Living biosensor designs
Engineer safe bacteria into living sensors. Every design pairs a non-pathogenic BSL-1 / GRAS chassis with a CRISPR-based sensing circuit (dCas9 / CRISPRi) that detects an analyte and produces a readable output. Clone any design to adapt it to your target.
Alkane/oil sensor (AlkS + CRISPRa)
Detects medium-chain alkanes (diesel / crude-oil contamination). The AlkS regulator gates a CRISPRa circuit driving a fluorescent reporter, in the solvent-tolerant chassis P. putida KT2440.
Androgen sensor (AR + CRISPRa)
Detects androgens (testosterone and anabolic-steroid mimics) in water and sport/clinical samples using the human androgen receptor expressed in GRAS yeast — a eukaryotic sensing class bacteria cannot do — gating a CRISPRa circuit driving a fluorescent reporter.
Arsenic AND mercury gate (dual heavy-metal)
A two-input AND gate that fires only when BOTH arsenic and mercury are present — reducing false positives and flagging co-contaminated water. ArsR drives the sgRNA and MerR drives dCas9, so CRISPRi repression (and the readout) needs both metals.
Arsenic ratiometric quantifier
Quantifies arsenic with two reporters: an arsenic-driven green channel over a constitutive red channel. The green/red ratio cancels out cell number, growth, and instrument variation — giving a robust, self-normalizing readout for field quantitation.
Arsenic water sensor (ArsR + CRISPRi)
Detects arsenite in drinking water. The validated ArsR/Pars sensing module gates an sgRNA that, with dCas9, represses a constitutive sfGFP reporter (CRISPRi inverter). Built in safe E. coli K-12.
Bacterial contamination sensor (AI-2 + CRISPRi)
Flags general bacterial contamination by sensing autoinducer-2 (AI-2), the inter-species quorum signal made by most bacteria. The LsrR/AI-2 system gates a CRISPRi circuit driving a visible pigment, in safe E. coli K-12.
Benzoate sensor (BenM + CRISPRi)
Detects benzoate, a common aromatic pollutant and degradation intermediate. The BenM LysR-family regulator gates a CRISPRi circuit driving a visible pigment, in P. putida KT2440.
Cadmium sensor (CadC + CRISPRi)
Detects toxic cadmium Cd(II) in water and soil. The CadC metal-responsive repressor gates a CRISPRi circuit driving sfGFP, in spore-forming Bacillus subtilis 168 for field-storable testing.
Cadmium sensor (CadR + CRISPRi)
Detects cadmium in industrial wastewater. A CadR/CadC metal-responsive regulator gates a CRISPRi circuit driving a fluorescent reporter, in the robust GRAS industrial chassis Corynebacterium glutamicum.
Cholera sensor (CAI-1 + CRISPRa)
Detects Vibrio cholerae by sensing its species-specific quorum signal CAI-1. The CqsS receptor gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12 — no live pathogen required.
Choline sensor (BetI + CRISPRi)
Detects choline, a dietary precursor of the cardiovascular-risk metabolite TMA/TMAO in the gut. The Marionette BetI sensor gates a CRISPRi circuit driving a fluorescent reporter, in the probiotic E. coli Nissle 1917.
Chromate sensor (ChrR + CRISPRi)
Detects toxic hexavalent chromium (chromate) in industrial water. The ChrR chromate-responsive regulator gates a CRISPRi circuit driving a fluorescent reporter, in the robust GRAS industrial chassis Corynebacterium glutamicum.
Copper sensor (ACE1 + CRISPRa)
Detects copper in water using the native yeast copper-responsive activator ACE1 and its CUP1 promoter, gating a CRISPRa circuit driving a fluorescent reporter, in GRAS baker's yeast.
Copper soil sensor (CueR + CRISPRi)
Detects bioavailable copper Cu(I)/Cu(II) in soil and water. The CueR copper-responsive regulator gates a CRISPRi circuit driving a visible chromoprotein, in the robust environmental chassis P. putida KT2440.
Crown-gall sensor (TraR/3OC8-HSL + CRISPRi)
Detects the plant pathogen Agrobacterium tumefaciens via its 3-oxo-C8-HSL quorum signal. The TraR receptor gates a CRISPRi circuit driving a visible pigment, in the soil chassis P. putida KT2440 — for agricultural crown-gall surveillance.
Cuminate sensor (CymR + CRISPRa)
Detects cuminate (p-isopropylbenzoate), a terpenoid-degradation marker. The native P. putida CymR sensor gates a CRISPRa circuit driving a fluorescent reporter, in P. putida KT2440.
DAPG biocontrol sensor (PhlF + CRISPRi)
Detects 2,4-diacetylphloroglucinol (DAPG), an antibiotic made by biocontrol pseudomonads in soil. The Marionette PhlF sensor gates a CRISPRi circuit driving a visible pigment, in the soil chassis P. putida KT2440 — useful for monitoring soil biocontrol activity.
EHEC sensor (AI-3/QseC + CRISPRi)
Detects enterohemorrhagic E. coli (EHEC) signalling via the AI-3 / host-adrenergic pathway. The QseC/QseB sensor gates a CRISPRi circuit driving a fluorescent reporter, in the probiotic gut chassis E. coli Nissle 1917.
Estrogen / endocrine-disruptor sensor (ERα + CRISPRa)
Detects estrogens and estrogenic endocrine-disrupting chemicals in water. Uses the human estrogen receptor (ERα) expressed in GRAS baker's yeast — a eukaryotic sensing class bacteria cannot do — gating a CRISPRa circuit driving a fluorescent reporter.
Explosives/landmine sensor (YqjF + CRISPRa)
Detects buried explosives by sensing DNT vapour (a TNT degradation product that leaks from landmines). The YqjF sensor gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12.
Fluoride sensor (riboswitch + CRISPRa)
Detects fluoride in drinking water using a natural fluoride riboswitch as the sensor, gating a CRISPRa circuit driving a fluorescent reporter, in the food-grade GRAS chassis Lactococcus lactis.
Formaldehyde sensor (HxlR + CRISPRa)
Detects toxic formaldehyde in water, air, and materials. The native B. subtilis HxlR formaldehyde regulator gates a CRISPRa circuit driving a fluorescent reporter, in spore-forming Bacillus subtilis 168.
GI bleeding sensor (heme + CRISPRa)
An ingestible sensor for heme, a marker of gastrointestinal bleeding. The validated HrtR heme sensor gates a CRISPRa circuit driving a luminescent reporter, in the probiotic E. coli Nissle 1917.
Glucose sensor (CRP/cAMP + CRISPRi)
Reports glucose via catabolite repression (CRP/cAMP). When glucose is low, cAMP-CRP activates its promoters; when glucose is high, it switches off. CRP gates a CRISPRi circuit driving a fluorescent reporter, in the probiotic E. coli Nissle 1917 — relevant to gut/metabolic monitoring.
Gut acid/pH sensor (GadE + CRISPRa)
Reports gut acidity / low pH (linked to short-chain-fatty-acid load and dysbiosis). The acid-responsive Gad system gates a CRISPRa circuit driving a fluorescent reporter, in the food-grade acid-tolerant chassis Lactococcus lactis.
Gut inflammation memory recorder (tetrathionate)
Records a transient gut-inflammation episode and remembers it. A recombinase memory switch, triggered by the tetrathionate sensor, flips a DNA state that persists after the signal is gone — so a single exposure is still detectable days later in stool.
Gut inflammation memory sensor (tetrathionate + CRISPRi)
An ingestible sensor for tetrathionate, a biomarker of gut inflammation. The validated TtrSR sensor gates a CRISPRi circuit driving a fluorescent reporter, in the probiotic E. coli Nissle 1917. Complements the thiosulfate sensor as a second inflammation marker.
Gut inflammation sensor (thiosulfate + CRISPRi)
An ingestible sensor for gut inflammation. The validated thiosulfate two-component sensor (ThsSR) gates a CRISPRi amplifier driving a fluorescent reporter, in the human probiotic E. coli Nissle 1917.
Gut nitric-oxide sensor (NsrR + CRISPRi)
An ingestible sensor for nitric oxide, a marker of intestinal inflammation. The native NsrR NO-sensing repressor gates a CRISPRi circuit driving a fluorescent reporter, in the probiotic E. coli Nissle 1917.
Gut sulfide sensor (CstR + CRISPRa)
An ingestible sensor for hydrogen sulfide / persulfide, a gut-microbial metabolite linked to colitis and colorectal risk. The CstR persulfide-sensing repressor gates a CRISPRa circuit driving a fluorescent reporter, in the probiotic E. coli Nissle 1917.
Iron sensor (Fur + CRISPRi)
Reports bioavailable iron via the Fur ferric-uptake regulator, gating a CRISPRi circuit driving a fluorescent reporter, in the robust environmental chassis P. putida KT2440. Useful for soil/water iron and process monitoring.
Lactate sensor (LldR + CRISPRi)
Detects L-lactate, a fermentation and clinical metabolite. The LldR lactate-responsive regulator gates a CRISPRa circuit driving a fluorescent reporter, in the food-grade GRAS chassis Lactococcus lactis.
Lead water sensor (PbrR + CRISPRi)
Detects lead Pb(II) in water. The PbrR metal-responsive regulator gates a CRISPRi circuit driving sfGFP, in spore-forming Bacillus subtilis 168 for rugged, field-storable testing.
Lysine sensor (LysG + CRISPRa)
Detects L-lysine — the flagship amino-acid product of C. glutamicum. The native LysG transcriptional sensor (used in the classic pSenLys biosensor) gates a CRISPRa circuit driving a fluorescent reporter, for strain screening and process monitoring.
Manganese sensor (MntR + CRISPRi)
Detects manganese in water and soil. The native B. subtilis MntR manganese-responsive regulator gates a CRISPRi circuit driving a fluorescent reporter, in spore-forming Bacillus subtilis 168.
Mercury soil/water sensor (MerR + CRISPRi)
Detects ionic mercury Hg(II) in soil and water. The MerR/PmerT sensing module gates a CRISPRi circuit driving a visible chromoprotein, in the rugged environmental chassis P. putida KT2440.
Naringenin/flavonoid sensor (FdeR + CRISPRa)
Detects naringenin and related flavonoids (dietary and nutraceutical compounds). The Marionette FdeR sensor gates a CRISPRa circuit driving a fluorescent reporter, in the food-grade GRAS chassis Lactococcus lactis.
Nickel/cobalt sensor (RcnR + CRISPRi)
Detects nickel and cobalt in water. The native E. coli RcnR metal-responsive repressor gates a CRISPRi circuit driving a visible chromoprotein, in safe E. coli K-12.
Nitrate sensor (NarL + CRISPRi)
Detects nitrate in water and food. The native E. coli NarX/NarL nitrate two-component system gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12.
Oxidative-stress sensor (OxyR + CRISPRa)
An ingestible sensor for hydrogen peroxide / oxidative stress, a marker of gut inflammation. The native OxyR peroxide sensor gates a CRISPRa circuit driving a fluorescent reporter, in the probiotic E. coli Nissle 1917.
P. aeruginosa quorum sensor (LasR + CRISPRi)
Flags contamination by Pseudomonas aeruginosa by sensing its quorum-sensing signal 3-oxo-C12-HSL. The LasR sensor gates a CRISPRi inverter driving a pigment reporter, in safe E. coli K-12.
P. aeruginosa sensor (PQS/PqsR + CRISPRi)
Detects Pseudomonas aeruginosa via its quinolone signal (PQS). The PqsR (MvfR) receptor gates a CRISPRi circuit driving a visible pigment, in the safe Pseudomonas relative P. putida KT2440.
Phenol sensor (DmpR + CRISPRa)
Detects phenol and methylphenols in water/soil. The DmpR aromatic sensor gates a CRISPRa circuit driving a fluorescent reporter, in the phenol-tolerant chassis P. putida KT2440.
Phosphate sensor (PhoPR + CRISPRa)
Reports phosphate status (relevant to water-quality and eutrophication monitoring). The native B. subtilis PhoP/PhoR phosphate-starvation system gates a CRISPRa circuit driving a fluorescent reporter, in spore-forming Bacillus subtilis 168.
Riboflavin (B2) sensor (FMN riboswitch + CRISPRa)
Detects riboflavin / FMN (vitamin B2) in food and the gut. The natural FMN riboswitch gates a CRISPRa circuit driving a fluorescent reporter, in the gut-persistent probiotic Lactiplantibacillus plantarum.
S. aureus sensor (AIP/AgrC + CRISPRa)
Detects Staphylococcus aureus by sensing its autoinducing peptide (AIP). The AgrC/AgrA quorum receptor gates a CRISPRa circuit driving a fluorescent reporter, in safe Gram-positive Bacillus subtilis 168 — no live pathogen handled.
Salicylate sensor (NahR + CRISPRi)
Detects salicylate (a naphthalene-degradation marker and drug metabolite). The NahR LysR-family activator gates a CRISPRi circuit driving a visible pigment, in safe E. coli K-12.
Self-powered arsenic sensor (ArsR + CRISPRi)
A self-powered water arsenic sensor. The native cyanobacterial ArsR regulator gates a CRISPRi circuit driving a fluorescent reporter, in photosynthetic Synechocystis — which runs on light and CO2, so it can be deployed long-term without added nutrients.
Self-powered phosphate sensor (SphS/SphR + CRISPRa)
A self-powered sensor for phosphate status in water (eutrophication-relevant). The native cyanobacterial SphS/SphR phosphate two-component system gates a CRISPRa circuit driving a fluorescent reporter, in photosynthetic Synechocystis.
Streptococcus sensor (CSP/ComD + CRISPRa)
Detects Streptococcus via its competence-stimulating peptide (CSP). The ComD/ComE quorum system gates a CRISPRa circuit driving a fluorescent reporter, in the food-grade Gram-positive chassis Lactococcus lactis.
Tetracycline sensor (TetR + CRISPRi)
Detects tetracycline antibiotic contamination in water and food. The classic TetR sensor gates a CRISPRi circuit driving a visible pigment, in safe E. coli K-12.
Theophylline sensor (riboswitch + CRISPRa)
Detects theophylline, an asthma drug with a narrow therapeutic window. The well-characterized synthetic theophylline riboswitch gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12 — a model for low-cost therapeutic drug monitoring.
Thiamine (B1) sensor (TPP riboswitch + CRISPRi)
Detects thiamine pyrophosphate (vitamin B1) in food and the gut using the natural TPP riboswitch — the most widespread riboswitch class — gating a CRISPRi circuit driving a fluorescent reporter, in probiotic Lactiplantibacillus plantarum.
Toluene/BTEX sensor (XylR + CRISPRi)
Detects toluene and related BTEX aromatic pollutants. The native XylR/Pu regulator gates a CRISPRi circuit driving a visible pigment, in P. putida KT2440 — a natural toluene-degrader and rugged environmental chassis.
Tryptophan sensor (TrpR + CRISPRi)
Detects tryptophan, a dietary amino acid and precursor of gut-microbial indole/serotonin metabolites. The classic TrpR repressor gates a CRISPRi circuit driving a fluorescent reporter, in the food-grade GRAS chassis Lactococcus lactis.
Vanillate sensor (VanR + CRISPRa)
Detects vanillate/vanillin (lignin-degradation and food/flavour marker). The Marionette VanR sensor gates a CRISPRa circuit driving a fluorescent reporter, in safe E. coli K-12.
Vibrio sensor (LuxR/3OC6-HSL + CRISPRa)
Detects Vibrio-type contamination via the 3-oxo-C6-homoserine-lactone quorum signal. The classic LuxR receptor gates a CRISPRa circuit driving a luminescent reporter, in safe E. coli K-12.
Vitamin B12 sensor (cobalamin riboswitch + CRISPRa)
Detects vitamin B12 (cobalamin) in food and the gut. The natural cobalamin riboswitch gates a CRISPRa circuit driving a fluorescent reporter, in the gut-persistent probiotic Lactiplantibacillus plantarum.
Water nitrogen sensor (NtcA + CRISPRa)
A self-powered sensor for nitrogen status in water bodies (relevant to eutrophication and algal blooms). The native cyanobacterial NtcA nitrogen regulator gates a CRISPRa circuit driving a fluorescent reporter, in the photosynthetic chassis Synechocystis — which runs on light and CO2.
Zinc band-pass sensor (healthy-window)
Fires only when zinc sits within a target concentration window — not too low, not too high — using an incoherent feed-forward loop. Useful for flagging deviations from a healthy/optimal range rather than mere presence.
Zinc sensor (ZitR + CRISPRi)
Detects zinc, a nutritional and water-quality marker. The native L. lactis ZitR zinc regulator gates a CRISPRi circuit driving a fluorescent reporter, in the food-grade GRAS chassis Lactococcus lactis.
Zinc-limitation/calprotectin sensor (Zur + CRISPRa)
An ingestible sensor for host nutritional immunity: the host inflammation protein calprotectin sequesters zinc, and the Zur zinc-uptake regulator reports the resulting zinc limitation. Zur gates a CRISPRa circuit driving a fluorescent reporter, in the probiotic E. coli Nissle 1917.