What Bioinformatic approach is suitable to identify unique genetic potentials (gene/metabolic function) between two groups of bacterial genus or species?

Question

[zahir_vet]

Hi everyone, What Bioinformatic approach is suitable to identify unique genetic potentials (gene/metabolic function) between two groups of bacterial genus or species? I have two sets of human gut bacterial genus: setA and setB. Each set comprises at least 10 genus. I want to download complete genome of all human gut microbiome species belonging to these two set of genus (one genome per species). Because, my main aim is to identify exclusive gene/metabolic functions in these two set of human gut microbiome members. My question- Is there any strait forward way to download complete genome of all human gut microbiome species under these two set of genus? Are there any idea/approach that can help me accomplishing my goals? Thank you very much for your thought.

[andres.firrincieli]

Hi Zahir,

The design is not clear but the most basic approach would be: 1) identify a core genome representative of both set A and B; 2) check for unique or enriched functions between the two set of genomes. Have a look at Anvio; it has a very nice workflow for microbial pangenomic.

ps. one genome per genus is not enough. You should include all type/reference strains of that genus

[zahir_vet]

Hi Andres, Thanks a lot for sharing your ideas. I will try this.

Answer 1

[3335098459]

Hi Zahir,

Hopefully these suggestions could help you.

1. Try ncbi-genome-download tool for downloading genomes by mentioning genus or accession nos.

2. Build a core phylogeny as mentioned previously or try different pangenome analysing pipelines.

Regards

Awan

[zahir_vet]

Hi Awan, Thank you very much for sharing your ideas.