MAGs and contigs composing them

Question

[Jonathan Yoou]

Hi all.

I started to work with MGS and have some questions on MAGs.

I got complete MAGs through tools for assembly, binning, and quality assessment, and there are 100~130 MAGs. Does this mean I have same number of recovered genomes, so that same number of species from the sample? If so, isn't it too small existing in the sample (human gut)?

Contigs composing each MAG are regarded as fragments from same genome. Then does this mean that they are collapsed without any order so that it is impossible to BLAST them and taxonomic profiling or gene profiling? I mean, in complete genome in NCBI or somewhere, their sequence is composed of ...ATGG(geneA)-TTGC(geneC)... but they are collapsed into ...TT-ATGG(geneA)-GC...

I'm quite new to de novo world, so a bit confused with my previous experience of dealing with 16S and reference sequences :(

Thank you in advance for all your helps

Answer 1

[Mensur Dlakic]

I am guessing that you mean 100-130 bins, which doesn't necessarily mean that you have that many MAGs. For a difference between a MAG and a bin, see the similar posts listed on the right side of this page. In general, 100-130 bins sounds very low for a human gut sample. It could be because of poor sample quality, poor assembly (lots of fragmentation), poor binning (lots of data not clustered and left out) or many of your bins contain more than one genome that can't be separated cleanly. I guess it is also possible that some human gut samples are not very diverse, especially if the sample was taken around a time when a major GI event occured.

Contigs in a bin/MAG are not in any particular order. That doesn't preclude taxonomic profiling, but it is advisable to first make sure that the bins are reasonably complete and not significantly contaminated. CheckM will provide that information.