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Dispersal and philopatry are fundamental processes influencing the genetic structure and persistence of populations, and might be affected by isolation and habitat perturbation. Habitat degradation induced by human activities could have detrimental consequences on the genetic structure of populations. Therefore, it is crucial to understand the role of human impact in promoting or disrupting the genetic structure. Here, we conducted a genetic analysis using 12 polymorphic microsatellite markers of 70 lesser kestrels F alco naumanni from 10 breeding colonies of two subpopulations in Sicily (southern Italy). Genetic differentiation between the two subpopulations was negligible, and linear distances played no role in the level of genetic relatedness recorded in the two sites. Linear distances between nests also resulted in no effects on the relatedness recorded within and between colonies in the largest subpopulation. Clusters of more-versus less-related individuals resulted when the two-dimensional positions of colonies (i.e., latitude and longitude) were tested as predictors of genetic proximity instead of linear distances. Specifically, analyses of colony features showed colony size and human disturbance as factors negatively affecting the relatedness among chicks from different nests. Regardless of colony size, less-related individuals were born in colonies located in the core of the agricultural plain, where we quantified a higher level of human disturbance. In contrast, more related individuals were in colonies located in the marginal, less disturbed, agricultural area. Given the high philopatry of this species, our results are consistent with disruption of colony fidelity related to intensification of agricultural practices. We discuss the possible implications of long-term effects of genetic variability in small and disturbed colonies on fitness and population viability. [ABSTRACT FROM AUTHOR]

Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication., Competing Interests: Declaration of interests D.O. is an employee of QIAGEN GmbH. E.S.K. is an employee of BaseClear B.V., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. ( Fs ), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. Analysis of the prevalence and abundance of Fs in >20,000 human metagenomic samples shows that it is a low-prevalence member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche, and given its interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.

Amphibians are particularly sensitive to habitat loss and fragmentation caused by the intensification and modernization of farming occurring in the second half of the twentieth century in the Mediterranean basin. However, artificial water bodies, associated with traditional husbandry, proved to be important surrogate for amphibian feeding and reproduction. Here, multilocus genotypes were used to investigate the spatial population structure of Lissotriton vulgaris meridionalis and the role of drinking troughs in supporting viable breeding populations within a rural landscape interested by traditional husbandry and agriculture. Our genetic analysis highlighted the conservation value and the potential stepping-stone function of artificial aquatic sites in the dispersal of the species and for the gene flow maintenance. Indeed, populations of drinking troughs show allelic richness and heterozygosity levels comparable to those from natural ponds and there is no great evidence of genetic bottlenecks. A complex system of artificial aquatic sites and few natural wetlands was identified sustaining a well-structured network of demes highly interconnected with themselves and natural aquatic sites. The conservation of the identified genetic clusters may be useful to prevent further population declines and future loss of genetic diversity within the study area characterized by scarce natural wetlands that frequently dried because of agricultural practices and strong seasonality. Site-specific protection measures are needed to contrast the progressive disappearance of drinking troughs observed in the last years in Italy because of the abandonment of traditional farming practices in favour of modern agriculture and intensive farming., (© 2023. The Author(s).)

Background: Understanding which intrinsic and extrinsic factors dictate decision-making processes such as leaving the natal area or not (migratory vs resident strategy), departure time, and non-breeding destination are key-issues in movement ecology. This is particularly relevant for a partially migratory meta-population in which only some individuals migrate., Methods: We investigated these decision making-processes for 40 juvenile greater flamingos Phoenicopterus roseus fledged in three Mediterranean colonies and equipped with GPS-GSM devices., Results: Contrary to the body size and the dominance hypotheses, juveniles in better body condition were more likely to migrate than those in worse conditions, which opted for a residence strategy. Flamingo probability of departure was not associated with an increase in local wind intensity, but rather with the presence of tailwinds with departure limited to night-time mostly when the wind direction aligned with the migratory destination. Moreover, a positive interaction between tailwind speed and migration distance suggested that juveniles opted for stronger winds when initiating long-distance journeys. In contrast to previous studies, the prevailing seasonal winds were only partially aligned with the migratory destination, suggesting that other factors (e.g., adults experience in mix-aged flocks, availability of suitable foraging areas en route, density-dependence processes) may be responsible for the distribution observed at the end of the first migratory movement. We found potential evidence of sex-biased timing of migration with females departing on average 10 days later and flying ca. 10 km/h faster than males. Female flight speed, but not male one, was positively influenced by tailwinds, a pattern most likely explained by sexual differences in mechanical power requirements for flight (males being ca. 20% larger than females). Furthermore, juveniles considerably reduced their flight speeds after 400 km from departure, highlighting a physiological threshold, potentially linked to mortality risks when performing long-distance non-stop movements., Conclusion: These results suggest that not only intrinsic factors such as individual conditions and sex, but also extrinsic factors like weather, play critical roles in triggering migratory behaviour in a partially migratory metapopulation. Furthermore, social factors, including conspecific experience, should be taken into consideration when evaluating the adaptive processes underlying migration phenology, flight performance, and final destination selection., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Most cell type-specific genes are regulated by the interaction of enhancers with their promoters. The identification of enhancers is not trivial as enhancers are diverse in their characteristics and dynamic in their interaction partners. We present Esearch3D, a new method that exploits network theory approaches to identify active enhancers. Our work is based on the fact that enhancers act as a source of regulatory information to increase the rate of transcription of their target genes and that the flow of this information is mediated by the folding of chromatin in the three-dimensional (3D) nuclear space between the enhancer and the target gene promoter. Esearch3D reverse engineers this flow of information to calculate the likelihood of enhancer activity in intergenic regions by propagating the transcription levels of genes across 3D genome networks. Regions predicted to have high enhancer activity are shown to be enriched in annotations indicative of enhancer activity. These include: enhancer-associated histone marks, bidirectional CAGE-seq, STARR-seq, P300, RNA polymerase II and expression quantitative trait loci (eQTLs). Esearch3D leverages the relationship between chromatin architecture and transcription, allowing the prediction of active enhancers and an understanding of the complex underpinnings of regulatory networks. The method is available at: https://github.com/InfOmics/Esearch3D and https://doi.org/10.5281/zenodo.7737123., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Strigiformes are affected by a substantial decline mainly caused by habitat loss and destruction, poaching, and trapping. Moreover, the increasing trend in bird trade and the growing interest in wild-caught rather than captive-bred birds are expected to encourage illegal trade. The biomolecular investigation represents a valuable tool to track illegal trade and to explore the genetic variability to preserving biodiversity. Microsatellite loci (STRs) are the most used markers to study genetic variability. Despite the availability of species-specific microsatellite loci in Strigiformes, a unique panel permitting the description of the genetic variability across species has not been identified yet. We tested 32 highly polymorphic microsatellite markers to evaluate the reliability of a unique microsatellite panel in different species of Strigiformes and its use for conservation and forensic purposes. We included in the study 84 individuals belonging to 28 parental groups and 11 species of Strigiformes. After screening polymorphic microsatellite loci, the description of genetic variability, and the kinship assessment, we characterized a final panel of 12 microsatellite loci able to identify individuals in 9 Strigiformes species. This STR panel might support the authorities in the forensic investigation for suspected smugglers and false parental claims; moreover, it can be useful to evaluate relatedness among individuals in captive-bred populations and to implement research projects finalized to the description of the genetic variability in wild populations.

This study aimed to characterise the gut microbiome composition of European hares ( Lepus europaeus ) and its potential changes after a short-term diet modification. The high sensitivity of European hare to habitat changes makes this species a good model to analyse possible alterations in gut microbiome after the introduction of additional nourishment into the diet. In total, 20 pairs were chosen for the experiments; 10 pairs formed the control group and were fed with standard fodder. The other 10 pairs represented the experimental group, whose diet was integrated with apples and carrots. The DNA from fresh faecal pellets collected after 4 days from the start of the experiment was extracted and the V3-V4 hypervariable regions were amplified and sequenced using the Illumina MiSeq ® platform. The obtained amplicon sequence variants were classified into 735 bacterial genera belonging to 285 families and 36 phyla. The control and the experimental groups appeared to have a homogenous dispersion for the two taxonomic levels analysed with the most abundant phyla represented by Bacteroidetes and Firmicutes. No difference between control and experimental samples was detected, suggesting that the short-term variation in food availability did not alter the hares' gut microbiome. Further research is needed to estimate significant time threshold.

Columba livia is a wild bird whose domestication has led to a large number of pigeon breeds. The occasional loss or straying of domestic birds determined the origin of feral pigeons, which are now widespread all around the world. In this study, we assumed that the main contribution to feral populations is provided by domestic breeds reared in the same areas. We tested this hypothesis by analysing the variability of 12 microsatellite loci in nine Italian feral populations sampled in areas with different intensities of breeding and selecting domestic breeds. We included in the analysis samples belonging to ten domestic lineages commonly bred in Italy. The pattern of geographic differentiation of feral populations turned out to be rather complex and only partially explained by the geographic distance between populations. This pattern can be understood only when the domestic breeds were included in the analysis. In particular, feral populations located in regions with a long-lasting tradition of pigeon breeding showed a high level of admixture with domestic breeds, in particular with Racing Homer and Piacentino. Ferals from Bolzano, Venice and Sassari were characterized by unique genetic components, mostly not shared by other feral populations and by the considered domestic breeds. Our results further emphasize the complex genetic structure of feral populations whose origin can be properly investigated by taking into account the pool of domestic pigeons bred in the considered area., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes must thus be efficiently scalable and sensitive from closely related strains to divergent phyla. We present PhyloPhlAn 3.0, an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences. For individual clades of interest, it reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers. At the other extreme of resolution, it scales to large phylogenies comprising >17,000 microbial species. Examples including Staphylococcus aureus isolates, gut metagenomes, and meta-analyses demonstrate the ability of PhyloPhlAn 3.0 to support genomic and metagenomic analyses.

Habitat loss and fragmentation are threatening amphibians by increasing population isolation. However, artificial waterbodies created for livestockmay contrast this phenomenon by providing surrogate habitats for amphibians. Here, we performed a genetic study on an amphibian species, Lissotriton vulgaris meridionalis , in a rural area in central Italy where natural wetlands are disappearing and drinking troughs for cattle watering are widespread. Specifically, we tested a panel of microsatellite markers to identify a suitable tool for addressing conservation genetic issues of this species that is undergoing severe local decline. Twelve of the 20 tested loci produced reliable amplifications and were polymorphic. Three distinct units with a low level of gene flow were distinguished and the population genetic structuring overlapped with geographic distribution. Such loci will be useful to assess the genetic diversity of the species across multiscale levels for its management and conservation.

A paternity test was used to investigate a robbery case involving captive individuals of Greek tortoise (Testudo graeca). Six tortoises were allegedly stolen from a private breeder and offered for sale on the web by the supposed thief. The stolen tortoises were confiscated by the rangers of the State Forestry Corps (CFS). A panel of 14 autosomal microsatellite loci was used to genotype the seized tortoises and ten individuals assumed to be legally owned by the breeder. Kinship analyses reliably reconstructed the tortoise pedigree, demonstrating parent-offspring relationships among the owned and the stolen tortoises. As correctly declared by the breeder, four of the six stolen individuals belonged to the same family group of the ten legally owned tortoises. Results indicate that genetic identification procedures can provide valuable evidence and give useful support against illegal wildlife traffic., (Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.)