The Spermophilus dauricus, the wild Daurian ground squirrel, is known to exhibit seasonal breeding behavior. Although the importance of gut microbiota in animal digestion, metabolism, and immunity is well-established, the correlation between gut microbiota and seasonal breeding in this species remains inadequately explored. In the present study, using metagenomic sequencing technology, the compositions and functions of the gut microbiota of wild Daurian ground squirrels in different breeding seasons were explored. The dominant gut microbial phyla were Firmicutes and Bacteroidetes. The Firmicutes were predominant in the breeding season, whereas Bacteroidetes were predominant in the non-breeding season. At the genus level, Lactobacillus accumulated during the breeding season, whereas Odoribacter and Alistipes increased during the non-breeding season. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genome) annotations indicated that genes in gut samples were highly associated with metabolic functions. The differential expression gene analysis showed that genes related to the phosphotransferase system, cysteine, and methionine metabolism were highly expressed during the breeding season, whereas the non-breeding season upregulated genes were enriched in starch and sucrose metabolism and bacterial chemotaxis pathways. In conclusion, this study could provide a reference for investigating gut microbiota in seasonal breeding animals and offer new insight into gut microbial function.

The gut microbiota plays a crucial role in the nutrition, metabolism, and immune function of the host animal. The muskrat (Ondatra zibethicus) is a typical seasonal breeding animal. The present study performed a metagenomic analysis of cecum contents from muskrats in the breeding and non-breeding seasons. The results indicated that the breeding muskrats and non-breeding muskrats differed in gut microbiota structure and function. During the breeding season, the relative abundance of phylum Bacteroidetes, genus Prevotella, and genus Alistipes increased, while the relative abundance of phylum Firmicutes and phylum Actinobacteria decreased. The muskrat gut microbiota was enriched in the metabolism-related pathways, especially amino acid and vitamin metabolism, and genetically related metabolites in the breeding season. We presumed that the muskrat gut microbiota might seasonally change to secure reproductive activity and satisfy the metabolic demands of different seasons. This study could explore potential mechanisms by which gut microbiota affects reproduction. Moreover, this study may provide a new theoretical basis for the management of muskrat captive breeding.

Hibernating mammals confront seasonal and harsh environmental shifts, prompting a cycle of pre-hibernation feeding and subsequent winter fasting. These adaptive practices induce diverse physiological adjustments within the animal’s body. With the gut microbiota’s metabolic activity being heavily reliant on the host’s diet, this cycle’s primary impact is on this microbial community. When the structure and composition of the gut microbiota changes, corresponding alterations in the interactions occur between these microorganisms and their host. These successive adaptations significantly contribute to the host’s capacity to sustain relatively stable metabolic and immune functions in severe environmental conditions. A thorough investigation into the reciprocal interplay between the host and gut microbiota during hibernation-induced adaptive changes holds promise for unveiling new insights. Understanding the underlying mechanisms driving these interactions may potentially unlock innovative approaches to address extreme pathological conditions in humans.

The Sox (SRY-related high-mobility group box) gene family encodes transcription factors characterized by a conserved high-mobility group (HMG) box DNA-binding domain and plays essential roles in metazoan development, including sex determination, embryogenesis, neurogenesis, organogenesis, and reproductive regulation. Seasonal breeders provide valuable models for investigating reproductive regulation. The Daurian ground squirrel (Spermophilus dauricus) is a typical species for studying seasonal reproductive adaptation. In this study, Sox genes were identified at the genome-wide level in the Daurian ground squirrel. A total of 11 genes were identified and classified into 5 subfamilies, SoxC (SdSox4, SdSox11), SoxD (SdSox5, SdSox6, SdSox13), SoxE (SdSox8, SdSox9, SdSox10), SoxF (SdSox17, SdSox18), SoxG (SdSox15). Structural and evolutionary analyses revealed conserved HMG domains along with diversification among subfamilies. The genetic homology of the Sox family between the Daurian ground squirrel and the Thirteen-lined ground squirrel (Ictidomys tridecemlineatus) was discovered through collinearity analysis. Furthermore, hematoxylin and eosin (HE) staining revealed seasonal morphological changes in the testes of the adult Daurian ground squirrel. The seasonal expression patterns of 7 reproduction-related Sox genes were analyzed in testicular tissues. All analyzed genes exhibited significantly higher expression levels in the breeding season than the non-breeding season. Notably, SdSox5, SdSox6, SdSox8, and SdSox13 showed pronounced seasonal differences in expression by the real-time quantitative polymerase chain reaction (RT-qPCR). This study provides new insights into the evolutionary characteristics and potential roles of Sox genes in seasonal reproductive regulation in mammals.

Hibernation is one of the most striking survival strategies in animals, a state in which metabolism drops to levels that would ordinarily threaten viability while tissues remain unexpectedly stable. Although the research to date has described many relevant molecular and physiological features of significance, most studies have examined these layers in isolation, which has limited our ability to understand how the process unfolds across time and across biological scales. In this review, we trace the historical trajectory of hibernation research and examine hibernation across complementary omics dimensions, introducing Hibernomics as a research framework that studies the phenomenon of hibernation through the dynamic integration of multi-omic technologies and approaches. This perspective allows hibernation to be viewed not as a collection of independent traits but as a coordinated and highly structured adaptation, shaped by its temporal rhythm. When examined through this lens, three interlinked core research threads emerge: energy metabolism, focusing on hypothermic metabolic reprogramming from genome to metabolites; neuroendocrine-immune regulation, centered on integrating environmental cues, endocrine signaling and immune remodeling to coordinate systemic physiological transitions; and cold tolerance, concentrating on the preservation of tissue integrity and functional resilience during prolonged hypothermia and rewarming. These themes appear across species even though individual mechanisms vary, which suggests that evolution has assembled different workable solutions to the same physiological challenge. Important gaps remain, including the difficulty of harmonizing heterogeneous datasets, incomplete grasp of the neural events that initiate hibernation, the technical obstacles in terms of resolution, dynamics, and different species, the wide translational gap from animal models to human application, and certain enduring enigmas of basic physiology and evolution. Advances in high-resolution technologies such as single-cell and spatial omics coupled with strategies for dynamic sampling and monitoring, are beginning to address these challenges, which are further being empowered by novel experimental platforms such as organoids and organs-on-chips, targeted perturbation tools, and computational methods capable of inferring or proving causal relationships. Together, these developments position Hibernomics to move from descriptive synthesis towards a predictive, mechanism-oriented framework, one that may eventually guide innovations in organ preservation, metabolic medicine, trauma care and the management of long-duration spaceflight towards transformative applications.