Reporting novel species from environmental samples

Question

[Dunois]

(I am asking this on behalf of someone.)

They have a set of bacterial species that have been isolated from the roots of a plant. The genomes were sequenced and assembled, and GTDBTK was used to establish identities for these genomes.

Some of the species seem to be novel; they did not get species assignments and their ANI was below 95%.

Now the question is: how should these novel species be reported and how should they be referred to in other analyses. Are there any tutorials/guides that can be followed here?

Any help would be much appreciated!

Answer 1

[Mensur Dlakic]

Some of the species seem to be novel; they did not get species assignments and their ANI was below 95%.

Novel species within a known order or family are discovered frequently in environmental metagenomes. I see probably 1-2 new species in each metagenome that has > 50 MAGs. Whether they are worth reporting or not depends on the degree of novelty.

The reporting is usually based only on genomic sequence, which commonly includes predictions about their metabolic potential. That alone is not worth very much. When they can be grown in a (near-)pure culture, imaged by microscopy and studied metabolically, that increases the value. At some point they may have to be named:

• https://academic.oup.com/femsre/article/23/2/231/524593
• https://www.nature.com/articles/s41564-020-0733-x
• https://eddev.eol.org/articles/names.pdf

[Dunois]

Thank you for your prompt answer Dr. Dlakic!

The study is not focused on the bacteria themselves and will not be focusing on characterizing the isolates further.

From your third link, we found the SeqCode paper (https://www.nature.com/articles/s41564-022-01214-9?fromPaywallRec=false). It seems that this approach would be vialble for the data at hand as SeqCode seems to be designed for identifying novel species on the basis of high quality genomes alone. Do you have any thoughts on this approach?

[Mensur Dlakic]

SeqCode approach is fine.

[Dunois]

Thank you so much!

[Crisp]

But most microorganisms can't be grown in a (near-)pure culture