Corrigendum: Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli

The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes are mosaics that only share a small subset of gene-sequences (core genome) even among members of the same species. It has been reported that the presence of essential genes is highly variable between closely related bacteria and even among members of the same species, due to the phenomenon known as “non-orthologous gene displacement” that refers to the coding for an essential function by genes with no sequence homology due to horizontal gene transfer (HGT). The existence of dormant forms among bacteria and the high incidence of HGT have been proposed to be driving forces of bacterial evolution, and they might have a role in the low level of conservation of essential genes among related bacteria by non-orthologous gene displacement, but this correlation has not been recognized. The aim of this mini-review is to give a brief overview of the approaches that have been taken to define and study essential genes, and the implications of non-orthologous gene displacement in bacterial evolution, focusing mainly in the case of Escherichia coli. To this end, we reviewed the available literature, and we searched for the presence of the essential genes defined by mutagenesis in the genomes of the 63 best-sequenced E. coli genomes that are available in NCBI database. We could not document specific cases of non-orthologous gene displacement among the E. coli strains analyzed, but we found that the quality of the genome-sequences in the database is not enough to make accurate predictions about the conservation of essential-genes among members of this bacterial species

Tracking the Origins of <i>Pseudomonas aeruginosa</i> Phylogroups by Diversity and Evolutionary Analysis of Important Pathogenic Marker Genes

Pseudomonas aeruginosa is a widespread environmental bacterium and an opportunistic pathogen that represents a health hazard due to its production of virulence factors and its high antibiotic resistance. The genome of most of the strains belonging to this bacterial species is highly conserved, and genes coding for virulence-associated traits are part of the species core-genome. Recently, the existence of phylogroups has been documented based on the analysis of whole genome sequences of hundreds of isolates. These clades contain both clinical and environmental strains, which show no particular geographical distribution. The major phylogroups (clades 1 and 2) are characterized by the nearly mutually exclusive production of the virulence effectors secreted by the type three secretion system (T3SS) ExoS and ExoU, respectively. Clade 3 is the most genetically diverse and shares with clade 5, which is closely related to clades 1 and 2, the production of the pore-forming exolysin A, and the lack of T3SS, among other characteristics. Here we analyze the 4955 P. aeruginosa genomes deposited in the Pseudomonas Genome Database and present some hypotheses on the origins of four of the five phylogroups of this bacterial species

Tracking the Origins of Pseudomonas aeruginosa Phylogroups by Diversity and Evolutionary Analysis of Important Pathogenic Marker Genes

Pseudomonas aeruginosa is a widespread environmental bacterium and an opportunistic pathogen that represents a health hazard due to its production of virulence factors and its high antibiotic resistance. The genome of most of the strains belonging to this bacterial species is highly conserved, and genes coding for virulence-associated traits are part of the species core-genome. Recently, the existence of phylogroups has been documented based on the analysis of whole genome sequences of hundreds of isolates. These clades contain both clinical and environmental strains, which show no particular geographical distribution. The major phylogroups (clades 1 and 2) are characterized by the nearly mutually exclusive production of the virulence effectors secreted by the type three secretion system (T3SS) ExoS and ExoU, respectively. Clade 3 is the most genetically diverse and shares with clade 5, which is closely related to clades 1 and 2, the production of the pore-forming exolysin A, and the lack of T3SS, among other characteristics. Here we analyze the 4955 P. aeruginosa genomes deposited in the Pseudomonas Genome Database and present some hypotheses on the origins of four of the five phylogroups of this bacterial species

Enrichment experiment changes microbial interactions in an ultra-oligotrophic environment

The increase of nutrients in water bodies, in particular nitrogen (N) and phosphorus (P) due to the recent expansion of agricultural and other human activities is accelerating environmental degradation of these water bodies, elevating the risk of eutrophication and reducing biodiversity. To evaluate the ecological effects of the influx of nutrients in an oligotrophic and stoichiometrically imbalanced environment, we performed a replicated in situ mesocosm experiment. We analyzed the effects of a N- and P-enrichment on the bacterial interspecific interactions in an experiment conducted in the Cuatro Cienegas Basin (CCB) in Mexico. This is a desert ecosystem comprised of several aquatic systems with a large number of microbial endemic species. The abundance of key nutrients in this basin exhibits strong stoichiometric imbalance (high N:P ratios), suggesting that species diversity is maintained mostly by competition for resources. We focused on the biofilm formation and antibiotic resistance of 960 strains of cultivated bacteria in two habitats, water and sediment, before and after three weeks of fertilization. The water habitat was dominated by Pseudomonas, while Halomonas dominated the sediment. Strong antibiotic resistance was found among the isolates at time zero in the nutrient-poor bacterial communities, but resistance declined in the bacteria isolated in the nutrient-rich environments, suggesting that in the nutrient-poor original environment, negative inter-specific interactions were important, while in the nutrient-rich environments, competitive interactions are not so important. In water, a significant increase in the percentage of biofilm-forming strains was observed for all treatments involving nutrient addition

Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT

International audienceBackground : Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications. Methods : Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading. Results : AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community. Conclusions : Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses