Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

Abstract

BackgroundLittle is known regarding the pool of mobile genetic elements associated with the human gut microbiome. In this study we employed the culture independent TRACA system to isolate novel plasmids from the human gut microbiota, and a comparative metagenomic analysis to investigate the distribution and relative abundance of functions encoded by these plasmids in the human gut microbiome.ResultsNovel plasmids were acquired from the human gut microbiome, and homologous nucleotide sequences with high identity (>90%) to two plasmids (pTRACA10 and pTRACA22) were identified in the multiple human gut microbiomes analysed here. However, no homologous nucleotide sequences to these plasmids were identified in the murine gut or environmental metagenomes. Functions encoded by the plasmids pTRACA10 and pTRACA22 were found to be more prevalent in the human gut microbiome when compared to microbial communities from other environments. Among the most prevalent functions identified was a putative RelBE toxin-antitoxin (TA) addiction module, and subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes. A broad phylogenetic distribution of RelE toxin genes was observed in gut associated bacterial species (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria), but no RelE homologues were identified in gut associated archaeal species. We also provide indirect evidence for the horizontal transfer of these genes between bacterial species belonging to disparate phylogenetic divisions, namely Gram negative Proteobacteria and Gram positive species from the Firmicutes division.ConclusionsThe application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. In particular the increased relative abundance and broad phylogenetic distribution was identified for a putative RelBE toxin/antitoxin addiction module, a putative phosphohydrolase/phosphoesterase, and an ORF of unknown function. Our analysis also indicates that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (America, Japan and Europe), and are potentially unique to the human gut microbiome. Further investigation of the plasmid population associated with the human gut is likely to provide important insights into the development, functioning and evolution of the human gut microbiota.

Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes

“…While the relative abundance of plasmids or pollution-related accessory genes has been compared between polluted and clean control sites, no studies have so far compared gene contents of plasmids (64,(69)(70)(71)(72). The recently developed metagenomics approaches to assess the "plasmidome" or "metamobilome" (73,74) present one way to assess accessory gene content independent of what the plasmids encode, but obtaining reliable, closed genome sequences for large self-transmissible plasmids is still a challenge (75). Using the triparental mating approach, we showed the presence of diverse self-transmissible plasmids that do not carry known host-beneficial genes in natural environments.…”

Interplay between gut microbiota and antibiotics

“…The aph (2′′)-Ib gene was associated with mobile elements and was harboured by a strain from the genus Subdoligranulum that includes members of the group of anaerobic commensal microbiota. Our results suggested that these genetic mobile elements can be mobilized and/or have been acquired through horizontal gene transfer, as reported previously for members of the Firmicutes (Jones et al, 2010), which could contribute to the risk of transfer of antibiotic resistance genes from commensals to potential pathogens. It cannot be excluded that the increase of aminoglycoside resistance genes may also be an effect of the SDD therapy since tobramycin is used as part as the cocktail administrated to the patients.…”

“…This observation suggests that these resistance genes may be part of larger genetic elements that can be mobilised and/or which have been acquired through horizontal gene transfer. Evidence for the extensive transfer of antibiotic resistance genes in the gut microbiota has been observed before in Bacteroidetes and Firmicutes (Shoemaker et al, 2001;Jones et al, 2010). Consequently, the enrichment of antibiotic resistance genes in the patient's gut microbiota during SDD and their association with mobile genetic elements is a cause of concern as this may facilitate transfer of resistance genes to aerobic nosocomial pathogens.…”

Probiotics and health: An evidence-based review

“…The intestinal microbiota (a term that has now replaced the old denomination of "microflora" [1,2]) is an ecosystem formed by a variety of ecological niches, made of several bacterial species and a very large amount of strains [3][4][5][6][7][8]. The microbiota is in close contact with the intestinal mucosa or epithelial interface which is, after the respiratory area, the largest surface of the body, occupying approximately 250-400 m 2 .…”

“…The human gut microbiota is currently the focus of very advanced research techniques -including studies on the bacterial genome (microbiome) -whose results are published in prestigious scientific journals [3][4][5][6][7][8]. Two major projects, based on systematic DNA sequencing of the microbiota, are currently in progress: (a) the Human Microbiome Project (HMP), in the USA and (b) the Metagenomics of the Human Intestine (metaHIT), held in Europe.…”