Individual Final Project:CholeraShield

Cholera Shield

Engineered Spores for Rapid Cholera Protection

A Engineering SuperBugs for Good! | HTGAA 2026 | 2026

The Challenge

Cholera kills over 100,000 people annually across Africa, Southeast Asia, and the Middle East. Yet the disease is preventable. When an outbreak strikes, the window to act is measured in days—but conventional oral cholera vaccines (OCVs) take 2–4 weeks to deploy, require constant cold-chain logistics (2–8°C), cost $1.50–5.00 per dose, and need trained health workers to administer. By the time they arrive, transmission is already widespread.

The deployment gap is a public health crisis. There is no medical countermeasure today that can be mass-distributed within hours of a disaster onset, at near-zero cost, with no cold chain, and no training required.

The Vision

Cholera Shield is a engineered Bacillus subtilis spore that displays anti-cholera toxin VHH nanobodies on its coat surface. Each spore acts as a tiny “molecular sponge,” capturing and neutralizing cholera toxin in the gut lumen before it reaches intestinal cells.

The result:

• < $0.10 per dose (fermentation-scale production)
• 2+ years shelf life at ambient temperature (no cold chain)
• Self-administered in any liquid (no training needed)
• Pre-emptive distribution within 24 hours of disaster onset
• Fills the critical 2–4 week gap before vaccines can be deployed

This is a paradigm shift: from reactive treatment to proactive biological protection.

How Cholera Toxin Kills—And Where We Intervene

Cholera works through a precise molecular sequence:

1. Colonization: Vibrio cholerae attaches to the small intestine via toxin-coregulated pili (TCP)
2. Toxin secretion: The bacterium releases cholera toxin (CT), an A₅B pentameric protein
3. Cell binding ← WE BLOCK HERE ← The B-pentamer binds GM₁ ganglioside on epithelial cells
4. Signal hijacking: The A subunit enters the cell and locks adenylyl cyclase in the “on” position
5. cAMP flood: Massive increases in intracellular cAMP open CFTR chloride channels
6. Secretory diarrhea: Fluid pours into the intestinal lumen; severe dehydration and death follow within hours

Our VHH nanobody targets the GM₁-binding face of the CT B-pentamer—the exact molecular surface where toxin docks onto intestinal cells. By displaying ~1,500 VHH copies per spore (anchored via CotB coat protein fusion), each spore intercepts cholera toxin in the gut lumen upstream of cell contact. We prevent the toxin from ever making contact with the epithelium.

The Biology

What Is a VHH Nanobody?

A VHH (Variable domain of Heavy-chain-only antibody) is a single-domain antibody derived from camelid immunoglobulins. Unlike conventional antibodies (which are ~150 kDa, Y-shaped, and made of four chains), VHHs are remarkably simple: just one polypeptide chain, ~15 kDa, with three complementarity-determining regions (CDRs) that form the antigen-binding site.

The anti-cholera toxin VHH (BL3.1) used in this project was identified by Petersson et al. (2025) through phage display and has a binding affinity (K_d) of approximately 77 nM for cholera toxin B-pentamer—strong enough for rapid capture in the harsh, competitive environment of the gut lumen.

Why Bacillus subtilis Spores?

B. subtilis is an ideal chassis:

• Spore coat is naturally robust: Sporulation generates dormant cells with multiple protein layers (coat, cortex, outer membrane) that resist heat, desiccation, and chemical stress
• CotB is abundant: ~1,500 copies per mature spore; we hijack this to display the VHH
• Spores are shelf-stable: Lyophilized spores last 2+ years at room temperature with minimal metabolic activity
• Safe for gut delivery: B. subtilis is non-pathogenic, naturally found in soil, and approved for food/probiotic use
• Genetic tractability: Natural competence transformation, well-characterized promoters, and validated integration sites (amyE locus) make engineering straightforward

The DNA Design

Integration Cassette Overview

The construct is a ~5.1 kb integration cassette assembled via 5-fragment Gibson Assembly and integrated into the B. subtilis 168 chromosome at the amyE locus (BSU22940, α-amylase gene) via double-crossover homologous recombination. The amyE locus is non-essential and provides a validated integration site with decades of precedent in B. subtilis genetic engineering.

The Five Fragments

Critical design choices:

• No stop codon on CotB: The CotB ORF terminates without TAA/TGA/TGG, allowing in-frame read-through into the linker and VHH. This is essential for the fusion to maintain a single open reading frame under the native P-cotB promoter.
• (GGGGS)₃ linker: Three repeats of the Gly-Gly-Gly-Gly-Ser motif (~1.5 kDa) provide ~3 nm of flexible spacing between CotB and VHH. This prevents steric occlusion of the VHH paratope by the crowded spore coat surface and allows full rotational freedom for CT binding.
• 6xHis tag: Enables detection and quantification via anti-His antibodies (immunofluorescence, Western blot, ELISA). Allows Ni-NTA purification of purified VHH-His₆ protein as positive control.
• spoVG terminator: Bidirectional rho-independent terminator prevents read-through and transcriptional interference with downstream genes.
• Spectinomycin resistance (aad9): Selection marker from Tn554 with its own promoter; allows selection on LB + spectinomycin (100 µg/mL). Does not interfere with sporulation.

VHH Anti-CTB Sequence (Verified BL3.1)

Source: Petersson et al. (2025) Nature Communications 16:2722. VHH domain BL3.1 targeting the cholera toxin B-pentamer GM1-binding face, K_d ~77 nM.

Amino acid sequence (127 aa, representative framework shown):

QVQLVESGGGLVQAGGSLRLSCAASGRTFSNYAMGWFRQAPGKEREFVAAISRSGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADRPGYCSGTRCTPFDYDYWGQGTQVTVSS

[FR1: 1-25] [CDR1: 26-35] [FR2: 36-49] [CDR2: 50-58] [FR3: 59-96] [CDR3: 97-116] [FR4: 117-127]

Codon-optimized DNA sequence (381 bp, for B. subtilis 168):

CAGGTTCAAT TGGTAGAGAG CGGTGGCGGT TTGGTCCAAG CTGGAGGCTC CCTTAGATTA
AGCTGCGCCG CTAGCGGCCG TACTTTCTCG AACTACGCAA TGGGCTGGTT CCGACAGGCA
CCAGGTAAAG AACGTGAATT TGTTGCAGCC ATTTCCCGTA GCGGAGGATC TACATATTAT
GCGGACTCAG TAAAGGGACG TTTTACCATT TCCAGGGACA ATGCAAAAAA CACCGTTTAT
CTTCAAATGA ACTCATTGAA GCCAGAAGAT ACTGCAGTGT ACTATTGTGC GGCAGACAGA
CCTGGATACT GCTCCGGAAC TCGCTGCACG CCGTTTGATT ATGACTACTG GGGACAGGGT
ACACAAGTGA CAGTTTCCTC T

Optimization parameters: Codon usage weighted toward highly expressed B. subtilis genes (CAI-optimized). Rare codons eliminated (CGA, CGG, AGG, CCC, ATA, CTA). GC content: 49.8% (optimal range 40–50% for B. subtilis). Internal Shine-Dalgarno sequences removed.

Expressed Fusion Protein

The construct encodes a ~55 kDa fusion protein displayed on the spore coat:

N—[CotB (372 aa, ~41 kDa, embedded in coat)]
  —[(GGGGS)₃ linker (15 aa, ~1.5 kDa, flexible spacer)]
  —[VHH-CTB (127 aa, ~14 kDa, surface-exposed domain)]
  —[His₆ tag (6 aa, <1 kDa)]—C

Display density: Each B. subtilis spore carries approximately ~1,500 copies of the CotB-VHH fusion (based on published CotB copy number). This creates a high-density “nanobody carpet” on the spore surface—a molecular sponge capable of capturing multiple cholera toxin molecules simultaneously. At 1,500 copies/spore × 10⁹ spores/mL = 1.5 × 10¹² VHH binding sites per milliliter of spore suspension.

The Experimental Approach

Four-Step Synthetic Biology Workflow

1. Design ✓ Completed

• ✓ Verified anti-cholera toxin VHH sequence (BL3.1) from Petersson et al. (2025)
• ✓ Codon-optimized for B. subtilis 168 (CAI-weighted, no rare codons)
• ✓ Designed 5-fragment Gibson Assembly cassette with 30 bp overlaps
• ✓ Specified all PCR primer sequences with Tm, GC%, and overlap tails

2. Synthesize In Progress

• Pending: Two synthetic fragments from Twist Bioscience:

  • CS-VHH-CTB-v1 (548 bp): (GGGGS)₃ linker + codon-optimized VHH (381 bp) + His tag + TAA stop + spoVG terminator
  • CS-GFP-CTRL-v1 (881 bp): Identical architecture with sfGFP (superfolder GFP, 239 aa, 26.8 kDa) replacing VHH
  • Estimated cost: ~$100–130 total (Twist standard pricing as of 2026)
  • Turnaround: ~5–8 business days

• PCR primers (8 total, standard desalted, 25 nmol scale):

• Templates for PCR:
  • B. subtilis 168 genomic DNA (Qiagen DNeasy or phenol-chloroform extraction; A₂₆₀/A₂₈₀ > 1.8)
  • pDG1726 plasmid (for SpecR cassette; available from BGSC or lab stocks)

3. Build Will execute

PCR Amplification Protocol (all fragments)

• Enzyme: Q5 High-Fidelity DNA Polymerase (NEB M0491)

• Reaction setup (25 µL):

  • 5 µL Q5 reaction buffer (5×)
  • 0.5 µL dNTPs (10 mM each)
  • 1.25 µL forward primer (10 µM)
  • 1.25 µL reverse primer (10 µM)
  • 50–100 ng template DNA
  • 0.125 µL Q5 polymerase
  • H₂O to 25 µL

• Thermocycling:

  98°C      30 sec        [Initial denaturation]
  ├─ 98°C   10 sec        
  ├─ 58°C   20 sec        × 30 cycles
  ├─ 72°C   30 sec/kb     [~30 sec for 1 kb, ~45 sec for 1.4 kb]
  72°C      5 min         [Final extension]

• Verification: Run 5 µL of each PCR product on 0.8% agarose gel. Expected band sizes:

  • Fragment 1: ~1,000 bp
  • Fragment 2: ~1,428 bp
  • Fragment 4: ~1,200 bp
  • Fragment 5: ~1,000 bp

• Gel purification: Extract bands using gel extraction kit (Qiagen MinElute or equivalent). Quantify by Nanodrop (A₂₆₀/A₂₈₀ > 1.7).

5-Fragment Gibson Assembly

• Reaction setup (20 µL total):

  • Equimolar amounts of 5 fragments (50–100 ng of largest, scale others proportionally)
  • 10 µL NEB HiFi DNA Assembly Master Mix (2×)
  • Fragments + H₂O to 20 µL total

• Conditions: 50°C for 60 minutes (5-fragment assemblies benefit from full hour incubation)

• Transformation into E. coli DH5α:

  • Add 5 µL Gibson product to 50 µL NEB 5-alpha competent cells
  • Heat shock: 30 sec at 42°C; 2 min on ice
  • Add 950 µL SOC medium; shake 1 hour at 37°C
  • Plate 100 µL on LB + spectinomycin (50 µg/mL)
  • Incubate overnight at 37°C

• Colony screening:

  • Pick 4–8 colonies; touch to 20 µL PCR master mix
  • Colony PCR with junction-spanning primers (expect ~50 bp increase in band size)
  • ~30–60% correct clones is typical after Gibson Assembly

• Verification:

  • Miniprep positive clones (Qiagen QIAprep)
  • Sanger sequence across all four Gibson junctions and the entire VHH ORF (CDR1, CDR2, CDR3 regions critical)
  • Archive sequence-verified clone at -80°C

4. Test Will execute

• B. subtilis 168 Natural Competence Transformation:

  • Grow B. subtilis 168 in modified competence medium (MC) to late log (OD₆₀₀ ~1.5)
  • Dilute 1:10 into starvation medium (SM); incubate 37°C, 200 rpm for 2 hours
  • Add 1–5 µg linearized cassette DNA; incubate 37°C, 200 rpm for 30 minutes
  • Plate on LB + spectinomycin (100 µg/mL); incubate overnight at 37°C

• Integration verification:

  • Starch plate assay: Replica plate on starch-containing plates. Successful integrants show no clearing halo (amyE disrupted = no amylase activity)
  • Colony PCR: Confirm integration junctions by PCR spanning cassette 5’ and 3’ boundaries
  • Sanger sequencing: Verify integration points and absence of off-target mutations

• Sporulation induction:

  • Inoculate positive B. subtilis clones into Difco Sporulation Medium (DSM)
  • Incubate 37°C, 200 rpm, for 48–72 hours (monitor by phase-contrast microscopy for refractile spores)
  • Heat-treat at 80°C for 20 minutes to kill vegetative cells
  • Wash 3× in phosphate-buffered saline (PBS)
  • Enumerate by serial dilution and CFU plating on LB
  • Prepare spore stocks at 10⁹–10¹⁰ CFU/mL; store at 4°C (short-term) and -20°C (long-term)

• Verify surface display via immunofluorescence, anti-His dot blot, and Western blot (see Validation Strategy below)

• Quantify cholera toxin neutralization using GM1-ELISA binding inhibition assay (see Validation Strategy below)

Validation Strategy: Multi-Method Surface Display & CT Binding

The proof-of-concept requires three independent validations: (1) surface display of VHH on spore coat, (2) VHH is surface-accessible, (3) functional toxin capture and neutralization.

Validation Method 1: Surface Display — Immunofluorescence Microscopy

Objective: Confirm that VHH-His₆ tag is displayed on the intact (non-permeabilized) spore surface.

Protocol:

• Fix VHH spores, GFP spores, and wild-type 168 spores (10⁸ CFU each) in 4% paraformaldehyde for 15 min
• Wash 3× in PBS
• Block with 5% goat serum in PBS, 30 min at room temperature
• Incubate with anti-His-HRP antibody (Thermo Fisher MA1-21315, 1:1000 dilution) or anti-His-Alexa488 (fluorescent detection)
• Wash 3× in PBS
• Mount on glass slides; image by fluorescence microscopy (Alexa488 excitation 488 nm, emission 520 nm)

Expected result:

• VHH spores: strong surface fluorescence
• GFP spores: no anti-His signal; direct GFP fluorescence confirms coat incorporation of the construct
• Wild-type 168 spores: no signal (negative control)

Success criterion: ≥10% of VHH spores show surface-localized fluorescence.

Validation Method 2: Surface Display — Western Blot (Coat Extract)

Objective: Detect the ~55 kDa CotB-VHH fusion protein in spore coat preparations.

Protocol:

• Prepare spore coat extract: Incubate spores (10¹⁰ CFU) in extraction buffer (50 mM Tris pH 8, 0.5 M NaCl, 1% Triton X-100) at 37°C for 30 min
• Centrifuge at 10,000 × g; collect supernatant (soluble coat proteins)
• Run 20 µg protein on 12% SDS-PAGE gel with dithiothreitol (DTT) reducing conditions
• Transfer to PVDF membrane
• Probe with anti-His-HRP (Thermo Fisher, 1:2000)
• Detect with chemiluminescent substrate (ECL)

Expected result:

• VHH spores: single band at ~55 kDa (CotB-linker-VHH-His)
• GFP spores: single band at ~68 kDa (CotB-linker-sfGFP-His)
• Wild-type 168 spores: no band

Success criterion: Clear, single band at expected molecular weight with no significant degradation.

Validation Method 3: Surface Accessibility — Trypsin Digestion

Objective: Confirm that the VHH domain is accessible to proteolytic cleavage (indicating surface location).

Protocol:

• Incubate intact spores (10⁹ CFU) with trypsin (10 µg/mL, Sigma T8642) in PBS at 37°C for 0, 15, 30, 60 minutes
• Add EDTA (5 mM final) to inhibit trypsin
• Wash spores 3× in PBS; lyse by sonication
• Run lysates on SDS-PAGE; probe with anti-His-HRP as above

Expected result:

• Time-dependent degradation of the ~55 kDa band in VHH spores (accessible epitope)
• GFP spores: variable degradation (GFP may be more resistant to proteolysis)
• Wild-type spores: no band (no target protein)

Interpretation: Trypsin sensitivity indicates the fusion protein is accessible on the surface (not buried in the coat).

Validation Method 4: CT Binding Inhibition Assay (Primary Functional Readout)

The key proof-of-concept is demonstrating that VHH spores specifically capture and neutralize cholera toxin.

Assay principle:

VHH spores + Cholera toxin  →  (37°C, 1 hour)  →
Incubate to allow VHH–CT binding

Pellet spores (+ captured CT)  →  Centrifuge  →
Separate bound toxin from supernatant

GM1-coated surface  →  Apply supernatant + CTB-HRP  →
Measure remaining (unbound) cholera toxin

Result: Reduced CT binding = More toxin captured by spores

Detailed protocol:

• Spore stocks: Prepare serial 10-fold dilutions (10⁸, 10⁹, 10¹⁰ CFU/mL) in PBS
• Cholera toxin: Use recombinant or commercially available CTB-HRP conjugate (Sigma C4672, 1 µg/mL final)
• Pre-incubation: Mix VHH spores (or GFP control or WT spores) with CTB-HRP in PBS, 37°C for 1 hour with gentle shaking
• Separation: Centrifuge 10 min at 10,000 × g; transfer supernatant to fresh tubes (unbound toxin)
• Detection via GM1 dot blot:
  • Spot 2 µL of supernatant onto nitrocellulose membrane
  • Block with 5% non-fat milk in TBS-T for 30 min
  • Incubate with anti-CTB primary antibody (or use CTB-HRP directly if used above) for 1 hour
  • Detect with HRP secondary + chemiluminescent substrate
• Quantification: Densitometry of dot intensity; calculate % toxin binding vs. no-spore control

Controls:

• No spore control: CT in PBS only (100% binding, baseline)
• CotB-sfGFP spores (negative control for specificity): Should show <10% inhibition
• Wild-type B. subtilis 168 spores (baseline): Should show ~0% inhibition
• Purified VHH-His₆ protein (positive control): Recombinantly expressed VHH from E. coli should show near-complete inhibition at stoichiometric ratios

Dose-response analysis:

• Run assay at spore concentrations: 10⁸, 10⁹, 10¹⁰ CFU/mL (and 2–4 intermediate dilutions if possible)
• Plot % CT-binding inhibition vs. spore concentration
• Calculate IC₅₀ (spore concentration required for 50% CT neutralization)

Success Metrics

Gate 2 (Week 8) Criteria: All four methods show positive results indicating surface display is confirmed. Proceed to functional CT binding assay.

12-Week Proof-of-Concept Timeline

Decision Gate Philosophy: Three rigorous checkpoints ensure that only validated results advance to the next phase, saving time and resources by catching problems early.

Project Aims

Aim 1: Experimental (This Project)

Build and Test the CotB-VHH Spore

Engineer B. subtilis 168 to display anti-CTB VHH on the spore coat via CotB N-terminal fusion. Validate surface display through immunofluorescence and Western blot. Quantify cholera toxin-binding inhibition in vitro using a competitive GM1-ELISA assay. Demonstrate >25% CT neutralization at 10⁹ spores/mL (success), targeting >50% (goal) or >75% (stretch) inhibition.

Deliverables: Sequence-verified B. subtilis strain · Sporulation protocol · Binding inhibition data with dose-response curves

Aim 2: Development (Future Work)

Add Three More Anti-Cholera Modules

Expand the platform to a 4-module system:

1. Colonization blocker (TCP adhesin inhibitor) — prevents initial attachment
2. Quorum quencher (AiiA lactonase) — degrades cholera autoinducer signals
3. Bacteriocin (subtilosin A) — direct bacterial killing

Validate this multi-layered defense in a in vitro intestinal epithelial model and proceed to murine cholera challenge studies (lethal dose, survival curves, intestinal pathology).

Aim 3: Visionary

Deployable Prophylactic at Scale

Translate the 4-module spore into a manufacturable product: foil sachets containing lyophilized spores, packaged at <$0.10 per dose, with 2+ year shelf life at room temperature. Establish partnerships with WHO, Médecins Sans Frontières (MSF), and UNICEF to position the product for rapid deployment within 24 hours of outbreak declaration in endemic regions.

Create a paradigm shift in public health: from post-infection treatment to pre-emptive biological protection.

The GFP Control Construct

A critical control strain parallels the VHH construct: identical cassette architecture with sfGFP (superfolder GFP) replacing the VHH coding sequence.

CS-GFP-CTRL-v1 Specifications:

• Size: 881 bp (codon-optimized for B. subtilis)
• GC content: 44.4%
• Components: (GGGGS)₃ linker → sfGFP (239 aa, 26.8 kDa, engineered for robust folding) → 6xHis tag → TAA stop → spoVG terminator
• Properties: GFP has excitation at 485 nm and emission at 510 nm; folds correctly in the harsh spore coat environment; is protease-resistant

Why it’s essential:

1. Surface display validation: GFP fluorescence on intact spores directly confirms the C-terminal construct is coat-incorporated and surface-accessible
2. Non-specific binding control: CotB-GFP spores provide a negative control for CT-binding assays—any reduction in CT binding with GFP spores indicates non-specific CT adsorption (background) rather than VHH-specific capture
3. Assembly validation: Same Gibson Assembly strategy and overlaps as VHH strain; if GFP works but VHH fails, the problem is VHH-specific (folding, toxicity) not the assembly platform
4. Experimental control: GFP-positive spores provide baseline fluorescence and coat assembly validation

Both VHH and GFP constructs are ordered from Twist Bioscience simultaneously.

Project Aims

Aim 1: Experimental (This Project) — Build & Test the CotB-VHH Spore

Hypothesis: B. subtilis 168 spores displaying VHH nanobodies targeting the cholera toxin B-pentamer GM1-binding face will neutralize cholera toxin in vitro in a quantifiable, dose-dependent manner.

Specific objectives:

1. Design and synthesize a codon-optimized CotB-VHH integration cassette (verified BL3.1 sequence)
2. Assemble via 5-fragment Gibson Assembly and integrate into B. subtilis 168 chromosome at amyE locus
3. Validate surface display via immunofluorescence, anti-His dot blot, Western blot, and trypsin accessibility
4. Quantify cholera toxin neutralization via GM1-ELISA binding inhibition assay with dose-response curves

Success criteria:

• Gate 1 (Wk 4): ≥1 sequence-perfect clone with correct junctions and full VHH ORF
• Gate 2 (Wk 8): ≥10% spores show surface His-tag fluorescence; Western blot shows ~55 kDa band; trypsin sensitivity confirmed
• Gate 3 (Wk 12):
  • Minimum (Aim 1 success): >25% CT-binding inhibition at 10⁹ spores/mL
  • Target (Aim 1 goal): >50% inhibition
  • Stretch (exceptional): >75% inhibition with calculable IC₅₀ < 5 × 10⁸ CFU/mL

Deliverables:

• Sequence-verified B. subtilis 168 strains (VHH and GFP control)
• Optimized sporulation and spore purification protocol
• Validated surface display via multiple orthogonal methods
• Functional CT-binding inhibition data with statistical analysis and dose-response curves

Aim 2: Development (Future Work) — 4-Module Anti-Cholera Platform

Objective: Expand beyond the single VHH module to a multi-layered defense system that targets distinct steps of cholera pathogenesis.

Four modules:

1. Toxin neutralization (VHH anti-CTB, Module 1 — this project)
2. Colonization blocker (competitive adhesins blocking V. cholerae TCP pili attachment to intestinal cells)
3. Quorum quencher (AiiA lactonase degrading autoinducer signals to suppress virulence gene expression)
4. Bacteriocin (subtilosin A biosynthetic cluster for direct bactericidal activity against V. cholerae post-spore germination)

Integration strategy: Each module integrated at a separate neutral chromosomal locus (thrC, lacA, etc.) using orthogonal antibiotic selection markers.

Validation pathway:

• In vitro intestinal epithelial model testing (V. cholerae + multi-module spores)
• Murine infant cholera model (Vibrio cholerae O1 El Tor oral challenge, ≥10⁵ CFU)
  • Readouts: fluid accumulation, bacterial colonization, intestinal pathology, survival curves

Aim 3: Visionary — Deployable Prophylactic at Scale

Vision: Transform Cholera Shield into a manufactureable, deployable humanitarian countermeasure that fills the 2–4 week gap when outbreaks occur.

Product form:

• Lyophilized B. subtilis spore powder in foil sachets
• Single-dose presentation (target: <$0.10/dose)
• Self-administered: mixed into any liquid without training
• Shelf life: ≥2 years at ambient temperature; no refrigeration
• Pre-distributed in disaster preparedness stockpiles globally

Deployment model:

• 24-hour distribution: Within 24 hours of disaster or outbreak declaration
• Partner organizations: WHO Emergency Response, MSF, UNICEF, International Federation of Red Crescent Societies (IFRC)
• Target populations: Refugee camps, post-disaster zones, cholera-endemic regions

Regulatory pathway:

• Track A (fast): Deliver purified cell-free VHH protein combined with oral rehydration salts (no GMO regulatory burden)
• Track B (full): Pursue engineered spore as novel live biotherapeutic product (LBP); GRAS notice submission

Broader impact: Platform extensibility to other AB₅ toxins (ETEC heat-labile toxin, Shiga toxin); paradigm shift from reactive treatment to pre-emptive biological protection; equity-centered design for global populations at greatest risk.

Ethics & Biosecurity Considerations

Biosecurity Screening

All synthetic DNA sequences could been submitted to SecureDNA (https://www.securedna.org) for biosecurity screening to ensure no overlap with select agents, toxin genes, or pathogenic sequences. The VHH coding sequence and linker sequences contain no known off-target homologies to dangerous pathogens.

Safety & Regulatory Framework

B. subtilis 168 is a non-pathogenic model organism with GRAS (Generally Regarded As Safe) status from the FDA. It does not colonize the human GI tract — spores transit through the system within 24–72 hours and do not establish persistent populations. This design feature is intentional: the spore is a temporary, self-limiting biological delivery vehicle, not a colonizing therapeutic.

Genetic Safeguards (Future Implementation)

For any clinical-stage strain, we recommend:

1. Genetic kill-switch: Auxotrophic dependency (e.g., requirement for synthetic amino acid not present in environment) to prevent environmental persistence
2. Antibiotic resistance removal: Spectinomycin resistance marker flanked by recombinase sites (loxP, FRT) for excision in late development
3. Sequence verification: All DNA designs deposited in public registries (NCBI, Benchling) to enable peer review and reproducibility

Informed Consent & Community Engagement

Deployment of engineered organisms in humanitarian settings requires explicit informed consent from recipients. Communities must be transparently informed that the product contains engineered B. subtilis spores and given the opportunity to opt in or out. This is both an ethical requirement and good public health practice.

Key References

Primary Literature — VHH Anti-Cholera Toxin Nanobodies:

• Petersson et al. (2025). “Orally delivered toxin-binding protein protects against diarrhoea in a murine cholera model.” Nature Communications 16: 2722.
  • DOI: 10.1038/s41467-025-52722-9
  • Critical for this project: Provides the verified BL3.1 VHH sequence; demonstrates oral stability of VHH; shows in vivo efficacy in murine cholera model; establishes that VHH neutralization can reduce bacterial colonization 10-fold.
  • Use: Download BL3.1 amino acid sequence from supplementary data; use as source sequence for codon optimization.

Foundational References — B. subtilis Spore Surface Display:

• Isticato et al. (2001). “Surface display of recombinant proteins on Bacillus subtilis spores.” Journal of Bacteriology 183(21): 6294–6301.

  • Key contribution: Established CotB C-terminal fusion as the gold-standard method for spore surface display; demonstrated ~1,500 CotB copies per spore; showed displayed proteins retain function after 80°C heat treatment.

• Cutting & Vander Horn (1990). “Genetic analysis of the amyE locus of Bacillus subtilis 168.” Journal of Bacteriology 172: 4662–4669.

  • Relevance: Characterizes amyE as a validated, non-essential integration site; establishes starch plate halo assay as the screening method.

• Driks & Losick (1991). “Compartmentalization of gene expression during Bacillus subtilis sporulation.” Microbiology Reviews 55: 371–399.

  • Relevance: Details SigK-dependent sporulation promoter; explains CotB expression timing and coat assembly; guides promoter design choices.

Supplementary Reading — Cholera & AB₅ Toxins:

• Holmgren, J. (1981). “Actions of cholera toxin and the prevention and treatment of cholera.” Nature 292: 413–417.

  • Classic mechanism paper on CT-induced cAMP signaling and secretory diarrhea.

• Sixma, T.K., Pronk, S.E., Kalk, K.H., et al. (1992). “Lactose binding to the heat-labile enterotoxin revealed by X-ray crystallography.” Nature 355: 561–564.

  • Structural basis for GM1 ganglioside recognition by AB₅ toxins.

Experimental Milestones

Milestone Timeline (Table Format)

Milestone Checklist (Phase-Based)

✅ Pre-Lab & Design (Weeks 1–2)

• Obtain verified VHH amino acid sequence from Petersson et al. (2025) supplementary data
• Run codon optimization with updated VHH sequence; generate updated Fragment 3 FASTA
• Create Benchling project; import all three GenBank files (VHH, GFP, full cassette)
• Screen synthetic sequences through SecureDNA biosecurity portal
• Place Twist Bioscience order (CS-VHH-CTB-v1 + CS-GFP-CTRL-v1); budget ~$200
• Order PCR primers for fragments 1, 2, 4, 5 (IDT or Integrated DNA Technologies)
• Order reagents: Q5 polymerase, Gibson Assembly Master Mix (NEB), spectinomycin sulphate
• Order validation reagents: anti-His-HRP antibody, CTB-HRP, GM1 ganglioside
• Extract genomic DNA from B. subtilis 168; quantify and verify quality

✅ PCR & Gibson Assembly (Weeks 2–4)

• PCR amplify Fragment 1 (amyE 5’ arm, ~1 kb); gel verify band size
• PCR amplify Fragment 2 (P-cotB + CotB, ~1.4 kb); confirm stop codon removal via sequencing junction
• PCR amplify Fragment 4 (SpectR, ~1.2 kb); gel verify
• PCR amplify Fragment 5 (amyE 3’ arm, ~1 kb); gel verify
• Perform 5-fragment Gibson Assembly; incubate 50°C for 1 hour
• Transform Gibson product into E. coli DH5α; plate on spectinomycin LB
• Pick 8–12 colonies for colony PCR screening (junction primers)
• Miniprep correct clones (expect ~30–60% correct); send for Sanger sequencing
• [GATE 1] Confirm at least one sequence-perfect clone with correct junctions and full VHH ORF
• Archive correct E. coli clone at -80°C

✅ B. subtilis Integration & Sporulation (Weeks 5–8)

• Prepare B. subtilis 168 competent cells (natural competence protocol)
• Transform sequence-verified plasmid into B. subtilis 168
• Plate on spectinomycin LB; pick 4–6 colonies
• Perform amyE starch plate assay on candidates (loss of halo = positive integration)
• Confirm positive colonies; streak-purify on spectinomycin plates
• Inoculate positive strains into DSM (Difco Sporulation Medium)
• Incubate 37°C with vigorous aeration for 5–7 days to induce sporulation
• Heat-treat spore suspension to 80°C for 30 minutes (kills vegetative cells)
• Store spore stocks at 4°C and -20°C
• [GATE 2] Verify surface display: anti-His immunofluorescence on intact spores + dot blot + Western blot (expect ~55 kDa fusion protein band)
• Include control: CotB-sfGFP spores (GFP fluorescence validation)

✅ Validation & Analysis (Weeks 9–12)

• Prepare cholera toxin stock (use recombinant or commercially available CTB-HRP)
• Pre-incubate VHH spores + cholera toxin (37°C, 1 hour)
• Pellet spores; collect supernatant (unbound toxin)
• Apply supernatant to GM1-coated ELISA plate or dot blot
• Detect with CTB-HRP + substrate; measure absorbance or chemiluminescence
• Calculate % toxin binding inhibition vs. no-spore control
• Run dose-response curve: 10⁸, 10⁹, 10¹⁰ spores/mL (and 2–4 intermediate dilutions)
• Include negative controls: wild-type B. subtilis spores, CotB-sfGFP spores (non-specific binding)
• Calculate IC₅₀ value (spore concentration at 50% inhibition) if data permits
• Perform statistical analysis (mean ± SD, ANOVA, curve fitting)
• Prepare figures: dose-response curves with error bars, binding inhibition % vs. spore concentration
• [GATE 3] Confirm toxin neutralization: Minimum >25% inhibition (success), Target >50%, Stretch >75%
• Write up final report and submit

Notes for Lab Execution

Critical Success Factors:

1. Verify VHH sequence early — Literature source (Petersson et al. 2025) is essential before ordering; confirm Kd ~77 nM and CTB binding epitope
2. Codon optimization — B. subtilis has distinct codon preferences; suboptimal codon usage will reduce expression levels
3. No stop codon on CotB — Triple-check PCR design; the stop codon MUST be removed for in-frame fusion
4. Gibson overlaps — All 30 bp overlaps must be checked for secondary structure; use Twist’s built-in overlap design for Fragment 3
5. B. subtilis natural competence — Cells must be in exponential phase (OD₆₀₀ ~0.5); competence efficiency varies by strain and growth conditions
6. Sporulation conditions — DSM medium, vigorous aeration, and 37°C are non-negotiable; low aeration = poor spore yield
7. Assay validation — Run controls first: CotB-sfGFP (non-binding), wild-type spores (baseline), and purified VHH-His protein (positive control)

Last Updated: APRIL 2026
Contact: fionaconn@icloud.com

Group Final Project