MadSci Network: Microbiology
Query:

Re: does cutoff value for 16S rDNA match is same for full and short sequences

Date: Mon May 7 01:09:44 2012
Posted By: Brian Foley, Molecular Genetics Staff Scientist
Area of science: Microbiology
ID: 1336219531.Mi
Message:

Hi Sara!

Excellent question!! As I have said before, "Excellent question" is the scientific term for "There is no answer." Or maybe more correctly there are dozens of areas of research the question leads into, all of which have vast areas of interesting new findings awaiting.

First of all, the definition of "species" or "Genus" is not currently and probably should not ever be precisely defined in any way that one single rule would work well for all types of bacteria. With sexually reproducing eukaryotes such as vertebrates or flowering plants, it makes some sense to define a "species" as a group of organisms that can mate and produce fertile offspring. We then generally use the term "subspecies" for groups that are reproductively isolated but can be forced to mate by humans using unnatural means.

For most asexual organisms including archaebacteria, eubacteria, many protists, many plants, viruses, etc. this definition of "species" does not work. Phylogenetic methods (counting the mutations or DNA percent identity between the same the same gene in different individuals is the very most simple beginning of phylogenetic analysis) offer many promising insights into the evolutionary history and natural history of groups of organisms. However, these methods should never be taken alone, or applied without regard to many other important aspects of life on earth. Modern humans classify themselves as being different species from Chimpanzees and Gorillas with very good reason, and testing to see if a lab-made chimp/human or chimp/gorilla or gorilla/human hybrid would be fertile is not a good idea for at least several dozen reasons. We consider the domestic dog to be a separate species (rather than just a subspecies) of Arctic wolf for many good reasons even though they can very easily mate even without human intervention. Making up some number like 99% or 97% or 98.235% DNA sequence identity of some gene, would be seen as silly and very counterproductive for the classification and nomenclature of vertebrates. It is an equally bad idea for any other branch of life.

Even within the eubacteria, a single group such as the gammaproteobacteria will contain some organisms that are completely isolated from each other at a very high DNA percent identity, and others that have great diversity and yet are still very able to exchange genetic material on a daily basis via sharing phages and plasmids or even fusing and splitting in a manner quite similar to eukaryotic sex. One example of a mechanism for eubacterial isolation is when a branch of the organism adapts to life within a specific host, either as a pathogen (Mycobacterium tuberculosis for humans, Mycobacterium bovis for cattle) or symbiont (some lineages of E. coli are very host specific).

Human exploration of the microbial world has only very recently begun. So far we have focused first on pathogens of economic importance to humans, such as those that cause plagues of humans or of economically important livestock. We have also done a lot of work with organisms used for economic benefit of humans such as Saccharomyces (beer, wine and other fermenters; bread yeasts). A bit of work has been done with organisms that are easy to culture in the laboratory. We are only beginning to learn about many organisms that cannot yet be cultured in the lab.

Classification and nomenclature systems exist to help humans make some sense of, and be able to discuss, things that do not necessarily fit into neat categories. We live in an analog world, but find it useful to digitize information. The visible light spectrum is continuous, but it is very handy for us to be able to talk about "yellow", "red" and "blue" as if there were neat boundaries in the rainbow. Likewise, it is very handy to be able to use terms like "coliform bacteria", "E. coli", "E. coli O175:H7" or even to get more specific about a the lineage that caused a particular gastroenteritis outbreak in humans such as "the Jack-in-the-Box isolate of E. coli O157:H7".

The system that makes the most sense for humans, is the system that should be used by humans. If a cut-off of 98% for species works well for Escherichia genus, we might declare that we will use that for Escherichia, even if we think 95% is more useful to us for describing species within the Clostridium genus.

If we do come up with a strict "cut-off" value for within and between species, we certainly need to define exactly which region of the genome we are going to use. If we say "98%" but do not specify whether we are basing this on the variable loops of 16S or the complete 16S rRNA gene, we have made a system that is worse than useless, it is inconsistent, confusing, and counterproductive.


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