tag:blogger.com,1999:blog-10781944.post8803531098820263088..comments2024-03-28T00:36:36.460-07:00Comments on The Tree of Life: Uggh: "Barcoding" researchers keep ignoring microbes and history #antimicrobiites #annoyingJonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger12125tag:blogger.com,1999:blog-10781944.post-1338917377529152712011-08-24T07:18:34.805-07:002011-08-24T07:18:34.805-07:00The fact that people are unfamiliar with the work ...<em>The fact that people are unfamiliar with the work in microbes and think that all work in microbes is sequence based is part of the problem here. Barcoding does not seem to me to be significantly distinct from prior work on microbes.</em><br /><br />The fact that people are not familiar with the background and current research in barcoding is also part of the problem. :-)T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-81405541195254647602011-08-13T03:25:34.334-07:002011-08-13T03:25:34.334-07:00Quick! Alert Williams and Ebach! They will no doub...Quick! Alert Williams and Ebach! They will no doubt wish to include this in the next edition of <i>Foundations of Systematics and Biogeography</i>.<br /><br />Meanwhile, I'm going to check to see if I have any coupons for Maalox.Russell Necheshttps://www.blogger.com/profile/00253304712038983943noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-51718359517540004232011-08-09T10:04:47.981-07:002011-08-09T10:04:47.981-07:00Still not getting it Ryan.
How is barcoding dif...Still not getting it Ryan. <br /><br />How is barcoding different from things like taking a collection of strains of microbes for which their is some taxonomy (based on chemistry, morphology, pathogenicity and other phenotypes) and sequencing rRNA genes from them and trying to define cutoffs to use to delineate what is species 1 vs. species 2 and then using the sequence instead of the phenotypes? <br /><br />This approach has been done with microbes for many many years. Sure morphological and other taxonomy works better in many cases in plants and animals. But molecular approaches have routinely been used to supplement phenotypic data as part of the formal description process for new taxa. This is even codified in the IJSEM and other organizations. <br /><br />See for example http://www.ncbi.nlm.nih.gov/pubmed/10551170 -- just something I pulled out almost randomly. Or look at hundreds of papers by Stackebrandt like http://www.ncbi.nlm.nih.gov/pubmed/1693659. <br /><br />Since the 80s people have been trying to develop calibrated, standardized methods to integrate molecular data and phenotypic data in the identification and classification of species of microbes. <br /><br />The fact that people are unfamiliar with the work in microbes and think that all work in microbes is sequence based is part of the problem here. Barcoding does not seem to me to be significantly distinct from prior work on microbes.Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-91241416942730429972011-08-09T09:36:47.794-07:002011-08-09T09:36:47.794-07:00#1 - I was referring to microbes generally. There ...<em>#1 - I was referring to microbes generally. There was much work on rRNA environmental surveys of microbial eukaryotes before the barcoding stuff came along. So to say all the rRNA stuff was about bacteria is wrong. There was plenty on euks and archaea.</em><br /><br />Environmental surveys are not barcoding, so the point is somewhat moot. Barcoding is, by definition, a standardized identification system that uses DNA sequences to identify species. DNA taxonomy is not the same thing. However, more recently "barcodes" have been used to identify clusters that can be considered putative species and considered on that basis in ecological or other work. But they don't get called "barcodes" in GenBank without meeting the strict criteria.<br /><br /><em>#2 - Woese used rRNA sequencing of cultured isolates to study phylogeny of all organisms, not just bacteria. And he started doing it in the 1970s. And after a few years this was standardized. And there are 1000s of papers using rRNA sequencing or other genes in standardized ways to do taxonomy of all sorts of organisms. So again, how is what became known as "barcoding" different than this?</em><br /><br />1) Barcoding is not phylogeny. 2) Barcoding is comprehensive (i.e., there are efforts to cover entire taxa, not a broad sampling). 3) Barcoding is not used to delimit new species by itself, it is calibrated against existing taxonomy and putative species are subject to formal description as well. 4) Animals (the initial focus of barcoding, now including plants and fungi) have never had a standardized DNA based system for identification.<br /><br /><em>#3 - Blaxter does generally a great job of linking barcoding and other studies using DNA to do taxonomy (e.g., http://filogeografia.dna.ac/PDFs/barcode/Blaxter_04_DNAtaxonomy.pdf). Many others however do not do a good job. I stand by my critiques of many in the field. I think they purposefully or ignorantly do not refer to other similar work with the effect of making their work seem more unique. It is unnecessary. And annoying.</em><br /><br />Exactly. Because what Blaxter does with nematodes is very similar to the work on microbes, in that there is no existing morphological taxonomy and very few morphological characters to base a taxonomic system on. It's DNA taxonomy and he even uses a similarity threshold approach similar to microbial studies. So it's very appropriate for him to draw a connection. Barcoding in the main sense is a means of identifying existing species and pointing out possible new ones that can be formally described by taxonmists. It's controversial enough, I can't imagine how it would go over if people just scooped up fishes and said "there are 50 MOTUs in this net, but nevermind formal names" and left it at that, rather than what FISH-BOL is actually doing.T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-29080835054714523822011-08-08T21:32:52.968-07:002011-08-08T21:32:52.968-07:00#1 - I was referring to microbes generally. There...#1 - I was referring to microbes generally. There was much work on rRNA environmental surveys of microbial eukaryotes before the barcoding stuff came along. So to say all the rRNA stuff was about bacteria is wrong. There was plenty on euks and archaea.<br /><br />#2 - Woese used rRNA sequencing of cultured isolates to study phylogeny of all organisms, not just bacteria. And he started doing it in the 1970s. And after a few years this was standardized. And there are 1000s of papers using rRNA sequencing or other genes in standardized ways to do taxonomy of all sorts of organisms. So again, how is what became known as "barcoding" different than this?<br /><br />#3 - Blaxter does generally a great job of linking barcoding and other studies using DNA to do taxonomy (e.g., http://filogeografia.dna.ac/PDFs/barcode/Blaxter_04_DNAtaxonomy.pdf). Many others however do not do a good job. I stand by my critiques of many in the field. I think they purposefully or ignorantly do not refer to other similar work with the effect of making their work seem more unique. It is unnecessary. And annoying.Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-68155725224751003042011-08-08T21:17:12.961-07:002011-08-08T21:17:12.961-07:00Sure now some people talk about barcoding fungi an...<em>Sure now some people talk about barcoding fungi and microbes. But really, how is this different from rRNA surveys? And why does it need to be called something new?</em><br /><br />Really? Well, taxonomy in animals, plants, fungi, etc., has a few hundred years behind it based for the most part on morphology. The rRNA work often uses *only* DNA data. DNA barcodes in eukaryotes are, by definition (according to GenBank as well), standardized, linked to a voucher, etc. People have used DNA in taxonomy in a different way in bacteria, sure. And people have used DNA to supplement eukaryote taxonomy, obviously. But a standardized system across entire kingdoms? That's new for eukaryotes.T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-27817018310218043812011-08-08T21:13:56.293-07:002011-08-08T21:13:56.293-07:00To answer your question, the Syst Biol paper was i...To answer your question, the Syst Biol paper was invited, based on a conference "debate", and it included a list of questions that we were asked to answer.<br /><br />Others have written papers specifically about barcoding in protists, algae, and fungi. Bacteria are different in the way DNA is used, as you noted. So, in that sense, it's not DNA barcoding and is not directly relevant to the point that it must be mentioned constantly. Do you mention the human genome in every environmental genomics paper?T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-84979273931330300572011-08-08T20:58:35.390-07:002011-08-08T20:58:35.390-07:00Oh and re PLoS One --- I am surprised they got awa...Oh and re PLoS One --- I am surprised they got away with some of this in a PLoS One paper. In a recent paper of mine there they made us take out any claims of "this is the biggest" or "this is the first" because they said PLoS One was about reporting what you did and unless we could document all previous studies we could not state which was biggest ...Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-69308200864325179702011-08-08T20:57:04.983-07:002011-08-08T20:57:04.983-07:00I like some papers on barcoding but overall the fi...I like some papers on barcoding but overall the field seems to ignore the work already done on rRNA surveys of microbes. <br /><br />I note - as an aside - in my first class I taught at UC Davis students had to pick a paper to present and discuss with the class. One of them presented this paper: http://www.erin.utoronto.ca/~w3bio/bio443/seminar_papers/promise_of_dna_barcoding.pdf. By you and Paul Hebert. And they all asked "Why is there no mention of microbes in this paper?" I said I had no idea but I would look into it. And every time I look into it it seems to me that the barcoding field does not give enough credit to Pace, Sogin, and the entire history of work on rRNA studies and now metagenomics. Sure now some people talk about barcoding fungi and microbes. But really, how is this different from rRNA surveys? And why does it need to be called something new?Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-12475084045164016462011-08-08T20:56:17.397-07:002011-08-08T20:56:17.397-07:00Fair enough. That paper seems like it should have ...Fair enough. That paper seems like it should have been revised during review to include mention of that. (It was a PLoS journal, no? Who edits/chooses reviewers?). But as I said, it doesn't reflect the real work being done even within the barcoding initiative, contra your criticism of the entire project.T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-38395188365059002702011-08-08T20:48:26.663-07:002011-08-08T20:48:26.663-07:00Really? There's not a single mention of micro...Really? There's not a single mention of microbes in the paper yet the paper is about estimating richness and such things which have been done w/ microbes for years.Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-91934988544476753482011-08-08T20:46:40.135-07:002011-08-08T20:46:40.135-07:00There are plenty of people within the barcoding wo...There are plenty of people within the barcoding world who work on microbes, including a working group on protists, others on fungi, and there is environmental "barcoding" of bacteria using next-gen sequencing.<br /><br />Seems like you're latching on to one (poorly worded) sentence here.T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.com