A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples
Gut metabolites are pivotal mediators of host-microbiome interactions and provide an important window on human physiology and disease. However, current methods to monitor gut metabolites rely on heavy and expensive technologies such as liquid chromatography-mass spectrometry (LC-MS). In that context...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-08-01
|
| Series: | Frontiers in Bioengineering and Biotechnology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fbioe.2022.859600/full |
| _version_ | 1798041947552612352 |
|---|---|
| author | Ana Zúñiga Geisler Muñoz-Guamuro Lucile Boivineau Pauline Mayonove Ismael Conejero Georges-Philippe Pageaux Romain Altwegg Jerome Bonnet |
| author_facet | Ana Zúñiga Geisler Muñoz-Guamuro Lucile Boivineau Pauline Mayonove Ismael Conejero Georges-Philippe Pageaux Romain Altwegg Jerome Bonnet |
| author_sort | Ana Zúñiga |
| collection | DOAJ |
| description | Gut metabolites are pivotal mediators of host-microbiome interactions and provide an important window on human physiology and disease. However, current methods to monitor gut metabolites rely on heavy and expensive technologies such as liquid chromatography-mass spectrometry (LC-MS). In that context, robust, fast, field-deployable, and cost-effective strategies for monitoring fecal metabolites would support large-scale functional studies and routine monitoring of metabolites biomarkers associated with pathological conditions. Living cells are an attractive option to engineer biosensors due to their ability to detect and process many environmental signals and their self-replicating nature. Here we optimized a workflow for feces processing that supports metabolite detection using bacterial biosensors. We show that simple centrifugation and filtration steps remove host microbes and support reproducible preparation of a physiological-derived media retaining important characteristics of human feces, such as matrix effects and endogenous metabolites. We measure the performance of bacterial biosensors for benzoate, lactate, anhydrotetracycline, and bile acids, and find that they are highly sensitive to fecal matrices. However, encapsulating the bacteria in hydrogel helps reduce this inhibitory effect. Sensitivity to matrix effects is biosensor-dependent but also varies between individuals, highlighting the need for case-by-case optimization for biosensors’ operation in feces. Finally, by detecting endogenous bile acids, we demonstrate that bacterial biosensors could be used for future metabolite monitoring in feces. This work lays the foundation for the optimization and use of bacterial biosensors for fecal metabolites monitoring. In the future, our method could also allow rapid pre-prototyping of engineered bacteria designed to operate in the gut, with applications to in situ diagnostics and therapeutics. |
| first_indexed | 2024-04-11T22:28:41Z |
| format | Article |
| id | doaj.art-ad091888091b46b883381d985bbc4b53 |
| institution | Directory Open Access Journal |
| issn | 2296-4185 |
| language | English |
| last_indexed | 2024-04-11T22:28:41Z |
| publishDate | 2022-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioengineering and Biotechnology |
| spelling | doaj.art-ad091888091b46b883381d985bbc4b532022-12-22T03:59:34ZengFrontiers Media S.A.Frontiers in Bioengineering and Biotechnology2296-41852022-08-011010.3389/fbioe.2022.859600859600A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samplesAna Zúñiga0Geisler Muñoz-Guamuro1Lucile Boivineau2Pauline Mayonove3Ismael Conejero4Georges-Philippe Pageaux5Romain Altwegg6Jerome Bonnet7Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, FranceCentre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, FranceHepatogastroenterology and Bacteriology Service at CHU Montpellier, University of Montpellier, Montpellier, FranceCentre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, FranceDepartment of Psychiatry, CHU Nimes, University of Montpellier, Montpellier, FranceHepatogastroenterology and Bacteriology Service at CHU Montpellier, University of Montpellier, Montpellier, FranceHepatogastroenterology and Bacteriology Service at CHU Montpellier, University of Montpellier, Montpellier, FranceCentre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, FranceGut metabolites are pivotal mediators of host-microbiome interactions and provide an important window on human physiology and disease. However, current methods to monitor gut metabolites rely on heavy and expensive technologies such as liquid chromatography-mass spectrometry (LC-MS). In that context, robust, fast, field-deployable, and cost-effective strategies for monitoring fecal metabolites would support large-scale functional studies and routine monitoring of metabolites biomarkers associated with pathological conditions. Living cells are an attractive option to engineer biosensors due to their ability to detect and process many environmental signals and their self-replicating nature. Here we optimized a workflow for feces processing that supports metabolite detection using bacterial biosensors. We show that simple centrifugation and filtration steps remove host microbes and support reproducible preparation of a physiological-derived media retaining important characteristics of human feces, such as matrix effects and endogenous metabolites. We measure the performance of bacterial biosensors for benzoate, lactate, anhydrotetracycline, and bile acids, and find that they are highly sensitive to fecal matrices. However, encapsulating the bacteria in hydrogel helps reduce this inhibitory effect. Sensitivity to matrix effects is biosensor-dependent but also varies between individuals, highlighting the need for case-by-case optimization for biosensors’ operation in feces. Finally, by detecting endogenous bile acids, we demonstrate that bacterial biosensors could be used for future metabolite monitoring in feces. This work lays the foundation for the optimization and use of bacterial biosensors for fecal metabolites monitoring. In the future, our method could also allow rapid pre-prototyping of engineered bacteria designed to operate in the gut, with applications to in situ diagnostics and therapeutics.https://www.frontiersin.org/articles/10.3389/fbioe.2022.859600/fullsynthetic biologydiagnosticswhole-cell biosensorengineered bacteriametabolite detectiongut microbiome |
| spellingShingle | Ana Zúñiga Geisler Muñoz-Guamuro Lucile Boivineau Pauline Mayonove Ismael Conejero Georges-Philippe Pageaux Romain Altwegg Jerome Bonnet A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples Frontiers in Bioengineering and Biotechnology synthetic biology diagnostics whole-cell biosensor engineered bacteria metabolite detection gut microbiome |
| title | A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples |
| title_full | A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples |
| title_fullStr | A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples |
| title_full_unstemmed | A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples |
| title_short | A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples |
| title_sort | rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples |
| topic | synthetic biology diagnostics whole-cell biosensor engineered bacteria metabolite detection gut microbiome |
| url | https://www.frontiersin.org/articles/10.3389/fbioe.2022.859600/full |
| work_keys_str_mv | AT anazuniga arapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT geislermunozguamuro arapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT lucileboivineau arapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT paulinemayonove arapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT ismaelconejero arapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT georgesphilippepageaux arapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT romainaltwegg arapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT jeromebonnet arapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT anazuniga rapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT geislermunozguamuro rapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT lucileboivineau rapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT paulinemayonove rapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT ismaelconejero rapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT georgesphilippepageaux rapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT romainaltwegg rapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples AT jeromebonnet rapidandstandardizedworkflowforfunctionalassessmentofbacterialbiosensorsinfecalsamples |