostridium perfringens-induced chicken necrotic enteritis through attenuating inflammatory cyclooxygenase signaling. Sci. Rep. 9, 14541 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Scott, S. A., Fu, J. & Chang, P. V. Dopamine receptor D2 confers colonization resistance via microbial metabolites. Nature 628, 180–185 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Caballero-Flores, G., Pickard, J. M. & Núñez, G. Microbiota-mediated colonization resistance: mechanisms and regulation. Nat. Rev. Microbiol. 21, 347–360 (2023).

Article 
CAS 
PubMed 

Google Scholar
 

Djukovic, A. et al. Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae. Nat. Commun. 13, 5617 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Foley, M. H. et al. Differential modulation of post-antibiotic colonization resistance to Clostridioides difficile by two probiotic Lactobacillus strains. mBio 16, e0146825 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

von Meijenfeldt, F. A. B., Hogeweg, P. & Dutilh, B. E. A social niche breadth score reveals niche range strategies of generalists and specialists. Nat. Ecol. Evol. 7, 768–781 (2023).

Article 

Google Scholar
 

Bakkeren, E., Piskovsky, V., Lee, M. N. Y., Jahn, M. T. & Foster, K. R. Strain displacement in microbiomes via ecological competition. Nat. Microbiol. 10, 3122–3135 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Heilbronner, S., Krismer, B., Brötz-Oesterhelt, H. & Peschel, A. The microbiome-shaping roles of bacteriocins. Nat. Rev. Microbiol. 19, 726–739 (2021).

Article 
CAS 
PubMed 

Google Scholar
 

Tang, Q. et al. Current sampling methods for gut microbiota: a call for more precise devices. Front. Cell. Infect. Microbiol. 10, 151 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, P. Influence of foods and nutrition on the gut microbiome and implications for intestinal health. Int. J. Mol. Sci. 23, 9588 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Tompkins, T. A., Mainville, I. & Arcand, Y. The impact of meals on a probiotic during transit through a model of the human upper gastrointestinal tract. Benef. Microbes 2, 295–303 (2011).

Article 
CAS 
PubMed 

Google Scholar
 

Fan, P. et al. Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation. ISME J. 14, 302–317 (2020).

Article 
CAS 
PubMed 

Google Scholar
 

Federici, S. et al. Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation. Cell 185, 2879–2898.e24 (2022).

Article 
CAS 
PubMed 

Google Scholar
 

Zuo, T. et al. Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome. Gut 67, 634–643 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Shimizu, K. et al. Identification of genes essential for bile acid resistance in the probiotic Lacticaseibacillus paracasei strain Shirota. Lett. Appl. Microbiol. 76, ovad062 (2023).

Article 
CAS 
PubMed 

Google Scholar
 

Mays, Z. J. S., Chappell, T. C. & Nair, N. U. Quantifying and engineering mucus adhesion of probiotics. ACS Synth. Biol. 9, 356–367 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Khan, M. T. et al. Synergy and oxygen adaptation for development of next-generation probiotics. Nature 620, 381–385 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Burrows, K. et al. A gut commensal protozoan determines respiratory disease outcomes by shaping pulmonary immunity. Cell 188, 316–330.e12 (2025).

Article 
CAS 
PubMed 

Google Scholar
 

Kruger, K. et al. Evaluation of inter- and intra-variability in gut health markers in healthy adults using an optimised faecal sampling and processing method. Sci. Rep. 14, 24580 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Rothwell, P. M. External validity of randomised controlled trials: ‘to whom do the results of this trial apply?’. Lancet 365, 82–93 (2005).

Article 
PubMed 

Google Scholar
 

Chuang, Y.-F. et al. Precision probiotics supplement strategy in aging population based on gut microbiome composition. Brief. Bioinform. 25, bbae351 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Latif, A. et al. Probiotics: mechanism of action, health benefits and their application in food industries. Front. Microbiol. 14, 1216674 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Khailova, L. et al. Lactobacillus rhamnosus GG and Bifidobacterium longum attenuate lung injury and inflammatory response in experimental sepsis. PLoS ONE 9, e97861 (2014).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Spacova, I. et al. Lactobacillus rhamnosus probiotic prevents airway function deterioration and promotes gut microbiome resilience in a murine asthma model. Gut Microbes 11, 1729–1744 (2020).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Walocha, R., Kim, M., Wong-Ng, J., Gobaa, S. & Sauvonnet, N. Organoids and organ-on-chip technology for investigating host–microorganism interactions. Microbes Infect. 26, 105319 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Yata, V. K. Ex vivo and miniaturized in vitro models to study microbiota–gut–brain axis. 3 Biotech 14, 280 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Krautkramer, K. A., Fan, J. & Bäckhed, F. Gut microbial metabolites as multi-kingdom intermediates. Nat. Rev. Microbiol. 19, 77–94 (2021).

Article 
CAS 
PubMed 

Google Scholar
 

Mousa, W. K., Chehadeh, F. & Husband, S. Recent advances in understanding the structure and function of the human microbiome. Front. Microbiol. 13, 825338 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Ebigbo, N. et al. Optimizing precision probiotics for mitigating graft-versus-host disease. Microorganisms 13, 706 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sanam, M. et al. Bridging two worlds: host microbiota crosstalk in health and dysregulation. Innate Immun. 31, 17534259251392993 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Garcia-Vello, P. et al. The lipooligosaccharide of the gut symbiont Akkermansia muciniphila exhibits a remarkable structure and TLR signaling capacity. Nat. Commun. 15, 8411 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Zhu, J. et al. Efficacy and safety of Lactobacillus acidophilus LA85 in preventing antibiotic-associated diarrhea: a randomized, placebo-controlled study. Food Sci. Nutr. 13, e70490 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

García, G. et al. Randomized clinical trials demonstrate the safety assessment of Alkalihalobacillus clausii AO1125 for use as a probiotic in humans. Microorganisms 12, 2299 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Quin, C. et al. Probiotic supplementation and associated infant gut microbiome and health: a cautionary retrospective clinical comparison. Sci. Rep. 8, 8283 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Mugambi, M. N., Musekiwa, A., Lombard, M., Young, T. & Blaauw, R. Association between funding source, methodological quality and research outcomes in randomized controlled trials of synbiotics, probiotics and prebiotics added to infant formula: a systematic review. BMC Med. Res. Methodol. 13, 137 (2013).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Rijkers, G. T. et al. Health benefits and health claims of probiotics: bridging science and marketing. Br. J. Nutr. 106, 1291–1296 (2011).

Article 
CAS 
PubMed 

Google Scholar
 

Lerner, A., Benzvi, C. & Vojdani, A. The potential harmful effects of genetically engineered microorganisms (GEMs) on the intestinal microbiome and public health. Microorganisms 12, 238 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Boyle, R. J. et al. Effects of Lactobacillus GG treatment during pregnancy on the development of fetal antigen-specific immune responses. Clin. Exp. Allergy 38, 1882–1890 (2008).

Article 
CAS 
PubMed 

Google Scholar
 

Gao, X. W., Mubasher, M., Fang, C. Y., Reifer, C. & Miller, L. E. Dose-response efficacy of a proprietary probiotic formula of Lactobacillus acidophilus CL1285 and Lactobacillus casei LBC80R for antibiotic-associated diarrhea and Clostridium difficile-associated diarrhea prophylaxis in adult patients. Am. J. Gastroenterol. 105, 1636–1641 (2010).

Article 
PubMed 

Google Scholar
 

Mohan, R. et al. Effects of Bifidobacterium lactis Bb12 supplementation on body weight, fecal pH, acetate, lactate, calprotectin, and IgA in preterm infants. Pediatr. Res. 64, 418–422 (2008).

Article 
PubMed 

Google Scholar
 

Olivares, M., Castillejo, G., Varea, V. & Sanz, Y. Double-blind, randomised, placebo-controlled intervention trial to evaluate the effects of Bifidobacterium longum CECT 7347 in children with newly diagnosed coeliac disease. Br. J. Nutr. 112, 30–40 (2014).

Article 
CAS 
PubMed 

Google Scholar
 

Pellino, G. et al. Early postoperative administration of probiotics versus placebo in elderly patients undergoing elective colorectal surgery: a double-blind randomized controlled trial. BMC Surg. 13, S57 (2013).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Yang, Y. et al. Within-host evolution of a gut pathobiont facilitates liver translocation. Nature 607, 563–570 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Montassier, E. et al. Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. Nat. Microbiol. 6, 1043–1054 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Mukhopadhya, I. et al. Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii. Environ. Microbiol. 20, 324–336 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Uemura, K. et al. Rapid and integrated bacterial evolution analysis unveils gene mutations and clinical risk of Klebsiella pneumoniae. Nat. Commun. 16, 2917 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Martin, F.-P. J. et al. Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. Mol. Syst. Biol. 4, 157 (2008).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Rottinghaus, A. G., Ferreiro, A., Fishbein, S. R. S., Dantas, G. & Moon, T. S. Genetically stable CRISPR-based kill switches for engineered microbes. Nat. Commun. 13, 672 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

George, D. R. et al. A bumpy road ahead for genetic biocontainment. Nat. Commun. 15, 650 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bansal, T. & Garg, S. Probiotics: from functional foods to pharmaceutical products. Curr. Pharm. Biotechnol. 9, 267–287 (2008).

Article 
CAS 
PubMed 

Google Scholar
 

Cheng, A. G. et al. Design, construction, and in vivo augmentation of a complex gut microbiome. Cell 185, 3617–3636.e19 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Furuichi, M. et al. Commensal consortia decolonize Enterobacteriaceae via ecological control. Nature 633, 878–886 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Tanoue, T. et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 565, 600–605 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Huang, X. et al. Multi-kingdom gut microbiota analyses define bacterial-fungal interplay and microbial markers of pan-cancer immunotherapy across cohorts. Cell Host Microbe 31, 1930–1943.e4 (2023).

Article 
CAS 
PubMed 

Google Scholar
 

Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl Acad. Sci. USA 105, 16731–16736 (2008).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bredon, M. et al. Faecalibaterium prausnitzii strain EXL01 boosts efficacy of immune checkpoint inhibitors. Oncoimmunology 13, 2374954 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Wende, M. et al. Suppression of gut colonization by multidrug-resistant Escherichia coli clinical isolates through cooperative niche exclusion. Nat. Commun. 16, 5426 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Depommier, C. et al. Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study. Nat. Med. 25, 1096–1103 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Atarashi, K. et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337–341 (2011).

Article 
CAS 
PubMed 

Google Scholar
 

Atarashi, K. et al. Th17 cell induction by adhesion of microbes to intestinal epithelial cells. Cell 163, 367–380 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Suez, J. et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature 514, 181–186 (2014).

Article 
CAS 
PubMed 

Google Scholar
 

Zeevi, D. et al. Personalized nutrition by prediction of glycemic responses. Cell 163, 1079–1094 (2015).

Article 
CAS 
PubMed 

Google Scholar
 

Bedu-Ferrari, C. et al. In-depth characterization of a selection of gut commensal bacteria reveals their functional capacities to metabolize dietary carbohydrates with prebiotic potential. mSystems 9, e0140123 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Wu, Z. et al. Fecal microbiota transplantation reverses insulin resistance in type 2 diabetes: a randomized, controlled, prospective study. Front. Cell. Infect. Microbiol. 12, 1089991 (2022).

Article 
CAS 
PubMed 

Google Scholar
 

Qin, X. et al. Gut microbiota predict retinopathy in patients with diabetes: a longitudinal cohort study. Appl. Microbiol. Biotechnol. 108, 497 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Hu, Y. et al. Causal relationship between gut microbiota and diabetic neuropathy: a Mendelian randomization and 16S rRNA sequencing analysis. Front. Endocrinol. 16, 1632406 (2025).

Article 

Google Scholar
 

Xu, M. et al. Causal effects of gut microbiota on diabetic neuropathy: a two-sample Mendelian randomization study. Front. Endocrinol. 15, 1388927 (2024).

Article 

Google Scholar
 

Zhang, L. et al. Alterations of the gut microbiota in patients with diabetic nephropathy. Microbiol. Spectr. 10, e0032422 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Kaye, D. M. et al. Deficiency of prebiotic fiber and insufficient signaling through gut metabolite-sensing receptors leads to cardiovascular disease. Circulation 141, 1393–1403 (2020).

Article 
CAS 
PubMed 

Google Scholar
 

Marques, F. Z. et al. High-fiber diet and acetate supplementation change the gut microbiota and prevent the development of hypertension and heart failure in hypertensive mice. Circulation 135, 964–977 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

Chi, J. et al. Precision probiotics regulate blood glucose, cholesterol, body fat percentage, and weight under eight-week high-fat diet. Metabolites 15, 642 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, D. et al. Short-chain fatty acids in diseases. Cell Commun. Signal. 21, 212 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Kostic, A. D. et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14, 207–215 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Rubinstein, M. R. et al. Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/β-catenin signaling via its FadA adhesin. Cell Host Microbe 14, 195–206 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Liang, J. Q. et al. A probiotic formula for modulation of colorectal cancer risk via reducing CRC-associated bacteria. Cells 12, 1244 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Chowdhury, S. et al. Programmable bacteria induce durable tumor regression and systemic antitumor immunity. Nat. Med. 25, 1057–1063 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655–662 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Franzosa, E. A. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat. Microbiol. 4, 293–305 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Ning, L. et al. Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts. Nat. Commun. 14, 7135 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Govaert, M. et al. Survival of probiotic bacterial cells in the upper gastrointestinal tract and the effect of the surviving population on the colonic microbial community activity and composition. Nutrients 16, 2791 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Cao, F. et al. Engineering clinically relevant probiotics with switchable ‘nano-promoter’ and ‘nano-effector’ for precision tumor therapy. Adv. Mater. 36, e2304257 (2024).

Article 
PubMed 

Google Scholar
 

Mainali, K., Bewick, S., Vecchio-Pagan, B., Karig, D. & Fagan, W. F. Detecting interaction networks in the human microbiome with conditional Granger causality. PLoS Comput. Biol. 15, e1007037 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Angermueller, C., Pärnamaa, T., Parts, L. & Stegle, O. Deep learning for computational biology. Mol. Syst. Biol. 12, 878 (2016).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, Y. et al. Screening antimicrobial peptides and probiotics using multiple deep learning and directed evolution strategies. Acta Pharm. Sin. B 14, 3476–3492 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Hanson, B. et al. Garbage in, garbage out: mitigating risks and maximizing benefits of AI in research. Nature 623, 28–31 (2023).

Article 
CAS 
PubMed 

Google Scholar
 

Wu, G. et al. A core microbiome signature as an indicator of health. Cell 187, 6550–6565.e11 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Passaro, S. et al. Boltz-2: towards accurate and efficient binding affinity prediction. Preprint at bioRxiv https://doi.org/10.1101/2025.06.14.659707 (2025).

Zhao, H. et al. Protein–peptide docking with a rational and accurate diffusion generative model. Nat. Mach. Intell. 7, 1308–1321 (2025).

Article 

Google Scholar
 

Mooney, C., Haslam, N. J., Pollastri, G. & Shields, D. C. Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity. PLoS ONE 7, e45012 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Fernández-Díaz, R. et al. AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors. Bioinformatics 40, btae555 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Du, Z., Ding, X., Xu, Y. & Li, Y. UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity. Brief. Bioinform. 24, bbad135 (2023).

Article 
PubMed 

Google Scholar
 

Pronk, S. et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845–854 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Dominguez, C., Boelens, R. & Bonvin, A. M. J. J. HADDOCK: a protein–protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125, 1731–1737 (2003).

Article 
CAS 
PubMed 

Google Scholar
 

Stark, H. et al. BoltzGen: toward universal binder design. Preprint at bioRxiv https://doi.org/10.1101/2025.11.20.689494 (2025).

Graber, D. et al. Resolving data bias improves generalization in binding affinity prediction. Nat. Mach. Intell. 7, 1713–1725 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Wu, L. et al. Data-driven prediction of colonization outcomes for complex microbial communities. Nat. Commun. 15, 2406 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Carr, A., Baliga, N. S., Diener, C. & Gibbons, S. M. Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut. Cell Syst. 16, 101367 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Heinken, A. et al. Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Nat. Biotechnol. 41, 1320–1331 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Quinn-Bohmann, N. et al. Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the human gut. Preprint at bioRxiv https://doi.org/10.1101/2023.02.28.530516 (2023).

Silva-Andrade, C. et al. A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information. PeerJ 13, e19296 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Gutierrez, M. W. et al. Early-life gut mycobiome core species modulate metabolic health in mice. Nat. Commun. 16, 1467 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Pattaroni, C. et al. Early life inter-kingdom interactions shape the immunological environment of the airways. Microbiome 10, 34 (2022).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Aminian-Dehkordi, J., Parsa, M., Dickson, A. & Mofrad, M. R. K. SIMBA-GNN: mechanistic graph learning for microbiome prediction. npj Syst. Biol. Appl. 12, 8 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Huang, H. et al. The mycobiome as integral part of the gut microbiome: crucial role of symbiotic fungi in health and disease. Gut Microbes 16, 2440111 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Sulaimany, S., Farahmandi, K. & Mafakheri, A. Computational prediction of new therapeutic effects of probiotics. Sci. Rep. 14, 11932 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Matsubara, V. H., Wang, Y., Bandara, H. M. H. N., Mayer, M. P. A. & Samaranayake, L. P. Probiotic lactobacilli inhibit early stages of Candida albicans biofilm development by reducing their growth, cell adhesion, and filamentation. Appl. Microbiol. Biotechnol. 100, 6415–6426 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Thiele, I. et al. Personalized whole-body models integrate metabolism, physiology, and the gut microbiome. Mol. Syst. Biol. 16, e8982 (2020).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Quinn, R. A. et al. Niche partitioning of a pathogenic microbiome driven by chemical gradients. Sci. Adv. 4, eaau1908 (2018).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Mougi, A. pH adaptation stabilizes bacterial communities. npj Biodivers. 3, 32 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Harcombe, W. R. et al. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell Rep. 7, 1104–1115 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

McCoubrey, L. E. et al. Active machine learning for formulation of precision probiotics. Int. J. Pharm. 616, 121568 (2022).

Article 
CAS 
PubMed 

Google Scholar
 

Cenikj, G. et al. From language models to large-scale food and biomedical knowledge graphs. Sci. Rep. 13, 7815 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Shin, E., Bhat, A. G. & Ramanathan, M. Large language models for clinical trial protocol assessments. Clin. Pharmacol. Ther. 119, 393–402 (2026).

Article 
PubMed 

Google Scholar
 

Athaluri, S. A. et al. Exploring the boundaries of reality: investigating the phenomenon of artificial intelligence hallucination in scientific writing through ChatGPT references. Cureus 15, e37432 (2023).

PubMed 
PubMed Central 

Google Scholar
 

Hatem, R., Simmons, B. & Thornton, J. E. A call to address AI ‘hallucinations’ and how healthcare professionals can mitigate their risks. Cureus 15, e44720 (2023).

PubMed 
PubMed Central 

Google Scholar
 

Jiang, J. et al. Artificial intelligence in bioinformatics: a survey. Brief. Bioinform. 26, bbaf576 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Anh-Hoang, D., Tran, V. & Nguyen, L.-M. Survey and analysis of hallucinations in large language models: attribution to prompting strategies or model behavior. Front. Artif. Intell. 8, 1622292 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Lin, S., Hilton, J. & Evans, O. TruthfulQA: measuring how models mimic human falsehoods. In Proc. 60th Annu. Meet. Assoc. Comput. Linguist. 3266–3289 (ACL, 2022).

Zhao, Y. & Zhang, Y. HalluClean: a unified framework to combat hallucinations in LLMs. Proc. AAAI Conf. Artif. Intell. 40, 36092–36100 (2026).


Google Scholar
 

Matsumoto, N. et al. KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models. Bioinformatics 40, btae353 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Gargari, O. K. & Habibi, G. Enhancing medical AI with retrieval-augmented generation: a mini narrative review. Digit. Health 11, 20552076251337177 (2025).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Pan, G., Chodnekar, V., Roy, A. & Wang, H. A cost–benefit analysis of on-premise large language model deployment: breaking even with commercial LLM services. Preprint at https://doi.org/10.48550/arXiv.2509.18101 (2025).

World Health Organization. Ethics and Governance of Artificial Intelligence for Health: Guidance on Large Multi-Modal Models (WHO, 2024).

Baliga, S., Muglikar, S. & Kale, R. Salivary pH: a diagnostic biomarker. J. Indian Soc. Periodontol. 17, 461–465 (2013).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Brinck, J. E. et al. Intestinal pH: a major driver of human gut microbiota composition and metabolism. Nat. Rev. Gastroenterol. Hepatol. 22, 639–656 (2025).

Article 
PubMed 

Google Scholar
 

Lin, Y.-P., Chen, W.-C., Cheng, C.-M. & Shen, C.-J. Vaginal pH value for clinical diagnosis and treatment of common vaginitis. Diagnostics 11, 1996 (2021).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Brooks, S. G., Mahmoud, R. H., Lin, R. R., Fluhr, J. W. & Yosipovitch, G. The skin acid mantle: an update on skin pH. J. Invest. Dermatol. 145, 509–521 (2025).

Article 
CAS 
PubMed 

Google Scholar
 

Dickson, R. P. et al. Radiographic honeycombing and altered lung microbiota in patients with idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 200, 1544–1547 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Nicola, T. et al. A lactobacilli-based inhaled live biotherapeutic product attenuates pulmonary neutrophilic inflammation. Nat. Commun. 15, 7113 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zawistowska-Rojek, A. et al. Evaluating the quality of selected commercial probiotic products, both dietary supplements and foods for special medical purposes. Foods 15, 373 (2026).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Drago, L., Rodighiero, V., Celeste, T., Rovetto, L. & De Vecchi, E. Microbiological evaluation of commercial probiotic products available in the USA in 2009. J. Chemother. 22, 373–377 (2010).

Article 
CAS 
PubMed 

Google Scholar
 

Vesa, T., Pochart, P. & Marteau, P. Pharmacokinetics of Lactobacillus plantarum NCIMB 8826, Lactobacillus fermentum KLD, and Lactococcus lactis MG 1363 in the human gastrointestinal tract. Aliment. Pharmacol. Ther. 14, 823–828 (2000).

Article 
CAS 
PubMed 

Google Scholar
 

Cai, S. et al. Lactobacillus rhamnosus GG activation of dendritic cells and neutrophils depends on the dose and time of exposure. J. Immunol. Res. 2016, 7402760 (2016).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Weese, J. S. & Martin, H. Assessment of commercial probiotic bacterial contents and label accuracy. Can. Vet. J. 52, 43–46 (2011).

PubMed 
PubMed Central 

Google Scholar
 

Oozeer, R. et al. Survival of Lactobacillus casei in the human digestive tract after consumption of fermented milk. Appl. Environ. Microbiol. 72, 5615–5617 (2006).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Arioli, S., Koirala, R., Taverniti, V., Fiore, W. & Guglielmetti, S. Quantitative recovery of viable Lactobacillus paracasei CNCM I-1572 (L. casei DG®) after gastrointestinal passage in healthy adults. Front. Microbiol. 9, 1720 (2018).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Goossens, D. et al. Survival of the probiotic, L. plantarum 299v and its effects on the faecal bacterial flora, with and without gastric acid inhibition. Dig. Liver Dis. 37, 44–50 (2005).

Article 
CAS 
PubMed 

Google Scholar
 

Wang, J., Zhang, J., Liu, W., Zhang, H. & Sun, Z. Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut. npj Biofilms Microbiomes 7, 55 (2021).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Basu, S., Paul, D. K., Ganguly, S., Chatterjee, M. & Chandra, P. K. Efficacy of high-dose Lactobacillus rhamnosus GG in controlling acute watery diarrhea in Indian children: a randomized controlled trial. J. Clin. Gastroenterol. 43, 208–213 (2009).

Article 
PubMed 

Google Scholar
 

Salamat, S., Jahan-Mihan, A., Gharibvand, L., Reza Tabandeh, M. & Mansoori, A. Multi-species synbiotic supplementation increased fecal short chain fatty acids and anti-inflammatory cytokine interleukin-10 in adult men with dyslipidemia; a randomized, double-blind, clinical trial. Cytokine 179, 156608 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Alander, M. et al. Persistence of colonization of human colonic mucosa by a probiotic strain, Lactobacillus rhamnosus GG, after oral consumption. Appl. Environ. Microbiol. 65, 351–354 (1999).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Goossens, D. et al. The effect of Lactobacillus plantarum 299v on the bacterial composition and metabolic activity in faeces of healthy volunteers: a placebo-controlled study on the onset and duration of effects. Aliment. Pharmacol. Ther. 18, 495–505 (2003).

Article 
CAS 
PubMed 

Google Scholar
 

Radicioni, M. et al. Survival of L. casei DG® (Lactobacillus paracasei CNCMI1572) in the gastrointestinal tract of a healthy paediatric population. Eur. J. Nutr. 58, 3161–3170 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Yin, X., Lee, B., Zaragoza, J. & Marco, M. L. Dietary perturbations alter the ecological significance of ingested Lactobacillus plantarum in the digestive tract. Sci. Rep. 7, 7267 (2017).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Maltby, R., Leatham-Jensen, M. P., Gibson, T., Cohen, P. S. & Conway, T. Nutritional basis for colonization resistance by human commensal Escherichia coli strains HS and Nissle 1917 against E. coli O157:H7 in the mouse intestine. PLoS ONE 8, e53957 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Deriu, E. et al. Probiotic bacteria reduce Salmonella typhimurium intestinal colonization by competing for iron. Cell Host Microbe 14, 26–37 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Jankowska, A., Laubitz, D., Antushevich, H., Zabielski, R. & Grzesiuk, E. Competition of Lactobacillus paracasei with Salmonella enterica for adhesion to Caco-2 cells. J. Biomed. Biotechnol. 2008, 357964 (2008).

PubMed 
PubMed Central 

Google Scholar
 

Orlando, A., Linsalata, M., Notarnicola, M., Tutino, V. & Russo, F. Lactobacillus GG restoration of the gliadin induced epithelial barrier disruption: the role of cellular polyamines. BMC Microbiol. 14, 19 (2014).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Guo, S. et al. Secretions of Bifidobacterium infantis and Lactobacillus acidophilus protect intestinal epithelial barrier function. J. Pediatr. Gastroenterol. Nutr. 64, 404–412 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

Gao, J. et al. A novel postbiotic from Lactobacillus rhamnosus GG with a beneficial effect on intestinal barrier function. Front. Microbiol. 10, 477 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Prete, R. et al. Beneficial bile acid metabolism from Lactobacillus plantarum of food origin. Sci. Rep. 10, 1165 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Gui, L. et al. Lactobacillus rhamnosus GG maintains gut microbiota stability and promotes intestinal adaptation via activated intestinal farnesoid X receptor signaling in short bowel syndrome. Commun. Biol. 8, 816 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Yao, L. et al. A selective gut bacterial bile salt hydrolase alters host metabolism. eLife 7, e37182 (2018).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Makishima, M. et al. Identification of a nuclear receptor for bile acids. Science 284, 1362–1365 (1999).

Article 
CAS 
PubMed 

Google Scholar
 

Boonma, P. et al. Probiotic VSL#3 treatment reduces colonic permeability and abdominal pain symptoms in patients with irritable bowel syndrome. Front. Pain Res. 2, 691689 (2021).

Article 

Google Scholar
 

Ahlroos, T. & Tynkkynen, S. Quantitative strain-specific detection of Lactobacillus rhamnosus GG in human faecal samples by real-time PCR. J. Appl. Microbiol. 106, 506–514 (2009).

Article 
CAS 
PubMed 

Google Scholar
 

Sequeira, I. R., Lentle, R. G., Kruger, M. C. & Hurst, R. D. Standardising the lactulose mannitol test of gut permeability to minimise error and promote comparability. PLoS ONE 9, e99256 (2014).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Adriaanse, M. P. M. et al. Serum I-FABP as marker for enterocyte damage in coeliac disease and its relation to villous atrophy and circulating autoantibodies. Aliment. Pharmacol. Ther. 37, 482–490 (2013).

Article 
CAS 
PubMed 

Google Scholar
 

Tibble, J. A., Sigthorsson, G., Foster, R., Forgacs, I. & Bjarnason, I. Use of surrogate markers of inflammation and Rome criteria to distinguish organic from nonorganic intestinal disease. Gastroenterology 123, 450–460 (2002).

Article 
PubMed 

Google Scholar
 

D’Haens, G. et al. Fecal calprotectin is a surrogate marker for endoscopic lesions in inflammatory bowel disease. Inflamm. Bowel Dis. 18, 2218–2224 (2012).

Article 
PubMed 

Google Scholar
 

Borruel, N. et al. Increased mucosal tumour necrosis factor α production in Crohn’s disease can be downregulated ex vivo by probiotic bacteria. Gut 51, 659–664 (2002).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhou, S. et al. Probiotic treatment induces changes in intestinal microbiota but does not alter SCFA levels in peritoneal dialysis patients — a randomized, placebo-controlled trial. Sci. Rep. 14, 31413 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Gibson, G. R., Beatty, E. R., Wang, X. & Cummings, J. H. Selective stimulation of bifidobacteria in the human colon by oligofructose and inulin. Gastroenterology 108, 975–982 (1995).

Article 
CAS 
PubMed 

Google Scholar
 

Kruse, H. P., Kleessen, B. & Blaut, M. Effects of inulin on faecal bifidobacteria in human subjects. Br. J. Nutr. 82, 375–382 (1999).

Article 
CAS 
PubMed 

Google Scholar
 

Anzawa, D. et al. Effects of synbiotics containing Bifidobacterium animalis subsp. lactis GCL2505 and inulin on intestinal bifidobacteria: a randomized, placebo-controlled, crossover study. Food Sci. Nutr. 7, 1828–1837 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar