Can metabat be used to bin eukaryotes from metagenomes

[Silas Kieser]

Hallo I wonder if in theory metabat can be used to bin small eukaryotes from mixed metagenome data?

I didn’t found anything in the paper that would speak against it. Do you have experience with it?

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Kind regards

Silas

[Rob Egan]

Hi Silas, In theory, yes it should work, but we have not performed much testing on this.

The TNF measure is at least partially related to the codon frequency that the organism has evolved to use which still applies to eukaryotes and the abundances should be completely agnostic to the type of organism. We have seen that metabat does a reasonable job clustering fungi within metagenomes. although the completeness may be lower due to their genomic size (and hence higher random chances of false negative heuristics excluding contigs from the cluster), and possibly different TNF profiles between the chromosomes too.