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Introduction: Paracoccus yeei is the first species in the genus Paracoccus to be implicated in opportunistic infections in humans. As a result, P. yeei strains provide a valuable model for exploring how bacteria shift from a saprophytic to a pathogenic lifestyle, as well as for investigating the role of horizontally transferred DNA in this transition. In order to gain deeper insights into the unique characteristics of this bacterium and the molecular mechanisms underlying its opportunistic behavior, a comparative physiological and genomic analysis of P. yeei strains was performed. Results: Complete genomic sequences of 7 P. yeei isolates (both clinical and environmental) were obtained and analyzed. All genomes have a multipartite structure comprising numerous extrachromosomal replicons (59 different ECRs in total), including large chromids of the DnaA-like and RepB families. Within the mobile part of the P. yeei genomes (ECRs and transposable elements, TEs), a novel non-autonomous MITE-type element was identified. Detailed genus-wide comparative genomic analysis permitted the identification of P. yeei -specific genes, including several putative virulence determinants. One of these, the URE gene cluster, determines the ureolytic activity of P. yeei strains—a unique feature among Paracoccus spp. This activity is induced by the inclusion of urea in the growth medium and is dependent on the presence of an intact nikR regulatory gene, which presumably regulates expression of nickel (urease cofactor) transporter genes. Discussion: This in-depth comparative analysis provides a detailed insight into the structure, composition and properties of P. yeei genomes. Several predicted virulence determinants (including URE gene clusters) were identified within ECRs, indicating an important role for the flexible genome in determining the opportunistic properties of this bacterium. [ABSTRACT FROM AUTHOR]

Background: Important industrial traits have been linked to plasmids in Lactococcus lactis. Results: The dairy isolate L. lactis subsp. lactis biovar diacetylactis FM03P was sequenced revealing the biggest plasmidome of all completely sequenced and published L. lactis strains up till now. The 12 plasmids that were identified are: pLd1 (8277 bp), pLd2 (15,218 bp), pLd3 (4242 bp), pLd4 (12,005 bp), pLd5 (7521 bp), pLd6 (3363 bp), pLd7 (30,274 bp), pLd8 (47,015 bp), pLd9 (15,313 bp), pLd10 (39,563 bp), pLd11 (9833 bp) and pLd12 (3321 bp). Structural analysis of the repB promoters and the RepB proteins showed that eleven of the plasmids replicate via the theta-type mechanism, while only plasmid pLd3 replicates via a rolling-circle replication mechanism. Plasmids pLd2, pLd7 and pLd10 contain a highly similar operon involved in mobilisation of the plasmids. Examination of the twelve plasmids of L. lactis FM03P showed that 10 of the plasmids carry putative genes known to be important for growth and survival in the dairy environment. These genes encode technological functions such as lactose utilisation (lacR-lacABCDFEGX), citrate uptake (citQRP), peptide degradation (pepO and pepE) and oligopeptide uptake (oppDFBCA), uptake of magnesium and manganese (2 mntH, corA), exopolysaccharides production (eps operon), bacteriophage resistance (1 hsdM, 1 hsdR and 7 different hsdS genes of a type I restriction-modification system, an operon of three genes encoding a putative type II restriction-modification system and an abortive infection gene) and stress resistance (2 uspA, cspC and cadCA). Acquisition of these plasmids most likely facilitated the adaptation of the recipient strain to the dairy environment. Some plasmids were already lost during a single propagation step signifying their instability in the absence of a selective pressure. Conclusions: Lactococcus lactis FM03P carries 12 plasmids important for its adaptation to the dairy environment. Some of the plasmids were easily lost demonstrating that propagation outside the dairy environment should be minimised when studying dairy isolates of L. lactis. [ABSTRACT FROM AUTHOR]

An approach based on quantitative reverse transcriptase PCR (RT-qPCR) was developed for monitoring two strains of lactococci in co-culture in milk by measuring the expression of specific genes identified by suppression subtractive hybridization (SSH). SSH was used to identify strain-specific genes of Lactococcus lactis ssp. cremoris SK11 and ATCC 19257. RT-qPCR was then employed to validate gene specificity and compare the expression of selected specific genes (glycosyltransferase and amidase genes for L. lactis ssp. cremoris ATCC 19257 and a hypothetical protein for SK11) identified by SSH. The time profile of changes in gene expression relative to ldh transcription differed between pure and mixed cultures as well as between media. At the stationary phase, gene expression of mixed cultures in GM17 attained the highest proportion of ldh transcription while mixed cultures in milk peaked at the postexponential phase. Strain ratios expressed as RNA proportion appear to favour SK11 in GM17 medium, while ATCC 19257 dominated in milk co-cultures. This approach was useful to determine the contribution of strain SK11 in relation to strain ATCC 19257 during co-culture in milk compared to rich medium. The ability to track the metabolic contribution of each lactococcal strain during fermentation of milk or cheese ripening will extend our understanding of the impact of process parameters on the production performance of strains. [ABSTRACT FROM AUTHOR]