Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

Abstract

Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.

The human gut resistome

“…Interestingly, transfer of CTnDOT is triggered by exposure to low levels of tetracycline [ 66 ], thereby directly linking antibiotic use and the spread of antibiotic resistance determinants. In addition to the strictly anaerobic gut commensals discussed above, facultatively anaerobic bacteria, in particular the lactic acid bacteria (enterococci, streptococci and lactobacilli), appear to be important conduits of horizontal gene transfer in the intestinal tract [ 67 ]. Enterococci appear to be exceptionally well suited to function as ‘drug resistance gene traffickers’ in the human gut [ 68 ].…”

Antimicrobial resistance in chronic liver disease

“…This densely populated microbial ecosystem resident in the intestinal luminal environment provides frequent opportunity for the horizontal transfer of resistance genes amongst microbes, through several different mechanisms including conjugation and transduction, with most AMR genes harboured by strictly anerobic intestinal commensals. Facultatively anerobic bacteria, in particular, those that produce lactic acid such as enterococci, streptococci and lactobacilli, are also involved in horizontal gene transfer within the gut [65]. This is particularly relevant to cirrhosis because enterococci, which are known to be enriched in the feces of patients with CLD, appear to behave as efficient 'drug resistance gene traffickers' in the gut [66], and thus may have an impact on development of enteric AMR, with emerging data confirming increasing prevalence of MDRO including vancomycin-resistant strains [3,25,67].…”

Drug Resistance in Bacteria, Fungi, Malaria, and Cancer

“…Conjugation is a mating process in which exchange of genetic material takes place through a conjugative bridge. Conjugation, transformation, and transduction serve as mechanisms that aid the spread of drug resistance in a population either from pathogens to commensals and vice versa or between the commensals themselves such as lactic acid bacteria are also involved in channeling gene transfer in the intestinal tract (Ogilvie et al 2012). Transduction is mediated by bacteriophages.…”