taxonomic assignment of metagenomic bins and detect 16S rRNA gene in metagenomic bins

Question

[luyang1005]

Hi, community,

I have Hiseq metagenomic data. I have used MEGAHIT assembly the reads, then I binned the contigs which results to 500 bins. I have used CheckM to assess the genome bins. All bins with <10% contamination and >70% completeness were saved and BLASTN to SILVA 132 SSU database. Most bins can detect 16S genes. However, some bins got hit to different taxonomy, such as one contig got hit with 'FUBE01000005.37491.40675 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia-Shigella;Shigella sonnei', one contig in the bin got hit to '> CP016073.2513631.2516362 Bacteria;Firmicutes;Bacilli;Bacillales;Stapyhlococcaceae;Staphylococcus;Staphylococcus pseudintermedius'. May I know what is the reason? Anything wrong with me?

Answer 1

[SilentGene]

Hi there, apart from using blastn against nr databases to assign taxonomy of the metagenomic bins. I recommend you to try out the following 2 software:

1. phylophlan. This software could help you integrate metagenomic bins in the 'tree of life' which has already involved over 3000 microbial genomes according to the universal conserved proteins in your bins. And you can probably know the taxonomy of the new bins according to the phylogenetic relationship shown by the supertree.

2. JSpeciesWS. This is a really handy online tool that can search genomes against their entire genomes reference database GenomesDB according to the Tetra Correlation. The database in JSpeciesWS is really large, which allow you to find more potential of the taxonomy.

Cheers, H