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Bioprocess Optimization

Smart cultivation in TFTAK

TFTAK offers outstanding support in manufacturing of microorganisms offering microbial fermentation contract manufacturing. We have developed solutions for some of the best industrial strain manufacturers in the world.

TFTAK is a strategic partner in focus on developing cultivation and bioprocess capabilities for “next-generation” probiotics (NGPs).

TFTAK has over 15 years of experience in detailed analysis of metabolism and optimization of microbial bioprocesses. We can use different cultivation approaches e.g. continuous cultivation, fed-batch and conventional batch depending on the clients needs. We are well equipped and experienced in handling strict anaerobes and also developing full aerobic processes.

Bioprocess Optimization

Focus and Advantages


TFTAK is your ideal bioprocess engineering partner, offering outstanding support in microbial fermentation contract manufacturing. We have developed solutions for some of the best industrial strain manufacturers in the world.


We are focused on offering agile solutions in the following cases:

Our approach starts from the species of interest of our clients. To develop lab-scale (1L) bioprocess and optimized down-stream processing the following steps are made:

  • For isolated microbial species that cannot be commercialized using simple optimization but instead need in-depth analysis

  • For the development of an efficient bioprocess for manufacturing consortia

  • For the improvement of growth properties of microbial species of interest with laboratory evolution and subsequent process development

You will enjoy two major advantages while working with us:

  • Time efficiency

Our experts can develop a flexible pipeline for the cultivation procedure that will take 2-3 months.

  • Full pipeline

Our approach is distinct in that we offer all services from DNA sequencing to the development of industrially feasible bacteria in one pipeline, as an integrated service.

Our method of cultivating microorganisms combines a synergetic and high-throughput pipeline of DNA sequencing methods, metabolic modelling, analytical (omics) methods and cultivation for full bioprocess control.

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Cultivation Technology

Approach and Work


Our approach to the cultivation of microorganisms:

Our unique approach is to develop a flexible pipeline for cultivation of microorganisms which are difficult to cultivate, e.g. strictly anaerobic human gut colonizing species, and design robust consortia or media for efficient co-culturing of multiple species in a single bioprocess.

Our work involves three main steps:

  • Genomic analysis. We analyze annotated genes to construct functional metabolic pathway maps and metabolic models. The latter helps us to gather essential information about potential auxotrophies and medium requirements for the screening phase and bioreactor process optimization.

  • Medium component screening with a microtiter plate reader, shake flask or isothermal microcalorimetry (IMC). IMC is the preferred method for anaerobes, which determines microbial growth by heat generated by metabolism. The strengths of the method are its excellent reproducibility and the fact that IMC also works in opaque environments. In the case of aerobic microbes, a shake flask or microtiter plate reader is preferred.

  • Bioreactor production process and downstream processing optimization. Here we optimize high culture density viable cell production. Sugar, yeast extract and peptone concentrations are optimized. Possible depletion of key medium components (e.g., amino acids) is determined and, based on the results, the final process is defined. We can also optimize the down-stream process including lyophilization procedures.

Filamentous Fungi

Solutions and



Cultivation technology of filamentous fungi:

Meat, fish and dairy alternatives are a fast-growing field. We have established a laboratory for growing filamentous fungi and use submerged as well as solid state fermentation to produce nutritional and protein-rich biomass. 

Current plant-based product development is typically focused on plant proteins and cultivated meat technologies. Fungal biomass is one of the upcoming alternatives for conventional meat and fish. We have experience in utilizing defined media, plant-based raw materials as well as food industry side-streams as feedstocks.

Solutions offered by our team at TFTAK:

  • Cultivation by submerged fermentation. The 1 L and 7 L bioreactors are dedicated to the bioprocess optimization of filamentous fungi.

  • Cultivation by solid-state fermentation. To obtain protein-rich biomass for meat and fish alternative development, solid-state fermentation on various plant-based raw materials as well as food industry side-streams can be utilized.

  • Metabolic characterization and growth medium optimization. Relying on our strong understanding of fungal metabolism, the growth medium and parameters are optimized to obtain the highest biomass yield.

  • Comprehensive biomass description and biomass characterization. Chemical, physical, and sensory properties are thoroughly evaluated using our in-house analytical methods and equipment.

  • Fungal biomass post-treatment and product formulation. Physical and chemical processes and treatments are applied to obtain high-quality fungal biomass and to reduce RNA, resulting in suitable biomass for fish and meat alternative development.

Our main strengths:

  • Thorough bioinformatic characterization of strains. Our team has extensive knowledge of various bioinformatic tools to assemble the genome and study the metabolism of fungi for process optimization.

  • Comprehensive chemical and sensory evaluation of fungal biomass with novel analytical equipment.

  • Bioprocess up-scaling. Our team provides support to transfer the lab-scale and pilot-scale fungal biomass production to the industrial level.

  • Downstream processing.

Human Gut

Model Consortium


The human microbiome has vast potential in several areas, including being a source of naturally evolved drug candidates. The importance of the microbiome for human health is enhanced by technological advances in microbiology and genomics which lead to a rapid increase in interest and demand for cultivating microorganisms.

TFTAK offers a fast and cost-effective in vitro gut microbiome analysis service for the prebiotics industry to determine which product modifications have the most significant effect on human gut microbiota.

In order to test the effect of different prebiotics on human microbiome, we have developed:

  • A model consortium of 25 species of microorganisms

  • A technology for isothermal microcalorimetry-based serial batch screening

This technological breakthrough will allow the screening of tens of dietary fiber mixtures within a week. The information could then be used to choose a product for testing in human trials and microbial fermentation contract manufacturing.











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Cultivation equipment

Fermenters and isothermal microcalorimeters are indispensable
to scale up the microbial cell culture development

  • Isothermal microcalorimetry - a perfect tool for growth medium screening and other applications.

Isothermal microcalorimeter determines heat produced during microbial growth with high precision. The main strength of the device is the fact that it could be used in opaque environments that optical density based devices cannot handle. This is our main tool for medium screening experiments.

  • Fermentation systems and applications

TFTAK has seven Applikon 1L bioreactors and one 7L system. The bioreactors are equipped with off-gas analysis and turbidity probes and ready for continuous, fed-batch and batch fermentation at controlled pH, temperature and gas environment. We have excellence in cultivation of both aerobes and strict anaerobes.

  • Cultivation of strict anaerobes

Strict anaerobes demand oxygen free environment.
TFTAK has Coy type B anaerobic chamber that makes it possible to handle species that do not tolerate oxygen.

Microbial cell culture services team is open for collaboration in challenging projects

"Our microbial cell culture services team is constantly growing and acquiring new knowledge. We have reached outstanding results in collaboration with world leading companies and are open to experiment with fresh ideas and projects that no-one has done before."

Ranno NAHKU, PhD

Director of Bioprocess Research

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