Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization.

The fungal gut microbiota (mycobiota) has been implicated in diseases that disturb gut homeostasis, such as inflammatory bowel disease. However, little is known about functional relationships between bacteria and fungi in the gut during infectious colitis. Here we investigated the role of fungal metabolites during infection with the intestinal pathogen Salmonella enterica serovar Typhimurium, a major cause of gastroenteritis worldwide. We found that, in the gut lumen, both the mycobiota and fungi present in the diet can be a source of siderophores, small molecules that scavenge iron from the host. The ability to use fungal siderophores, such as ferrichrome and coprogen, conferred a competitive growth advantage to Salmonella strains expressing the fungal siderophore receptors FhuA or FhuE in vitro and in a mouse model. Our study highlights the role of inter-kingdom cross-feeding between fungi and Salmonella and elucidates an additional function of the gut mycobiota, revealing the importance of these understudied members of the gut ecosystem during bacterial infection.

Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut.

Zinc is an essential cofactor for bacterial metabolism, and many Enterobacteriaceae express the zinc transporters ZnuABC and ZupT to acquire this metal in the host. However, the probiotic bacterium Escherichia coli Nissle 1917 (or "Nissle") exhibits appreciable growth in zinc-limited media even when these transporters are deleted. Here, we show that Nissle utilizes the siderophore yersiniabactin as a zincophore, enabling Nissle to grow in zinc-limited media, to tolerate calprotectin-mediated zinc sequestration, and to thrive in the inflamed gut. We also show that yersiniabactin's affinity for iron or zinc changes in a pH-dependent manner, with increased relative zinc binding as the pH increases. Thus, our results indicate that siderophore metal affinity can be influenced by the local environment and reveal a mechanism of zinc acquisition available to commensal and pathogenic Enterobacteriaceae.

The canine skin and ear microbiome: A comprehensive survey of pathogens implicated in canine skin and ear infections using a novel next-generation-sequencing-based assay.

This study analyzed the complex bacterial and fungal microbiota of healthy and clinically affected canine ear and skin samples. A total of 589 canine samples were included: 257 ear swab samples (128 healthy vs. 129 clinically affected) and 332 skin swab samples (172 healthy vs. 160 clinically affected) were analyzed using next-generation sequencing (NGS) to determine both relative and absolute abundances of bacteria and fungi present in the samples. This study highlighted the canine microbiota of clinically affected cases was characterized by an overall loss of microbial diversity, high microbial biomass, with overgrowth of certain members of the microbiota. The observed phenotype of these samples was best described by the combination of both relative and absolute microbial abundances. Compared to healthy samples, 78.3% of the clinically affected ear samples had microbial overgrowth; 69.8% bacterial overgrowth, 16.3% fungal overgrowth, and 7.0% had both bacterial and fungal overgrowth. The most important microbial taxa enriched in clinically affected ears were Malassezia pachydermatis, Staphylococcus pseudintermedius, Staphylococcus schleiferi, and a few anaerobic bacteria such as Finegoldia magna, Peptostreptococcus canis, and Porphyromonas cangingivalis. The anaerobic microbes identified here were previously not commonly recognized as pathogens in canine ear infections. Similar observations were found for skin samples, but yeasts and anaerobes were less abundant when compared to clinically affected cases. Results highlighted herein, signify the potential of NGS-based methods for the accurate quantification and identification of bacterial and fungal populations in diagnosing canine skin and ear infections, and highlight the limitations of traditional culture-based testing.