Tag: annoying

Barcoding is a technique in which researchers sequence a small region of the genome of an organism and use this sequence information as a “tag” to identify species/types.   The term barcoding is most commonly associated with sequencing a small portion of the mitochondrial genome of a multicellular eukaryote.  There is a new paper in PLoS One discussing barcoding: Neotropical Bats: Estimating Species Diversity with DNA Barcodes.  The paper seems potentially interesting.  But I could not get past the part where they write “To the best of our knowledge, it is one of the largest molecular surveys of biodiversity.”

Let’s examine this statement a bit.  In the study here the authors did a heroic task – they did barcoding for some 9000 individuals.  It is impressive, in many ways.  But one can only call it a large molecular survey of biodiversity if one thinks  biodiversity = plants and animals. If however you include microbes, as of course you should, then this new study is not even remotely the “largest molecular survey of biodiversity.”  In fact, one could argue that 100s if not 1000s of studies of biodiversity of microbes are “larger” in many ways than this study.  In microbial studies 9000 “individuals” are characterized routinely in most studies via the use of collecting DNA from environmental samples and sequencing genes from 100s -1000s to even billions of individual cells in a sample.  This is done routinely in both metagenomic work (where one collects DNA from the environment and randomly sequences it) or ribosomal RNA PCR surveys where one collects DNA and then sequences rRNA genes from the sample.  Overall, hundreds of microbial studies cover more biodiversity than this one – more species – wider phylogenetic diversity – more samples even.

So – could it be that the authors of the current paper are not aware of the microbial work?  I don’t know – for they do not even mention it in this paper.  This is amazing / startling / annoying / disappointing.  After all, molecular studies of biodiversity were first done in microbial studies in the mid 1980s – pioneered by people like Norm Pace and colleagues surveying ribosomal RNA from mixed communities like Yellowstone hotsprings (e.g., see here and here). And in the 80s and 90s microbial work covered incredibly diverse ecosystems with many studies determining 100s-1000s of sequences. As sequencing got cheaper and cheaper, molecular studies of microbial biodiversity expanded to go beyond just single genes to studies of “metagenomes” from the environment. And in single gene studies, researchers now routinely sequence millions to billions of representatives of single genes using rRNA PCR and Illumina sequencing, for example.

Should these authors here be discussing microbes?  I think so.  After all, not only would this give their paper historical context.  But it would almost certainly give it scientific context and value since there are hundreds of papers on microbes looking at species richness, biodiversity metrics, and such ((a simple pubmed search found 1357 papers using rRNA PCR and diversity as the query, for example).  And since the work here is on mitochondrial DNA there may be even more parallels to microbes than one might think at first blush. 

I note – this is not the first time Paul Hebert, the senior author on this study has gotten on my nerves about barcoding in terms of not mentioning microbes. I even posted a “dissent” regarding one of his earlier papers on Faculty of 1000 (which I used to contribute to before they become non open access). I am not sure what the explanation is, but the lack of referencing the historical work on using DNA to study diversity is disappointing (though I note in at least one of the first papers by Hebert, there was more brief mention of microbes). Not mentioning the 25 years of work on molecular studies of biodiversity in microbes gives the impression that Hebert invented using DNA to study biodiversity.  And that is not needed.  Barcoding has some nice features and uses.  No need to purposefully or accidentally make it seem like it is something new.

Are microbial studies the same as the barcoding studies being done?  No.  Many barcoding studies have things like individual voucher specimens and museum collections.  And microbial studies frequently have mixed samples like soil or water and DNA.  So what.  The general point of many of these studies is the same – using molecular data to infer information about species richness, beta diversity, phylogenetic patterns, etc.  And for this, studies of microbes long preceded the barcoding approach.  And there is a lot of useful literature out there as well as tools, methods and concepts.  I for one peruse the barcoding papers to see if there is anything useful there for my work.  It would almost certainly be good for the barcoding researchers to check out the microbial literature.  And if the leaders in the barcoding arena continue to not mention microbes, well that would be unfortunate.