Week 1 HW: Microalgae-Derived Coffee

Microalgae-Derived Coffee-Like Powder

For my first biomanufacturing project, I would like to explore whether engineered microalgae could be used to produce a coffee-like beverage powder. The idea is not to reproduce a conventional coffee bean, but instead to use the microalgal biomass itself as the basis of a new product with some of the functional and sensory characteristics associated with coffee.

1. What would I like to biomanufacture and why?

I would like to biomanufacture a coffee-like powder from engineered microalgal biomass.

The concept is to engineer a Chlorella species so that, while producing biomass, it also accumulates selected compounds associated with coffee, potentially including caffeine and relevant flavor or aroma precursors. After cultivation, the biomass would be harvested, dried, mildly roasted, milled, and packaged as a concentrated powder that could be used to prepare a coffee-like beverage.

I am interested in this idea because it combines two things that are usually considered separately: biomanufacturing and food production.

Instead of growing a plant for years and harvesting only a particular part of it, microalgae can rapidly generate biomass in controlled cultivation systems. This creates the possibility of producing a high-value beverage ingredient using a relatively compact and highly controlled production platform.

Another interesting aspect is that the biomass itself could be part of the final product. Chlorella biomass contains proteins, lipids, carbohydrates, pigments, and other cellular components, and its composition can change depending on the cultivation conditions [3]. Therefore, the goal would not necessarily be to imitate coffee perfectly, but to create a new functional beverage ingredient that combines coffee-associated properties with the nutritional characteristics of microalgal biomass.

At this stage, I do not assume that microalgal coffee would automatically be cheaper or more sustainable than conventional coffee. Cultivation, harvesting, drying, and processing microalgae can also require substantial resources. Instead, one purpose of the project would be to determine whether biological production and process optimization could eventually make this concept competitive.

2. What living system would I use?

I would use an engineered strain of Chlorella sp. as the biological manufacturing chassis.

I would initially investigate a mixotrophic cultivation strategy. Under mixotrophic conditions, the microalgae can use light and inorganic carbon while simultaneously using an organic carbon source, such as glucose. Mixotrophic cultivation has been shown to substantially increase biomass productivity in some Chlorella strains compared with purely photoautotrophic cultivation [3].

At a simplified level, the process would be:

Light + CO2 + organic carbon + nutrients + water

↓

Engineered Chlorella

↓

Biomass + production of selected coffee-associated compounds

↓

Harvesting

↓

Drying

↓

Mild roasting

↓

Milling

↓

Microalgae-derived coffee-like powder

The engineered cells would ideally accumulate selected target molecules during biomass production. These could include caffeine as an initial functional target and, later, selected flavor or aroma precursors.

One advantage of this concept is that the desired compounds would not necessarily need to be secreted into the culture medium and purified individually. Because the biomass itself is intended to become the final ingredient, the cells would simultaneously act as the manufacturing system and part of the product.

The exact metabolic pathways and concentrations of the coffee-associated compounds are not defined yet. At this stage, I assume that an engineered strain capable of producing at least one major functional compound, such as caffeine, while maintaining reasonable biomass productivity could be developed.

3. How would I use automation?

Automation would be useful at two different stages of the project: development of the biological system and production of the final biomass.

During development, automated liquid handling could be used to test different engineered strains and cultivation conditions in parallel. For example, a desktop liquid-handling platform such as an Opentrons robot could prepare cultures with different carbon-source concentrations, nutrient compositions, or other experimental conditions.

These small-scale experiments could be combined with automated measurements of biomass growth and, when possible, the concentration of the target compounds. This would allow a Design-Build-Test-Learn workflow in which many conditions could be compared systematically rather than testing each one manually. High-throughput automation, parallel bioreactors, and automated analytics are increasingly important tools for accelerating biomanufacturing development [1,4].

Once a viable engineered strain had been selected, I would automate the bioreactor itself.

Sensors could continuously monitor variables such as:

• temperature;
• pH;
• dissolved oxygen;
• cell density;
• CO2 supply;
• nutrient availability;
• illumination;
• mixing and aeration.

A programmable control system could use these measurements to automatically adjust culture conditions, nutrient feeding, gas flow, illumination, and mixing.

The downstream process could also be integrated into the automated workflow. When the desired biomass concentration is reached, the process could proceed to harvesting, controlled drying, roasting, milling, and eventually packaging.

The complete production workflow would therefore be approximately:

automated cultivation → monitoring and feedback control → harvesting → drying → controlled roasting → milling → packaging

The automation technology used during the research phase would therefore be different from the technology used during production. Laboratory automation would focus primarily on screening and optimization, while manufacturing automation would focus on process control, reproducibility, and continuous monitoring.

4. How much would I need to make, and how long would it take?

4.1 Defining a meaningful production scale

For an initial demonstration, I define a meaningful scale as producing one 250 g package of microalgae-derived coffee-like powder.

I will assume that one package can prepare approximately 15 cups.

Therefore:

250 g / 15 cups = approximately 16.7 g per cup

My manufacturing target is therefore:

15 cups × 16.7 g/cup ≈ 250 g of final powder

This is intended as a first prototype-scale calculation rather than an industrial production target.

4.2 Biomass productivity assumptions

Biomass productivity can vary substantially depending on the Chlorella strain and cultivation conditions.

For example, Yun et al. [3] reported approximately 0.35 g/L/day biomass productivity for Chlorella vulgaris KNUA104 under photoautotrophic conditions, while an optimized mixotrophic condition with glucose reached approximately 2.99 g/L/day.

Instead of assuming that my engineered strain would immediately reach the best reported performance, I will use a more conservative design range:

The 1.4 g/L/day working estimate is the midpoint between the poor and enhanced scenarios.

I will also assume:

Cultivation time = 15 days

and an overall downstream biomass recovery of:

85%

The 85% recovery is an engineering assumption that accounts for losses during harvesting, transfers, drying, roasting, and milling. It would need to be experimentally measured.

4.3 Enhanced scenario

At 2.0 g/L/day:

2.0 g/L/day × 15 days = 30 g/L dry biomass

For a 10 L culture:

30 g/L × 10 L = 300 g dry biomass

After 85% recovery:

300 g × 0.85 = 255 g final powder

Therefore, under enhanced conditions, approximately 10 L of culture could produce one 250 g package.

More precisely:

250 g / (30 g/L × 0.85) ≈ 9.8 L

4.4 Poor-condition scenario

For a deliberately pessimistic scenario, I assume only 0.8 g/L/day:

0.8 g/L/day × 15 days = 12 g/L dry biomass

A 10 L culture would therefore produce:

12 g/L × 10 L = 120 g dry biomass

After 85% recovery:

120 g × 0.85 = 102 g final powder

This would produce only approximately:

102 g / 16.7 g per cup ≈ 6 cups

To produce the complete 250 g package under these conditions:

250 g / (12 g/L × 0.85) ≈ 24.5 L

Therefore, approximately 25 L of culture would be required in the poor-condition scenario.

4.5 Working midpoint estimate

For my main engineering estimate, I will use the midpoint productivity of 1.4 g/L/day.

After 15 days:

1.4 g/L/day × 15 days = 21 g/L dry biomass

To obtain 250 g of final product with 85% recovery, I first need:

250 g / 0.85 ≈ 294 g dry biomass

The required culture volume is therefore:

294 g / 21 g/L ≈ 14 L

I would therefore design the first production system around approximately a 15 L working-volume bioreactor.

At 15 L:

21 g/L × 15 L = 315 g dry biomass

After 85% recovery:

315 g × 0.85 ≈ 268 g final powder

This provides a small production margin above the desired 250 g package.

Summary of the production estimate

Therefore, my preliminary design would use a 15 L culture as the central estimate, while recognizing that the actual requirement could plausibly range from approximately 10 to 25 L depending on strain performance.

4.6 How long would production take?

I estimate approximately 16 to 18 days from inoculation to finished product.

The main production stage would consist of:

15 days of mixotrophic cultivation

followed by approximately:

1-2 days for harvesting, drying, mild roasting, milling, and packaging

Therefore:

18 days cultivation + ~2 day downstream processing = ~20 days per batch

This does not mean that a larger manufacturing facility would produce only one package every 20 days. Multiple bioreactors could operate simultaneously or in staggered batches.

For example, once the process was established, several reactors could be started on different days so that biomass would become available for processing at regular intervals. Industrial production could also use larger-volume reactors, although productivity would need to be experimentally verified during scale-up.

5. What don’t I know yet?

There are three major technical unknowns that would need to be investigated before determining whether this concept is feasible.

5.1 Can the engineered cells produce enough coffee-associated compounds without losing biomass productivity?

Introducing new metabolic pathways into Chlorella could create a metabolic burden on the cells.

A strain that produces a large amount of caffeine or flavor precursors might grow more slowly than the original strain. This is particularly important because the calculation above assumes an average biomass productivity of approximately 1.4 g/L/day.

I would therefore need to experimentally measure both:

biomass productivity and target-compound concentration

for the engineered strain.

The important parameter would not simply be how fast the algae grow, but how much useful final product can be generated per liter and per day.

5.2 Will dried and roasted microalgal biomass actually taste like an acceptable coffee-like beverage?

Coffee aroma and flavor are chemically complex and are strongly influenced by reactions that occur during roasting.

Therefore, it may not be necessary, or even desirable, for the microalgae to directly biosynthesize every molecule found in coffee. The engineered cells could instead produce selected compounds and biochemical precursors that are transformed during the roasting process.

This creates an important experimental question:

Which compounds need to be produced biologically, and which desirable flavors can be generated during processing?

To answer this, I would need to compare different engineered strains and roasting conditions using chemical characterization of the volatile and non-volatile compounds followed eventually by sensory evaluation of the beverage.

5.3 Can the productivity observed at small scale be maintained in a 15 L reactor and later at larger scales?

Scaling microalgal cultivation is not simply a matter of increasing the volume.

As cultures become larger and denser, several physical conditions change, including light penetration, mixing, oxygen transfer, CO2 availability, nutrient distribution, and temperature.

Biomanufacturing scale-up is a major challenge because biological performance observed at laboratory scale is not necessarily maintained in larger reactors [1].

I would therefore need to test the process progressively, for example:

small screening cultures → laboratory photobioreactor → ~15 L reactor → pilot scale

At each scale, I would measure biomass productivity and the concentration of the desired coffee-associated compounds.

The final feasibility of this project would depend on whether acceptable biomass productivity, chemical composition, sensory properties, and process reproducibility can be maintained simultaneously.

References

[1] Asin-Garcia, E., Fawcett, J. D., Batianis, C., & Martins dos Santos, V. A. P. (2025). A snapshot of biomanufacturing and the need for enabling research infrastructure. Trends in Biotechnology, 43(5), 1000–1014. DOI: 10.1016/j.tibtech.2024.10.014.

[2] Karim, A. S., & Jewett, M. C. (2021). Toward sustainable, cell-free biomanufacturing. Current Opinion in Biotechnology, 69, 136–144. DOI: 10.1016/j.copbio.2020.12.012.

[3] Yun, H.-S., Kim, Y.-S., & Yoon, H.-S. (2021). Effect of different cultivation modes (photoautotrophic, mixotrophic, and heterotrophic) on the growth of Chlorella sp. and biocompositions. Frontiers in Bioengineering and Biotechnology, 9, 774143. DOI: 10.3389/fbioe.2021.774143.

[4] Petzold, C. J., & Mukhopadhyay, A. (2025). From bench to biofactory: High-throughput technologies and automated workflows to accelerate biomanufacturing. Current Opinion in Biotechnology, 94, 103320. DOI: 10.1016/j.copbio.2025.103320.

AI Use

I used ChatGPT (OpenAI, GPT-5.6 Sol) as an AI-assisted learning and writing tool while developing this assignment. The AI was used to help organize the initial concept, improve clarity and English writing, structure the engineering assumptions, perform and check the back-of-the-envelope calculations, and identify questions that should be experimentally tested.

I reviewed, discussed, and edited the generated material and made the final decisions regarding the proposed biological system, assumptions, production scale, and project concept.

Representative prompts used during the development of this assignment included:

“I’ll tell you my short answers for questions 1–3 so you can help me expand them and then we’ll build the answers for 4–5 accordingly.”

“Please elaborate a plausible answer for question 4 defining enough powder to prepare 15 cups of microalgal coffee, which is roughly the amount of cups per 250 g package, considering a 15-day culture of the biomass in enhanced conditions.”

“Calculate the same, but for below-average conditions to simulate a worse-case scenario, and then make the estimates meet halfway.”

“Can we move on to question 5 or is there anything else to adjust?”

The AI-assisted content was checked against the course assignment and relevant scientific literature before inclusion.