The role of the gut microbiome in human health and disease is being increasingly recognized. Gut microbes (including bacteria, fungi and viruses) can be genetically modified to diagnose (as biosensors) and treat (detoxification, controlled biosynthesis and precision targeting) the dysbiosis of the microbiome, which has been linked to several cancers and metabolic, autoimmune and infectious diseases. However, conventional manipulation of single microbial strains is often insufficient, and engineering a mutually supportive and collaborative network of gut microbes — ‘a keystone consortium’ — could be more effective. In this Review, we summarize gut microbiome engineering strategies against selected diseases and critically discuss their translational potential. We focus mainly on genetic engineering approaches, but we also discuss complementary strategies such as encapsulation, coupling with electronic devices, orthogonal diet engineering and faecal microbiota transplantation.
The human gastrointestinal (GI) tract contains thousands of microbial species, including bacteria, fungi and viruses, the dysbiosis of which has been linked to the pathogenesis of many diseases.
The microbiome can be engineered to treat various pathologies including cancer, metabolic and autoimmune diseases.
‘Holistic’ modulation of the gut microbiome through orthogonal approaches and/or engineering mutually supportive and collaborative networks of gut microbes is an emerging and promising alternative to engineering single microbes.
Proper biocontainment and precision targeting are among the main challenges to be overcome for the clinical translation of gut microbiome engineering strategies.
This is a preview of subscription content, access via your institution
Subscribe to this journal
Receive 12 digital issues and online access to articles
$99.00 per year
only $8.25 per issue
Rent or buy this article
Prices vary by article type
Prices may be subject to local taxes which are calculated during checkout
Lynch, S. V. & Pedersen, O. The human intestinal microbiome in health and disease. N. Engl. J. Med. 375, 2369–2379 (2016). This article reviews the role of the gut microbiome in human health and disease.
Zuo, T., Kamm, M. A., Colombel, J. F. & Ng, S. C. Urbanization and the gut microbiota in health and inflammatory bowel disease. Nat. Rev. Gastroenterol. Hepatol. 15, 440–452 (2018).
Postler, T. S. & Ghosh, S. Understanding the holobiont: how microbial metabolites affect human health and shape the immune system. Cell Metab. 26, 110–130 (2017).
Neish, A. S. Microbes in gastrointestinal health and disease. Gastroenterology 136, 65–80 (2009).
Grenham, S., Clarke, G., Cryan, J. F. & Dinan, T. G. Brain–gut–microbe communication in health and disease. Front. Physiol. 2, 94 (2011).
Arnold, J. W., Roach, J. & Azcarate-Peril, M. A. Emerging technologies for gut microbiome research. Trends Microbiol. 24, 887–901 (2016).
Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D. & Lawley, T. D. Massive expansion of human gut bacteriophage diversity. Cell 184, 1098–1109.e1099 (2021).
Sokol, H. et al. Fungal microbiota dysbiosis in IBD. Gut 66, 1039–1048 (2017).
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).
Sommer, F. & Backhed, F. The gut microbiota — masters of host development and physiology. Nat. Rev. Microbiol. 11, 227–238 (2013).
Pinero-Lambea, C., Ruano-Gallego, D. & Fernandez, L. A. Engineered bacteria as therapeutic agents. Curr. Opin. Biotechnol. 35, 94–102 (2015).
Wu, G., Zhao, N., Zhang, C., Lam, Y. Y. & Zhao, L. Guild-based analysis for understanding gut microbiome in human health and diseases. Genome Med. 13, 22 (2021).
Zhao, L. et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science 359, 1151–1156 (2018).
Isabella, V. M. et al. Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria. Nat. Biotechnol. 36, 857–864 (2018).
Kurtz, C. B. et al. An engineered E. coli Nissle improves hyperammonemia and survival in mice and shows dose-dependent exposure in healthy humans. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.aau7975 (2019).
Zhao, R. et al. Engineered Escherichia coli Nissle 1917 with urate oxidase and an oxygen-recycling system for hyperuricemia treatment. Gut Microbes 14, 2070391 (2022).
Adolfsen, K. J. et al. Improvement of a synthetic live bacterial therapeutic for phenylketonuria with biosensor-enabled enzyme engineering. Nat. Commun. 12, 6215 (2021).
Puurunen, M. K. et al. Safety and pharmacodynamics of an engineered E. coli Nissle for the treatment of phenylketonuria: a first-in-human phase 1/2a study. Nat. Metab. 3, 1125–1132 (2021).
Pontes, D. S. et al. Lactococcus lactis as a live vector: heterologous protein production and DNA delivery systems. Protein Expr. Purif. 79, 165–175 (2011).
Hidalgo-Cantabrana, C., Goh, Y. J., Pan, M., Sanozky-Dawes, R. & Barrangou, R. Genome editing using the endogenous type I CRISPR–Cas system in Lactobacillus crispatus. Proc. Natl Acad. Sci. USA 116, 15774–15783 (2019).
Zhou, D. et al. CRISPR/Cas9-assisted seamless genome editing in Lactobacillus plantarum and its application in N-acetylglucosamine production. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.01367-19 (2019).
Goh, Y. J. & Barrangou, R. Portable CRISPR-Cas9(N) system for flexible genome engineering in Lactobacillus acidophilus, Lactobacillus gasseri, and Lactobacillus paracasei. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.02669-20 (2021).
Huang, H., Song, X. & Yang, S. Development of a RecE/T-assisted CRISPR–Cas9 toolbox for Lactobacillus. Biotechnol. J. 14, e1800690 (2019).
Myrbraten, I. S. et al. CRISPR interference for rapid knockdown of essential cell cycle genes in Lactobacillus plantarum. mSphere https://doi.org/10.1128/mSphere.00007-19 (2019).
Steidler, L. et al. Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science 289, 1352–1355 (2000).
Chappell, T. C. & Nair, N. U. Engineered lactobacilli display anti-biofilm and growth suppressing activities against Pseudomonas aeruginosa. npj Biofilms Microbiomes 6, 48 (2020).
Mao, N., Cubillos-Ruiz, A., Cameron, D. E. & Collins, J. J. Probiotic strains detect and suppress cholera in mice. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.aao2586 (2018).
Taniguchi, S. In situ delivery and production system (iDPS) of anti-cancer molecules with gene-engineered bifidobacterium. J. Pers. Med. https://doi.org/10.3390/jpm11060566 (2021).
Carvalho, A. L. et al. Use of bioengineered human commensal gut bacteria-derived microvesicles for mucosal plague vaccine delivery and immunization. Clin. Exp. Immunol. 196, 287–304 (2019).
Hickey, C. A. et al. Colitogenic Bacteroides thetaiotaomicron antigens access host immune cells in a sulfatase-dependent manner via outer membrane vesicles. Cell Host Microbe 17, 672–680 (2015).
Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 568, 499–504 (2019).
Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2021).
McCarty, N. S. & Ledesma-Amaro, R. Synthetic biology tools to engineer microbial communities for biotechnology. Trends Biotechnol 37, 181–197 (2019).
Riglar, D. T. & Silver, P. A. Engineering bacteria for diagnostic and therapeutic applications. Nat. Rev. Microbiol. 16, 214–225 (2018).
Jin, W. B. et al. Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome. Cell 185, 547–562 e522 (2022).
Sun, Z., Baur, A., Zhurina, D., Yuan, J. & Riedel, C. U. Accessing the inaccessible: molecular tools for bifidobacteria. Appl. Environ. Microbiol. 78, 5035–5042 (2012).
Zuo, F., Chen, S. & Marcotte, H. Engineer probiotic bifidobacteria for food and biomedical applications — current status and future prospective. Biotechnol. Adv. 45, 107654 (2020).
Sekirov, I., Russell, S. L., Antunes, L. C. & Finlay, B. B. Gut microbiota in health and disease. Physiol. Rev. 90, 859–904 (2010).
Durmusoglu, D. et al. In situ biomanufacturing of small molecules in the mammalian gut by probiotic Saccharomyces boulardii. ACS Synth Biol 10, 1039–1052 (2021).
Hudson, L. E. et al. Functional heterologous protein expression by genetically engineered probiotic yeast Saccharomyces boulardii. PLoS One 9, e112660 (2014).
Scott, B. M. et al. Self-tunable engineered yeast probiotics for the treatment of inflammatory bowel disease. Nat. Med. 27, 1212–1222 (2021). This article describes how engineered microbes self-regulate the expression of target proteins according to the surrounding environment.
Zhang, J. et al. A microbial supply chain for production of the anti-cancer drug vinblastine. Nature 609, 341–347 (2022). This article shows the predominance of engineering fungi for the de novo synthesis of complex, multistep molecules.
Cao, Z. et al. The gut virome: a new microbiome component in health and disease. eBioMedicine 81, 104113 (2022).
Salmond, G. P. & Fineran, P. C. A century of the phage: past, present and future. Nat. Rev. Microbiol. 13, 777–786 (2015).
Kilcher, S. & Loessner, M. J. Engineering bacteriophages as versatile biologics. Trends Microbiol. 27, 355–367 (2019).
Martel, B. & Moineau, S. CRISPR–Cas: an efficient tool for genome engineering of virulent bacteriophages. Nucleic Acids Res. 42, 9504–9513 (2014).
Marinelli, L. J. et al. BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes. PLoS One 3, e3957 (2008).
Shin, J., Jardine, P. & Noireaux, V. Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS Synth. Biol. 1, 408–413 (2012).
Kilcher, S., Studer, P., Muessner, C., Klumpp, J. & Loessner, M. J. Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria. Proc. Natl Acad. Sci. USA 115, 567–572 (2018).
Ando, H., Lemire, S., Pires, D. P. & Lu, T. K. Engineering modular viral scaffolds for targeted bacterial population editing. Cell Syst. 1, 187–196 (2015).
Lu, T. K. & Collins, J. J. Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl Acad. Sci. USA 104, 11197–11202 (2007).
Bikard, D. et al. Exploiting CRISPR–Cas nucleases to produce sequence-specific antimicrobials. Nat. Biotechnol. 32, 1146–1150 (2014).
Dunne, M. et al. Reprogramming bacteriophage host range through structure-guided design of chimeric receptor binding proteins. Cell Rep. 29, 1336–1350.e1334 (2019).
Bertozzi Silva, J., Storms, Z. & Sauvageau, D. Host receptors for bacteriophage adsorption. FEMS Microbiol. Lett. https://doi.org/10.1093/femsle/fnw002 (2016).
Donath, E. Biosensors: Viruses for ultrasensitive assays. Nat. Nanotechnol. 4, 215–216 (2009).
Park, J. S. et al. A highly sensitive and selective diagnostic assay based on virus nanoparticles. Nat. Nanotechnol. 4, 259–264 (2009).
Yeh, M. T. et al. Engineering the live-attenuated polio vaccine to prevent reversion to virulence. Cell Host Microbe 27, 736–751 e738 (2020).
Vesikari, T. et al. Safety and efficacy of a pentavalent human-bovine (WC3) reassortant rotavirus vaccine. N. Engl. J. Med. 354, 23–33 (2006).
De Vos, B. et al. Live attenuated human rotavirus vaccine, RIX4414, provides clinical protection in infants against rotavirus strains with and without shared G and P genotypes: integrated analysis of randomized controlled trials. Pediatr. Infect. Dis. J. 28, 261–266 (2009).
Vela Ramirez, J. E., Sharpe, L. A. & Peppas, N. A. Current state and challenges in developing oral vaccines. Adv. Drug Deliv. Rev. 114, 116–131 (2017).
Taddio, A. et al. Survey of the prevalence of immunization non-compliance due to needle fears in children and adults. Vaccine 30, 4807–4812 (2012).
Lin, I. Y., Van, T. T. & Smooker, P. M. Live-attenuated bacterial vectors: tools for vaccine and therapeutic agent delivery. Vaccines 3, 940–972 (2015).
Dabrowska, K. Phage therapy: what factors shape phage pharmacokinetics and bioavailability? Systematic and critical review. Med. Res. Rev. 39, 2000–2025 (2019).
Stavropoulou, E. & Bezirtzoglou, E. Probiotics in medicine: a long debate. Front. Immunol. 11, 2192 (2020).
Freedman, S. B. et al. Multicenter trial of a combination probiotic for children with gastroenteritis. N. Engl. J. Med. 379, 2015–2026 (2018).
Cristofori, F., Indrio, F., Miniello, V. L., De Angelis, M. & Francavilla, R. Probiotics in celiac disease. Nutrients https://doi.org/10.3390/nu10121824 (2018).
Stenuit, B. & Agathos, S. N. Deciphering microbial community robustness through synthetic ecology and molecular systems synecology. Curr. Opin. Biotechnol. 33, 305–317 (2015).
Tsoi, R. et al. Metabolic division of labor in microbial systems. Proc. Natl Acad. Sci. USA 115, 2526–2531 (2018).
Bassler, B. L. & Losick, R. Bacterially speaking. Cell 125, 237–246 (2006).
McCarty, N. S., Graham, A. E., Studena, L. & Ledesma-Amaro, R. Multiplexed CRISPR technologies for gene editing and transcriptional regulation. Nat. Commun. 11, 1281 (2020).
Patel, J. R., Oh, J., Wang, S., Crawford, J. M. & Isaacs, F. J. Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome. Cell 185, 1487–1505.e1414 (2022). This article reports that the same synthetic genetic elements can function simultaneously in prokaryotes and eukaryotes.
Vo, P. L. H. et al. CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering. Nat. Biotechnol. 39, 480–489 (2021).
Rubin, B. E. et al. Species- and site-specific genome editing in complex bacterial communities. Nat. Microbiol. 7, 34–47 (2022).
Cazares, A., Figueroa, W. & Cazares, D. Diversity of microbial defence systems. Nat. Rev. Microbiol. 20, 191 (2022).
Huang, M. et al. The activation and limitation of the bacterial natural transformation system: the function in genome evolution and stability. Microbiol. Res. 252, 126856 (2021).
Rodriguez-Grande, J. & Fernandez-Lopez, R. Measuring plasmid conjugation using antibiotic selection. Methods Mol. Biol. 2075, 93–98 (2020).
Lam, K. N. et al. Phage-delivered CRISPR–Cas9 for strain-specific depletion and genomic deletions in the gut microbiome. Cell Rep. 37, 109930 (2021).
Brophy, J. A. N. et al. Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria. Nat. Microbiol. 3, 1043–1053 (2018).
Waller, M. C., Bober, J. R., Nair, N. U. & Beisel, C. L. Toward a genetic tool development pipeline for host-associated bacteria. Curr. Opin. Microbiol. 38, 156–164 (2017).
Ronda, C., Chen, S. P., Cabral, V., Yaung, S. J. & Wang, H. H. Metagenomic engineering of the mammalian gut microbiome in situ. Nat. Methods 16, 167–170 (2019).
Pansegrau, W. et al. Complete nucleotide sequence of Birmingham IncP alpha plasmids. Compilation and comparative analysis. J. Mol. Biol. 239, 623–663 (1994).
Shen, T. C. et al. Engineering the gut microbiota to treat hyperammonemia. J Clin. Invest. 125, 2841–2850 (2015).
Walser, M. & Bodenlos, L. J. Urea metabolism in man. J. Clin. Invest. 38, 1617–1626 (1959).
Mobley, H. L. & Hausinger, R. P. Microbial ureases: significance, regulation, and molecular characterization. Microbiol. Rev. 53, 85–108 (1989).
Riordan, S. M. & Williams, R. Treatment of hepatic encephalopathy. N. Engl. J. Med. 337, 473–479 (1997).
Tanoue, T. et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 565, 600–605 (2019).
Atarashi, K. et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500, 232–236 (2013).
Cheng, A. G. et al. Design, construction, and in vivo augmentation of a complex gut microbiome. Cell https://doi.org/10.1016/j.cell.2022.08.003 (2022).
Stein, R. R. et al. Computer-guided design of optimal microbial consortia for immune system modulation. eLife https://doi.org/10.7554/eLife.30916 (2018).
Wang, L. et al. Engineering consortia by polymeric microbial swarmbots. Nat. Commun. 13, 3879 (2022).
El-Salhy, M., Hatlebakk, J. G., Gilja, O. H., Brathen Kristoffersen, A. & Hausken, T. Efficacy of faecal microbiota transplantation for patients with irritable bowel syndrome in a randomised, double-blind, placebo-controlled study. Gut 69, 859–867 (2020).
DeFilipp, Z. et al. Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant. N. Engl. J. Med. 381, 2043–2050 (2019).
Wolter, M. et al. Leveraging diet to engineer the gut microbiome. Nat. Rev. Gastroenterol. Hepatol. 18, 885–902 (2021).
Kearney, S. M., Gibbons, S. M., Erdman, S. E. & Alm, E. J. Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal. Cell Rep. 24, 1842–1851 (2018).
Lam, S. et al. Roles of the gut virome and mycobiome in faecal microbiota transplantation. Lancet Gastroenterol. Hepatol. 7, 472–484 (2022). This article reviews the roles of non-bacteria components of the gut microbiome in human health and faecal microbiota transplantation.
Oliva, M. et al. Tumor-associated microbiome: where do we stand? Int. J. Mol. Sci. https://doi.org/10.3390/ijms22031446 (2021).
Zheng, J. H. & Min, J. J. Targeted cancer therapy using engineered Salmonella typhimurium. Chonnam. Med. J. 52, 173–184 (2016).
Nguyen, V. H. & Min, J. J. Salmonella-mediated cancer therapy: roles and potential. Nucl. Med. Mol. Imaging 51, 118–126 (2017).
Brown, J. M. Tumor hypoxia in cancer therapy. Methods Enzymol. 435, 297–321 (2007).
St Jean, A. T., Zhang, M. & Forbes, N. S. Bacterial therapies: completing the cancer treatment toolbox. Curr. Opin. Biotechnol. 19, 511–517 (2008).
Liang, K. et al. Genetically engineered Salmonella Typhimurium: recent advances in cancer therapy. Cancer Lett. 448, 168–181 (2019).
Ganai, S., Arenas, R. B., Sauer, J. P., Bentley, B. & Forbes, N. S. In tumors Salmonella migrate away from vasculature toward the transition zone and induce apoptosis. Cancer Gene Ther. 18, 457–466 (2011).
Li, C. X. et al. ‘Obligate’ anaerobic Salmonella strain YB1 suppresses liver tumor growth and metastasis in nude mice. Oncol. Lett. 13, 177–183 (2017).
Zhou, S. et al. Suppression of pancreatic ductal adenocarcinoma growth by intratumoral delivery of attenuated Salmonella typhimurium using a dual fluorescent live tracking system. Cancer Biol. Ther. 17, 732–740 (2016).
Yue, Y. et al. Antigen-bearing outer membrane vesicles as tumour vaccines produced in situ by ingested genetically engineered bacteria. Nat. Biomed. Eng. 6, 898–909 (2022).
Harimoto, T. et al. A programmable encapsulation system improves delivery of therapeutic bacteria in mice. Nat. Biotechnol. https://doi.org/10.1038/s41587-022-01244-y (2022).
Liu, X., Jiang, S., Piao, L. & Yuan, F. Radiotherapy combined with an engineered Salmonella typhimurium inhibits tumor growth in a mouse model of colon cancer. Exp. Anim. 65, 413–418 (2016).
Zheng, D. W. et al. Phage-guided modulation of the gut microbiota of mouse models of colorectal cancer augments their responses to chemotherapy. Nat. Biomed. Eng. 3, 717–728 (2019).
Fluckiger, A. et al. Cross-reactivity between tumor MHC class I-restricted antigens and an enterococcal bacteriophage. Science 369, 936–942 (2020).
Gilbert, J. A. et al. Current understanding of the human microbiome. Nat. Med. 24, 392–400 (2018).
Sedlmayer, F., Aubel, D. & Fussenegger, M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat. Biomed. Eng. 2, 399–415 (2018).
Pedrolli, D. B. et al. Engineering microbial living therapeutics: the synthetic biology toolbox. Trends Biotechnol. 37, 100–115 (2019).
Hicks, M., Bachmann, T. T. & Wang, B. Synthetic biology enables programmable cell-based biosensors. ChemPhysChem 21, 132–144 (2020).
Vigouroux, A. & Bikard, D. CRISPR tools to control gene expression in bacteria. Microbiol. Mol. Biol. Rev. https://doi.org/10.1128/MMBR.00077-19 (2020).
Landry, B. P. & Tabor, J. J. Engineering diagnostic and therapeutic gut bacteria. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.BAD-0020-2017 (2017).
Sheth, R. U. & Wang, H. H. DNA-based memory devices for recording cellular events. Nat. Rev. Genet. 19, 718–732 (2018).
Schmidt, F. et al. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 376, eabm6038 (2022).
Daeffler, K. N. et al. Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Mol. Syst. Biol. 13, 923 (2017).
Archer, E. J., Robinson, A. B. & Suel, G. M. Engineered E. coli that detect and respond to gut inflammation through nitric oxide sensing. ACS Synth. Biol. 1, 451–457 (2012).
Kimura, H. et al. Increased nitric oxide production and inducible nitric oxide synthase activity in colonic mucosa of patients with active ulcerative colitis and Crohn’s disease. Dig. Dis. Sci. 42, 1047–1054 (1997).
Riglar, D. T. et al. Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Nat. Biotechnol. 35, 653–658 (2017).
Kotula, J. W. et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl Acad. Sci. USA 111, 4838–4843 (2014).
Mimee, M. et al. An ingestible bacterial-electronic system to monitor gastrointestinal health. Science 360, 915–918 (2018). This article combines gut microbiome engineering and microelectronics to monitor gastrointestinal health.
Fedorak, R. N. et al. Recombinant human interleukin 10 in the treatment of patients with mild to moderately active Crohn’s disease. The Interleukin 10 Inflammatory Bowel Disease Cooperative Study Group. Gastroenterology 119, 1473–1482 (2000).
Steidler, L. et al. Biological containment of genetically modified Lactococcus lactis for intestinal delivery of human interleukin 10. Nat. Biotechnol. 21, 785–789 (2003).
Waeytens, A. et al. Paracellular entry of interleukin-10 producing Lactococcus lactis in inflamed intestinal mucosa in mice. Inflamm. Bowel Dis. 14, 471–479 (2008).
Benbouziane, B. et al. Development of a stress-inducible controlled expression (SICE) system in Lactococcus lactis for the production and delivery of therapeutic molecules at mucosal surfaces. J. Biotechnol. 168, 120–129 (2013).
Llosa, M., Schroder, G. & Dehio, C. New perspectives into bacterial DNA transfer to human cells. Trends Microbiol. 20, 355–359 (2012).
Spisni, E. et al. Cyclooxygenase-2 silencing for the treatment of colitis: a combined in vivo strategy based on RNA interference and engineered Escherichia coli. Mol. Ther. 23, 278–289 (2015).
Breyner, N. M. et al. Microbial anti-inflammatory molecule (MAM) from Faecalibacterium prausnitzii shows a protective effect on DNBS and DSS-induced colitis model in mice through inhibition of NF-κB pathway. Front. Microbiol. 8, 114 (2017).
Hamady, Z. Z. et al. Xylan-regulated delivery of human keratinocyte growth factor-2 to the inflamed colon by the human anaerobic commensal bacterium Bacteroides ovatus. Gut 59, 461–469 (2010).
Hamady, Z. Z. et al. Treatment of colitis with a commensal gut bacterium engineered to secrete human TGF-β1 under the control of dietary xylan 1. Inflamm. Bowel Dis. 17, 1925–1935 (2011).
Agarwal, P., Khatri, P., Billack, B., Low, W.-K. & Shao, J. Oral delivery of glucagon like peptide-1 by a recombinant Lactococcus lactis. Pharm. Res. 31, 3404–3414 (2014).
Hendrikx, T. et al. Bacteria engineered to produce IL-22 in intestine induce expression of REG3G to reduce ethanol-induced liver disease in mice. Gut 68, 1504–1515 (2019).
Koh, E. et al. Engineering probiotics to inhibit Clostridioides difficile infection by dynamic regulation of intestinal metabolism. Nat. Commun. 13, 3834 (2022).
Paton, A. W., Morona, R. & Paton, J. C. A new biological agent for treatment of Shiga toxigenic Escherichia coli infections and dysentery in humans. Nat. Med. 6, 265–270 (2000).
Theriot, C. M., Bowman, A. A. & Young, V. B. Antibiotic-induced alterations of the gut microbiota alter secondary bile acid production and allow for Clostridium difficile spore germination and outgrowth in the large intestine. mSphere https://doi.org/10.1128/mSphere.00045-15 (2016).
Selle, K. et al. In vivo targeting of Clostridioides difficile using phage-delivered CRISPR–Cas3 antimicrobials. mBio https://doi.org/10.1128/mBio.00019-20 (2020).
Edgar, R., Friedman, N., Molshanski-Mor, S. & Qimron, U. Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Appl. Environ. Microbiol. 78, 744–751 (2012).
Lee, J. W., Chan, C. T. Y., Slomovic, S. & Collins, J. J. Next-generation biocontainment systems for engineered organisms. Nat. Chem. Biol. 14, 530–537 (2018).
Torres, L., Kruger, A., Csibra, E., Gianni, E. & Pinheiro, V. B. Synthetic biology approaches to biological containment: pre-emptively tackling potential risks. Essays Biochem. 60, 393–410 (2016).
Hosseini, S., Curilovs, A. & Cutting, S. M. Biological containment of genetically modified Bacillus subtilis. Appl. Environ. Microbiol. https://doi.org/10.1128/AEM.02334-17 (2018).
Chan, C. T., Lee, J. W., Cameron, D. E., Bashor, C. J. & Collins, J. J. ‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment. Nat. Chem. Biol. 12, 82–86 (2016). This article describes strategies for the biocontainment of engineered microbes.
Sasaki, T. et al. Genetically engineered Bifidobacterium longum for tumor-targeting enzyme-prodrug therapy of autochthonous mammary tumors in rats. Cancer Sci 97, 649–657 (2006).
Reghu, S. & Miyako, E. Nanoengineered Bifidobacterium bifidum with optical activity for photothermal cancer immunotheranostics. Nano Lett. 22, 1880–1888 (2022).
Neil, K. et al. High-efficiency delivery of CRISPR–Cas9 by engineered probiotics enables precise microbiome editing. Mol. Syst. Biol. 17, e10335 (2021).
Leffler, D. A. & Lamont, J. T. Clostridium difficile infection. N. Engl. J. Med. 372, 1539–1548 (2015).
Olsen, S. J. et al. A nosocomial outbreak of fluoroquinolone-resistant salmonella infection. N. Engl. J. Med. 344, 1572–1579 (2001).
Low, K. B. et al. Lipid A mutant Salmonella with suppressed virulence and TNFα induction retain tumor-targeting in vivo. Nat. Biotechnol. 17, 37–41 (1999).
Low, K. B. et al. Construction of VNP20009: a novel, genetically stable antibiotic-sensitive strain of tumor-targeting Salmonella for parenteral administration in humans. Methods Mol. Med. 90, 47–60 (2004).
Rosenberg, S. A., Spiess, P. J. & Kleiner, D. E. Antitumor effects in mice of the intravenous injection of attenuated Salmonella typhimurium. J. Immunother. 25, 218–225 (2002).
Claesen, J. & Fischbach, M. A. Synthetic microbes as drug delivery systems. ACS Synth. Biol. 4, 358–364 (2015).
Kurtz, C. et al. Translational development of microbiome-based therapeutics: kinetics of E. coli Nissle and engineered strains in humans and nonhuman primates. Clin. Transl. Sci. 11, 200–207 (2018).
Joeres-Nguyen-Xuan, T. H., Boehm, S. K., Joeres, L., Schulze, J. & Kruis, W. Survival of the probiotic Escherichia coli Nissle 1917 (EcN) in the gastrointestinal tract given in combination with oral mesalamine to healthy volunteers. Inflamm. Bowel Dis. 16, 256–262 (2010).
Russell, B. J. et al. Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes. Cell 185, 3263–3277.e3215 (2022). This article describes approaches of engineering and re-delivering native microbes in the host’s gut, proving that foreign microbes can colonize the original gut microbiome without disrupting the gut environment.
Yang, X. et al. Physiologically inspired mucin coated Escherichia coli Nissle 1917 enhances biotherapy by regulating the pathological microenvironment to improve intestinal colonization. ACS Nano 16, 4041–4058 (2022).
Lubkowicz, D. et al. An engineered bacterial therapeutic lowers urinary oxalate in preclini cal models and in silico simulations of enteric hyperoxaluria. Mol. Syst. Biol. 18, e10539 (2022).
Darsley, M. J. et al. The oral, live attenuated enterotoxigenic Escherichia coli vaccine ACE527 reduces the incidence and severity of diarrhea in a human challenge model of diarrheal disease. Clin. Vaccine Immunol. 19, 1921–1931 (2012).
Limaye, S. A. et al. Phase 1b, multicenter, single blinded, placebo-controlled, sequential dose escalation study to assess the safety and tolerability of topically applied AG013 in subjects with locally advanced head and neck cancer receiving induction chemotherapy. Cancer 119, 4268–4276 (2013).
Schmitz-Winnenthal, F. H. et al. Anti-angiogenic activity of VXM01, an oral T-cell vaccine against VEGF receptor 2, in patients with advanced pancreatic cancer: a randomized, placebo-controlled, phase 1 trial. OncoImmunology 4, e1001217 (2015).
Clark, L. C., Jr. & Lyons, C. Electrode systems for continuous monitoring in cardiovascular surgery. Ann. NY Acad. Sci. 102, 29–45 (1962).
Jackson, D. A., Symons, R. H. & Berg, P. Biochemical method for inserting new genetic Information into DNA of simian virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli. Proc. Natl Acad. Sci. 69, 2904–2909 (1972).
Cohen, S. N., Chang, A. C., Boyer, H. W. & Helling, R. B. Construction of biologically functional bacterial plasmids in vitro. Proc. Natl Acad. Sci. 70, 3240–3244 (1973).
Alyas, J. et al. Human insulin: history, recent advances, and expression systems for mass production. Biomed. Res. Ther. 8, 4540–4561 (2021).
Ishino, Y., Krupovic, M. & Forterre, P. History of CRISPR-Cas from encounter with a mysterious repeated sequence to genome editing technology. J. Bacteriol. 200, https://doi.org/10.1128/jb.00580-17 (2018).
Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000).
Weiss, R. & Knight Jr, T. F. in DNA Computing: 6th International Workshop on DNA-Based Computers (DNA 2000) 1–16 (Springer, 2001).
Guet, C. C., Elowitz, M. B., Hsing, W. & Leibler, S. Combinatorial synthesis of genetic networks. Science 296, 1466–1470 (2002).
Martin, V. J., Pitera, D. J., Withers, S. T., Newman, J. D. & Keasling, J. D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nature Biotechnol. 21, 796–802 (2003).
Isaacs, F. J. et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnol. 22, 841–847 (2004).
Levskaya, A. et al. Synthetic biology: engineering Escherichia coli to see light. Nature 438, 441–442 (2005).
Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).
Anderson, J. C., Clarke, E. J., Arkin, A. P. & Voigt, C. A. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355, 619–627 (2006).
Wang, H. H. et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460, 894–898 (2009).
Friedland, A. E. et al. Synthetic gene networks that count. Science 324, 1199–1202 (2009).
Danino, T., Mondragón-Palomino, O., Tsimring, L. & Hasty, J. A synchronized quorum of genetic clocks. Nature 463, 326–330 (2010).
Gibson, D. G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56 (2010).
Dymond, J. S. et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477, 471–476 (2011).
Paddon, C. J. et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496, 528–532 (2013).
Annaluru, N. et al. Total synthesis of a functional designer eukaryotic chromosome. Science 344, 55–58 (2014).
Rovner, A. J. et al. Recoded organisms engineered to depend on synthetic amino acids. Nature 518, 89–93 (2015).
Nielsen, A. A. K. et al. Genetic circuit design automation. Science 352, aac7341 (2016).
Shao, Y. et al. Creating a functional single-chromosome yeast. Nature 560, 331–335 (2018).
Fredens, J. et al. Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514–518 (2019).
Feuerstadt, P. et al. SER-109, an oral microbiome therapy for recurrent Clostridioides difficile infection. New Engl. J. Med. 386, 220–229 (2022).
Canale, F. P. et al. Metabolic modulation of tumours with engineered bacteria for immunotherapy. Nature 598, 662–666 (2021).
Hatakeyama, M. Helicobacter pylori CagA and gastric cancer: a paradigm for hit-and-run carcinogenesis. Cell Host Microbe 15, 306–316 (2014).
Kostic, A. D. et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14, 207–215 (2013).
Zuo, T. et al. Human–gut–DNA virome variations across geography, ethnicity, and urbanization. Cell Host Microbe 28, 741–751.e744 (2020).
Bai, X. et al. Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population. Microbiome 10, 147 (2022).
Sun, Y. et al. Population-level configurations of gut mycobiome across 6 ethnicities in urban and rural China. Gastroenterology 160, 272–286.e211 (2021).
T.Z. discloses support for publication of this work from the National Natural Science Foundation of China (NSFC grant numbers 82172323 and 32100134), the Municipal Key Research and Development Program of Guangzhou (grant number 202206010014). We acknowledge intellectual support from the Key Laboratory of Human Microbiome and Chronic diseases (Sun Yat-sen University), Ministry of Education, China.
The authors declare no competing interests.
Peer review information
Nature Reviews Bioengineering thanks Hiroshi Ohno and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Bai, X., Huang, Z., Duraj-Thatte, A.M. et al. Engineering the gut microbiome. Nat Rev Bioeng 1, 665–679 (2023). https://doi.org/10.1038/s44222-023-00072-2