Enhancements of symbiotic adhesion and antibiotic efficacy observed by the metabolic crosstalk within cell-bacteria cocultured on a microfluidic gut chip

Jingyang Li; Yuxuan Li; Shulang Chen; Gaowa Xing; Yingrui Zhang; Xianli Meng; Yi Zhang; Yukmi Cai; Jin-Ming Lin

doi:10.1016/j.jpha.2026.101641

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Jingyang Li, Yuxuan Li, Shulang Chen, Gaowa Xing, Yingrui Zhang, Xianli Meng, Yi Zhang, Yukmi Cai, Jin-Ming Lin. Enhancements of symbiotic adhesion and antibiotic efficacy observed by the metabolic crosstalk within cell-bacteria cocultured on a microfluidic gut chip[J]. Journal of Pharmaceutical Analysis. doi: 10.1016/j.jpha.2026.101641

Citation:

Jingyang Li, Yuxuan Li, Shulang Chen, Gaowa Xing, Yingrui Zhang, Xianli Meng, Yi Zhang, Yukmi Cai, Jin-Ming Lin. Enhancements of symbiotic adhesion and antibiotic efficacy observed by the metabolic crosstalk within cell-bacteria cocultured on a microfluidic gut chip[J]. Journal of Pharmaceutical Analysis. doi: 10.1016/j.jpha.2026.101641

Citation:

Jingyang Li, Yuxuan Li, Shulang Chen, Gaowa Xing, Yingrui Zhang, Xianli Meng, Yi Zhang, Yukmi Cai, Jin-Ming Lin. Enhancements of symbiotic adhesion and antibiotic efficacy observed by the metabolic crosstalk within cell-bacteria cocultured on a microfluidic gut chip[J]. Journal of Pharmaceutical Analysis. doi: 10.1016/j.jpha.2026.101641

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Enhancements of symbiotic adhesion and antibiotic efficacy observed by the metabolic crosstalk within cell-bacteria cocultured on a microfluidic gut chip

doi: 10.1016/j.jpha.2026.101641

a. State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China;
b. Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China;
c. School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China;
d. Center for Infectious Disease Research, School of Medicine, Tsinghua University Beijing 100084 China

Funds:

This work was supported by National Key R&

D Program of China (Grant No.: 2022YFC3400700), National Natural Science Foundation of China (Grant No.: U23A20520) and the Natural Science Foundation of Sichuan Province (Grant No.: 2024NSFSC0701).

Received Date: Dec. 26, 2025
Accepted Date: Apr. 18, 2026
Rev Recd Date: Apr. 17, 2026
Available Online: Apr. 22, 2026

Abstract

Abstract

The gut cells and symbiotic bacteria play a critical role in maintaining gut health and influencing disease development, with metabolic interactions among its constituents warranting further investigation. In this study, we developed a cell-bacteria coculture system on a microfluidic gut chip to simulate the human gut microenvironment and performed multi-omics analyses to elucidate the metabolic crosstalk within the system. The results revealed that the coculture significantly enhances the adhesion and biofilm formation of symbiotic bacteria to gut epithelial cells through activation of the glucose-pyruvate-acetate metabolic cycle. This coculture promotes glucose consumption and acetate secretion while remaining resilient to antibiotics. Moreover, the coculture protected symbiotic bacterial biofilms from antibiotic-induced disruption, thereby enhancing colonization resistance and improving the efficacy of antibiotics against pathogens. Our findings highlight the importance of cell-bacteria interactions in driving the glucose-pyruvate-acetate metabolic cycle, enhancing symbiotic adhesion, and optimizing antibiotic efficacy.
- Cell-bacteria coculture,
- microfluidic gut chip,
- metabolic crosstalk,
- symbiotic adhesion,
- antibiotics efficacy

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References(71)

References

[1]	F.C. Ross, D. Patangia, G. Grimaud, et al., The interplay between diet and the gut microbiome: implications for health and disease, Nat. Rev. Microbiol. 22 (2024) 671-686.
[2]	K.A. Krautkramer, J. Fan, F. Backhed, Gut microbial metabolites as multi-kingdom intermediates, Nat Rev Microbiol. 19 (2021) 77-94.
[3]	R.N. Carmody, J.E. Bisanz, Roles of the gut microbiome in weight management, Nat. Rev. Microbiol. 21 (2023) 535-550.
[4]	Y.E. Martinez-Lopez, D.A. Esquivel-Hernandez, J.P. Sanchez-Castaneda, et al., Type 2 diabetes, gut microbiome, and systems biology: A novel perspective for a new era, Gut Microbes 14 (2022), 2111952.
[5]	S. Ha, V.W. Wong, X. Zhang, et al., Interplay between gut microbiome, host genetic and epigenetic modifications in MASLD and MASLD-related hepatocellular carcinoma, Gut 74 (2025) 141-152.
[6]	M. Lee, E.B. Chang, Inflammatory bowel diseases (IBD) and the microbiome: searching the crime scene for clues, Gastroenterology 160 (2021) 524-537.
[7]	N. Daniel, F. Genua, M. Jenab, et al., The role of the gut microbiome in the development of hepatobiliary cancers, Hepatology 80 (2024) 1252-1269.
[8]	C.C. Wong, J. Yu, Gut microbiota in colorectal cancer development and therapy, Nat. Rev. Clin. Oncol. 20 (2023) 429-452.
[9]	Y. Tong, H. Gao, Q. Qi, et al., High fat diet, gut microbiome and gastrointestinal cancer, Theranostics 11 (2021) 5889-5910.
[10]	S. Moossavi, M.C. Arrieta, A. Sanati-Nezhad, et al., Gut-on-chip for ecological and causal human gut microbiome research, Trends Microbiol. 30 (2022) 710-721.
[11]	M. Lucchetti, K.O. Aina, L. Grandmougin, et al., An organ-on-chip platform for simulating drug metabolism along the gut-liver axis, Adv. Healthc. Mater. 13 (2024), 2303943.
[12]	A. Kriaa, V. Mariaule, C. De Rudder, et al., From animal models to gut-on-chip: the challenging journey to capture inter-individual variability in chronic digestive disorders, Gut Microbes 16 (2024), 2333434.
[13]	L. Sardelli, M. Campanile, L. Boeri, et al., A novel on-a-chip system with a 3D-bioinspired gut mucus suitable to investigate bacterial endotoxins dynamics, Mater. Today Bio 24 (2024), 100898.
[14]	F. Siwczak, E. Loffet, M. Kaminska, et al., Intestinal stem cell-on-chip to study human host-microbiota interaction, Front. Immunol. 12 (2021), 798552.
[15]	V. De Gregorio, C. Sgambato, F. Urciuolo, et al., Immunoresponsive microbiota-gut-on-chip reproduces barrier dysfunction, stromal reshaping and probiotics translocation under inflammation, Biomaterials 286 (2022), 121573.
[16]	S. Jalili-Firoozinezhad, F.S. Gazzaniga, E.L. Calamari, et al., A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip, Nat. Biomed. Eng. 3 (2019) 520-531.
[17]	M. Horne, I. Woolley, J.S.Y. Lau, The use of long-term antibiotics for suppression of bacterial infections, Clin. Infect. Dis. 79 (2024) 848-854.
[18]	L. Maier, C.V. Goemans, J. Wirbel, et al., Unravelling the collateral damage of antibiotics on gut bacteria, Nature 599 (2021) 120-124.
[19]	H. Szajewska, K.P. Scott, T. de Meij, et al., Antibiotic-perturbed microbiota and the role of probiotics, Nat. Rev. Gastroenterol. Hepatol. 22 (2025) 155-172.
[20]	R.Y.K. Chang, S.C. Nang, H.K. Chan, et al., Novel antimicrobial agents for combating antibiotic-resistant bacteria, Adv. Drug. Deliv. Rev. 187 (2022), 114378.
[21]	P. Piewngam, M. Otto, Staphylococcus aureus colonisation and strategies for decolonisation, Lancet Microbe 5 (2024) e606-e618.
[22]	P. Paone, P.D. Cani, Mucus barrier, mucins and gut microbiota: The expected slimy partners? Gut 69 (2020) 2232-2243.
[23]	M.R. Kudelka, S.R. Stowell, R.D. Cummings, et al., Intestinal epithelial glycosylation in homeostasis and gut microbiota interactions in IBD, Nat. Rev. Gastroenterol. Hepatol. 17 (2020) 597-617.
[24]	Y. Zhang, Y. Cai, X. Jin, et al., Persistent glucose consumption under antibiotic treatment protects bacterial community, Nat. Chem. Biol. 21 (2025) 238-246.
[25]	Y. Zhang, Y. Cai, B. Zhang, et al., Spatially structured exchange of metabolites enhances bacterial survival and resilience in biofilms, Nat. Commun. 15 (2024), 7575.
[26]	Y. Zhang, Y. Cai, Z. Chen, Community-specific diffusion characteristics determine resistance of biofilms to oxidative stress, Sci. Adv. 9 (2023), eade2610.
[27]	W. Shin, H.J. Kim, 3D in vitro morphogenesis of human intestinal epithelium in a gut-on-a-chip or a hybrid chip with a cell culture insert, Nat. Protoc. 17 (2022) 910-939.
[28]	Y. Jang, H. Kim, J. Oh, An array of carbon nanofiber bundle_based 3D in vitro intestinal microvilli for mimicking functional and physical activities of the small intestine, Small 20 (2024), 2404842.
[29]	A.S. Riegert, F.M. Raushel, Functional and structural characterization of the UDP-glucose dehydrogenase involved in capsular polysaccharide biosynthesis from Campylobacter jejuni, Biochemistry 60 (2021) 725-734.
[30]	S. van Harten, R. Brito, A.M. Almeida, et al., Gene expression of regulatory enzymes involved in the intermediate metabolism of sheep subjected to feed restriction, Animal 7 (2013) 439-455.
[31]	J.J. Kenyon, S.Y.N. Senchenkova, A.S. Shashkov, et al., K17 capsular polysaccharide produced by Acinetobacter baumannii isolate G7 contains an amide of 2-acetamido-2-deoxy-d-galacturonic acid with d-alanine, Int. J. Biol. Macromol. 144 (2020) 857-862.
[32]	D. Cimini, R. Russo, S. D'Ambrosio, et al., Physiological characterization and quantitative proteomic analyses of metabolically engineered E. coli K4 strains with improved pathways for capsular polysaccharide biosynthesis, Biotechnol. Bioeng. 115 (2018) 1801-1814.
[33]	D. Wang, G.C. Fletcher, D. Gagic, et al., Comparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus, Food Res. Int. 166 (2023), 112605.
[34]	Y. Li, H. Yao, S. Chen, et al., Effect of tryptophan metabolites on cell damage revealed by bacteria-cell interactions in hydrogel microspheres, Anal. Chem. (2023), acs.analchem.2c04355.
[35]	Z. Wu, Y. Zheng, L. Lin, et al., Multicompartmental hydrogel microspheres as a tool for multicomponent analysis, Anal. Chem. 95 (2023) 11047-11051.
[36]	M. Lucchetti, G. Werr, S. Johansson, et al., Integration of multiple flexible electrodes for real-time detection of barrier formation with spatial resolution in a gut-on-chip system, Microsyst. Nanoeng. 10 (2024), 18.
[37]	A. Boquet-Pujadas, T. Feaugas, A. Petracchini, et al., 4D live imaging and computational modeling of a functional gut-on-a-chip evaluate how peristalsis facilitates enteric pathogen invasion, Sci. Adv. 8 (2022), eabo5767.
[38]	J. Lee, N. Menon, C.T. Lim, Dissecting gut-microbial community interactions using a gut microbiome-on-a-chip, Adv. Sci. 11 (2024), 2302113.
[39]	W. Wang, Y. Liu, Z. Yao, et al., A microfluidic-based gut-on-a-chip model containing the gut microbiota of patients with depression reveals physiological characteristics similar to depression, Lab a Chip 24 (2024) 2537-2550.
[40]	M.S. Jeon, Y.Y. Choi, S.J. Mo, et al., Contributions of the microbiome to intestinal inflammation in a gut-on-a-chip, Nano Convergence 9 (2022), 8.
[41]	J. Elzinga, M. Grouls, G.J.E.J. Hooiveld, et al., Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions, Arch. Toxicol. 97 (2023) 737-753.
[42]	M.T. Nelson, M.R. Charbonneau, H.G. Coia, et al., Characterization of an engineered live bacterial therapeutic for the treatment of phenylketonuria in a human gut-on-a-chip, Nat. Commun. 12 (2021), 2805.
[43]	A. Apostolou, R.A. Panchakshari, A. Banerjee, et al., A novel microphysiological colon platform to decipher mechanisms driving human intestinal permeability, Cell. Mol. Gastroenterol. Hepatol. 12 (2021) 1719-1741.
[44]	M.T. Nelson, H.G. Coia, C. Holt, et al., Evaluation of human performance aiding live synthetically engineered bacteria in a gut-on-a-chip, ACS Biomater. Sci. Eng. 9 (2023) 5136-5150.
[45]	E.J. Howard, T.K.T. Lam, F.A. Duca, The gut microbiome: connecting diet, glucose homeostasis, and disease, Annu. Rev. Med. 73 (2022) 469-481.
[46]	W. Yang, T. Yu, X. Liu, et al., Microbial metabolite butyrate modulates granzyme B in tolerogenic IL-10 producing Th1 cells to regulate intestinal inflammation, Gut Microbes 16 (2024), 2363020.
[47]	T. Takeuchi, E. Miyauchi, T. Kanaya, et al., Acetate differentially regulates IgA reactivity to commensal bacteria, Nature 595 (2021) 560-564.
[48]	P. Millard, T. Gosselin-Monplaisir, S. Uttenweiler-Joseph, et al., Acetate is a beneficial nutrient for E. coli at low glycolytic flux, EMBO J. 42 (2023), EMBJ2022113079.
[49]	J. Wu, Y. Li, Z. Cai, et al., Pyruvate-associated acid resistance in bacteria, Appl. Environ. Microbiol. 80 (2014) 4108-4113.
[50]	B. Wei, S. Shin, D. LaPorte, et al., Global regulatory mutations in csrA and rpoS cause severe central carbon stress in Escherichia coli in the presence of acetate, J. Bacteriol. 182 (2000) 1632-1640.
[51]	A. Alvarez-Ordonez, M. Begley, C. Hill, Selection for loss of RpoS in Cronobacter sakazakii by growth in the presence of acetate as a carbon source, Appl. Environ. Microbiol. 79 (2013) 2099-2102.
[52]	L. Pan, Y. Sun, X. Dong, et al., Infant feces-derived Lactobacillus gasseri FWJL-4 mitigates experimental necrotizing enterocolitis via acetate production, Gut Microbes 16 (2024), 2430541.
[53]	Q. Song, X. Zhang, W. Liu, et al., Bifidobacterium pseudolongum-generated acetate suppresses non-alcoholic fatty liver disease-associated hepatocellular carcinoma, J. Hepatol. 79 (2023) 1352-1365.
[54]	L. Hu, L. Sun, C. Yang, et al., Gut microbiota-derived acetate attenuates lung injury induced by influenza infection via protecting airway tight junctions, J. Transl. Med. 22 (2024), 570.
[55]	H. North, M. McLaughlin, A. Fiebig, et al., The Caulobacter NtrB-NtrC two-component system bridges nitrogen assimilation and cell development, J. Bacteriol. 205 (2023) e00181-e00123.
[56]	M.E.V. Johansson, H. Sjovall, G.C. Hansson, The gastrointestinal mucus system in health and disease, Nat. Rev. Gastroenterol. Hepatol. 10 (2013) 352-361.
[57]	J. Zhang, Q. Yu, D. Jiang, et al., Epithelial Gasdermin D shapes the host-microbial interface by driving mucus layer formation, Sci. Immunol. 7 (2022), eabk2092.
[58]	B.O. Schroeder, Fight them or feed them: How the intestinal mucus layer manages the gut microbiota, Gastroenterol. Rep. 7 (2019) 3-12.
[59]	Q. Li, R. Wang, Z. Ma, et al., Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants, ISME J. 16 (2022) 2535-2546.
[60]	Y. Nagara, D. Fujii, T. Takada, et al., Selective induction of human gut-associated acetogenic/butyrogenic microbiota based on specific microbial colonization of indigestible starch granules, ISME J. 16 (2022) 1502-1511.
[61]	F. Spragge, E. Bakkeren, M.T. Jahn, et al., Microbiome diversity protects against pathogens by nutrient blocking, Science 382 (2023), eadj3502.
[62]	H. Goodrich-Blair, Interactions of host-associated multispecies bacterial communities, Periodontol. 2000 86 (2021) 14-31.
[63]	A. Styczynski, C. Herzig, U.O. Luvsansharav,et al., Using colonization to understand the burden of antimicrobial resistance across low- and middle-income countries, Clin. Infect. Dis. 77 (2023) S70-S74.
[64]	N.S. Isles, A. Mu, J.C. Kwong, et al., Gut microbiome signatures and host colonization with multidrug-resistant bacteria, Trends Microbiol. 30 (2022) 853-865.
[65]	W. Guo, X. Zhou, X. Li, et al., Depletion of gut microbiota impairs gut barrier function and antiviral immune defense in the liver, Front Immunol. 12 (2021) 636803.
[66]	N.K. Das, A.J. Schwartz, G. Barthel, et al., Microbial metabolite signaling is required for systemic iron homeostasis, Cell Metab. 31 (2020) 115-130.e6.
[67]	M. Furuichi, T. Kawaguchi, M.M. Pust, et al., Commensal consortia decolonize Enterobacteriaceae via ecological control, Nature. 633 (2024) 878-886.
[68]	S. Singh, O.K. Koo, A Comprehensive review exploring the protective role of specific commensal gut bacteria against Salmonella, Pathogens 13 (2024), 642.
[69]	C.G. Cole, Z.J. Zhang, S.R. Dommaraju, et al., Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance, Cell Host Microbe 33 (2025) 2100-2114.e6.
[70]	S.M. Holmberg, R.H. Feeney, V. Prasoodanan P.K., et al., The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids, Nat. Commun. 15 (2024), 3502.
[71]	L. Fu, M. Wang, D. Li, et al., Microbial metabolites short chain fatty acids, tight junction, gap junction, and reproduction: A review, Front. Cell Dev. Biol. 13 (2025), 1624415.