5. Single gene knock outs

The Bactabolize sgk function

bactabolize sgk --model_fp input_assembly_model.json --media_type m9 --atmosphere_type aerobic --output_fp inut_assembly_model_sgk.tsv

Once a model has been generated, you can analyse model gene essentiality across growth environments e.g. a common use case would be to predict which genes are essential for growth in minimal media. Bactabolize will remove each gene one-by-one and evaluate growth. Predictions are based on Flux Balance Analysis (FBA), optimising the model's biomass objective function. If the optimised biomass objective value exceeds a predetermined threshold, the model is considered to predict positive growth.

bactabolize sgk is designed to facilitate prediction of gene essentiality phenotypes at scale. You can select the base media and atmosphere for your predictions and Bactabolize will remove a model gene one-by-one, and attempt to optimise for growth in these conditions.

Input files

One input is required:

1. A strain-specific metabolic model in BiGG compatible JSON format.

E.g. a model generated by bactabolize draft_model. Alternatively the SEED_to_BiGG_model_convert helper script can be used to convert third party models using SEED IDs into those compatible with Bactabolize.

Outputs

A single tab-delimited file will be output for each model. The file will contain 6 columns as follows:

Column name	Description
ids	Name of the removed model gene
growth	Biomass objective value as a result of gene removal
status	Status of the growth simulation

Command options

Required

--model_fp - Input model (.json) to perform FBA on.

--output_fp - Output filename for SGK results (tab-delimited).

Optional

--media_type - Growth media for initial model growth simulation test. One of: cdm_mendoza, bg11, lb, lb_carveme, m9, nutrient, pmm5_mendoza, pmm7_mendoza, tsa, tsa_sheep_blood. DEFAULT: m9. --atmosphere_type - Atmosphere for model testing. One of: aerobic, anaerobic. DEFAULT: aerobic.

Examples

# Perform SGK on M9 minimal media, aerobically
bactabolize sgk \
  --model_fp input_assembly_model.json \
  --media_type m9 \
  --atmosphere_type aerobic \
  --output_fp input_assembly_model_sgk_m9_O2.tsv

# Perform SGK on TSA media, anaerobically
bactabolize sgk \
  --model_fp input_assembly_model.json \
  --media_type tsa \
  --atmosphere_type anaerobic \
  --output_fp input_assembly_model_sgk_tsa_AnO2.tsv