How Probiotic Strains Are Brought From Lab to Market

The development of probiotic supplements is a complex yet well-orchestrated process that transforms scientific innovation into commercially viable products. From isolating novel human-derived strains to optimizing production and manufacturing multi-strain formulations, every stage demands precision, standardization, and tailored expertise. Companies like Creative Biolabs play a critical role in this pipeline, offering robust solutions for strain discovery, process optimization, and large-scale production.

This article outlines the key steps in bringing probiotic strains from the research lab to finished products, highlighting both scientific and manufacturing challenges, particularly in the development of multi-strain formulations.

Fig.1 The production of probiotics for dietary supplements and dairy starter culture strains.¹

Probiotic Strain Development: From Candidate to Contender

Developing a market-ready probiotic strain begins with discovery—either through isolation from natural environments or screening of microbial libraries. Promising candidates often originate from the human gut microbiota, fermented foods, or natural sources. The goal is to identify strains that exhibit beneficial properties and are safe for consumption. Initial screening focuses on:

• Tolerance to low pH and bile salts to survive gastrointestinal conditions
• Adhesion to intestinal epithelial cells, supporting transient colonization
• Antimicrobial activity through competitive exclusion or secretion of inhibitory substances
• Genetic safety, including absence of toxin genes and mobile antibiotic resistance elements

Modern tools such as whole-genome sequencing, comparative genomics, and bioinformatics pipelines are used to validate strain identity, rule out harmful traits, and assess functional potential. Creative Biolabs supports clients at this critical phase with proprietary strain libraries and screening services, enabling rapid identification and characterization of elite candidates.

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Isolation of Human-Derived Probiotic Strains

Many commercial probiotics are derived from the human microbiome, reflecting their ecological compatibility with the host. Isolating viable strains from human samples—primarily feces, saliva, or mucosal swabs—requires sterile collection, anaerobic culturing, and selective media.

Once isolated, strains are identified via 16S rRNA sequencing or WGS, then subjected to in vitro validation. Common methods include:

• Growth profiling under gastrointestinal-like stress
• Adhesion assays using human intestinal cell lines
• Hemolysis and cytotoxicity testing to rule out safety concerns
• Antibiotic susceptibility screening, ensuring the absence of transferable resistance

Not all isolates qualify. Only those demonstrating stable growth, safety, and resilience under simulated digestive conditions are considered viable candidates for scale-up. Creative Biolabs offers comprehensive services for strain isolation, functional screening, and safety profiling—streamlining the transition from isolation to development.

Overcoming Scale-Up Challenges in Probiotic Production

Scaling from a 100 mL lab flask to a 5,000 L fermenter introduces new biological and engineering complexities. Each probiotic strain responds differently to fermentation conditions, and preserving viability throughout the process is critical. Key scale-up challenges include:

• Non-linear fermentation dynamics: Larger tanks often develop gradients in pH, oxygen, or temperature, affecting bacterial metabolism.
• Shear stress from pumping, agitation, or filtration, which can damage sensitive cells.
• Extended hold times between steps—such as centrifugation and drying—can reduce cell viability.
• Contamination risks grow with scale, requiring tight environmental controls.

Creative Biolabs addresses these issues with pilot-scale fermentation studies, simulating industrial conditions to refine protocols and minimize risks. This includes adjusting agitation speeds, gas flow rates, and feeding strategies to match strain-specific growth patterns.

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Strain-Specific Optimization: Tailoring the Process

Probiotic manufacturing is not one-size-fits-all. Even closely related strains often require unique process conditions for optimal growth and preservation. Therefore, strain-specific process optimization is essential.

Fermentation Optimization

Fermentation parameters such as pH, temperature, agitation, and dissolved oxygen are adjusted to match the biological needs of the strain. Some lactic acid bacteria prefer a pH of 5.5–6.0, while others may require low-oxygen environments or specialized nutrient compositions.

Creative Biolabs conducts Design of Experiment (DoE) studies to quickly identify optimal fermentation conditions. This results in higher cell density, improved viability, and better downstream performance.

Preservation and Drying

After cultivation, cells are concentrated and stabilized—typically through freeze-drying (lyophilization) or spray drying. However, both methods expose bacteria to physical and osmotic stress, risking viability loss.

To counter this, cryoprotectants (e.g., trehalose, sucrose) and matrix excipients (e.g., skim milk, maltodextrin) are added to the cell suspension before drying. The lyophilization cycle itself—freezing rate, shelf temperature, and drying time—is adjusted to protect each strain's membrane integrity and functionality.

Through iterative testing, Creative Biolabs develops customized preservation protocols for each probiotic, ensuring that dried cells remain viable throughout storage and downstream handling.

Manufacturing Multi-Strain Probiotic Formulations

Multi-strain probiotics appeal to consumers seeking comprehensive microbiome support. However, combining different strains into a stable, effective product presents unique production challenges.

Separate Cultivation and Drying

To avoid antagonistic interactions, each strain is:

• Cultured separately under optimal conditions
• Harvested and preserved using strain-specific drying protocols
• Stored as an individual powder concentrate

Only after stabilization are the strains blended according to the formulation design.

Formulation Considerations

• Precise CFU Ratios: Manufacturers must ensure the correct quantity of each strain is delivered in every dose.
• Strain Compatibility: Some strains produce metabolites that inhibit others. Compatibility studies are required to ensure stability during storage.
• Excipient Selection: Carriers like inulin, microcrystalline cellulose, or resistant starch improve powder flow, dispersibility, and moisture resistance.

Creative Biolabs provides formulation and blending services, including strain compatibility testing and controlled environment packaging to preserve product potency. Our facilities support blending of high-count, multi-strain formulations under GMP-compliant conditions.

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Ensuring Quality and Long-Term Stability

Probiotics are only effective if viable organisms reach the consumer at the stated dose. Ensuring quality over the product's entire shelf life requires rigorous control measures at every stage.

Viability Testing

Producers often include CFU overages to account for degradation over time. However, stability studies are still essential to ensure strains remain above label claims until expiry. These studies include:

• Accelerated stability testing under elevated temperature and humidity
• Real-time monitoring over 12 to 24 months
• Water activity control to prevent metabolic reactivation

Strain Verification and Safety Testing

• Strain identity is verified via qPCR or genetic fingerprinting
• Contamination checks for pathogens and spoilage organisms
• Endotoxin and residual allergen screening to meet safety standards

Creative Biolabs conducts full analytical testing on raw materials and final products, including strain-specific CFU counts, identity confirmation, and safety validations. We help clients meet international quality standards and regulatory expectations.

Packaging and Delivery Formats

Once probiotic powders are stabilized and verified, they are encapsulated or packaged in dosage forms that support long-term viability. Popular delivery forms include:

• Capsules (standard or enteric-coated)
• Sachets for mixing with water or food
• Tablets or functional foods (subject to additional formulation challenges)

Proper packaging is essential. Moisture-barrier bottles, oxygen-absorbing sachets, and cold-chain storage (when needed) all contribute to shelf-life extension.

Creative Biolabs supports clients in choosing appropriate delivery systems and packaging materials that align with product goals and strain requirements.

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Related Services Recommendations

Bringing probiotic strains from the lab to market requires far more than just scientific discovery. It demands a coordinated effort in microbial identification, strain-specific process design, large-scale manufacturing, and stringent quality control.

From isolation of high-potential human strains to formulation of multi-strain capsules, Creative Biolabs offers full-spectrum support for probiotic development. Our services are built around scientific rigor, regulatory compliance, and manufacturing excellence—helping ensure that each product entering the market is effective, stable, and reliable. The followings are our main services:

• Microbial Isolation and Screening
• Microbial Identification
• Microbial Stabilization
• Microbial Fermentation
• Microbial Formulation
• Lab-scale Production
• Downstream Process Development
• QC Analytical Testing
• Final Product Assays
• Potency Test
• Antimicrobial Susceptibility Testing

FAQs

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References

1. Fenster, K., et al. "The production and delivery of probiotics: A review of a practical approach. Microorganisms 7." 2019, https://doi.org/10.3390/microorganisms7030083
2. Bazireh, Homa, et al. "Isolation of novel probiotic Lactobacillus and Enterococcus strains from human salivary and fecal sources." Frontiers in microbiology 11 (2020): 597946. https://doi.org/10.3389/fmicb.2020.597946
3. Distributed Under Open Access license CC BY 4.0, without modification.