Escherichia coli (E.coli): if you are an average member of the public you might think of this bacteria in terms of some really nasty food poisoning. The name might conjure up warnings on the news about spinach and sprouts. On the other hand if you, like me, are something of a microbiologist you know E. coli as the most studied bacteria on the globe, and possibly the organism we know the most about on earth. What is important to remember, however, is that all of this research wasn’t conducted with “E. coli” but with a specific strain of the bug: K-12.
In science we accept certain limitations. You can’t study everything and so in biology and in microbiology you tend to study “model organisms.” These are defined species that researchers concentrate their studies on. The benefit of this approach is that everyone can compare apples to apples (or zebrafish to zebrafish, as the case may be). It is useful, however, to remember that when you’re studying a nematode, you’re not studying “worms” you’re studying a nematode (which is a worm), and when you’re studying a mouse, you’re not studying “mammals”, you’re studying a mouse. Obviously it’s important to keep this in mind when drawing conclusions about the implications of research. The questionable applicability of studies into one species to a separate species is precisely why there is so much controversy both inside and outside scientific fields about animal drug testing and its value: a mouse is not a human.
In the bacterial world there is incredible diversity. There is a far greater number of bacterial species than of animal species. For this reason, it’s important to remember to take a look at just how wide a spectrum is being distilling down to one point by concentrating on one organism. I attended a recent talk by professor Erick Denamur who is interested in precisely this subject matter. His lab studies the diversity and “lifestyles” of E. coli from around the world, and how these variables relate to differences in their genetic makeup.
As a little bit of background, the scientific community has focused intense research effort into investigations of the K-12 strain of E.coli. This was isolated from the faeces of a single convalescent diphtheria patient in the early 20th century. To reiterate, this single strain is our basis for much of what we know about bacteria in general. E. coli does, however, have a much wider genetic and phenotypic range than this. The primary habitat for E. coli is as commensal organisms in the intestines of vertebrates. This means they live with us, without causing us any problems, and do the same for birds, pigs, and lots of other animals. They can also live in their secondary habitat: fresh water and sediments. This makes sense, as the contents of one’s intestine tend to end up on the ground if one is your average vertebrate. While these might seem a first glance to be two well defined habitats, there is actually great diversity in the conditions in the intestines of different species. Indeed, even in humans there are different “gut phenotypes” which support the growth of different bacteria in different individuals. Likewise, there are vast differences in conditions and available resources in different soil and water environments around the world. Studies conducted by professor Denamur show that to go along with all of this ecological diversity, the species E. coli also has massive genetic diversity. Depending on the strain, each one can have between 4300-5300 genes, and only just under 2000 are conserved in all the strains. This means that less than half of the genes can be compared in the same species of bacteria, and we’re extrapolating what we know about it to many other species.
As might be expected, Denamur’s lab also found that the different genotypes or genetic makeups correlated with different niches. For example, almost half of people sampled from the US are carriers of a specific strain whereas in a jungle in Africa, less than two percent of people carry the same strain. There are also different profiles for birds than for humans, and different levels of pathogenicity in the different strains: some kill mice, some don’t. This is all, of course, a product of the natural selection process.
So why is this a skeptical subject? Biological model organsisms are one of the most valuable tools that we can use such that each individual study contributes to a larger field, rather than each research group working on a different organism in isolation. Its a good idea, however, to do studies like those of professor Denamur to effectively take a skeptical look at the applicability of biological models by getting a handle on what you don’t know. Having a better idea of the diversity of the group that you’re using one member to represent allows us to more rationally draw conclusions about the group as a whole. Positive knowledge is great, but sometimes it can be just as powerful to estimate and accept the scope of what we don’t yet know.