CoChat
Sign Up
Cited by 50Microbial Metabolic Engineering and BioproductionMicrobial Fuel Cells and BioremediationMicrobial Applications in Construction Materials

Engineering Microbial Consortia as Living Materials: Advances and Prospectives

Open access
Wang, Shuchen, Zhan, Yuewei, Jiang, Xue, Lai, Yong·2024·ACS Synthetic Biology
DOI 10.1021/acssynbio.4c00313PMC PMC11421429
Open this paper in CoChat — free accountOpen PDF

Abstract

The field of Engineered Living Materials (ELMs) integrates engineered living organisms into natural biomaterials to achieve diverse objectives. Multiorganism consortia, prevalent in both naturally occurring and synthetic microbial cultures, exhibit complex functionalities and interrelationships, extending the scope of what can be achieved with individual engineered bacterial strains. However, the ELMs comprising microbial consortia are still in the developmental stage. In this Review, we introduce two strategies for designing ELMs constituted of microbial consortia: a top-down strategy, which involves characterizing microbial interactions and mimicking and reconstructing natural ecosystems, and a bottom-up strategy, which entails the rational design of synthetic consortia and their assembly with material substrates to achieve user-defined functions. Next, we summarize technologies from synthetic biology that facilitate the efficient engineering of microbial consortia for performing tasks more complex than those that can be done with single bacterial strains. Finally, we discuss essential challenges and future perspectives for microbial consortia-based ELMs.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1021/acssynbio.4c00313

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Industrial sites often experience fluctuating conditions such as changes in temperature, pH, and contaminant concentrations, which can impact microbial performance.

    “Industrial sites often experience fluctuating conditions such as changes in temperature, pH, and contaminant concentrations, which can impact microbial performance [4,369,370,372].”

    From Harnessing bacterial consortia for effective bioremediation: targeted removal of heavy metals, hydrocarbons, and persistent pollutants (2025) · cites this paper as [372]

    The “Expanding the Lifespan and Sustainability of Consortia-Based ELMs” section says unfavorable environmental conditions can threaten microbial viability and long-term performance. The “Understanding the Interactions” section also anticipates more complex, less predictable growth environments. Neither passage establishes that industrial sites often fluctuate specifically in temperature, pH, or contaminant concentrations (page numbers unavailable). (LLM, conf=0.84)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

1 retracted

Flagged first, then by citations

Research works printed but not linked: 136

  1. Granier C.; Tardieu F. Multi-Scale Phenotyping of Leaf Expansion in Response to Environmental Changes: The Whole Is More than the Sum of Parts. Plant Cell Environ 2009, 32 (9), 1175– 1184. 10.1111/j.1365-3040.2009.01955.x. 19210637 · DOI
  2. Duda G. N.; Geissler S.; Checa S.; Tsitsilonis S.; Petersen A.; Schmidt-Bleek K. The Decisive Early Phase of Bone Regeneration. Nat. Rev. Rheumatol. 2023, 19 (2), 78– 95. 10.1038/s41584-022-00887-0. 36624263 · DOI
  3. Lories B.; Roberfroid S.; Dieltjens L.; De Coster D.; Foster K. R.; Steenackers H. P. Biofilm Bacteria Use Stress Responses to Detect and Respond to Competitors. Curr. Biol. 2020, 30 (7), 1231– 1244.e4. 10.1016/j.cub.2020.01.065. 32084407 PMC7322538 · DOI
  4. Hays S. G.; Patrick W. G.; Ziesack M.; Oxman N.; Silver P. A. Better Together: Engineering and Application of Microbial Symbioses. Curr. Opin. Biotechnol. 2015, 36, 40– 49. 10.1016/j.copbio.2015.08.008. 26319893 · DOI
  5. Penesyan A.; Paulsen I. T.; Kjelleberg S.; Gillings M. R. Three Faces of Biofilms: A Microbial Lifestyle, a Nascent Multicellular Organism, and an Incubator for Diversity. npj Biofilms Microbiomes 2021, 7 (1), 1– 9. 10.1038/s41522-021-00251-2. 34759294 PMC8581019 · DOI
  6. Molinari S.; Tesoriero R. F.; Ajo-Franklin C. M. Bottom-up Approaches to Engineered Living Materials: Challenges and Future Directions. Matter 2021, 4 (10), 3095– 3120. 10.1016/j.matt.2021.08.001. · DOI
  7. Gilbert C.; Ellis T. Biological Engineered Living Materials: Growing Functional Materials with Genetically Programmable Properties. ACS Synth. Biol. 2019, 8 (1), 1– 15. 10.1021/acssynbio.8b00423. 30576101 · DOI
  8. Nguyen P. Q.; Courchesne N. M. D.; Duraj-Thatte A.; Praveschotinunt P.; Joshi N. S. Engineered Living Materials: Prospects and Challenges for Using Biological Systems to Direct the Assembly of Smart Materials. Adv. Mater. 2018, 30 (19), 1704847 10.1002/adma.201870134. PMC6309613 29430725 · DOI
  9. Liu X.; Inda M. E.; Lai Y.; Lu T. K.; Zhao X.; Liu X.; Zhao X.; Inda M. E.; Lai Y.; Lu T. K. Engineered Living Hydrogels. Adv. Mater. 2022, 34 (26), 2201326 10.1002/adma.202201326. PMC9250645 35243704 · DOI
  10. Rodrigo-Navarro A.; Sankaran S.; Dalby M. J.; del Campo A.; Salmeron-Sanchez M. Engineered Living Biomaterials. Nat. Rev. Mater. 2021, 6 (12), 1175– 1190. 10.1038/s41578-021-00350-8. · DOI
  11. Dong X.; Wu W.; Pan P.; Zhang X. Z. Engineered Living Materials for Advanced Diseases Therapy. Adv. Mater. 2023, 2304963 10.1002/adma.202304963. 37436776 · DOI
  12. Heveran C. M.; Hernandez C. J. Make Engineered Living Materials Carry Their Weight. Matter 2023, 6 (11), 3705– 3718. 10.1016/j.matt.2023.07.023. · DOI
  13. An B.; Wang Y.; Huang Y.; Wang X.; Liu Y.; Xun D.; Church G. M.; Dai Z.; Yi X.; Tang T. C.; Zhong C. Engineered Living Materials For Sustainability. Chem. Rev. 2023, 123 (5), 2349– 2419. 10.1021/acs.chemrev.2c00512. 36512650 · DOI
  14. Stenuit B.; Agathos S. N. Deciphering Microbial Community Robustness through Synthetic Ecology and Molecular Systems Synecology. Curr. Opin. Biotechnol. 2015, 33 (1), 305– 317. 10.1016/j.copbio.2015.03.012. 25880923 · DOI
  15. Boucher D. H.; James S.; Keeler K. H. The Ecology of Mutualism. Annu. Rev. Ecol. Syst. 1982, 13, 315– 347. 10.1146/annurev.es.13.110182.001531. · DOI
  16. Raina J. B.; Fernandez V.; Lambert B.; Stocker R.; Seymour J. R. The Role of Microbial Motility and Chemotaxis in Symbiosis. Nat. Rev. Microbiol. 2019, 17 (5), 284– 294. 10.1038/s41579-019-0182-9. 30923350 · DOI
  17. Michielsen S.; Vercelli G. T.; Cordero O. X.; Bachmann H. Spatially Structured Microbial Consortia and Their Role in Food Fermentations. Curr. Opin. Biotechnol. 2024, 87, 103102 10.1016/j.copbio.2024.103102. 38461750 · DOI
  18. Adam B.; Baillie G. S.; Douglas L. J. Mixed Species Biofilms of Candida Albicans and Staphylococcus Epidermidis. J. Med. Microbiol. 2002, 51 (4), 344– 349. 10.1099/0022-1317-51-4-344. 11926741 · DOI
  19. Abas A. A Systematic Review on Biomonitoring Using Lichen as the Biological Indicator: A Decade of Practices. Progress and Challenges. Ecol. Indic. 2021, 121, 107197 10.1016/j.ecolind.2020.107197. · DOI
  20. Krespach M. K. C.; García-Altares M.; Flak M.; Schoeler H.; Scherlach K.; Netzker T.; Schmalzl A.; Mattern D. J.; Schroeckh V.; Komor A.; Mittag M.; Hertweck C.; Brakhage A. A. Lichen-like Association of Chlamydomonas Reinhardtii and Aspergillus Nidulans Protects Algal Cells from Bacteria. ISME J. 2020, 14 (11), 2794– 2805. 10.1038/s41396-020-0731-2. 32753730 PMC7784976 · DOI
  21. Duran-Nebreda S.; Valverde S. Composition, Structure and Robustness of Lichen Guilds. Sci. Rep. 2023, 13 (1), 1– 14. 10.1038/s41598-023-30357-w. 36841885 PMC9968342 · DOI
  22. Hom E. F. Y.; Murray A. W. Niche Engineering Demonstrates a Latent Capacity for Fungal-Algal Mutualism. Science 2014, 345 (6192), 94– 98. 10.1126/science.1253320. 24994654 PMC4409001 · DOI
  23. Yu X.; Polz M. F.; Alm E. J. Interactions in Self-Assembled Microbial Communities Saturate with Diversity. ISME J. 2019, 13 (6), 1602– 1617. 10.1038/s41396-019-0356-5. 30809013 PMC6775987 · DOI
  24. Correa-Galeote D.; Marco D. E.; Tortosa G.; Bru D.; Philippot L.; Bedmar E. J. Spatial Distribution of N-Cycling Microbial Communities Showed Complex Patterns in Constructed Wetland Sediments. FEMS Microbiol Ecol. 2013, 83 (2), 340– 351. 10.1111/j.1574-6941.2012.01479.x. 22928965 · DOI
  25. Khan M. T.; Dwibedi C.; Sundh D.; Pradhan M.; Kraft J. D.; Caesar R.; Tremaroli V.; Lorentzon M.; Bäckhed F. Synergy and Oxygen Adaptation for Development of Next-Generation Probiotics. Nature 2023, 620 (7973), 381– 385. 10.1038/s41586-023-06378-w. 37532933 PMC10412450 · DOI
  26. Van Huynh V.; Ngo M. T. T.; Itayama T.; Nguyen M. B.; Vo T. D. H.; Vo T. K. Q.; Le V. G.; You S. j.; Nguyen P. T.; Bui X. T. Dynamic of Microbial Community in Simultaneous Nitrification and Denitrification Process: A Review. Bioresour. Technol. Rep. 2023, 22, 101415 10.1016/j.biteb.2023.101415. · DOI
  27. Thomas T.; Rusch D.; DeMaere M. Z.; Yung P. Y.; Lewis M.; Halpern A.; Heidelberg K. B.; Egan S.; Steinberg P. D.; Kjelleberg S. Functional Genomic Signatures of Sponge Bacteria Reveal Unique and Shared Features of Symbiosis. ISME J. 2010, 4 (12), 1557– 1567. 10.1038/ismej.2010.74. 20520651 · DOI
  28. Webster N. S.; Taylor M. W. Marine Sponges and Their Microbial Symbionts: Love and Other Relationships. Environ. Microbiol. 2012, 14 (2), 335– 346. 10.1111/j.1462-2920.2011.02460.x. 21443739 · DOI
  29. Li T.; Jiang L.; Hu Y.; Paul J. T.; Zuniga C.; Zengler K.; Betenbaugh M. J. Creating a Synthetic Lichen: Mutualistic Co-Culture of Fungi and Extracellular Polysaccharide-Secreting Cyanobacterium Nostoc PCC 7413. Algal. Res. 2020, 45, 101755 10.1016/j.algal.2019.101755. · DOI
  30. Das A. A. K.; Bovill J.; Ayesh M.; Stoyanov S. D.; Paunov V. N. Fabrication of Living Soft Matter by Symbiotic Growth of Unicellular Microorganisms. J. Mater. Chem. B 2016, 4 (21), 3685– 3694. 10.1039/C5TB02489G. 32263307 · DOI
  31. Gilbert C.; Tang T. C.; Ott W.; Dorr B. A.; Shaw W. M.; Sun G. L.; Lu T. K.; Ellis T. Living Materials with Programmable Functionalities Grown from Engineered Microbial Co-Cultures. Nat. Mater. 2021, 20 (5), 691– 700. 10.1038/s41563-020-00857-5. 33432140 · DOI
  32. Shaw W. M.; Yamauchi H.; Mead J.; Gowers G. O. F.; Bell D. J.; Öling D.; Larsson N.; Wigglesworth M.; Ladds G.; Ellis T. Engineering a Model Cell for Rational Tuning of GPCR Signaling. Cell 2019, 177 (3), 782– 796.e27. 10.1016/j.cell.2019.02.023. 30955892 PMC6476273 · DOI
  33. Lee M. E.; DeLoache W. C.; Cervantes B.; Dueber J. E. A Highly Characterized Yeast Toolkit for Modular. Multipart Assembly. ACS Synth. Biol. 2015, 4 (9), 975– 986. 10.1021/sb500366v. 25871405 · DOI
  34. Goosens V. J.; Walker K. T.; Aragon S. M.; Singh A.; Senthivel V. R.; Dekker L.; Caro-Astorga J.; Buat M. L. A.; Song W.; Lee K. Y.; Ellis T. Komagataeibacter Tool Kit (KTK): A Modular Cloning System for Multigene Constructs and Programmed Protein Secretion from Cellulose Producing Bacteria. ACS Synth. Biol. 2021, 10 (12), 3422– 3434. 10.1021/acssynbio.1c00358. 34767345 · DOI
  35. McBee R. M.; Lucht M.; Mukhitov N.; Richardson M.; Srinivasan T.; Meng D.; Chen H.; Kaufman A.; Reitman M.; Munck C.; Schaak D.; Voigt C.; Wang H. H. Engineering Living and Regenerative Fungal–Bacterial Biocomposite Structures. Nat. Mater. 2022, 21 (4), 471– 478. 10.1038/s41563-021-01123-y. 34857911 · DOI
  36. Khakhar A. A Roadmap for the Creation of Synthetic Lichen. Biochem. Biophys. Res. Commun. 2023, 654, 87– 93. 10.1016/j.bbrc.2023.02.079. 36898228 · DOI
  37. Marco M. L.; Heeney D.; Binda S.; Cifelli C. J.; Cotter P. D.; Foligné B.; Gänzle M.; Kort R.; Pasin G.; Pihlanto A.; Smid E. J.; Hutkins R. Health Benefits of Fermented Foods: Microbiota and Beyond. Curr. Opin. Biotechnol. 2017, 44, 94– 102. 10.1016/j.copbio.2016.11.010. 27998788 · DOI · Paper page
  38. Duncker K. E.; Holmes Z. A.; You L. Engineered Microbial Consortia: Strategies and Applications. Microb. Cell Factories 2021, 20 (1), 1– 13. 10.1186/s12934-021-01699-9. PMC8597270 34784924 · DOI · Paper page
  39. Song H.; Ding M. Z.; Jia X. Q.; Ma Q.; Yuan Y. J. Synthetic Microbial Consortia: From Systematic Analysis to Construction and Applications. Chem. Soc. Rev. 2014, 43 (20), 6954– 6981. 10.1039/C4CS00114A. 25017039 · DOI
  40. Cheng A. G.; Ho P. Y.; Aranda-Díaz A.; Jain S.; Yu F. B.; Meng X.; Wang M.; Iakiviak M.; Nagashima K.; Zhao A.; Murugkar P.; Patil A.; Atabakhsh K.; Weakley A.; Yan J.; Brumbaugh A. R.; Higginbottom S.; Dimas A.; Shiver A. L.; Deutschbauer A.; Neff N.; Sonnenburg J. L.; Huang K. C.; Fischbach M. A. Design, Construction, and in Vivo Augmentation of a Complex Gut Microbiome. Cell 2022, 185 (19), 3617– 3636.e19. 10.1016/j.cell.2022.08.003. 36070752 PMC9691261 · DOI
  41. Cordero O. X.; Datta M. S. Microbial Interactions and Community Assembly at Microscales. Curr. Opin. Microbiol. 2016, 31, 227– 234. 10.1016/j.mib.2016.03.015. 27232202 PMC5157693 · DOI
  42. Li L.; Yang C.; Ma B.; Lu S.; Liu J.; Pan Y.; Wang X.; Zhang Y.; Wang H.; Sun T.; Liu D. Hydrogel-Encapsulated Engineered Microbial Consortium as a Photoautotrophic “Living Material” for Promoting Skin Wound Healing. ACS Appl. Mater. Interfaces 2023, 15 (5), 6536– 6547. 10.1021/acsami.2c20399. 36708324 · DOI
  43. Zheng D.-W.; Qiao J.-Y.; Ma J.-C.; An J.-X.; Yang C.-H.; Zhang Y.; Cheng Q.; Rao Z.-Y.; Zeng S.-M.; Wang L.; Zhang X.-Z. A Microbial Community Cultured in Gradient Hydrogel for Investigating Gut Microbiome-Drug Interaction and Guiding Therapeutic Decisions. Adv. Mater. 2023, 35 (22), 2300977 10.1002/adma.202300977. 37029611 · DOI
  44. Connell J. L.; Ritschdorff E. T.; Whiteley M.; Shear J. B. 3D Printing of Microscopic Bacterial Communities. Proc. Natl. Acad. Sci. U. S. A. 2013, 110 (46), 18380– 18385. 10.1073/pnas.1309729110. 24101503 PMC3832025 · DOI
  45. Schaffner M.; Rühs P. A.; Coulter F.; Kilcher S.; Studart A. R. 3D Printing of Bacteria into Functional Complex Materials. Sci. Adv. 2017, 3 ((12),). 10.1126/sciadv.aao6804. PMC5711516 29214219 · DOI
  46. Gao H.; Wang H.; Zhang Y.; Wang Y.; Liu G.; Zhao Q.; Yu Z.; Xin F.; Zhang W. Design and Optimization of Artificial Light-Driven Microbial Consortia for the Sustainable Growth and Biosynthesis of 2-Phenylethanol. J. Chem. Eng. 2023, 466, 143050 10.1016/j.cej.2023.143050. · DOI
  47. Birnbaum D. P.; Manjula-Basavanna A.; Kan A.; Tardy B. L.; Joshi N. S. Hybrid Living Capsules Autonomously Produced by Engineered Bacteria. Adv. Sci. 2021, 8 ((11),). 10.1002/advs.202004699. PMC8188213 34141524 · DOI
  48. Qiao J. Y.; Zeng R. Y.; Chen Q. W.; Zheng D.; Hao P. L.; Liu X. H.; Zhao F.; Zhang X. Z. Autonomously Assembled Living Capsules by Microbial Coculture for Enhanced Bacteriotherapy of Inflammatory Bowel Disease. Nano Lett. 2023, 23 (10), 4375– 4383. 10.1021/acs.nanolett.3c00657. 37159332 · DOI
  49. Liu J.; Zhou X.; Wang T.; Fan L.; Liu S.; Wu N.; Xu A.; Qian X.; Li Z.; Jiang M.; Zhou J.; Dong W. Construction and Comparison of Synthetic Microbial Consortium System (SMCs) by Non-Living or Living Materials Immobilization and Application in Acetochlor Degradation. J. Hazard. Mater. 2022, 438, 129460 10.1016/j.jhazmat.2022.129460. 35803189 · DOI
  50. Wang L.; Zhang X.; Tang C.; Li P.; Zhu R.; Sun J.; Zhang Y.; Cui H.; Ma J.; Song X.; Zhang W.; Gao X.; Luo X.; You L.; Chen Y.; Dai Z. Engineering Consortia by Polymeric Microbial Swarmbots. Nat. Commun. 2022, 13 (1), 1– 13. 10.1038/s41467-022-31467-1. 35790722 PMC9256712 · DOI
  51. Jeong Y.; Irudayaraj J. Hierarchical Encapsulation of Bacteria in Functional Hydrogel Beads for Inter- and Intra- Species Communication. Acta Biomater. 2023, 158, 203– 215. 10.1016/j.actbio.2023.01.003. 36632875 PMC10209895 · DOI
  52. Wang Y.; Liu Y.; Li J.; Chen Y.; Liu S.; Zhong C. Engineered Living Materials (ELMs) Design: From Function Allocation to Dynamic Behavior Modulation. Curr. Opin. Chem. Biol. 2022, 70, 102188 10.1016/j.cbpa.2022.102188. 35970133 · DOI
  53. Ivaškė A.; Gribniak V.; Jakubovskis R.; Urbonavičius J. Bacterial Viability in Self-Healing Concrete: A Case Study of Non-Ureolytic Bacillus Species. Microorganisms 2023, 11 (10), 2402 10.3390/microorganisms11102402. 37894059 PMC10609539 · DOI
  54. Fang X.; Kalathil S.; Divitini G.; Wang Q.; Reisner E. A Three-Dimensional Hybrid Electrode with Electroactive Microbes for Efficient Electrogenesis and Chemical Synthesis. Proc. Natl. Acad. Sci. U. S. A. 2020, 117 (9), 5074– 5080. 10.1073/pnas.1913463117. 32051251 PMC7060665 · DOI
  55. Sawa M.; Fantuzzi A.; Bombelli P.; Howe C. J.; Hellgardt K.; Nixon P. J. Electricity Generation from Digitally Printed Cyanobacteria. Nat. Commun. 2017, 8 (1), 1– 10. 10.1038/s41467-017-01084-4. 29109396 PMC5673893 · DOI
  56. Kehe J.; Kulesa A.; Ortiz A.; Ackerman C. M.; Thakku S. G.; Sellers D.; Kuehn S.; Gore J.; Friedman J.; Blainey P. C. Massively Parallel Screening of Synthetic Microbial Communities. Proc. Natl. Acad. Sci. U. S. A. 2019, 116 (26), 12804– 12809. 10.1073/pnas.1900102116. 31186361 PMC6600964 · DOI
  57. Hsu R. H.; Clark R. L.; Tan J. W.; Ahn J. C.; Gupta S.; Romero P. A.; Venturelli O. S. Microbial Interaction Network Inference in Microfluidic Droplets. Cell Syst. 2019, 9 (3), 229– 242.e4. 10.1016/j.cels.2019.06.008. 31494089 PMC6763379 · DOI
  58. Jo C.; Bernstein D. B.; Vaisman N.; Frydman H. M.; Segrè D. Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions. mSystems 2023, 8 ((2),). 10.1128/msystems.00017-21. PMC10134821 36802169 · DOI
  59. Pacheco A. R.; Osborne M. L.; Segrè D. Non-Additive Microbial Community Responses to Environmental Complexity. Nat. Commun. 2021, 12 (1), 1– 11. 10.1038/s41467-021-22426-3. 33888697 PMC8062479 · DOI
  60. Poyet M.; Groussin M.; Gibbons S. M.; Avila-Pacheco J.; Jiang X.; Kearney S. M.; Perrotta A. R.; Berdy B.; Zhao S.; Lieberman T. D.; Swanson P. K.; Smith M.; Roesemann S.; Alexander J. E.; Rich S. A.; Livny J.; Vlamakis H.; Clish C.; Bullock K.; Deik A.; Scott J.; Pierce K. A.; Xavier R. J.; Alm E. J. A Library of Human Gut Bacterial Isolates Paired with Longitudinal Multiomics Data Enables Mechanistic Microbiome Research. Nat. Med. 2019, 25 (9), 1442– 1452. 10.1038/s41591-019-0559-3. 31477907 · DOI
  61. van den Berg N. I.; Machado D.; Santos S.; Rocha I.; Chacón J.; Harcombe W.; Mitri S.; Patil K. R. Ecological Modelling Approaches for Predicting Emergent Properties in Microbial Communities. Nat. Ecol. Evol. 2022, 6 (7), 855– 865. 10.1038/s41559-022-01746-7. 35577982 PMC7613029 · DOI
  62. San León D.; Nogales J. Toward Merging Bottom–up and Top–down Model-Based Designing of Synthetic Microbial Communities. Curr. Opin. Microbiol. 2022, 69, 102169 10.1016/j.mib.2022.102169. 35763963 · DOI
  63. Qian Y.; Lan F.; Venturelli O. S. Towards a Deeper Understanding of Microbial Communities: Integrating Experimental Data with Dynamic Models. Curr. Opin. Microbiol. 2021, 62, 84– 92. 10.1016/j.mib.2021.05.003. 34098512 PMC8286325 · DOI
  64. Venturelli O. S.; Carr A. V.; Fisher G.; Hsu R. H.; Lau R.; Bowen B. P.; Hromada S.; Northen T.; Arkin A. P. Deciphering Microbial Interactions in Synthetic Human Gut Microbiome Communities. Mol. Syst. Biol. 2018, 14 (6), e8517 10.15252/msb.20178157. PMC6011841 29930200 · DOI
  65. Buffie C. G.; Bucci V.; Stein R. R.; McKenney P. T.; Ling L.; Gobourne A.; No D.; Liu H.; Kinnebrew M.; Viale A.; Littmann E.; Van Den Brink M. R. M.; Jenq R. R.; Taur Y.; Sander C.; Cross J. R.; Toussaint N. C.; Xavier J. B.; Pamer E. G. Precision Microbiome Reconstitution Restores Bile Acid Mediated Resistance to Clostridium Difficile. Nature 2015, 517 (7533), 205– 208. 10.1038/nature13828. 25337874 PMC4354891 · DOI · Paper page
  66. Marino S.; Baxter N. T.; Huffnagle G. B.; Petrosino J. F.; Schloss P. D. Mathematical Modeling of Primary Succession of Murine Intestinal Microbiota. Proc. Natl. Acad. Sci. U. S. A. 2014, 111 (1), 439– 444. 10.1073/pnas.1311322111. 24367073 PMC3890833 · DOI
  67. Goldford J. E.; Lu N.; Bajić D.; Estrela S.; Tikhonov M.; Sanchez-Gorostiaga A.; Segrè D.; Mehta P.; Sanchez A. Emergent Simplicity in Microbial Community Assembly. Science 2018, 361 (6401), 469– 474. 10.1126/science.aat1168. 30072533 PMC6405290 · DOI
  68. MacArthur R. Species Packing and Competitive Equilibrium for Many Species. Theor. Popul. Biol. 1970, 1 (1), 1– 11. 10.1016/0040-5809(70)90039-0. 5527624 · DOI
  69. Dukovski I.; Bajić D.; Chacón J. M.; Quintin M.; Vila J. C. C.; Sulheim S.; Pacheco A. R.; Bernstein D. B.; Riehl W. J.; Korolev K. S.; Sanchez A.; Harcombe W. R.; Segrè D. A Metabolic Modeling Platform for the Computation of Microbial Ecosystems in Time and Space (COMETS). Nat. Protoc. 2021, 16 (11), 5030– 5082. 10.1038/s41596-021-00593-3. 34635859 PMC10824140 · DOI
  70. García-Jiménez B.; García J. L.; Nogales J. FLYCOP: Metabolic Modeling-Based Analysis and Engineering Microbial Communities. Bioinformatics 2018, 34 (17), i954– i963. 10.1093/bioinformatics/bty561. 30423096 PMC6129290 · DOI
  71. Borer B.; Ataman M.; Hatzimanikatis V.; Or D. Modeling Metabolic Networks of Individual Bacterial Agents in Heterogeneous and Dynamic Soil Habitats (IndiMeSH). PLoS Comput. Bio.l 2019, 15 (6), e1007127 10.1371/journal.pcbi.1007127. PMC6583959 31216273 · DOI
  72. Shin S.; Venturelli O. S.; Zavala V. M. Scalable Nonlinear Programming Framework for Parameter Estimation in Dynamic Biological System Models. PLoS Comput. Biol. 2019, 15 (3), e1006828 10.1371/journal.pcbi.1006828. 30908479 PMC6467427 · DOI
  73. Clark R. L.; Connors B. M.; Stevenson D. M.; Hromada S. E.; Hamilton J. J.; Amador-Noguez D.; Venturelli O. S. Design of Synthetic Human Gut Microbiome Assembly and Butyrate Production. Nat. Commun. 2021, 12 (1), 1– 16. 10.1038/s41467-021-22938-y. 34059668 PMC8166853 · DOI
  74. Karkaria B. D.; Fedorec A. J. H.; Barnes C. P. Automated Design of Synthetic Microbial Communities. Nat. Commun. 2021, 12 (1), 1– 12. 10.1038/s41467-020-20756-2. 33510148 PMC7844305 · DOI
  75. Federici F.; Rudge T. J.; Pollak B.; Haseloff J.; Gutiérrez R. A. Synthetic Biology: Opportunities for Chilean Bioindustry and Education. Biol. Res. 2013, 46 (4), 383– 393. 10.4067/S0716-97602013000400010. 24510141 · DOI
  76. Anzalone A. V.; Koblan L. W.; Liu D. R. Genome Editing with CRISPR–Cas Nucleases, Base Editors, Transposases and Prime Editors. Nat. Biotechnol. 2020, 38 (7), 824– 844. 10.1038/s41587-020-0561-9. 32572269 · DOI · Paper page
  77. Miller J. C.; Tan S.; Qiao G.; Barlow K. A.; Wang J.; Xia D. F.; Meng X.; Paschon D. E.; Leung E.; Hinkley S. J.; Dulay G. P.; Hua K. L.; Ankoudinova I.; Cost G. J.; Urnov F. D.; Zhang H. S.; Holmes M. C.; Zhang L.; Gregory P. D.; Rebar E. J. A TALE Nuclease Architecture for Efficient Genome Editing. Nat. Biotechnol. 2011, 29 (2), 143– 148. 10.1038/nbt.1755. 21179091 · DOI · Paper page
  78. Urnov F. D.; Rebar E. J.; Holmes M. C.; Zhang H. S.; Gregory P. D. Genome Editing with Engineered Zinc Finger Nucleases. Nat. Rev. Genet. 2010, 11 (9), 636– 646. 10.1038/nrg2842. 20717154 · DOI · Paper page
  79. del Solar G.; Giraldo R.; Ruiz-Echevarría M. J.; Espinosa M.; Díaz-Orejas R. Replication and Control of Circular Bacterial Plasmids. Microbiol. Mol. Biol. Rev. 1998, 62 (2), 434– 464. 10.1128/MMBR.62.2.434-464.1998. 9618448 PMC98921 · DOI
  80. Gilbert C.; Crits-Christoph A.; Ledieu-Dherbécourt E.; Kang S. C.; Brumwell S. L.; Lee H. H.; Ostrov N. Design and Construction towards a Pan-Microbial Toolkit. bioRxiv 2024, 2024.02.23.58174 10.1101/2024.02.23.581749. · DOI
  81. Angelici B.; Mailand E.; Haefliger B.; Benenson Y. Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells. Cell. Rep. 2016, 16 (9), 2525– 2537. 10.1016/j.celrep.2016.07.061. 27545896 PMC5009115 · DOI
  82. Hanko E. K. R.; Paiva A. C.; Jonczyk M.; Abbott M.; Minton N. P.; Malys N. A Genome-Wide Approach for Identification and Characterisation of Metabolite-Inducible Systems. Nat. Commun. 2020, 11 (1), 1– 14. 10.1038/s41467-020-14941-6. 32139676 PMC7057948 · DOI
  83. Lai Y.; Hayashi N.; Lu T. K. Engineering the Human Gut Commensal Bacteroides Thetaiotaomicron with Synthetic Biology. Curr. Opin. Chem. Biol. 2022, 70, 102178 10.1016/j.cbpa.2022.102178. 35759819 · DOI
  84. Mitchell M. J.; Billingsley M. M.; Haley R. M.; Wechsler M. E.; Peppas N. A.; Langer R. Engineering Precision Nanoparticles for Drug Delivery. Nat. Rev. Drug Discovery 2021, 20 (2), 101– 124. 10.1038/s41573-020-0090-8. 33277608 PMC7717100 · DOI · Paper page
  85. Sugianto W.; Altin-Yavuzarslan G.; Tickman B. I.; Kiattisewee C.; Yuan S. F.; Brooks S. M.; Wong J.; Alper H. S.; Nelson A.; Carothers J. M. Gene Expression Dynamics in Input-Responsive Engineered Living Materials Programmed for Bioproduction. Mater. Today. Bio. 2023, 20, 100677 10.1016/j.mtbio.2023.100677. PMC10239009 37273790 · DOI
  86. Liu S.; Xu W. Engineered Living Materials-Based Sensing and Actuation. Front. Sens. 2020, 1, 586300 10.3389/fsens.2020.586300. · DOI
  87. Bressler E. M.; Adams S.; Liu R.; Colson Y. L.; Wong W. W.; Grinstaff M. W. Boolean Logic in Synthetic Biology and Biomaterials: Towards Living Materials in Mammalian Cell Therapeutics. Clin. Transl. Med. 2023, 13 (7), e1244 10.1002/ctm2.1244. 37386762 PMC10310979 · DOI
  88. Stanton B. C.; Nielsen A. A. K.; Tamsir A.; Clancy K.; Peterson T.; Voigt C. A. Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates. Nat. Chem. Biol. 2014, 10 (2), 99– 105. 10.1038/nchembio.1411. 24316737 PMC4165527 · DOI
  89. Tringe S. G. A Toolkit for Microbial Community Editing. Nat. Rev. Microbiol. 2022, 20 (7), 383– 383. 10.1038/s41579-022-00747-4. 35581476 · DOI
  90. Chen Z.; Jin W.; Hoover A.; Chao Y.; Ma Y. Decoding the Microbiome: Advances in Genetic Manipulation for Gut Bacteria. Trends Microbiol. 2023, 31 (11), 1143– 1161. 10.1016/j.tim.2023.05.007. 37394299 · DOI
  91. Burstein D.; Harrington L. B.; Strutt S. C.; Probst A. J.; Anantharaman K.; Thomas B. C.; Doudna J. A.; Banfield J. F. New CRISPR–Cas Systems from Uncultivated Microbes. Nature 2017, 542 (7640), 237– 241. 10.1038/nature21059. 28005056 PMC5300952 · DOI
  92. Van Der Helm E.; Genee H. J.; Sommer M. O. A. The Evolving Interface between Synthetic Biology and Functional Metagenomics. Nat. Chem. Biol. 2018, 14 (8), 752– 759. 10.1038/s41589-018-0100-x. 30013060 · DOI
  93. Anzalone A. V.; Koblan L. W.; Liu D. R. Genome Editing with CRISPR–Cas Nucleases, Base Editors, Transposases and Prime Editors. Nat. Biotechnol. 2020, 38 (7), 824– 844. 10.1038/s41587-020-0561-9. 32572269 · DOI · Paper page
  94. Citorik R. J.; Mimee M.; Lu T. K. Sequence-Specific Antimicrobials Using Efficiently Delivered RNA-Guided Nucleases. Nat. Biotechnol. 2014, 32 (11), 1141– 1145. 10.1038/nbt.3011. 25240928 PMC4237163 · DOI · Paper page
  95. Bikard D.; Euler C. W.; Jiang W.; Nussenzweig P. M.; Goldberg G. W.; Duportet X.; Fischetti V. A.; Marraffini L. A. Exploiting CRISPR-Cas Nucleases to Produce Sequence-Specific Antimicrobials. Nat. Biotechnol. 2014, 32 (11), 1146– 1150. 10.1038/nbt.3043. 25282355 PMC4317352 · DOI · Paper page
  96. Thibault D.; Jensen P. A.; Wood S.; Qabar C.; Clark S.; Shainheit M. G.; Isberg R. R.; van Opijnen T. Droplet Tn-Seq Combines Microfluidics with Tn-Seq for Identifying Complex Single-Cell Phenotypes. Nat. Commun. 2019, 10 (1), 5729 10.1038/s41467-019-13719-9. 31844066 PMC6914776 · DOI
  97. Jana B.; Liu X.; Dénéréaz J.; Park H.; Leshchiner D.; Liu B.; Gallay C.; Veening J.-W.; van Opijnen T.; Zhu J. CRISPRi-TnSeq: A Genome-Wide High-Throughput Tool for Bacterial Essential-Nonessential Genetic Interaction Mapping. Nat. Microbiol. 2024, 543074 10.1038/s41564-024-01759-x. PMC11371651 39030344 · DOI
  98. Morin M.; Pierce E. C.; Dutton R. J. Changes in the Genetic Requirements for Microbial Interactions with Increasing Community Complexity. Elife 2018, 7, e37032 10.7554/eLife.37072. PMC6175579 30211673 · DOI
  99. English M. A.; Alcantar M. A.; Collins J. J. A Self-propagating, Barcoded Transposon System for the Dynamic Rewiring of Genomic Networks. Mol. Syst. Biol. 2023, 19 (6), 11398 10.15252/msb.202211398. PMC10258560 36970845 · DOI
  100. Miravet-Verde S.; Mazzolini R.; Segura-Morales C.; Broto A.; Lluch-Senar M.; Serrano L. ProTInSeq: Transposon Insertion Tracking by Ultra-Deep DNA Sequencing to Identify Translated Large and Small ORFs. Nat. Commun. 2024, 15 (1), 1– 17. 10.1038/s41467-024-46112-2. 38453908 PMC10920889 · DOI
  101. Kirsch J. M.; Hryckowian A. J.; Duerkop B. A. A Metagenomics Pipeline Reveals Insertion Sequence-Driven Evolution of the Microbiota. Cell Host Microbe 2024, 32 (5), 739– 754.e4. 10.1016/j.chom.2024.03.005. 38565143 PMC11081829 · DOI
  102. Peng C.; Guo Y.; Ren S.; Li C.; Liu F.; Lu F. SPSED: A Signal Peptide Secretion Efficiency Database. Front. Bioeng. Biotechnol. 2022, 9, 819789 10.3389/fbioe.2021.819789. 35118058 PMC8804277 · DOI
  103. Gonzalez-Perez D.; Ratcliffe J.; Tan S. K.; Wong M. C. M.; Yee Y. P.; Nyabadza N.; Xu J. H.; Wong T. S.; Tee K. L. Random and Combinatorial Mutagenesis for Improved Total Production of Secretory Target Protein in Escherichia Coli. Sci. Rep. 2021, 11 (1), 1– 13. 10.1038/s41598-021-84859-6. 33674702 PMC7935960 · DOI
  104. Teufel F.; Almagro Armenteros J. J.; Johansen A. R.; Gíslason M. H.; Pihl S. I.; Tsirigos K. D.; Winther O.; Brunak S.; von Heijne G.; Nielsen H. SignalP 6.0 Predicts All Five Types of Signal Peptides Using Protein Language Models. Nat. Biotechnol. 2022, 40 (7), 1023 10.1038/s41587-021-01156-3. 34980915 PMC9287161 · DOI
  105. Glass D. S.; Riedel-Kruse I. H. A Synthetic Bacterial Cell-Cell Adhesion Toolbox for Programming Multicellular Morphologies and Patterns. Cell 2018, 174 (3), 649– 658.e16. 10.1016/j.cell.2018.06.041. 30033369 · DOI
  106. Ronda C.; Chen S. P.; Cabral V.; Yaung S. J.; Wang H. H. Metagenomic Engineering of the Mammalian Gut Microbiome in Situ. Nat. Methods 2019, 16 (2), 167– 170. 10.1038/s41592-018-0301-y. 30643213 PMC6467691 · DOI
  107. Rubin B. E.; Diamond S.; Cress B. F.; Crits-Christoph A.; Lou Y. C.; Borges A. L.; Shivram H.; He C.; Xu M.; Zhou Z.; Smith S. J.; Rovinsky R.; Smock D. C. J.; Tang K.; Owens T. K.; Krishnappa N.; Sachdeva R.; Barrangou R.; Deutschbauer A. M.; Banfield J. F.; Doudna J. A. Species- and Site-Specific Genome Editing in Complex Bacterial Communities. Nat. Microbiol. 2022, 7 (1), 34– 47. 10.1038/s41564-021-01014-7. 34873292 PMC9261505 · DOI
  108. Tsoi R.; Wu F.; Zhang C.; Bewick S.; Karig D.; You L. Metabolic Division of Labor in Microbial Systems. Proc. Natl. Acad. Sci. U. S. A. 2018, 115 (10), 2526– 2531. 10.1073/pnas.1716888115. 29463749 PMC5877992 · DOI
  109. Zhang H.; Li Z.; Pereira B.; Stephanopoulos G. Engineering E. Coli–E. Coli Cocultures for Production of Muconic Acid from Glycerol. Microb. Cell Fact. 2015, 14 (1), 134 10.1186/s12934-015-0319-0. 26369810 PMC4570557 · DOI
  110. Wang M.; Chen X.; Liu X.; Fang Y.; Zheng X.; Huang T.; Tang Y. Q.; Ackermann M.; Nie Y.; Wu X. L. Even Allocation of Benefits Stabilizes Microbial Community Engaged in Metabolic Division of Labor. Cell Rep. 2022, 40 (13), 111410 10.1016/j.celrep.2022.111410. 36170826 · DOI
  111. Gutiérrez Mena J.; Kumar S.; Khammash M. Dynamic Cybergenetic Control of Bacterial Co-Culture Composition via Optogenetic Feedback. Nat. Commun. 2022, 13 (1), 1– 16. 10.1038/s41467-022-32392-z. 35973993 PMC9381578 · DOI
  112. Fedorec A. J. H.; Karkaria B. D.; Sulu M.; Barnes C. P. Single Strain Control of Microbial Consortia. Nat. Commun. 2021, 12 (1), 1– 12. 10.1038/s41467-021-22240-x. 33785746 PMC8010080 · DOI
  113. Moraïs S.; Mazor M.; Tovar-Herrera O.; Zehavi T.; Zorea A.; Ifrach M.; Bogumil D.; Brandis A.; Walter J.; Elia N.; Gur E.; Mizrahi I. Plasmid-Encoded Toxin Defence Mediates Mutualistic Microbial Interactions. Nat. Microbiol. 2024, 9 (1), 108– 119. 10.1038/s41564-023-01521-9. 38151647 PMC10769881 · DOI
  114. Huang R.; Shao J.; Xu Z.; Chen Y.; Liu Y.; Wang D.; Feng H.; Xun W.; Shen Q.; Zhang N.; Zhang R. A Toxin-Mediated Policing System in Bacillus Optimizes Division of Labor via Penalizing Cheater-like Nonproducers. Elife 2023, 12, e84743 10.7554/eLife.84743. 37096874 PMC10171868 · DOI
  115. Liao M. J.; Din M. O.; Tsimring L.; Hasty J. Rock-Paper-Scissors: Engineered Population Dynamics Increase Genetic Stability. Science 2019, 365 (6457), 1045– 1049. 10.1126/science.aaw0542. 31488693 PMC6988775 · DOI
  116. Diao W.; Guo L.; Ding Q.; Gao C.; Hu G.; Chen X.; Li Y.; Zhang L.; Chen W.; Chen J.; Liu L. Reprogramming Microbial Populations Using a Programmed Lysis System to Improve Chemical Production. Nat. Commun. 2021, 12 (1), 1– 14. 10.1038/s41467-021-27226-3. 34824227 PMC8617184 · DOI
  117. Kim H. J.; Boedicker J. Q.; Choi J. W.; Ismagilov R. F. Defined Spatial Structure Stabilizes a Synthetic Multispecies Bacterial Community. Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (47), 18188– 18193. 10.1073/pnas.0807935105. 19011107 PMC2587551 · DOI
  118. Doshi A.; Shaw M.; Tonea R.; Moon S.; Minyety R.; Doshi A.; Laine A.; Guo J.; Danino T. Engineered Bacterial Swarm Patterns as Spatial Records of Environmental Inputs. Nat. Chem. Biol. 2023, 19 (7), 878– 886. 10.1038/s41589-023-01325-2. 37142806 · DOI
  119. Oliver Huidobro M.; Tica J.; Wachter G. K. A.; Isalan M. Synthetic Spatial Patterning in Bacteria: Advances Based on Novel Diffusible Signals. Microb. Biotechnol. 2022, 15 (6), 1685– 1694. 10.1111/1751-7915.13979. 34843638 PMC9151330 · DOI
  120. Basu S.; Gerchman Y.; Collins C. H.; Arnold F. H.; Weiss R. A Synthetic Multicellular System for Programmed Pattern Formation. Nature 2005, 434 (7037), 1130– 1134. 10.1038/nature03461. 15858574 · DOI
  121. Li X.; Rizik L.; Kravchik V.; Khoury M.; Korin N.; Daniel R. Synthetic Neural-like Computing in Microbial Consortia for Pattern Recognition. Nat. Commun. 2021, 12 (1), 1– 12. 10.1038/s41467-021-23336-0. 34035266 PMC8149857 · DOI
  122. Curatolo A. I.; Zhou N.; Zhao Y.; Liu C.; Daerr A.; Tailleur J.; Huang J. Cooperative Pattern Formation in Multi-Component Bacterial Systems through Reciprocal Motility Regulation. Nat. Phys. 2020, 16 (11), 1152– 1157. 10.1038/s41567-020-0964-z. · DOI
  123. Levskaya A.; Chevalier A. A.; Tabor J. J.; Simpson Z. B.; Lavery L. A.; Levy M.; Davidson E. A.; Scouras A.; Ellington A. D.; Marcotte E. M.; Voigt C. A. Engineering Escherichia Coli to See Light. Nature 2005, 438 (7067), 441– 442. 10.1038/nature04405. 16306980 · DOI
  124. Genetically Encoding Colors and Images into Bioengineered Microbial Materials. Nat. Biotechnol. 2024, 1– 2. 10.1038/s41587-024-02200-8. 38565974 · DOI
  125. Liang Y.; Ma A.; Zhuang G. Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles. Front. Microbiol. 2022, 13, 829717 10.3389/fmicb.2022.829717. 35283862 PMC8905317 · DOI · Paper page
  126. Chang C. Y.; Vila J. C. C.; Bender M.; Li R.; Mankowski M. C.; Bassette M.; Borden J.; Golfier S.; Sanchez P. G. L.; Waymack R.; Zhu X.; Diaz-Colunga J.; Estrela S.; Rebolleda-Gomez M.; Sanchez A. Engineering Complex Communities by Directed Evolution. Nat. Ecol. Evol. 2021, 5 (7), 1011– 1023. 10.1038/s41559-021-01457-5. 33986540 PMC8263491 · DOI
  127. Ponomarova O.; Gabrielli N.; Sévin D. C.; Mülleder M.; Zirngibl K.; Bulyha K.; Andrejev S.; Kafkia E.; Typas A.; Sauer U.; Ralser M.; Patil K. R. Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow. Cell Syst. 2017, 5 (4), 345– 357.e6. 10.1016/j.cels.2017.09.002. 28964698 PMC5660601 · DOI
  128. Lee J. W.; Chan C. T. Y.; Slomovic S.; Collins J. J. Next-Generation Biocontainment Systems for Engineered Organisms. Nat. Chem. Biol. 2018, 14 (6), 530– 537. 10.1038/s41589-018-0056-x. 29769737 · DOI
  129. Snow A. A. Transgenic Crops—Why Gene Flow Matters. Nat. Biotechnol. 2002, 20 (6), 542– 542. 10.1038/nbt0602-542. 12042845 · DOI
  130. Chilcutt C. F.; Tabashnik B. E. Contamination of Refuges by Bacillus Thuringiensis Toxin Genes from Transgenic Maize. Proc. Natl. Acad. Sci. U. S. A. 2004, 101 (20), 7526– 7529. 10.1073/pnas.0400546101. 15136739 PMC419639 · DOI
  131. Cooper R. M.; Tsimring L.; Hasty J. Inter-Species Population Dynamics Enhance Microbial Horizontal Gene Transfer and Spread of Antibiotic Resistance. Elife 2017, 6. 10.7554/eLife.25950. PMC5701796 29091031 · DOI
  132. Rovner A. J.; Haimovich A. D.; Katz S. R.; Li Z.; Grome M. W.; Gassaway B. M.; Amiram M.; Patel J. R.; Gallagher R. R.; Rinehart J.; Isaacs F. J. Recoded Organisms Engineered to Depend on Synthetic Amino Acids. Nature 2015, 518 (7537), 89– 93. 10.1038/nature14095. 25607356 PMC4590768 · DOI
  133. Stirling F.; Bitzan L.; O’Keefe S.; Redfield E.; Oliver J. W. K.; Way J.; Silver P. A. Rational Design of Evolutionarily Stable Microbial Kill Switches. Mol. Cell 2017, 68 (4), 686– 697.e3. 10.1016/j.molcel.2017.10.033. 29149596 PMC5812007 · DOI
  134. Hayashi N.; Lai Y.; Fuerte-Stone J.; Mimee M.; Lu T. K. Cas9-Assisted Biological Containment of a Genetically Engineered Human Commensal Bacterium and Genetic Elements. Nat. Commun. 2024, 15 (1), 1– 17. 10.1038/s41467-024-45893-w. 38453913 PMC10920895 · DOI
  135. Tang T. C.; Tham E.; Liu X.; Yehl K.; Rovner A. J.; Yuk H.; de la Fuente-Nunez C.; Isaacs F. J.; Zhao X.; Lu T. K. Hydrogel-Based Biocontainment of Bacteria for Continuous Sensing and Computation. Nat. Chem. Biol. 2021, 17 (6), 724– 731. 10.1038/s41589-021-00779-6. 33820990 PMC9269716 · DOI
  136. Shepherd E. S.; Deloache W. C.; Pruss K. M.; Whitaker W. R.; Sonnenburg J. L. An Exclusive Metabolic Niche Enables Strain Engraftment in the Gut Microbiota. Nature 2018, 557 (7705), 434– 438. 10.1038/s41586-018-0092-4. 29743671 PMC6126907 · DOI · Paper page

Cited by

Sorted by citations

Authors
Wang, S., Zhan, Y., Jiang, X., & Lai, Y.
Affiliations
  • Hong Kong University of Science and Technology (HK)
  • State Key Laboratory of Pharmaceutical Biotechnology (CN)
Corresponding author
Lai, Yong
ORCID
Venue
ACS Synthetic Biology
Publisher
American Chemical Society (ACS)
Published
2024-08-22
Volume
13
Issue
9
Pages
2653-2666
ISSN
2161-5063 (ISSN-L)
DOI
10.1021/acssynbio.4c00313
PMC
PMC11421429
OpenAlex
W4401744392
Cited by
50
References
6
Citations by year
2026: 30 · 2025: 19 · 2024: 1
FWCI
1.97
Type
journal article
Language
en
Open access
Licence
Locations
  • ACS Synthetic Biology (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
Funders
  • Research Grants Council, University Grants Committee (26100423)
  • Hong Kong University of Science and Technology (R9829)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
  • Physical Sciences › Environmental Science › Environmental Engineering › Microbial Fuel Cells and Bioremediation
  • Physical Sciences › Environmental Science › Environmental Engineering › Microbial Applications in Construction Materials
Keywords
engineered living materials, microbial consortia, synthetic microbial consortia, top-down design, bottom-up design, synthetic biology, biomaterials, microbial interactions, ecological reconstruction
MeSH terms
Bacteria, Ecosystem, Microbial Interactions, Synthetic Biology, Microbial Consortia

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review