Barnich, N. et al. Beneficial effects of natural mineral waters on intestinal inflammation and the mucosa-associated microbiota. Int. J. Mol. Sci. 22, 4336 (2021).
Böhmer, H., Müller, H. & Resch, K. L. Calcium supplementation with calcium-rich mineral waters: a systematic review and meta-analysis of its bioavailability. Osteoporos. Int. 11, 938–943 (2000).
Peng, H., Lu, T. T., Xiong, S., Ferrer, A. S. N. & Wang, Y. X. Calcium and magnesium in China’s public drinking water and their daily estimated average requirements. Environ. Geochem. Health 45, 3447–3464 (2023).
Willis, J. R. et al. Citizen science charts two major ‘stomatotypes’ in the oral microbiome of adolescents and reveals links with habits and drinking water composition. Microbiome 6, 218 (2018).
Guo, H. et al. High-efficiency capture and recovery of anionic perfluoroalkyl substances from water using PVA/PDDA nanofibrous membranes with near-zero energy consumption. Environ. Sci. Technol. Lett. 8, 350–355 (2021).
Chen, Y. et al. Protective effects of selenium nanoparticle-enriched Lactococcus lactis NZ9000 against enterotoxigenic Escherichia coli K88-induced intestinal barrier damage in mice. Appl. Environ. Microbiol. 87, e01636-21 (2021).
Liu, X. et al. Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome. Nat. Genet. 54, 52–61 (2022).
Chen, J. et al. Metasilicate-based alkaline mineral water confers diarrhea resistance in maternally separated piglets via the microbiota-gut interaction. Pharmacol. Res. 187, 106580 (2023).
Bowyer, R. C. E. et al. Associations between UK tap water and gut microbiota composition suggest the gut microbiome as a potential mediator of health differences linked to water quality. Sci. Total Environ. 739, 139697 (2020).
Vanhaecke, T., Bretin, O., Poirel, M. & Tap, J. Drinking water source and intake are associated with distinct gut microbiota signatures in US and UK populations. J. Nutr. 152, 171–182 (2022).
Wotzka, S. Y., Nguyen, B. D. & Hardt, W. D. Salmonella Typhimurium diarrhea reveals basic principles of enteropathogen infection and disease-promoted DNA exchange. Cell Host Microbe 21, 443–454 (2017).
Liou, M. J. et al. Host cells subdivide nutrient niches into discrete biogeographical microhabitats for gut microbes. Cell Host Microbe 30, 836–847 (2022).
Bratburd, J. R. et al. Gut microbial and metabolic responses to Salmonella enterica serovar Typhimurium and Candida albicans. mBio 9, 02032–18 (2018).
von Strempel, A. et al. Bacteriophages targeting protective commensals impair resistance against Salmonella Typhimurium infection in gnotobiotic mice. PLoS Pathog. 19, e1011600 (2023).
Cianfanelli, F. R., Monlezun, L. & Coulthurst, S. J. Aim, load, fire: the type VI secretion system, a bacterial nanoweapon. Trends Microbiol. 24, 51–62 (2016).
Sana, T. G. et al. Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut. Proc. Natl Acad. Sci. USA 113, E5044–E5051 (2016).
Weiss, A. S. et al. In vitro interaction network of a synthetic gut bacterial community. ISME J. 16, 1095–1109 (2022).
Zhang, J. et al. SecReT6 update: a comprehensive resource of bacterial type VI secretion systems. Sci. China Life Sci. 66, 626–634 (2023).
Lories, B. et al. Biofilm bacteria use stress responses to detect and respond to competitors. Curr. Biol. 30, 1231–1244 (2020).
Lories, B., Belpaire, T. E. R., Smeets, B. & Steenackers, H. P. Competition quenching strategies reduce antibiotic tolerance in polymicrobial biofilms. npj Biofilms Microbiomes 10, 23 (2024).
Speare, L., Jackson, A. & Septer, A. N. Calcium promotes T6SS-mediated killing and aggregation between competing symbionts. Microbiol. Spectr. 10, e01397-22 (2022).
Tang, M.-X. et al. Abiotic factors modulate interspecies competition mediated by the type VI secretion system effectors in Vibrio cholerae. ISME J. 16, 1765–1775 (2022).
Yang, J. et al. Xylooligosaccharides ameliorate insulin resistance by increasing Akkermansia muciniphila and improving intestinal barrier dysfunction in gestational diabetes mellitus mice. Food Funct. 15, 3122–3129 (2024).
Yoo, W. et al. Salmonella Typhimurium expansion in the inflamed murine gut is dependent on aspartate derived from ROS-mediated microbiota lysis. Cell Host Microbe 32, 887–899 (2024).
Jacobson, A. et al. A gut commensal-produced metabolite mediates colonization resistance to Salmonella infection. Cell Host Microbe 24, 296–307 (2018).
Jaeggi, T. et al. Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants. Gut 64, 731–742 (2015).
Bachmann, V. et al. Bile salts modulate the mucin-activated type VI secretion system of pandemic Vibrio cholerae. PLoS Negl. Trop. Dis. 9, e0004031 (2015).
Li, S. et al. c-di-GMP inhibits the DNA binding activity of H-NS in Salmonella. Nat. Commun. 14, 7502 (2023).
Li, S. et al. Autoinducer-2 and bile salts induce c-di-GMP synthesis to repress the T3SS via a T3SS chaperone. Nat. Commun. 13, 6684 (2022).
Pontes, M. H., Lee, E.-J., Choi, J. & Groisman, E. A. Salmonella promotes virulence by repressing cellulose production. Proc. Natl Acad. Sci. USA 112, 5183–5188 (2015).
Ferreira, R. M. et al. Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota. Gut 67, 226–236 (2018).
Wotzka, S. Y. et al. Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. Nat. Microbiol. 4, 2164–2174 (2019).
Walker, G. T. & Raffatellu, M. Salmonella respiration turns the tables on propionate. Trends Microbiol. 30, 206–208 (2022).
Corte-Real, J. & Bohn, T. Interaction of divalent minerals with liposoluble nutrients and phytochemicals during digestion and influences on their bioavailability – a review. Food Chem. 252, 285–293 (2018).
Funabashi, M. et al. A metabolic pathway for bile acid dehydroxylation by the gut microbiome. Nature 582, 566–570 (2020).
Wu, Q. et al. Intestinal hypoxia-inducible factor 2α regulates lactate levels to shape the gut microbiome and alter thermogenesis. Cell Metab. 33, 1988–2003 (2021).
Lee, E. J., Pontes, M. H. & Groisman, E. A. A bacterial virulence protein promotes pathogenicity by inhibiting the bacterium’s own F1F0 ATP synthase. Cell 154, 146–156 (2013).
Mills, E., Petersen, E., Kulasekara, B. R. & Miller, S. I. A direct screen for c-di-GMP modulators reveals a Salmonella Typhimurium periplasmic ʟ-arginine-sensing pathway. Sci. Signal 8, ra57 (2015).
Pickard, J. M. et al. Dietary amino acids regulate Salmonella colonization via microbiota-dependent mechanisms in the mouse gut. Nat. Commun. 16, 4225 (2025).
Lopes, A. A. et al. Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump. mBio 15, e03488-23 (2024).
Slipko, K. et al. Removal of extracellular free DNA and antibiotic resistance genes from water and wastewater by membranes ranging from microfiltration to reverse osmosis. Water Res. 164, 114916 (2019).
Mukherjee, A. G. et al. Elimination of microplastics from the aquatic milieu: a dream to achieve. Chemosphere 303, 135232 (2022).
Li, D. P. et al. Oral magnesium prevents acetaminophen-induced acute liver injury by modulating microbial metabolism. Cell Host Microbe 32, 48–62 (2024).
McLaughlin, P. A. et al. Inflammatory monocytes provide a niche for Salmonella expansion in the lumen of the inflamed intestine. PLoS Pathog. 15, e1007847 (2019).
Ivanov, I. I. et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485–498 (2009).
Ten Bruggencate, S. J., Bovee-Oudenhoven, I. M., Lettink-Wissink, M. L., Katan, M. B. & Van Der Meer, R. Dietary fructo-oligosaccharides and inulin decrease resistance of rats to Salmonella: protective role of calcium. Gut 53, 530–535 (2004).
Miller, A. L. et al. Nitrate is an environmental cue in the gut for Salmonella enterica serovar Typhimurium biofilm dispersal through curli repression and flagellum activation via cyclic-di-GMP signaling. mBio 13, e02886-21 (2022).
Crawford, R. W. et al. Very long O-antigen chains enhance fitness during Salmonella-induced colitis by increasing bile resistance. PLoS Pathog. 8, e1002918 (2012).
Liu, S. J. et al. Metabolomics and proteomics reveal blocking argininosuccinate synthetase 1 alleviates colitis in mice. Nat. Commun. 16, 6983 (2025).
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).
Chen, S. B. et al. Colonization mediated by T6SS-ClpV disrupts host gut microbiota and enhances virulence of Salmonella enterica serovar Typhimurium. J. Agric. Food Chem. 72, 19155–19166 (2024).
Yang, L. L. et al. Oligoribonuclease mediates high adaptability of P. aeruginosa through metabolic conversion. BMC Microbiol. 24, 25 (2024).
Ren, Y. et al. Majorbio Cloud: a one-stop, comprehensive bioinformatic platform for multiomics analyses. iMeta 1, e12 (2022).
Wu, M. et al. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science 350, aac5992 (2015).
Wang, X. et al. Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria. Microbiome 7, 109 (2019).