From engineered phage to live biotherapeutics—viability and precision at scale.

Aquaterra Biotech is a Québec-based CDMO built for the future of microbial medicine. We specialize in bacteriophage therapeutics, microbiome-based drugs, and next-generation live biotherapeutic products (LBPs)—domains where viability, genetic stability, and regulatory rigor make or break programs. Sponsors come to us because fragile biology cannot survive ordinary manufacturing; it requires engineered processes, custom analytics, and GMP lines designed to keep pace with regulators worldwide.

This page outlines the full spectrum of our phage and microbiome CDMO services—from strain engineering and high-titer fermentation to stabilization, fill-finish, release testing, and regulatory submissions. You’ll see why Aquaterra is the partner of choice for innovators building the next era of microbial therapies.

Why Phage & Microbiome Matter Now

• Antibiotic resistance crisis: Phages and engineered microbiome interventions are at the center of alternatives to antibiotics.
• Regulatory clarity emerging: The FDA, EMA, and Health Canada now recognize LBPs, with frameworks for INDs and IMPDs.
• Investment boom: Billions in venture and pharma partnerships are flowing into engineered bacteria, consortia, and phage biocontrol.
• Manufacturing gap: Few CDMOs can scale these modalities under cGMP while preserving viability and genetic integrity.

Aquaterra fills this gap with precision microbial fermentation, phage engineering expertise, and integrated QA/regulatory systems that move programs cleanly from concept to clinic.

Our Phage & Microbiome Services at a Glance

• Phage Engineering & Production
  High-titer bacteriophage fermentation, purification, and characterization.
• Live Biotherapeutic Products (LBPs)
  Anaerobe and consortia fermentation, stabilization, and GMP release.
• Microbiome-Derived Postbiotics
  Cell-free fractions, metabolites, and paraprobiotics with functional assays.
• Formulation & Fill-Finish
  Vials, capsules, sachets, bulk frozen bags—designed for shelf life.
• Analytics & QA
  Infectivity, CFU/viability, genetic stability, host DNA clearance, potency assays.
• Regulatory & Tech Transfer
  IND/IMPD packages, GRAS/Novel Food dossiers, EU BPR submissions.

1. Phage Engineering & Therapeutics

Strain & Host Selection

Phage manufacturing begins with host bacteria—often Gram-negative species like E. coli, Klebsiella, or Pseudomonas. Our services include:

• Host-range editing and CRISPR-based tailoring for therapeutic phages.
• Resistance mapping and evolutionary stability profiling.
• Safe strain qualification (endotoxin profile, prophage-free, antibiotic markers).

Upstream: High-Titer Phage Production

• Controlled infection MOI (multiplicity of infection) optimization.
• Batch and fed-batch fermentations with DO/pH/temperature tight control.
• Host lysis kinetics modeled to maximize yield while minimizing debris.

Downstream: Purification

Phage DSP is delicate—removing host cell proteins, nucleic acids, and endotoxin without killing infectivity. Our toolkit includes:

• Tangential-flow filtration (TFF) with low-shear membranes.
• Endotoxin clearance strategies (anion exchange, affinity resins).
• Chromatography and polishing steps validated against potency loss.
• Final ultrafiltration/diafiltration into formulation buffer.

Analytics

• Infectivity assays (PFU, qPCR-based infectious unit assays).
• TEM imaging for morphology.
• Potency/stability across stress conditions.
• Host DNA/protein residuals and endotoxin quantification.

Formulation

• Liquid phage formulations for IV/PO delivery.
• Spray-dry and lyophilization for stability in oral delivery or agriculture.
• Encapsulation for targeted GI delivery.

2. Live Biotherapeutic Products (LBPs)

Anaerobe Fermentation

• Dedicated anaerobic suites with nitrogen/CO₂ headspace and deoxygenated media.
• Inline dissolved oxygen monitoring (<1 ppm).
• Continuous-flow and perfusion systems for fragile anaerobes.

Consortia Development

• Multi-strain programs engineered to maintain defined ratios.
• Staggered fermentations and proportional blending.
• Stability models to ensure ratio consistency over shelf life.

Stabilization

• Cryoprotectant matrices designed via DOE (trehalose, skim milk, amino acids).
• Microencapsulation (alginate, chitosan, lipid coatings) for gastric survival.
• Spray-dry and fluid-bed drying for shelf-stable spores.

Fill-Finish

• Bulk frozen bags, vials, sachets, capsules.
• Low-O₂ packaging with scavengers and desiccants.
• Cold chain validation and shipping simulations.

Analytics

• CFU counts with PMA/EMA-qPCR to distinguish live vs. dead.
• Genomic stability assays across passages.
• Potency assays (bile/acid resistance, adhesion surrogates, metabolite activity).
• Shelf-life modeling under ICH stability conditions.

3. Microbiome-Derived Postbiotics & Paraprobiotics

Not every microbiome therapy requires live, replicating organisms. Increasingly, sponsors are turning to postbiotics (cell-free metabolites, secreted factors, structural fragments) and paraprobiotics (inactivated or non-viable cells that still deliver immune or functional benefits). These products offer several advantages: enhanced stability, simpler distribution, reduced biosafety concerns, and clearer regulatory paths. At Aquaterra, we’ve built a reproducible framework for developing and manufacturing these next-generation modalities under controlled, audit-ready conditions.

Inactivation Strategies

The first step is creating consistency in how “non-viable” is defined and achieved. We validate inactivation methods with precision:

• Thermal inactivation: Controlled heat profiles, monitored with real-time thermocouples to establish validated kill curves while minimizing protein denaturation.
• UV and light-based inactivation: UV-C exposure in continuous-flow systems, balancing penetration depth with DNA damage efficiency.
• High-pressure processing (HPP): For paraprobiotics intended for food applications, offering gentle but complete inactivation.
• Chemical methods: Where appropriate, validated use of ethanol or other mild reagents with rigorous downstream clearance testing.

Each method is benchmarked against viability assays (PMA/EMA-qPCR, flow cytometry with membrane integrity dyes) to prove complete inactivation.

Fractionation & Metabolite Recovery

Many postbiotic effects arise not from whole cells but from their secretome. We fractionate supernatants using:

• Ultrafiltration membranes to enrich peptides, SCFAs, or exopolysaccharides.
• Chromatographic separation to isolate bioactive fractions (cation/anion exchange, HIC, SEC).
• Lyophilization or spray-drying for stable powders that preserve metabolite functionality.

This allows sponsors to define a “postbiotic fingerprint” and link functional claims to specific metabolite spectra.

Functional Validation

Postbiotics and paraprobiotics demand proof of activity beyond “absence of viability.” We conduct:

• Cytokine modulation assays with primary immune cells or reporter lines.
• Epithelial barrier integrity testing (TEER, tight junction protein assays).
• Anti-pathogen activity assays in co-culture.
• Metabolomic profiling to tie function to defined molecules.

These functional validations become central to dossiers—demonstrating not just safety but mechanistic benefit.

Safety & Quality Testing

Safety claims must stand up in regulatory and retailer audits. Our testing panels include:

• Residual DNA quantification and fragment analysis.
• Endotoxin/LPS testing (critical for Gram-negative paraprobiotics).
• Allergen content and cross-contact risk assessments.
• Mycotoxin, heavy metal, and residual solvent panels when required.

The result is a product that can be trusted by regulators, clinicians, and consumers alike.

4. Regulatory & Quality Framework

Aquaterra’s regulatory and QA infrastructure is designed to handle the gray zones of emerging microbiome therapies—where expectations straddle food, pharma, and agriculture.

IND/IMPD Support

For clinical programs, we provide:

• Process descriptions & master batch records with full traceability from inoculum to final vial.
• Comparability plans for bridging early research processes into GMP campaigns.
• Potency assay validation linking CFU or activity metrics to functional outcomes.
• Stability packages designed around ICH conditions (25 °C/60% RH, 30 °C/65% RH, 40 °C/75% RH).
• Host strain qualification (genetic stability, prophage screening, antibiotic marker absence).
• Impurity clearance data (residual proteins, DNA, host cell debris).

GRAS/Novel Food Dossiers

For food and nutrition products, we build GRAS and EU Novel Food submissions that include:

• Safety narrative (history of use, strain origin, toxicology evidence).
• Manufacturing descriptions with unit operations and controls.
• Final product specifications (identity, purity, potency).
• Toxicology summaries or literature-based safety equivalence.

EU BPR Submissions

For agricultural and environmental phage or enzyme products:

• Stability data under realistic storage/field conditions.
• Efficacy dossiers against target pathogens/pests.
• Environmental risk assessments and residue studies.
• Safety and exposure documentation across crop/animal uses.

QA Infrastructure

• GMP-compliant pilot scale (300–2,000 L): scalable fermentation, anaerobic handling, spray-dry and lyo capacity.
• LIMS traceability: Every sample, every lot tied into digital records with deviation dashboards.
• SOC-2–certified digital twin: Secure live data sharing with clients; IP firewall guarantees data segregation.

5. Why Sponsors Choose Aquaterra for Phage & Microbiome

Aquaterra brings together the full ecosystem of expertise under one roof—making us rare among CDMOs serving this space.

• Viability engineered, not left to chance. Whether preserving infectivity of a phage, or ensuring a paraprobiotic remains definitively “dead,” we design viability into the process.
• Anaerobe + phage expertise under one roof. Our team runs strict anaerobe fermentations and high-titer phage campaigns with the same GMP discipline.
• Full regulatory fluency. We cover pharma (IND/IMPD), food (GRAS/Novel Food), and ag-biocontrol (EU BPR). Few CDMOs can handle this cross-sector scope.
• Cost intelligence and transparency. Our dashboards surface media, resin, utility, and packaging costs early—informing sponsor decisions at every stage.
• Audit-ready documentation. Right-first-time records and deviation control reduce surprises during regulatory and partner audits.

Representative Programs

• Phage cocktail for MDR infections
  Multi-host fermentation, chromatographic polishing, GMP aseptic vialing.
• LBP consortia for metabolic disease
  Anaerobe co-fermentation, encapsulation strategies, cold chain validation, IND-ready.
• Spore-based veterinary LBP
  Sporulation control, spray-drying with validated heat profiles, stable sachets for ambient distribution.
• Postbiotic for skin barrier health
  Metabolite fractionation, cytokine modulation assays, validated cosmetic-grade specifications, regulatory dossier for international submission.

Program Onboarding: 30-Day Path

Week 1: Intake, manufacturability & risk assessment.
Week 2: DOE design (media, protectants, packaging).
Week 3: Bench/pilot runs, early stability initiation.
Week 4: Go/no-go + Phase Plan with Gantt + budget.

Let’s Build the Future of Microbial Medicine

Phage and microbiome programs demand more than ordinary fermentation. They demand engineered viability, regulatory foresight, and scale discipline. Aquaterra Biotech delivers all three—turning fragile, next-generation biology into regulated, ready-to-ship product.

Email us at info@aquaterrabiotech.com or come visit us in Montréal