Co-infection dynamics of a major food-borne zoonotic pathogen in chicken.

A major bottleneck in understanding zoonotic pathogens has been the analysis of pathogen co-infection dynamics. We have addressed this challenge using a novel direct sequencing approach for pathogen quantification in mixed infections. The major zoonotic food-borne pathogen Campylobacter jejuni, with an important reservoir in the gastrointestinal (GI) tract of chickens, was used as a model.

Alignment-independent comparisons of human gastrointestinal tract microbial communities in a multidimensional 16S rRNA gene evolutionary space.

We present a novel approach for comparing 16S rRNA gene clone libraries that is independent of both DNA sequence alignment and definition of bacterial phylogroups. These steps are the major bottlenecks in current microbial comparative analyses. We used direct comparisons of taxon density distributions in an absolute evolutionary coordinate space.

Quencher extension for single nucleotide polymorphism quantification in bacterial typing and microbial community analyses.

Quencher extension is a novel single-step closed tube real-time method to quantify single nucleotide polymorphisms (SNPs) in combination with primer extension. A probe with a 5'-reporter is single-base extended with a dideoxy nucleotide containing a quencher if the target SNP allele is present. The reaction is measured from the quenching (reduced fluorescence) of the reporter.

Alignment-independent bilinear multivariate modelling (AIBIMM) for global analyses of 16S rRNA gene phylogeny.

Alignment-independent phylogenetic methods have interesting properties for global phylogenetic reconstructions, particularly with respect to speed and accuracy. Here, we present a novel multimer-based alignment-independent bilinear mathematical modelling (AIBIMM) approach for global 16S rRNA gene phylogenetic analyses. In AIBIMM, jackknife cross-validated principal component analyses (PCA) are used to explain the variance in nucleotide n-mer frequency data.

Multiplex real-time single nucleotide polymorphism detection and quantification by quencher extension.

Multiplex quencher extension (multiplex-QEXT) is a novel closed tube single-step method for detection and quantification of several single nucleotide polymorphisms (SNPs) simultaneously. The principle of multiplex-QEXT is that 5' reporter-labeled probes are 3' single-base-extended with TAMRA dideoxy nucleotides if the respective SNP alleles are present. TAMRA can serve as either an energy acceptor (quencher-based detection) or donor [fluorescence resonance energy transfer (FRET)-based detection] for a wide range of different reporter fluorochromes.