Media definition for new isolated gut strains

[hongzhonglu]

Hi GapSeq developers [@jotech],
Could I ask a question about how to define the media used for the gap-filling phase because I have several isolated human gut strains but I did not know their detailed nutrient requirement?

Thanks a lot!

Best regards,
Hongzhong

[Waschina]

Dear Hongzhong,

our benchmark for bacterial fermentation products included also several human gut bacteria. Here we used the media stored in "dat/media/FT.csv". This medium contains a few sugars, small amounts of amino acids, nucleotides and vitamins. And of course the essential anorganics such as Water, sodium, potassium, etc.

You could try the FT medium for gapfilling on your genomes. e.g. by

model="my_genome_name"

# Reaction & pathway prediction
./gapseq find -p all -b 200 $model.fna.gz

# Transporter prediction
./gapseq find-transport -b 200 $model.fna.gz

# Draft network reconstruction 
./gapseq draft -r $model-all-Reactions.tbl -t $model-Transporter.tbl -p $model-all-Pathways.tbl -u 200 -l 100 -c $model.fna.gz

# Gapfilling using FT-medium
media_path="/path/to/gapseq/dat/media/FT.csv"
./gapseq fill -m $model-draft.RDS -n $media_path -c $model-rxnWeights.RDS -g $model-rxnXgenes.RDS -b 100

You may start directly with the Gapfilling step if you have already run the previous steps. Please note, that you need to adjust media_path, so it points directly to the FT.csv file in your gapseq directory.

Let me know if this works or if something is unclear.

Best regards
Silvio

[hongzhonglu]

Dear Silvio @Waschina ,
Great thanks for your information! Do you have references for the medium composition in "FT.csv" ? It is similar to the medium "Yeast Casitone Fatty Acids Broth" (YCFA) as I saw YCFA has been used in some human gut strains GEMs reconstruction.

Best regards,
Hongzhong

[Waschina]

The FT-medium is not based on a reference to a specific isolation medium definition, but a collection (although probably incomplete) of metabolites that have been described to be potential nutrients for bacteria in the human gut.
But thank you for pointing out the YCFA broth – it's a good idea to try this as well. I found this definition of by the DSMZ: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1611.pdf
I will prepare a gap-filling medium for gapseq based on this definition and commit it here to github later today.
Thank you!
Silvio

[hongzhonglu]

Thanks a lot! That will be cool.

Best regards,
Hongzhong

[hongzhonglu]

Hi Silvio,
In the DSMZ_medium, I see it also contains Casitone and Yeast extract, the compositions of these two components maybe not clear?

Here I have also a reference for you to check which have a composition of YCFA broth.

Journal of Bacteriology-2014-Heinken-3289.full.pdf

I extracted the YCFA media composition from this paper.
Media_Faecalibacterium_prausnitzii.xlsx

Best regards,
Hongzhong

[Waschina]

Hi Hongzhong,

thank you for this table and the reference. Here's a suggestion for the ycfa medium based on DZMZ definition, your table, and the reference you mentioned:
ycfa.xlsx

I did not include ammonia, as it is not part of the medium definition by DSMZ. Yet, I can reintroduce it if you say that this might be important as N-source. Perhaps you could have a quick look at the list if you find something odd or missing? Afterwards I can commit a first gapfill medium version for YCFA.

Best
Silvio

[hongzhonglu]

Hi Silvio,

Great thanks for your information.
I think ammonia is ok as it can be used as nitrogen source.
When I check other information, I found co2, Arsenate, chromate, Carbonate may be not essential? But I am not sure about it as I did not find reference for these four metabolites.

Best regards,
Hongzhong

[Waschina]

Yes you are right. I removed CO2, Arsenate and Chromate. Carbonate was kept as it is part of the YCFA formulation by DSMZ in form of NaHCO3. And I added ammonium as you suggested.

Thanks for your help!
Silvio

[hongzhonglu]

Thanks so much! That will be nice for us to build GEMs for gut strains using this media.

Best wishes,
Hongzhong