Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes

<p>Abstract</p> <p>Background</p> <p><it>Legionella pneumophila </it>is an intracellular pathogen of environmental protozoa. When humans inhale contaminated aerosols this bacterium may cause a severe pneumonia called Legionnaires' disease. Despite the abundance of dozens of <it>Legionella </it>species in aquatic reservoirs, the vast majority of human disease is caused by a single serogroup (Sg) of a single species, namely <it>L. pneumophila </it>Sg1. To get further insights into genome dynamics and evolution of Sg1 strains, we sequenced strains Lorraine and HL 0604 1035 (Sg1) and compared them to the available sequences of Sg1 strains Paris, Lens, Corby and Philadelphia, resulting in a comprehensive multigenome analysis.</p> <p>Results</p> <p>We show that <it>L. pneumophila </it>Sg1 has a highly conserved and syntenic core genome that comprises the many eukaryotic like proteins and a conserved repertoire of over 200 Dot/Icm type IV secreted substrates. However, recombination events and horizontal gene transfer are frequent. In particular the analyses of the distribution of nucleotide polymorphisms suggests that large chromosomal fragments of over 200 kbs are exchanged between <it>L. pneumophila </it>strains and contribute to the genome dynamics in the natural population. The many secretion systems present might be implicated in exchange of these fragments by conjugal transfer. Plasmids also play a role in genome diversification and are exchanged among strains and circulate between different <it>Legionella </it>species.</p> <p>Conclusion</p> <p>Horizontal gene transfer among bacteria and from eukaryotes to <it>L. pneumophila </it>as well as recombination between strains allows different clones to evolve into predominant disease clones and others to replace them subsequently within relatively short periods of time.</p

Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome

International audienceThe biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation

Perceived Access Problems Among Patients with Diabetes in Two Public Systems of Care

OBJECTIVE: We examined the prevalence of access problems among public clinic patients after participating in trials of automated telephone disease management with nurse follow-up. DESIGN: Randomized trial. SETTING: General medicine clinics of a county health care system and a Veterans Affairs (VA) health care system. PARTICIPANTS: Five hundred seventy adults with diabetes using hypoglycemic medication were enrolled and randomized; 520 (91%) provided outcome data at 12 months. INTERVENTION: Biweekly automated telephone assessments with telephone follow-up by diabetes nurse educators. MEASUREMENTS AND MAIN RESULTS: At follow-up, patients reported whether in the prior 6 months they had failed to obtain each of six types of health services because of a financial or nonfinancial access problem. Patients receiving the intervention were significantly less likely than patients receiving usual care to report access problems (adjusted odds ratio [AOR], 0.61; 95% confidence interval [CI], 0.43 to 0.97). The risk of reporting access problems was greater among county clinic patients than VA patients even when adjusting for their experimental condition, and socioeconomic and clinical risk factors (AOR, 1.61; 95% CI, 1.02 to 2.53). County patients were especially more likely to avoid seeking care because of a worry about the cost (AOR, 2.82; 95% CI, 1.48 to 5.37). CONCLUSIONS: Many of these public sector patients with diabetes reported that they failed to obtain health services because they perceived financial and nonfinancial access problems. Automated telephone disease management calls with telephone nurse follow-up improved patients' access to care. Despite the impact of the intervention, county clinic patients were more likely than VA patients to report access problems in several areas

Bacterial gene import and mesophilic adaptation in archaea

International audienceIt is widely believed that the archaeal ancestor was hyperthermophilic, but during archaeal evolution, several lineages - including haloarchaea and their sister methanogens, the Thaumarchaeota, and the uncultured Marine Group II and Marine Group III Euryarchaeota (MGII/III) - independently adapted to lower temperatures. Recent phylogenomic studies suggest that the ancestors of these lineages were recipients of massive horizontal gene transfer from bacteria. Many of the acquired genes, which are often involved in metabolism and cell envelope biogenesis, were convergently acquired by distant mesophilic archaea. In this Opinion article, we explore the intriguing hypothesis that the import of these bacterial genes was crucial for the adaptation of archaea to mesophilic lifestyles