How To Determine How Many Strains Of Ecoli In Metagenome

Question

[zeleniy.spb]

I have a human gut whole genome metagenomics reads. And i must answer the question - is there only one or several ecoli strains in it. How can i do it?

Answer 1

[Leszek]

I have seen recently paper/program that can help you.

Answer 2

[Manu Prestat]

You can also find some inspiration in that Banfield's Lab paper:

Morowitz, M. J., Denef, V. J., Costello, E. K., Thomas, B. C., Poroyko, V., Relman, D. A., & Banfield, J. F. (2011). Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proceedings of the National Academy of Sciences of the United States of America, 108(3), 1128–1133. doi:10.1073/pnas.1010992108

Answer 3

[WANG]

You can use the strain-profiling tool PStrain, it will profile the strains with different strain numbers and choose a reasonable one. So, you can know if there is a mix of strains. Hope it helps.