Shien Ren

Several rodent species are considered global pests owing to their broad dietary habits, with stable gut microbiota enterotypes playing a vital role in host digestion. This study examined the Gansu zokor, a subterranean pest rodent endemic to the Loess Plateau. By extensive sampling across seasons and habitats, we characterized the gut microbiota enterotypes and clarified the mechanisms underlying their adaptation to diverse dietary resources. The gut microbiota of the Gansu zokor was categorized into two distinct enterotypes (E1 and E2), whose distribution varied markedly by season and habitat. The α and β diversity differed notably between the two enterotypes. Although Bacillota (formerly Firmicutes) and Bacteroidota dominated both enterotypes, the Bacillota/Bacteroidota ratio was markedly higher in E2, and this higher ratio was correlated with greater host body weight and BMI. Probiotic biomarkers such as Muribaculum and Alistipes were enriched in E1, whereas E2 was enriched in the Lachnospiraceae NK4A136 group , Butyribacter , and Roseburia . Potential pathogens such as Bordetella , Acinetobacter , and Desulfovibrio also serve as key biomarkers. E1 was enriched with genes involved in lipid metabolism, transport, and catabolism, while E2 was characterized by genes related to terpenoid and polyketide metabolism. Co‐occurrence networks revealed more interconnected interactions in E1, but higher modularity in E2. Stochastic processes (e.g., drift) governed microbial assembly in E1, whereas deterministic processes (e.g., homogeneous selection) dominated in E2. Enterotype stratification was closely correlated with host body size parameters and microbial α diversity. Research identifies two distinct enterotypes of zokors, clarifying their traits and links to food resource utilization. These findings illuminate the ecological adaptations of subterranean rodents and offer a theoretical basis for developing microbe‐based pest control strategies.

Diet significantly influences gut microbiota composition. Grazing activities alter local vegetation communities, which in turn are related to changes in the availability of food resources for wildlife. However, the relationships between grazing and the dietary diversity and gut microbiota in subterranean rodents remain poorly understood. Using the plateau zokor ( Eospalax baileyi ) as a model species, chloroplast trnL and 16S rRNA gene sequencing were employed to characterize dietary composition and gastrointestinal microbial communities in zokors from grazing and non‐grazing (control) areas. The analysis revealed significant differences in dietary diversity and composition of zokors between grazing and non‐grazing areas. Meanwhile, the gastrointestinal microbial community diversity differed significantly between groups. Beneficial microbes (e.g., Lachnospiraceae and Christensenellaceae) showed higher abundance in the control group, while pathogenic Proteobacteria were enriched in the grazing groups. Notably, the complexity of stomach microbial co‐occurrence networks increased in the grazing group, and functional differentiation of the gastrointestinal microbiota was observed between the control and grazing groups. Community assembly analysis displayed that stochastic processes dominated the assembly of stomach and gut microbiota, though these processes diminished in the grazing group, where divergent ecological processes emerged. Furthermore, we identified robust associations between zokor diets and stomach/gut microbiota, with specific microbial taxa significantly correlated with particular plants. Collectively, these findings highlight that grazing is associated with dietary changes and gut microbiota shifts in subterranean rodents, thereby advancing our understanding of the ecological impacts of grazing on terrestrial ecosystems.

Dietary fiber (DF) is an important nutrient component in pig’s diet that remarkably influences their growth and slaughter performance. The ability of pigs to digest DF depends on the microbial composition of the intestinal tract, particularly in the hindgut. However, studies on how DF alters the growth and slaughter performance of pigs by shaping the gut microbial composition and metabolites are still limited. Therefore, this study aimed to investigate the effects of DF on microbial composition, functions, and metabolites, ultimately altering host growth and slaughter performance using Durco × Bamei crossbred pigs supplemented with 0%, 10%, 17%, and 24% broad bean silage in the basic diet. We found that the final weight, average daily gain, fat, and lean meat weight significantly decreased with increasing DF. Pigs with the lowest slaughter rate and fat weight were observed in the 24% fiber-supplemented group. Gut microbial communities with the highest alpha diversity were formed in the 17% fiber group. The relative abundance of fiber-degrading bacteria, bile acid, and succinate-producing bacteria, including Prevotella sp., Bacteroides sp., Ruminococcus sp., and Parabacteroides sp., and functional pathways, including the butanoate metabolism and the tricarboxylic acid [TCA] cycle, significantly increased in the high-fiber groups. The concentrations of several bile acids significantly decreased in the fiber-supplemented groups, whereas the concentrations of succinate and long-chain fatty acids increased. Our results indicate that a high-fiber diet may alter the growth and slaughter performance of Durco × Bamei crossbred pigs by modulating the composition of Prevotella sp., Bacteroides sp., Ruminococcus sp., Parabacteroides sp., and metabolite pathways of bile acids and succinate.

Captivity is an important and efficient technique for rescuing endangered species. However, it induces infertility, and the underlying mechanism remains obscure. This study used the plateau pika (Ochotona curzoniae) as a model to integrate physiological, metagenomic, metabolomic, and transcriptome analyses and explore whether dysbiosis of the gut microbiota induced by artificial food exacerbates infertility in captive wild animals. Results revealed that captivity significantly decreased testosterone levels and the testicle weight/body weight ratio. RNA sequencing revealed abnormal gene expression profiles in the testicles of captive animals. The microbial α-diversity and Firmicutes/Bacteroidetes ratio were drastically decreased in the captivity group. Bacteroidetes and Muribaculaceae abundance notably increased in captive pikas. Metagenomic analysis revealed that the alteration of flora increased the capacity for carbohydrate degradation in captivity. The levels of microbe metabolites’ short-chain fatty acids (SCFAs) were significantly high in the captive group. Increasing SCFAs influenced the immune response of captivity plateau pikas; pro-inflammatory cytokines were upregulated in captivity. The inflammation ultimately contributed to male infertility. In addition, a positive correlation was observed between Gastranaerophilales family abundance and testosterone concentration. Our results provide evidence for the interactions between artificial food, the gut microbiota, and male infertility in pikas and benefit the application of gut microbiota interference in threatened and endangered species.

The browning of white adipose tissue (WAT) is a promising area of research for treating metabolic disorders and obesity in the future. However, studies on plant secondary compounds promoting WAT browning are limited. Herein, we explored the effects of swainsonine (SW) on gut microbiota and WAT browning in captive pikas. SW inhibited body mass gain, increased brown adipose tissue (BAT) mass, and induced WAT browning in pikas. The 16S rDNA sequencing revealed a significant reduction in the alpha diversity and altered community structure of the gut microbiota in captive pikas. However, the addition of SW to the diet significantly increased the alpha diversity of gut microbiota and the relative abundance of Akkermansia, Prevotella, and unclassified_f__Lachnospiraceae, along with the complexity of the microbial co-occurrence network structure, which decreased in the guts of captive pikas. Functional profiles showed that SW significantly decreased the relative abundances of energy metabolism, lipid metabolism, and glycan biosynthesis and metabolism, which were enriched in captive pikas. Furthermore, SW decreased deterministic processes of gut microbiota assembly in July and increased them in November. Finally, the genera Prevotella and unclassified_f__Prevotellaceae were positively correlated with BAT mass. Our results highlighted that plant secondary compounds promote WAT browning by modulating the gut microbiota in small mammals.

Although fungi occupy only a small proportion of the microbial community in the intestinal tract of mammals, they play important roles in host fat accumulation, nutrition metabolism, metabolic health, and immune development. Here, we investigated the dynamics and assembly of gut fungal communities in plateau pikas inhabiting six altitudinal gradients across warm and cold seasons. We found that the relative abundances of Podospora and Sporormiella significantly decreased with altitudinal gradients in the warm season, whereas the relative abundance of Sarocladium significantly increased. Alpha diversity significantly decreased with increasing altitudinal gradient in the warm and cold seasons. Distance-decay analysis showed that fungal community similarities were significantly and negatively correlated with elevation. The co-occurrence network complexity significantly decreased along the altitudinal gradients as the total number of nodes, number of edges, and degree of nodes significantly decreased. Both the null and neutral model analyses showed that stochastic or neutral processes dominated the gut fungal community assembly in both seasons and that ecological drift was the main ecological process explaining the variation in the gut fungal community across different plateau pikas. Homogeneous selection played a weak role in structuring gut fungal community assembly during the warm season. Collectively, these results expand our understanding of the distribution patterns of gut fungal communities and elucidate the mechanisms that maintain fungal diversity in the gut ecosystems of small mammals.

Plants produce various plant secondary compounds (PSCs) to deter the foraging of herbivorous mammals. However, little is known about whether PSCs can reshape gut microbiota and promote gut homeostasis of hosts. Using 16S rDNA sequencing to investigate the effects of PSCs on the gut microbiota of small herbivorous mammals, we studied plateau pikas (Ochotona curzoniae) fed diets containing swainsonine (SW) extracted from Oxytropis ochrocephala. Our results showed that both long- and short-term treatment of a single artificial diet in the laboratory significantly reduced alpha diversity and significantly affected beta diversity, core bacteria abundance, and bacterial functions in pikas. After SW was added to the artificial diet, the alpha diversity significantly increased in the long-term treatment, and core bacteria (e.g., Akkermansiaceae) with altered relative abundances in the two treatments showed no significant difference compared with pikas in the wild. The complexity of the co-occurrence network structure was reduced in the artificial diet, but it increased after SW was added in both treatments. Further, the abundances of bacteria related to altered alanine, aspartate, and glutamate metabolism in the artificial diet were restored in response to SW. SW further decreased the concentration of short-chain fatty acids (SCFAs) in both treatments. Our results suggest that PSCs play a key role in regulating gut microbiota community and intestinal homeostasis, thereby maintaining host health. Key points: • Swainsonine improves the intestinal bacterial diversity of plateau pikas. • Swainsonine promotes the recovery of core bacterial abundances in the gut of plateau pikas. • Swainsonine promotes the restoration of intestinal bacterial functions of plateau pikas.