Dear all, 
I am a rookie in data analysis and stuck with my results dnt know how to interpret them.

I started with 7 metagenomic assemblies of different species of Azolla fern. The aim was to identify bacteria in leaf ecosytem of azolla different species. Out hypotheisis was, if there are similar bacteria which repeat within the azollas different species, they will cluster together when their genomes will be plotted in dendrogram or a tree.

The method used `spades` to get assemblies, `BWA` was used to do backmapping, `samtools` for sorting, `metabat` for binning and checkm for to see completeness and contamination of bins.

Then `prokka` was used to annotate the genomes and uniport ids were obtained and table was made of all uniport id of all the bins. the table was changed to binary table and then used to create a dendrogram in R.

The dendrogram and then tree made by using dendrogram in fig tree. In the tree i observed that the bacteria are clustering according to the metagenomic sample or plant host not on the basis of their similar taxonomical name eg rhizobiales is clustering with burkholderiales of same metagenomic assembly but not with rhizobiales of other host plant assembly.

Im on the dead end how to intrepret these results and what can i deduce from it.
and are there other ways to improve my approach? Can i compare similar taxonomical bins directly of different metagenomic assemblies any suggestions will be valuable.

kind regards

manpy student utrecht university holland

An alternative approach might be to calculate `mash` distances between all your genomes directly. Assuming your taxonomic assignments are largely correct, this would save you having to mess about with extracting the uniprot IDs, binary matrix etc.

Since you can’t align that many full genomes, mash distances are a good surrogate for genome similarity.

You can then draw your trees using pairwise mash distances among all your genomes.

I’m not 100% sure how much you’ll need to polish your genomes etc. You may need to reorder contigs and perhaps concatenate but if you read up on it I’m sure it’ll become clear.