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According to this paper, among 61 strains of E. coli they studied only 6% of the genes are common in all. Which means that the overwhelming majority of the genes are not shared.

And wikipedia defines E. coli like this:

... is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms).

Which is a phenotypic definition. My question is: what defines E. coli as a species: its genotype or its phenotype?

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    $\begingroup$ That's more like a morphological description. Pre-genomic microbiological classification relied a lot on serological and biochemical tests. $\endgroup$ – WYSIWYG Mar 6 at 13:00
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    $\begingroup$ Related, but possibly not a duplicate: biology.stackexchange.com/q/68853/36466 $\endgroup$ – rotaredom Mar 6 at 13:01
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    $\begingroup$ I think there's more than just a semantic question here, although indeed species definitions are a bit of an arbitrary construct to begin with, decisions have been made to call certain organisms E. coli and others not. $\endgroup$ – Bryan Krause Mar 6 at 16:29
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    $\begingroup$ @David in my experience, genotype can refer to an entire genome, most often with regard to a virus, as in HIV genotype, HCV genotype, etc. $\endgroup$ – De Novo supports GoFundMonica Mar 6 at 16:34
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    $\begingroup$ @David it's not sloppy usage. It's usage you're not familiar with :) $\endgroup$ – De Novo supports GoFundMonica Mar 6 at 17:46
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The context for identifying E. coli is primarily clinical Microbiology, and in the clinical lab the identification is primarily phenotypic, based on various properties such as growth and morphology on selective media, Gram stain appearance, biochemical characteristics, etc - only under unusual circumstances is genetic testing done. The latter is problematic because of extreme genetic diversity within the species and some overlap with others (even other genera).

The problems with the notion of "species" in E. coli in the context of 16s sequencing, horizontal gene transfer, mobile genetic elements, plasmids, etc is discussed at some length in Quammen's recent book The Tangled Tree.

For now, phenotypic species identification is the norm, as illustrated by the "Nomenclature" guidance to authors of the Journal of Bacteriology, a publication of the American Society for Microbiology.

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Surely both. Nowadays, with molecular technics avaiable with low effort, the typing is mainly done with genotyping. This can be done using the 16S rRNA gene, which is composed by hyper-variable regions, as reported in picture. This choice is justified because this gene is highly conserved into the bacterial phylum, giving perhaphs variation into some regions due to evolution. This concept is explained by the term "molecular clock" in evolutionary biology.

enter image description here

By designing specific primers (they already exists for more species) you could obtain only amplification by E.coli cells. This is just an example, exportable also to other bacterial species: by analyzing other conserved phenotypes for every strains of this species, is possible to do also some real-time PCR using other regions of the genome. Remember always that isolation and, by so, phenotyping is required while doing bacterial identification; the genotyping is the fastest and most accurate way to the first recognition step.

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I happened to encounter a related problem recently in answering a question regarding a paper on virus classification. I am not a microbiologist, so this answer may be flawed, however it raises a point that I don’t think has been made in the other answers. I welcome corrections.

First, however, it is obvious that bacteria were identified many, many years before their sequences were available, and, as indicated in the answer by @Argalatyr, classification could only be on phenotypic characteristics. The imprecision of this is acknowledged in a statement in a 2000 review article by Dijkshoorn et al. ‘Strain, clone and species: comments on three basic concepts of bacteriology’:

“A species consists of strains of common origin which are more similar to each other than they are to any other strain.”

The paper I came across previously was by Bobay and Ochman (2018) in which they state:

“Members of a biological species are defined by their ability to exchange genetic material

This definition — by its nature genotypic — clearly predates the DNA sequencing era. (In asexual organisms like bacteria, exchange of genetic material can occur by recombination of DNA.)

It should also be mentioned that this definition applied to bacteria does not require members of the same species to have the same number of genes (the concern of the question), only that they can recombine.

In their paper Dijkshoorn et al. go on to discuss current efforts to correlate what, I assume, is this accepted definition with DNA-based comparisons — 16S rRNA sequencing and overall DNA percentage identity.

“Recently, a comparison of DNA–DNA pairing data and 16S rRNA similarity data showed that strains with rRNA similarity less than c. 97% generally showed no significant DNA–DNA reassociation and thus belong to different species. Similarity >97% may or may not indicate close relationship. The use of this percentage as a rule of thumb has in many cases made rRNA sequencing replace the more cumbersome DNA–DNA pairing technique for the creation of new species. At present, either the 70% or the 97% rule is used to underpin most proposals for new species.”

The moral would seem to be that we have reached a stage where it is cheaper and easier to try to define species from DNA sequencing that to go into the laboratory and perform experiments to see whether they can exchange genetic material.

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  • $\begingroup$ Recombination and other genomic information exchange is arbitrary as a criterion; apart from the dichotomy of sexual vs asexual reproduction, recombination is often a biological not species characteristic. For example, HIV packages 2 copies of its genome - perhaps explaining its rampant recombination, whereas hepatitis C virus (HCV) recombination is a remarkably rare event. Ultimately, sequence similarity thresholds are arbitrary as well. Species definition is largely a convenience for humans, not an intrinsic biological grouping. $\endgroup$ – Argalatyr Jul 9 at 3:36
  • $\begingroup$ @Argalatyr — I thought it was evident from my answer that I regarded taxonomic distinctions as arbitrary human constructs. Perhaps we should both make this explicit. Both answers addressed the question of practice. Your answer stated that the ‘norm’ for species identification was phenotypic. I have never studied taxonomy (or indeed organismal biology) but my answer drew attention to papers that implied that a different — genotypic — criterion constituted the ‘norm’. I did not, and do not, claim that this or any other classification is absolute, only that it appears to be in use. $\endgroup$ – David Jul 9 at 10:17
  • $\begingroup$ I think we're in agreement that genotypic classification is rapidly getting cheaper, but the criteria for discuss definition remain somewhat nebulous. I don't think that exchange or genetic information will stand up as a species definition for the reasons that I provided. $\endgroup$ – Argalatyr Jul 10 at 10:40
  • $\begingroup$ @Argalatyr — I think that is generally recognized. The original virology paper Of the other question was concerned with the problem of horizontal transfer of individual genes. And I’m the last person to wish to be involved in controversies regarding what is or isn’t a species. $\endgroup$ – David Jul 10 at 10:48

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