> For the complete documentation index, see [llms.txt](https://help.sbtinstruments.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.sbtinstruments.com/mpd/workflows/mpd1.md). # Identify harvest time
BactoBox® skill levelTime to complete (E. coli)Hands-on timeRequirements
🎓 Intermediate⏳ 8-12 hours⏱️ 4 hours:hard-drive: 7.6a :floppy-disk: 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**](/encyclopedia/software/access/pages/measurement-group/growth-curve-group-type.md#cize)**:** The sphere-equivalent diameter of the cells at max cell concentration. In practice the workflow is very similar to [Track growth curve](/mpd/workflows/track-growth-curve.md), but instead of tracking lag and exponential phase, we measure primarily in the deceleration and stationary [growth phases](/mpd/cell-growth/growth-phases.md). {% hint style="success" %} ## 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. {% endhint %} {% hint style="info" icon="graduation-cap" %} ## 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](/mpd/workflows/bioprocess-workflows.md). {% endhint %} ## 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](#user-content-fn-1)[^1] 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. {% hint style="info" %} ## Real-time [PAT ](#user-content-fn-2)[^2]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](/mpd/cell-growth/harvest-window.md). {% endhint %} ## 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 ](#user-content-fn-3)[^3]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](/mpd/cell-growth/correlation-with-plate-counts.md) for [active cultures](/mpd/cell-growth/active-cultures.md) 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](/mpd/workflows/mpd1/plan-experimental-timeline.md) 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.

{% hint style="info" icon="hammer-brush" %} ## 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. :radio-tuner: Stay tuned. We are working on a when-to-harvest algorithm directly in Access. It will do all the tricky curve-fitting automatically. {% endhint %} ## Overview The overall steps in the workflow are given below. 1. [Plan experimental timeline](/mpd/workflows/mpd1/plan-experimental-timeline.md) 2. [Get things ready](/mpd/workflows/mpd1/get-things-ready.md) 3. [Create measurement group](/mpd/workflows/mpd1/create-measurement-group.md) 4. [Track deceleration phase](/mpd/workflows/mpd1/track-deceleration-phase.md) 5. [Track hourly](/mpd/workflows/mpd1/track-hourly.md) 6. [Conclude engineering run](/mpd/workflows/mpd1/conclude-engineering-run.md) 7. [Inspect data for harvest time](/mpd/workflows/mpd1/inspect-data-for-harvest-time.md) 8. [Summary](/mpd/workflows/mpd1/summary.md) ## Summary With this introduction you are now ready to [Plan experimental timeline](/mpd/workflows/mpd1/plan-experimental-timeline.md). [^1]: A production or pilot-scale fermentation carried out primarily to **test and validate the process, equipment, automation, and operational procedures** rather than to generate commercial product for release [^2]: Process Analytical Technology [^3]: High Performance Liquid Chromatography --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.sbtinstruments.com/mpd/workflows/mpd1.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.