Metagenomics with Illumina, all species genomes coverd by reads or not?

[mkoohim]

Hi All,

I am new in Metagenomics and want to ask a basic questions!

suppose we have a microbial community and use Illumina for WGS. We don't know any things about our community and don't know which species are there (Actually it is a de novo sequencing). I want to know is there any possibility that there are some parts of our unknown bacteria genome that is not covered by reads produced by Illumina? Or for sure all part of species genomes will be covered by reads?

P.S: I read some articles about the library preparation in Illumina WGS. I were wondering if there is any relation between this issue and library preparation?

Thank you,

[Brian Bushnell]

In a complex community, there will be a large variation in species abundance. Thus, you won't get good coverage of very rare organisms, and they won't assemble. There's also a gc-bias (low- and high-gc organisms may be underrepresented) but that won't matter nearly as much.

There are also differences in efficiency of lysing and DNA extraction for different organisms, so I'm sure that preparation plays some kind of role, but I don't know the details. This is quite important for single-cell work. I think abundance is probably much more important in metagenomes though.

[mkoohim]

Dear Brian,

Thank you for your answer and share your experience. Your answer is very comprehensive.

Thank you,

In a complex community, there will be a large variation in species abundance. Thus, you won't get good coverage of very rare organisms, and they won't assemble. There's also a gc-bias (low- and high-gc organisms may be underrepresented) but that won't matter nearly as much.

There are also differences in efficiency of lysing and DNA extraction for different organisms, so I'm sure that preparation plays some kind of role, but I don't know the details. This is quite important for single-cell work. I think abundance is probably much more important in metagenomes though.