Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota
Open accessAbstract
Engineering commensal organisms for challenging applications, such as modulating the gut ecosystem, is hampered by the lack of genetic parts. Here, we describe promoters, ribosome-binding sites, and inducible systems for use in the commensal bacterium Bacteroides thetaiotaomicron, a prevalent and stable resident of the human gut. We achieve up to 10,000-fold range in constitutive gene expression and 100-fold regulation of gene expression with inducible promoters and use these parts to record DNA-encoded memory in the genome. We use CRISPR interference (CRISPRi) for regulated knockdown of recombinant and endogenous gene expression to alter the metabolic capacity of B. thetaiotaomicron and its resistance to antimicrobial peptides. Finally, we show that inducible CRISPRi and recombinase systems can function in B. thetaiotaomicron colonizing the mouse gut. These results provide a blueprint for engineering new chassis and a resource to engineer Bacteroides for surveillance of or therapeutic delivery to the gut microbiome.
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Recent research in other non-PD conditions has highlighted the potential transferability of targeted approaches like engineered symbiotic bacteria, CRISPR-Cas9 technologies, and bacteriophages for targeting specific bacterial populations.
“Recent research in other non-PD conditions has highlighted the potential transferability of targeted approaches like engineered symbiotic bacteria, CRISPR-Cas9 technologies, and bacteriophages for targeting specific bacterial populations [171–173].”
From The gut–brain axis in early Parkinson’s disease: from prodrome to prevention (2025) · cites this paper as [173]
The Introduction describes engineering the commensal B. thetaiotaomicron and validating CRISPRi circuits in bacteria colonizing the mouse gut. The Discussion proposes future targeted microbiome therapeutics, but the paper does not demonstrate targeting specific bacterial populations. The accompanying citations may address the sentence’s other approaches; this paper supports the engineered-commensal example. (LLM, conf=0.82)
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“CRISPR interference (CRISPRi) employs a catalytically inactive version of the endonuclease Cas9 (dCas9) to regulate gene expression at target DNA sequences by blocking transcription by RNA polymerase (Qi et al., 2013).”
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“Recent research in other non-PD conditions has highlighted the potential transferability of targeted approaches like engineered symbiotic bacteria, CRISPR-Cas9 technologies, and bacteriophages for targeting specific bacterial populations [171–173].”
- Authors
- Mimee, M., Tucker, A. C., Voigt, C. A., & Lu, T. K.
- Affiliations
- Massachusetts Institute of Technology (US)
- Corresponding author
- Lu, Timothy K.
- Venue
- Cell Systems
- Publisher
- Elsevier BV
- Published
- 2015-07
- Volume
- 1
- Issue
- 1
- Pages
- 62-71
- ISSN
- 2405-4712 (ISSN-L)
- PMC
- PMC4762051
- OpenAlex
- W2124374420
- Cited by
- 387
- References
- 5
- Citations by year
- 2026: 29 · 2025: 38 · 2024: 41 · 2023: 41 · 2022: 42 · 2021: 31 · 2020: 41 · 2019: 31 · 2018: 29 · 2017: 34 · 2016: 24 · 2015: 6
- FWCI
- 13.47
- Type
- journal article
- Language
- en
- Update notices
- erratum (2016-03-23)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell Systems (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-nd)
- Funders
- Defense Advanced Research Projects Agency (CLIO N66001-12-C-4016)
- National Institutes of Health (GM095765, 1R01EB017755, 1DP2OD008435, P50GM098792)
- National Science Foundation (EEC-0540879)
- Office of Naval Research (N00014-13-1-0424)
- Defense Threat Reduction Agency (HDTRA1-14-1-0007)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- Bacteroides thetaiotaomicron, synthetic biology parts, inducible promoters, ribosome binding site, CRISPR interference, gene expression regulation, antimicrobial peptide resistance, metabolic engineering, commensal bacteria
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