Identify harvest time

MPD-1. Determine best harvest time for highest cell concentration in batch cultivation.

BactoBox® skill level	Time to complete (E. coli)	Hands-on time	Requirements
🎓 Intermediate	⏳ 8-12 hours	⏱️ 4 hours	7.6a v2026.02a

The goal of this workflow is to identify harvest time for a fixed-in-time batch bioprocess that involves production of bacteria. The outcome of the workflow is

• Harvest time: The incubation time needed to hit the highest cell concentration.

• Harvest time concentration: The max cell concentration that is obtainable with the bioprocess.

• Harvest time CIZE: The sphere-equivalent diameter of the cells at max cell concentration.

In practice the workflow is very similar to Track growth curve, but instead of tracking lag and exponential phase, we measure primarily in the deceleration and stationary growth phases.

Plan experiments carefully and use a tag-team approach for this workflow

MPD-1 is one of the more time-intensive workflows. It is therefore advisable to carefully plan the experimental timeline and organize personnel into shifts to ensure efficient execution.

This workflow requires intermediate BactoBox® skills

The skill level for this MPD is intermediate because you need skills for when to conclude the experiment and how to identify harvest time. If you are new to BactoBox® it may be better to start with one of the basic Workflows.

Fixed-in-time strategy to identify harvest time

In this workflow, we use the fixed-in-time strategy. The steps of this strategy are outlined briefly below

1. First an engineering run is done to identify the optimal harvest point. A panel of different analytical methods is used to characterize the bioprocess.

2. The data from the engineering run(s) are analyzed to determine the optimal incubation time where cell concentration peaks.

3. Once the optimal incubation time has been determined, the bioprocess is fixed in time for the subsequent production runs.

Real-time PAT methods provides more accurate harvest time for production runs

The fixed-in-time strategy assumes that all critical parameters are controllable to make the bioprocess repeatable. In practice it is very difficult to get consistent processes and it is advisable to use real-time PAT tools like BactoBox® to pinpoint harvest time in production runs. More information on this is available in the explainer Harvest window.

Existing methods to identify harvest time

It is far from trivial to determine optimal harvest time. The traditional methods used for this purpose have shortcomings.

• Plate counts: Inaccurate, labor-intensive, and long time-to-result.

• Light scattering methods: Proxy methods like optical density (OD) depend on additional factors than cell concentration, e.g. bacterial size, non-bacterial objects and pigment formation.

• Metabolite measurements: HPLC measurement on carbon source concentration and by-product formation typically takes more than two hours to complete. The cells may use alternative substrates than the supplied carbon source and therefore these concentrations do not necessarily indicate when to conclude the experiment.

• On-line analysis methods: Distinct patterns from pH, conductivity, off-gas, dissolved oxygen, and capacitance do not necessarily coincide with when to harvest.

For bioprocesses with bacteria as the product, place counting is presently one of the most important metrics to define harvest time.

BactoBox® measurements to identify harvest time

BactoBox® shows strong agreement with plate counts for active cultures and gives you real-time cell concentration data. You get the same insight as plate counts with >1,000 times faster results and better precision.

The real-time results are beneficial because they indicate when to conclude the engineering run. In contrast, plate counts provide no guidance on when to stop the run, since the time to result is several days. Light scattering methods and online sensors also do not provide reliable information on when to conclude the engineering run, as their signals are influenced by multiple factors beyond cell concentration.

Staphylococcus epidermidis example

Throughout this workflow we will use a S. epidermidis growth curve example to demonstrate when to harvest. The below plot shows the complete growth curve. You will Plan experimental timeline so that measurements are mainly done in the grey box below, i.e. during the deceleration and stationary phases.

• The low gauge icon highlights the deceleration phase where you should start the measurements.

• The magnifying glass highlights the best harvest points based on this example.

Staphylococcus epidermidis shake flask growth curve with TSB as growth medium. The grey box highlights where most measurements should be done. The magnifying glass is the identified harvest time. BactoBox® (lavender) and plate counts (yellow) were done using triplicate repeats (primary axis). CIZE (cyan) is represented on the secondary axis. Error bars represent standard deviation.

We are working on a harvest algorithm

The most rigorous approach to determine harvest time is to fit the data to a mathematical function. In the present workflow we use a more simplistic, rule-of-thumb approach.

Stay tuned. We are working on a when-to-harvest algorithm directly in Access. It will do all the tricky curve-fitting automatically.

Overview

The overall steps in the workflow are given below.

1. Plan experimental timeline

2. Get things ready

3. Create measurement group

4. Track deceleration phase

5. Track hourly

6. Conclude engineering run

7. Inspect data for harvest time

8. Summary

Summary

With this introduction you are now ready to Plan experimental timeline.