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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 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 Mar 6 at 17:46
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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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