The famous factoid, “we have more bacterial cells in our body than human cells,” can be attributed mostly by the amount of bacteria in the dense microbial community of the gut where more than 10^12 bacteria/gram live happily within your system. This community is collectively known as your microbiota. Your microbiota are not only numerous, they have profound effects on our nutrition (providing us with essential nutrients), physiology, and the immune system (generally suppressing the inflammation in the gut).

The make-up of your microbiota consists of several hundred different bacterial species – which consists of over 100,000 different genes total. The bacteria that make up your microbiota, including the Gram-negative Enterobacteriaceae, inherently engage in high levels of horizontal gene transfer (HGT). HGT or, “any process in which an organism incorporates genetic material from another species without being the offspring of that organism,” can result in bacterial antibiotic resistance or increased fitness (hypervirulence).

What kind of genetic elements are jumping from species to species?

There are multiple transferable genetic elements, however HGT generally involves plasmids. Plasmids are double-stranded extra-chromosomal genetic elements (pictured right) that can replicate independently of the chromosomal DNA, they are generally found in bacterial species (however, some have been found in eukaryotic organisms, specifically the yeast Saccharomyces cerevisiae), and have the ability to transfer from one bacterium to another.

Many plasmids encode machinery to self-transfer by conjugation (pictured below & above). Conjugation is initiated by contact with donor and recipient bacterium and subsequent plasmid transfer (via conjugation proteins).

The previously mentioned Enterobacteriaceae are a subclass of the microbiota that include pathogenic and non-pathogenic (commensal) bacterial species (ex: Salmonella and E. coli) and have high levels of HGT; however, mechanisms of HGT in Enterobacteriaceae are not fully understood.

What could be fueling the increased HGT of Enterobacteriaceae in the gut?

Stecher, et al. tackled this provocative question first by assessing the environment of the microbiota in the gut. Enterobacteriaceae genome sequencing, and microbiome analysis revealed an immense library of highly diverse plasmid-encoded accessory genes within these species – indicative of a high rate of HGT. One small problem, Enterobacteriaceae are found in low densities in the gut (<<10^8 bacteria/gram), which makes occurrence of plasmid transfer decrease immensely, since you need physical contact between donor and recipient bacterium for conjugation. Low density of Enterobacteriaceae may be due to the presence of obligate anaerobic bacteria (killed by oxygen) in the gut actively keeping the density of facultative anaerobic bacteria (Enterobacteriaceae – can persist with or with oxygen) to a minimum.

With this in mind, something must be occurring in the complex bacterial ecosystem of the gut to induce a higher density of Enterobacteriaceae, thus increasing HGT.

Stecher, et al. suggest “inflammatory host responses triggered by gut immune system (ex: in inflammatory bowel disease patients) or by pathogens such as Salmonella spp. strains […] can suppress the anaerobic microbiota and boost Enterobacteriaceae colonization densities”.

Using a mouse model, they found inflammation in the gut induced by infection with pathogenic Salmonella elicits an increase of pathogen and of resident commensal Escherichia coli (E. coli), and subsequently an increased rate of HGT in the gut.

They created a system that could detect HGT between pathogenic Salmonella and commensal E. coli. Interestingly, they found that when they studied E. coli strains isolated from the gut of the mouse infected with Salmonella and E. coli – 4/10 E. coli harbored a plasmid (p2) from Salmonella. They note, p2 originated from Salmonella and it carried all of the necessary conjugation abilities, indicating HGT between these two species.

Why would commensal E. coli want the Salmonella p2 plasmid?

Is the p2 harboring fitness-factors that would increase the growth or survival of the E. coli that picked it up?

In fact, p2 is harboring fitness-factors. They found p2 encodes for colicin production (cib) and immunity to colicins (imm). “Colicins are toxic proteins produced by and toxic for Enterobaceriaceae”. This way, bacteria harboring p2 are resistant to colicin-mediated killing because they carry the immunity proteins – however, their unlucky neighbors would be killed by the colicin production.

Since plasmid maintenance is generally costly for a bacterium, it is interesting that it provides protection against colicins – it gives a reason for E. coli to keep this extra-chromosomal DNA around.

Additionally, they wanted to test the frequency of plasmid conjugation in the mouse gut during a duel infection with pathogenic Salmonella and commensal E. coli without the benefit of colicin resistance. They deleted the colicin genes from p2 and infected the mice. What they found was near 100% conjugation frequency – nearly all of the E. coli harvested from the mouse harbored p2. This indicates that HGT occurs despite the added bonus of colicin resistance (or general increased fitness).

Interestingly, high rate of HGT between these two species was dependent on inflammation in the gut due to pathogenic Salmonella, and could not be recreated by an avirulent strain of Salmonella.

These studies provide evidence of how plasmids are maintained in bacterial populations over evolutionary time. They also indicate that the high rate of HGT is partly explained by the colicin-mediated fitness conferred by p2, but mostly by the high rate of intrinsic plasmid transfer and inflammation in the gut.





Bärbel Stechera,b,1, Rémy Denzlera, Lisa Maiera, Florian Berneta, Mandy J. Sandersc, Derek J. Pickardc, Manja Barthela,, Astrid M. Westendorfd, Karen A. Krogfelte, Alan W. Walkerc, Martin Ackermannf,g, Ulrich Dobrindth,i,, & Nicholas R. Thomsonc, and Wolf-Dietrich Hardta (2012). Gut in!ammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae Proceedings of the National Academy of Sciences of the United States of America, 109 (4), 1269-1274