Determining the antibiotic resistance potential of the indigenous oral microbiota of humans using a metagenomic approach

Abstract

Studies of the prevalence and identity of genes encoding resistance to antibiotics in a microbial community are usually carried out on only the cultivable members of the community. However, it is possible to include the as-yet-uncultivable organisms present by adopting a metagenomic approach to such studies. In this investigation, four metagenomic libraries of the oral microbiota were prepared from three groups of 20 adult humans and screened for antibiotic-resistant clones. Clones resistant to tetracycline and amoxycillin were present in all four libraries while gentamicin-resistant clones were found in three of the libraries. The genes encoding tetracycline resistance in the clones were identified and found to be tet(M), tet(O), tet(Q), tet(W), tet37 and tet(A). However, only the first three of these were detected in all three groups of individuals investigated.

Metabolic Network Model of a Human Oral Pathogen

“…Putative malonyl-CoAbased fatty acid extension reactions (13MMA, PMACP) were then used to produce 13-methyl-myristic acid and 15-methyl-palmitic acid. These molecules, in turn, form the basis of the C 15 and C 17 terminal branched chains that make up the exposed moieties of the lipidA molecule. Similarly, taking advantage of the detailed study by Takahashi et al (90), we could refine manually the details of the amino acid fermentation pathways (see below and also Fig.…”

“…Most notably, as sequencing technologies become increasingly approachable, a variety of organisms and community-level metagenomic samples are being sequenced (17,18,53). In parallel, the awareness of the importance of quantitative methods and system-level mathematical approaches is gradually percolating through different branches of biology and is going to be a fundamental component of the study of microbial physiology and pathology (24,63,64,76,77,92).…”

“…In the fight against infectious diseases, we are witnessing the discovery of novel connections between infection, inflammation, and systemic human diseases (2-4, 14, 29, 39, 48-50) and a rise in the evolution of antibiotic resistance (12,15,17). These threats reinforce the necessity to understand the mechanisms that underlie pathogenicity and the interactions between pathogenic and nonpathogenic microbes coexisting in our body as a means to identify novel drug targets for more aggressive and carefully targeted therapies.…”

From bacterial genomics to metagenomics: concept, tools and recent advances

“…Davies and co-workers in 2000, identifi ed a novel metabolite, Terragine from soil metagenome [90]. More recently, Diaz-Torres et al (2006) screened four metagenomic libraries made from the oral microfl ora of 20 adult human beings to identify novel tetracycline, amoxicillin and gentamycin resistant genes [65]. Piel and group reported a set of putative antitumor polyketide, pederin biosynthesis genes from a metagenomic library of Paederus fuscipes beetles and its associated bacteria [92].…”

“…This study of the collective microbial genomes contained in an environmental sample was fi rst termed as 'metagenomics' by Jo Handelsman [54] and subsequently explained as the statistical concept of meta-analysis (the process of statistically combining separate analyses) and genomics (comprehensive analysis of an organism's genetic material) [55,58,60]. More specifi cally, the study may be defi ned as the culture-independent analysis of the genomes of an assemblage of microorganisms from environmental sample which may include soil [61,62], aquatic habitats [63], gut [64], oral cavity [65], excreta [66] etc. Several other terms such as 'community genome' [67], 'environment DNA (eDNA) libraries' [63], 'recombinant environmental libraries' [68] etc.…”