Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging

Abstract Background Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut. Results We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut. Conclusions Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen

Responsible for the Irish potato famine of 1845–49, the oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the pathogen, the genome of the famine-era strain remains entirely unknown. Here we characterize temporal genomic changes in introduced P. infestans. We shotgun sequence five 19th-century European strains from archival herbarium samples—including the oldest known European specimen, collected in 1845 from the first reported source of introduction. We then compare their genomes to those of extant isolates. We report multiple distinct genotypes in historical Europe and a suite of infection-related genes different from modern strains. At virulence-related loci, several now-ubiquitous genotypes were absent from the historical gene pool. At least one of these genotypes encodes a virulent phenotype in modern strains, which helps explain the 20th century’s episodic replacements of European P. infestans lineages

Sale and purchase of immovable things between natural persons from the point of view of the Income Tax Act

Additional file 2. DAMe manual. This file contains the manual for DAMe, which describes in detail the parameters, inputs and output files of each tool

Mitogenomics of the Extinct Cave Lion, Panthera spelaea (Goldfuss, 1810), Resolve its Position within the Panthera Cats

The extinct cave lion (Panthera spelaea) was an apex predator of the Pleistocene, and one of the largest felid species ever to exist. We report the first mitochondrial genome sequences for this species, derived from two Beringian specimens, one of which has been radiocarbon dated to 29,860 ± 210 14C a BP. Phylogenetic analysis confirms the placement of the cave lion as the sister taxon to populations of the modern lion (P. leo). Using newly recovered stem pantherine fossils to calibrate a molecular clock, we estimate that P. spelaea and P. leo diverged about 1.89 million years ago (95% credibility interval: 1.23–2.93 million years), highlighting the likely position of this extinct carnivore as a distinct species