Associations of the gut mycobiome and its cross-kingdom interactions with estrus return in post-weaning sows revealed by metagenomic analysis.

Post-weaning estrus return is a critical determinant of reproductive efficiency in the swine industry. While the gut microbiome, particularly bacteria, has been significantly associated with estrus return in sows, the role of the gut mycobiome and its cross-kingdom interactions with bacteria in this context remains largely unexplored. Here, we employed fecal metagenomics to characterize the gut mycobiome in 85 sows and investigated its association with post-weaning estrus return. A total of 22 fungal species were significantly associated with estrus return. Normal-return sows were characterized by increased abundance of Arxiozyma slooffiae (formerly Kazachstania slooffiae) and decreased abundances of Malassezia pachydermatis and Alternaria rosae. Moreover, we uncovered cross-kingdom interactions between fungi and bacteria associated with estrus return, where Arxiozyma slooffiae showed a positive correlation with Prevotella spp. enriched in normal-return sows. These interactions were predicted to involve the exchange of metabolites, including Fe2+, thiamine, and nicotinate. Fungal biomarkers demonstrated good discriminatory power for distinguishing normal-return and non-return sows (AUC = 0.906), and the combination with bacterial biomarkers further enhanced the performance (AUC = 0.947). Integrated multi-omics analysis revealed extensive associations between gut fungi and hormones and hormone-related compounds, as well as microbial functional pathways. Notably, Arxiozyma slooffiae was positively correlated with phytoestrogens (including daidzein and genistein) and the steroid hormone biosynthesis pathway but negatively correlated with testosterone. Collectively, these findings provide comprehensive insights into the role of the gut mycobiome and its cross-kingdom interactions in sow reproductive performance.