Week 1 HW: Final Project Ideas

A Living Probiotic Community for Vitamin D Production and Absorption

Raul Duran De Alba — HTBAA Homework #1 — September 22, 2026

My proposal is a bacterial community designed to produce a small, controlled amount of vitamin D inside the gut and improve its absorption. This is an ambitious research concept: in-gut vitamin D production is an unresolved challenge, and the proposed functions must be distinguished from what has already been demonstrated.

1. What would I like to biomanufacture, and why?

I would like to biomanufacture a defined community of probiotic bacteria with two complementary functions: producing a small, controlled amount of vitamin D inside the intestine and helping the body absorb it. The final product would be a capsule containing selected bacterial strains, each assigned a specific role.

My motivation is an interest in personalized supplementation: using living systems to help address nutritional needs while accounting for differences between people’s microbiomes. I am particularly interested in its potential relevance to Mexico. An analysis of ENSANUT 2018–19 reported vitamin D deficiency in 31.6% and insufficiency in 46.1% of Mexican women aged 20–49, using the study’s definitions. These results identify a substantial problem in that population, although they should not be generalized to all Mexicans. Source: Contreras-Manzano et al., 2021.

For an initial engineering target, I would aim for 5 micrograms of vitamin D produced per person per day, equivalent to 200 IU. This is approximately one-third of the recommended daily intake of 15 micrograms for adults aged 19–70. It is a proposed production target, not a treatment dose, and the amount absorbed would need to be measured separately. Source: NIH vitamin D fact sheet.

2. What living system would I use?

I would begin with a two-member bacterial community:

A post hoc analysis of a randomized trial involving 127 adults with elevated cholesterol found increased circulating 25-hydroxyvitamin D after supplementation with L. reuteri NCIMB 30242. However, the study did not demonstrate that the bacteria synthesized vitamin D or directly prove increased intestinal absorption. Source: Jones et al., 2013.

The evidence is also strain-dependent: another trial found no additional vitamin D benefit from the tested probiotic combination compared with vitamin-D-fortified yogurt. Therefore, improved absorption would be a hypothesis to test. Source: randomized trial of probiotic- and vitamin-D-fortified yogurt.

At a high level, the intended process would be:

Available nutrients → bacterial metabolism → vitamin D production and release → intestinal absorption.

The hardest step is the conversion into vitamin D itself. Researchers have engineered yeast to produce 7-dehydrocholesterol, a vitamin D3 precursor, but conversion of that precursor into vitamin D3 requires UVB exposure. That route would not directly work inside the gut. Source: Metabolic engineering of Saccharomyces cerevisiae for 7-dehydrocholesterol overproduction.

My proposal therefore depends on discovering or engineering a pathway that functions without light under intestinal conditions. Producing a precursor alone would not count as successful vitamin D production. If this pathway cannot be established, the central concept would need redesign.

I would initially manufacture the strains separately and combine them at a measured ratio. This would make their proportions easier to control. Daily administration would be the starting model; permanent colonization would not be assumed.

3. How would I use automation?

I would use an Opentrons liquid-handling robot to prepare culture comparisons, distribute samples, and perform serial dilutions. These are established capabilities of the platform. Source: Opentrons documentation.

For example, one screening plate could contain:

24 candidate conditions × 3 replicates + 24 control wells = 96 wells.

The conditions could compare candidate strains, community ratios, and nutrient availability. Appropriate incubation equipment would maintain the required growth environment; the liquid handler would automate sample preparation.

Separate analytical instruments would measure bacterial viability and chemically identify vitamin D. Measuring growth alone would not demonstrate production. Subsequent intestinal models would test whether the product is released and available for uptake, comparing the community with each strain alone and with a matched amount of conventional vitamin D.

At manufacturing scale, automation would shift toward bioreactor monitoring and control, harvesting, drying, blending, and capsule filling. The desktop robot would mainly support development and quality-control workflows.

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

A. A meaningful initial scale

I would define a meaningful initial scale as a 30-day supply for 1,000 people.

The intended vitamin D output would be:

1,000 people × 30 days × 5 micrograms/person/day = 150,000 micrograms = 150 mg.

That is 150 mg produced collectively inside the gut over one month, assuming the system works. The factory would manufacture the bacteria.

For the bacterial product, I would assume one capsule per day containing 10¹⁰ colony-forming units (CFU), divided equally between the two strains. CFU estimates viable bacteria capable of forming colonies. This quantity and ratio are design assumptions, not validated effective doses.

The requirement would therefore be approximately 300 L of culture per strain. Both culture density and recovery would need experimental validation. If achievable density were ten times lower, the required volume would increase to 6,000 L.

B. Manufacturing time

For timing, assume two bioreactors, each with a 100 L working volume, operated in parallel with one strain per reactor. Three production cycles would provide 600 L total.

These are illustrative scheduling assumptions for an established process. They exclude the potentially much longer research period needed to develop and validate the strains.

C. Required output per active producer

The production target also sets a requirement for each active producer. Suppose 10⁹ producer cells remain metabolically active for a full day:

(5 × 10⁻⁶ g/day) / (10⁹ active cells) = 5 × 10⁻¹⁵ g/cell/day.

Each would need to release approximately 5 femtograms of vitamin D per day. This calculation defines a performance target; it does not establish that the biology can achieve it.

5. What are the three biggest unknowns?

Can the bacteria actually make vitamin D?

The largest uncertainty is a complete production pathway that functions without light under intestinal conditions. I would need chemical evidence of newly synthesized vitamin D, distinguishing it from precursors or vitamin D already present in the medium.

Will production occur where absorption is possible?

Vitamin D is absorbed in the small intestine. Production farther downstream cannot automatically be assumed to provide the same benefit. I would need to measure where the bacteria are active, whether they release vitamin D, and whether the partner strain improves uptake. Source: NIH vitamin D fact sheet.

Can the community deliver a predictable, controlled output?

Diet, microbiome composition, intestinal transit, and strain survival could change production substantially. I would need to establish dose consistency, shelf stability, strain compatibility, and a way to limit activity or persistence. A small average output would not by itself establish reliable control.

AI-use disclosure

AI client: OpenAI Codex. Date: September 22, 2026.

AI was used to develop the proposal, locate scientific sources, check engineering calculations, and format the homework for this website.

Prompts:

Help me make this homework. Let’s expand on the making a bacterial comunity for the probiotic supplementation wich produces a small amount of vitamin d and vitamin d absorbtion

Ambitious in-gut production

A follow-up request asked Codex to use computer control to add the homework to this page and correct its formatting.