Fermented Small Molecules

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Microbial fermentation for complex small molecules and metabolites

  • Agilent Advanced Therapeutics provides end-to-end microbial fermentation for small molecules, metabolites, and intermediates that support pharmaceuticals, bioconjugation, and specialty chemical applications.
  • With facilities in Charlottetown, PEI, Canada—including multiple fermentation suites up to 15,000 L—our teams support programs from early development through commercial manufacturing. Integrated chemistry, analytical capabilities, and downstream purification allow us to efficiently scale complex routes with consistency and regulatory confidence.
  • Large-scale fermentation capacity—Fermenters up to 15,000 L for reliable commercial supply.
  • Integrated chemistry and fermentation workflows—Process chemistry, route development, and fermentation under one organization.
  • Advanced downstream purification—Centrifugation, extraction, crystallization, and large-format chromatography (80 cm columns).
  • Microbial strain and process optimization—High-yield, robust fermentation processes to improve cost and efficiency.
  • Seamless scale-up—Fermentation development, pilot-scale, and commercial production across harmonized facilities.
  • Regulatory-ready production—GMP-aligned systems with proven commercial track record and global regulatory experience.

Fermented Small Molecules

Microbial fermentation of small molecules supported by in-house chemistry, purification, and expertise

Stainless steel bioreactors used in large-scale biologics manufacturing and fermentation within a modern pharmaceutical facility.

Features

Microbial fermentation for complex small molecules and metabolites

The Advanced Therapeutics advantage

50+ years' experience

in biopharma manufacturing

7 cGMP-aligned facilities

in U.S. and Canada are equipped for multiple modalities and projects

$1.65 billion

invested into CDMO business in 2023–2026

100+ successful audits

by platform biotech, big pharma, and global regulatory agencies

Specifications

Facility and equipment highlights

  • Charlottetown, PEI facilities with multiple fermentation suites
  • Commercial fermentation up to 15,000 L
  • Development-scale fermentation (30–1,000 L)
  • Stainless steel and single-use options in PD
  • High-capacity downstream processing including industrial centrifugation, solvent extraction, crystallization, 80 cm chromatography columns
  • Controlled-substance licensed facility

Capabilities and expertise

  • Microbial strain optimization
  • Fermentation route design and scale-up
  • Integrated chemistry and fermentation development
  • In-process monitoring (PAT)
  • Crude processing, extraction, and purification
  • Toxins, metabolites, and complex intermediates

Product applications

  • Small-molecule APIs and intermediates
  • Bioconjugation intermediates (PEGs, linkers, ADC precursors)
  • Microbial metabolites (bioactive compounds)
  • Bioreagents for the manufacture of diagnostic test kits and processing agents for biological application
  • Novel secondary metabolites for R&D or commercial programs

Quality and compliance

  • GMP manufacturing, aligned with ICH guidance
  • Harmonized quality system across all sites
  • Strong inspection record (FDA, Health Canada)
  • Cleaning validation, impurity profiling, stability programs
  • Comprehensive documentation packages for regulatory filings

Browse other areas of expertise

A cluster of connected circular nodes forming a branching structure, with a distinct end node, representing synthetic small molecules. Synthetic Small Molecules

Chemical steps to finalize or modify fermented intermediates.

Scalable production for downstream synthesis needs.

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Containment window with glove ports on an isolator used for safely handling highly potent APIs. Highly Potent APIs

Support for potent compounds derived from microbial pathways.

Contained processing for high-potency fermentation outputs.

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Circular biologics icon featuring an abstract DNA-like structure arranged in a ring. Microbial Fermentation

Expanded capacity for larger batches or alternate host systems.

Flexible platforms for metabolites, enzymes, and intermediates.

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A dropper releasing a droplet above three capped test tubes in a rack, representing bioreagents sample preparation. Bioreagents

High-quality reagents to optimize microbial growth and yield.

Reliable inputs for fermentation, purification, and analytics.

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Three small capped bottles with a dropper above the center one releasing a droplet into it, representing fill/finish. Fill/Finish

Aseptic filling for liquid or sterile small-molecule formulations.

Controlled handling for sensitive or high-value products.

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Frequently asked questions

Find helpful answers to common questions as you evaluate and advance your program

What types of small molecules can be produced by microbial fermentation?

We produce a range of fermented small molecules including metabolites, toxins, complex intermediates, and specialty compounds that benefit from biological production pathways.

What fermentation scales are available for small-molecule production?

We offer development-scale fermentation from 30–1,000 L and commercial-scale production up to 15,000 L.

Can Agilent Advanced Therapeutics support both fermentation and synthetic steps?

Yes. Our integrated model allows fermentation and synthetic chemistry teams to collaborate closely, supporting hybrid routes and efficient downstream processing.

How do you ensure consistency from batch to batch?

We use PAT monitoring, controlled feeding strategies, validated analytical methods, and harmonized process parameters across development and manufacturing suites.

Do you manufacture controlled substances?

Yes. Our Charlottetown site is licensed for controlled substances and maintains strict alignment with regulatory requirements.

Can fermentation be used to scale complex intermediates for ADC or biologics manufacturing?

Absolutely. Fermentation often provides higher yields and better impurity profiles for intermediates used in conjugation, linker synthesis, or bioreagents for the manufacture of diagnostic test kits.

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