Mobilization of vitamin B12 transporters alters competitive dynamics in a human gut microbe

Abstract

Highlights d Diverse mobile genetic elements in gut microbes encode vitamin B 12 transporters d Transfer of CTns with B 12 transporters complement transport-deficient strains d CTns with B 12 transporters offer competitive advantages during in vitro growth d In vivo conjugation restores ability to use B 12 in transportdeficient Bacteroides

Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota

“…The PUL-based clustering of species does not correlate to the overall Bacteroidetes phylogeny. Frye et al observed a similar phenomenon among the vitamin B 12 transport loci of Bacteroidetes ( 17 ). Both groups suggest the occurrence of interspecies HGT as a likely explanation.…”

Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution

“…Not only do distinct lineages of a species co-colonize, but so to do numerous isolates of the same clonal lineage that have diverged due to the acquisition or loss of genetic elements. The properties conferred by the genetic cargo of these MGE are beginning to be characterized and include the utilization of dietary polysaccharides, 19,20 , cofactor import, 26 antagonistic weapons, 27–29 protection from T6SS mediated antagonism, 30 transcriptional regulators that influence expression of chromosomal genes, 76 biofilm formation, and antibiotic resistance. 77,78 It can be anticipated that introduction of new Bacteroidales strains for therapeutic purposes will evolve differently in each ecosystem into which they are introduced and will also shape the Bacteroidales strains preexisting in or acquired by each ecosystem.…”

“…Another feature of gut Bacteroidales is their rapid evolution due to the exchange of DNA by conjugation. These mobile genetic elements encode numerous properties that affect strain fitness, including PUL that increase utilizable substrates, 19 transport cofactors, 26 Type VI secretion systems 27 and bacteriocins 28,29 that antagonize competing strains, along with protective immunity genes, 30 and antibiotic resistance genes, 31 to name a few. Although extensive conjugal DNA transfer between species within an individual’s gut microbiota has been documented, 32,33 there are few studies that examine the degree to which Bacteroidales strains evolve and differentiate in the human gut due to DNA acquisitions.…”

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

“…Here, we found some phylogenetic trends in corrinoid traits, but overall, the distribution of these traits is patchy across the phylogenetic tree, suggesting that gene loss has occurred at various evolutionary points, possibly due to the frequent emergence of corrinoid dependence and independence (9), or that horizontal gene transfer (HGT) is important in sustaining corrinoid biosynthesis and use. Indeed, corrinoid uptake genes in human gut Bacteroidetes are commonly found on mobile genetic elements (77), and Salmonella typhimurium and Lactobacillus reuteri biosynthesis genes are thought to have been acquired by HGT (78,79). The evolutionary history of corrinoids should be explored further to identify which processes have impacted the biosynthesis and use of these cofactors.…”