Probiotic acoustic biosensors for noninvasive imaging of gut inflammation
-
1.
California Institute of Technology
-
2.
Rice University
Abstract
Inflammatory bowel diseases (IBD) affect millions of people globally, result in severe symptoms, and are difficult to diagnose and monitor – often necessitating the use of invasive and costly methods such as colonoscopies or endoscopies. Engineered gut bacteria offer a promising alternative due to their ability to persist in the gastrointestinal (GI) tract and sense and respond to specific environmental signals. However, probiotics that have previously been engineered to report on inflammatory and other disease biomarkers in the Gl tract rely on fluorescent or bioluminescent reporters, whose signals cannot be resolved in situ due to the poor penetration of light in tissue, or on colorimetric reporters which rely on plating feces. To overcome this limitation, we introduce probiotic biosensors that can be imaged in situ using ultrasound – a widely available, inexpensive imaging modality providing sub-mm spatial resolution deep inside the body. These biosensors are based on the clinically approved probiotic bacterium E. coli Nissle, which we engineered to transiently colonize the GI tract, sense inflammatory biomarkers, and respond by expressing air-filled sound-scattering protein nanostructures called gas vesicles. After optimizing biomolecular signaling circuits to respond sensitively to the biomarkers thiosulfate and tetrathionate and produce strong and stable ultrasound contrast, we validated our living biosensors in vivo by noninvasively imaging antibiotic-induced inflammation in mice. By connecting cell-based diagnostic agents to ultrasound, these probiotic biosensors will potentially make it easier and cheaper to diagnose and monitor IBD or other GI conditions.
Copyright and License (English)
© The Author(s) 2025. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Acknowledgement (English)
The authors thank the Caltech Flow Cytometry & Cell Sorting Facility for assistance with flow cytometry, Dr. Nathan Dalleska & the Water and Environment Lab (WEL) at Caltech for assistance with IC-MS, and Dr. Genevieve Remmers & IDEXX Laboratories for assistance with histopathology sample preparation and interpretation. The authors would also like to thank Dr. Moshe Baruch for assistance with sending the initial thiosulfate and tetrathionate sensor plasmids.
Funding (English)
MTB was supported by an NSF GRFP fellowship. MTB was supported by an NSF GRFP fellowship. Related research in the Shapiro Laboratory is supported by the David and Lucille Packard Foundation and the Dreyfus Foundation. MGS is an investigator of the Howard Hughes Medical Institute.
Contributions (English)
M.T.B. and M.G.S. conceived the study. M.T.B., L.Z., and J.H.K. planned and performed experiments. M.T.B. analyzed data. J.J.T. provided reagents and input on the research design and manuscript. M.T.B. and M.G.S. wrote the manuscript with input from all other authors. M.G.S. supervised the research.
Data Availability (English)
Plasmids will be made available through Addgene upon publication (Addgene IDs 232468 – 232475). All data are available within the article, its Supplementary Information, and the Source Data file. Raw unprocessed data and other materials are available upon request from the corresponding author. Source data are provided with this paper.
Code Availability (English)
Ultrasound data acquisition and analysis code are available on the Shapiro Lab GitHub at https://github.com/shapiro-lab in the “Probiotic-GI-Imaging” repository113. Source data are provided with this paper.
Supplemental Material
Files
s41467-025-62569-1.pdf
Files
(59.9 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:1094108ac12f21e2e59acbeb49bac8aa
|
17.1 kB | Preview Download |
|
md5:65db41b2e67740cff23fa1446f31437d
|
91.8 kB | Download |
|
md5:0ae5fa4d7a000e46ba4ab6dd3016e706
|
5.5 MB | Preview Download |
|
md5:72139b8c289f5637e018f721652e7a45
|
87.1 kB | Preview Download |
|
md5:3702cdaa92c2aa5eebc131635b6f047b
|
9.6 MB | Preview Download |
|
md5:c410ce8265601aaeb65b2330bc27cd7e
|
9.2 MB | Preview Download |
|
md5:138448f51522d429652ecc28a19161c1
|
10.1 MB | Preview Download |
|
md5:4ad83bbf31d33c56b548d34830c19bef
|
10.9 MB | Preview Download |
|
md5:b23f9739c30a197f67733c1492338de5
|
10.2 MB | Preview Download |
|
md5:7f74aa41d00967ec65fde1301f9be9e9
|
13.9 kB | Download |
|
md5:614981db1867e9a39590309287ebdc52
|
118.0 kB | Preview Download |
|
md5:76e0c99247af9ae3299b13723b82fd99
|
4.0 MB | Preview Download |
Additional details
Identifiers
- PMCID
- PMC12379287
- PMID
- 40855083
Related works
- Describes
- Journal Article: https://rdcu.be/eFJQ6 (ReadCube)
- Journal Article: PMC12379287 (PMCID)
- Journal Article: 40855083 (PMID)
- Is new version of
- Discussion Paper: 10.1101/2024.09.23.614598 (DOI)
- Is supplemented by
- Software: https://github.com/shapiro-lab (URL)
Funding
- National Science Foundation
- Graduate Research Fellowship Program -
- Pew Charitable Trusts
- United States Army Research Office
- W911NF-19-D-0001
- National Institutes of Health
- NIAID R01AI155586
- David and Lucile Packard Foundation
- Camille and Henry Dreyfus Foundation
- Howard Hughes Medical Institute
Dates
- Accepted
-
2025-07-23