Generalist species able to exploit anthropogenic food sources are becoming increasingly common in urban environments. Coyotes (Canis latrans) are one such urban generalist that now resides in cities across North America, where diseased or unhealthy coyotes are frequently reported in cases of human-wildlife conflict. Coyote health and fitness may be related to habitat use and diet via the gut microbiome, which has far-reaching effects on animal nutrition and physiology. In this study, we used stomach contents, stable isotope analysis, 16S rRNA gene amplicon sequencing, and measures of body condition to identify relationships among habitat use, diet, fecal microbiome composition, and health in urban and rural coyotes. Three distinct relationships emerged: (1) Urban coyotes consumed more anthropogenic food, which was associated with increased microbiome diversity, higher abundances of Streptococcus and Enterococcus, and poorer average body condition. (2) Conversely, rural coyotes harbored microbiomes rich in Fusobacteria, Sutterella, and Anaerobiospirillum, which were associated with protein-rich diets and improved body condition. (3) Diets rich in anthropogenic food were associated with increased abundances of Erysipelotrichiaceae, Lachnospiraceae, and Coriobacteriaceae, which correlated with larger spleens in urban coyotes. Urban coyotes also had an increased prevalence of the zoonotic parasite Echinococcus multilocularis, but there were no detectable connections between parasite infection and microbiome composition. Our results demonstrate how the consumption of carbohydrate-rich anthropogenic food by urban coyotes alters the microbiome to negatively affect body condition, with potential relationships to parasite susceptibility and conflict-prone behavior.

Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.

In cities throughout North America, sightings of coyotes (Canis latrans) have become common. Reports of human-coyote conflict are also rising, as is the public demand for proactive management to prevent negative human-coyote interactions. Effective and proactive management can be informed by the direct observations of community members, who can report their interactions with coyotes and describe the location, time, and context that led to their interactions. To assess the predictors of human-coyote conflict, we used a web-based reporting system to collect 9,134 community-supplied reports of coyotes in Edmonton, Canada, between January 2012 and December 2021. We used a standardized ordinal ranking system to score each report on two indicators of human-coyote conflict: coyote boldness, based on the reported coyote behaviour, and human perceptions about coyotes, determined from the emotions expressed by reporters. We assigned greater conflict scores to behaviours where coyotes followed, approached, charged or contacted pets or people, and to perceptions where reporters expressed fear, worry, concern, discomfort or alarm. Using ordered logistic regression and chi-square tests, we compared conflict scores for each response variable to spatial, temporal and contextual covariates. Our analysis showed that coyotes were bolder in less developed open areas and during the pup rearing season, but human perceptions were most negative in residential areas and during the dispersal season. Reports that mentioned dogs or cats were more likely to describe bolder coyote behaviour, and those that mentioned pets or children had more negative perceptions about coyotes. Coyote boldness and human perceptions both indicated rising human-coyote conflict in Edmonton over the 10 years of reporting.