Simple SummaryPolar bears are native inhabitants of the Arctic ice. An increase in the ice-free season forces polar bears ashore and prompts them to invade human settlements and feed on human waste. Since their usual food objects (seals)differ extremely from human waste, the enforced diet shifts are considered to be stressful and may lead to intestinal dysbiosis and digestive disorders. To assess the resulting changes, we compared the gut bacterial community of bears feeding on their natural food and bears visiting the human waste dump. To our knowledge this is the first investigation of the fugal community in polar bears’ intestines. It turned out that feeding at the dump does not facilitate the development of dysbiosis in polar bears, but, on the contrary, leads to the formation of an adaptive microbial community similar to that of omnivorous animals. This is also confirmed by the high fat reserves in the animals attending the dump, which increases their chances of surviving the starvation period. However, in the structure of the fungal community, facultative pathogenic yeast species appear, which are theoretically capable of provoking various infections. Moreover, polar bears that do not visit human settlements do not harbor a specific fungal community.AbstractClimate changes cause a dramatical increase in the ice-free season in the Arctic, forcing polar bears ashore, closer to human settlements associated with new and non-natural food objects. Such a diet may crucially transform the intestinal microbiome and metabolism of polar bears. The aim of this study was to characterize changes in the gut bacterial and fungal communities resulting from the transition to anthropogenic food objects by the means of 16S and ITS metabarcoding. Thus, rectal samples from 16 wild polar bears from the Kara–Barents subpopulation were studied. Human waste consuming resulted in a significant increase in the relative abundance of fermentative bacteria (Lactobacillaceae, Leuconostocaceae, and Streptococcaceae) and a decrease in proteolytic Enterobacteriaceae. However, the alpha-diversity parameters remained similar. Also, for the first time, the composition of the fungal community of the polar bear intestine was determined. Diet change is associated with the displacement of eurybiontic fungi (Thelebolus,Dipodascus,Candida(sake), andGeotrichum) by opportunisticCandida (tropicalis),Kazachstania, andTrichosporon. Feeding on human waste does not cause any signs of dysbiosis and probably leads to adaptive changes in the bacterial microbiome. However, the emergence of fungal facultative pathogens increases the risk of infections.