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Campylobacteris a bacterial genus associated with community outbreaks and gastrointestinal symptoms. Studies onCampylobactergenerally focus on specific pathogenic species such asC. coliandC. jejuni. Currently, there are thousands of publicly availableCampylobactergenomes, allowing a more complete assessment of the genus diversity. In this work, we report a network-based analysis of all availableCampylobactergenomes to explore the genus structure and diversity, revealing potentially new species and elucidating genus features. We also hypothesize that the previously established Clade III ofC. coliis in fact a novel species (referred here asCampylobacter spp12). Finally, we found a negative correlation between pangenome fluidity and saturation coefficient, with potential implications to the lifestyles of distinctCampylobacterspecies. Since pangenome analysis depends on the number of available genomes, this correlation could help estimate pangenome metrics ofCampylobacterspecies with less sequenced genomes, helping understand their lifestyle and niche adaptation. Together, our results indicate that theCampylobactergenus should be re-evaluated, with particular attention to the interplay between genome structure and niche segregation.

The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida. Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7T to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic diversity and its potential for biotechnological applications.

Members of the Pseudomonas genus inhabit a wide variety of environments, which is correlated with their versatile genome and metabolic capacity. Pseudomonas putida is a saprophytic soil bacterium, known to bioremediate toxic compounds and to promote plant growth. Nevertheless, some clinical P. putida strains have been reported, raising concerns about the safety of this species for biotechnology applications. Despite the ability to occupy different niches, the population structure of P. putida remains unclear. Here, we report the population structure of P. putida for the first time, which is essential to better investigate its biology. We retrieved 11,025 Pseudomonas genomes and used P. putida KT2440 as a type strain to define P. putida sensu stricto, as well as to estimate its population structure and pangenome. By using network and average nucleotide identity analyses, we found that 90 of the 138 deposited P. putida genomes were misclassified, including some reference genomes. Further, we found 23 additional P. putida genomes that were not designated as such. P. putida has an open pangenome dominated by low-frequency genes. The population structure of P. putida is composed by at least 7 clonal complexes (CCs). Clinical isolates are not restricted to a specific CC, although CC4 has 6 out the 9 clinical isolates. Acquired resistance genes are present at low frequency, particularly in plasmids from clinical isolates. Virulence profiles support the higher potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. P. putida lacks key genes for indole-3-acetic acid production, indicating an incomplete or non-functional pathway. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. putida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. putida genetic diversity, which is key to assess its safety for environmental and biotechnology applications.