taxonomy – Jonathan Eisen's Lab

Just got this email:

Dear Jonathan , I am relatively new to phylogenetics and have developed a keen interest in bacterial phylogenies. I read one the papers which you have published in Nature on the same topic. I needed some help. Thing is, I have constructed a bacterial phylogeny based on 16s rRNA and have found that Candidatus species differ by a really great extent from one another, and appear to be in completely different clades. I need some way to verify this and was wondering if you could send me the phylogeny you have created in order for me to verify. Thank you

I have been arguing for years that the use of the term “Candidatus” to describe microbes is a bad idea. This email is exactly the kind of thing I worry about. Candidatus is a term used “for well characterized but as yet uncultured organisms.” (A nice description of the history of the term is here). The problem with Candidatus are many – including the confusion such as evidenced by this email – in that people who are not used to dealing with the term have no clue what it means. But in addition, the constraint that one is not “allowed” to name things unless they have been cultured is silly, outdated, and damaging to the field. But I can write about that some other time. For now, this email will suffice …