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30 September 2026, Volume 46 Issue 5

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REVIEWS

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Research progress and prospect on gut microbiome in Musteloidea

YUAN Ziyu, LIU Yixin, HU Yibo

2026, 46(5):  621-637.  DOI: 10.16829/j.slxb.151183

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Musteloidea is a taxonomically and morphologically diverse group within Carnivora, with marked variation in ecological adaptations. This superfamily includes the carnivorous Mustelidae, the mainly omnivorous Procyonidae and Mephitidae, and the strictly herbivorous Ailuridae. The wide variation in diet and habitat among these animals makes them a valuable system for investigating the relationships between host-associated factors and gut microbiome structure and function. Although studies using 16S rRNA sequencing, metagenomics, and multi-omics methods have become more common in recent years, research focusing specifically on the gut microbiome of Musteloidea is still rare and not yet systematic. This review summarizes recent progresses in this field by integrating and contrasting existing findings on gut microbiome composition and function across the four families (Mustelidae, Procyonidae, Mephitidae, and Ailuridae) in relation to their dietary adaptations, which provides a foundation for future research.

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Advances in bat gut microbiota research

HUANG Xinlei, LANG wei, FENG Jiang, LIU Boyu

2026, 46(5):  638-649.  DOI: 10.16829/j.slxb.151100

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Bats (Chiroptera) are one of the most species-diverse groups of mammals, boasting a wide variety of species and a broad geographic distribution. They not only exhibit diverse feeding habits but also possess a unique immune system and relatively long lifespans, which have led them to develop distinctive adaptive mechanisms over the course of evolution. Although bats serve as natural hosts for various pathogens, they seldom display clinical symptoms—a phenomenon that may indicate a high tolerance to these pathogens or unique immunoregulatory strategies. The composition and function of bat gut microbiota are influenced by multiple factors, including feeding habits, habitat, and seasonal variations, thereby exhibiting a certain degree of uniqueness. This review systematically summarizes the compositional characteristics of bat gut microbiota, explores its association with the host’s feeding habits, and analyzes the impact of the microbial community on host health, with the aim of providing a reference for research on bat gut microbiota.

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Cross-scale physiological and ecological effects of gut microbiota in small mammals under food restriction

ZHANG Tianxin, ZHU Wanlong

2026, 46(5):  650-669.  DOI: 10.16829/j.slxb.151139

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Food restriction (FR) is a key environmental stress influencing animal adaptive strategies, and its interaction mechanisms with gut microbiota have become a research hotspot in recent years. The gut microbiota, the host’s‘second genome’, is essential for assisting small mammals in adjusting to dietary limitations. The advantages benefits of using small mammals as research models for gut microbiome studies are explored in this paper. Subsequently, we examine the differential effects of various FR regimens on host gut microbiomes, including complete fasting, partial fasting, and nutritional restriction. We emphasize how FR mediates host physiological adaptation by reshaping microbial community structure, altering metabolic functions, and influencing microbe-host interactions. This paper integrates the multi-scale physiological and ecological effects of FR mediated by gut microbiota. At the individual level, it regulates energy balance, immune homeostasis, and cognitive behavior; and at the population level, it influences reproductive development and population dynamics. Further exploration should concentrate on understanding the molecular underpinnings of microbiome plasticity, clarifying the implications of intergenerational transmission, and expanding the application of these discoveries in wildlife management and conservation. The‘FR-gut microbiota-host phenotype-population dynamics’ framework established in this paper provides a new perspective for deepening our understanding of the physiological basis of animal adaptation to the environment.

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Proposed operational framework for fecal microbiota transplantation in wildlife: from theoretical foundation to conservation applications

SHEN Wenjing, ZHANG Xin, GAO Peng, WEN Jing, BO Tingbei

2026, 46(5):  670-687.  DOI: 10.16829/j.slxb.151213

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Fecal microbiota transplantation (FMT) can restore intestinal microbiota of wildlife and improve reintroduction success, but standardized protocols are still lacking in this field. Combined with microbial ecology theories and published FMT cases, this paper established an operational framework for wildlife conservation from three aspects: selection of donors, technical implementation, and effectiveness evaluation. Current practices are hindered by inadequate safety screening, non-standard techniques, and insufficient long-term monitoring. Potential risks including antibiotic resistance genes, opportunistic pathogens, and anthropogenic microbiota transmission should be fully considered. The proposed framework clarifies hierarchical operation rules and ethical principles, providing references for wildlife rescue, captive management, and reintroduction. Further long-term field verifications across more species are required to promote the transformation of FMT from preliminary exploration to scientific application based on ecological principles.

ORIGINAL PAPERS

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Effects of habitat type and seasonal changes on the gut microbiota of Brandt’s voles

ZHANG Zewei, WANG Siyu, LI Guoliang

2026, 46(5):  688-704.  DOI: 10.16829/j.slxb.151207

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The gut microbiota plays a crucial role in host physiological function and ecological adaptation. Investigating the impact of different habitat types and seasonal changes on its structure is of significant scientific importance for revealing the host-microbe interaction mechanism. This study collected fecal samples from Brandt’s voles (Lasiopodomys brandtii) under summer field, winter field, and summer indoor conditions, and analyzed the composition, co-occurrence network, assembly mechanism, and predicted metabolic function of the gut microbiota based on 16S rRNA gene amplicon sequencing. The results showed that both seasonal changes and habitat type significantly shaped the gut microbiota of Brandt’s voles, with seasonal factors having a more pronounced effect. In terms of habitat comparison, wild summer individuals, due to highly heterogeneous food intake and complex environmental stimuli, exhibited significantly higher alpha diversity and co-occurrence network complexity of gut microbiota than indoor summer individuals. Their community assembly was primarily driven by deterministic processes (homogeneous selection accounted for 77. 8%), while indoor individuals, living in a constant environment for extended periods, showed a looser network structure, with assembly patterns shifting towards stochastic processes (71. 1%). In terms of seasonal comparison, winter wild individuals showed the lowest microbial diversity, with a dramatic restructuring of the core microbial community. The relative abundance of Bacillota and other phyla decreased significantly, while Bacteroidota (mainly the family Muribaculaceae) experienced an explosive increase, leading to a significant decrease in the Bacillota/Bacteroidota ratio. Although the microbial network shrank in winter, its local aggregation (clustering coefficient) and the importance of key nodes increased significantly, intensifying antagonistic competition. Furthermore, community assembly mechanism analysis revealed that environmental directional selection pressure weakened from summer to winter, while the relative contribution of stochastic processes such as ecological drift increased. Functional predictions indicate that extreme winter cold and food scarcity broadly inhibited the basal metabolism and tricarboxylic acid cycle of the gut microbiota, while activating specific degradation pathways, such as D-arabinose and glycolic acid metabolism, to maintain host energy homeostasis. Furthermore, the outdoor environment, compared to indoor conditions, induced metabolic potential in the gut microbiota for cellular defense and multinutrient utilization, including cell membrane or wall synthesis and specific amino acid degradation. This study systematically reveals the structural reorganization and simultaneous functional remodeling of the gut microbiota of Brandt’s voles under extreme resource and environmental stress, providing important evidence for a deeper understanding of the ecological adaptation strategies of wild animals and host-microbe interactions.

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The role of gut microbiota differences in the coexistence of norway rats (Rattus norvegicus) and Asian house rats (Rattus tanezumi) in Hainan

GAO Xiaolong, ZHANG Wanxiang, ZHAI Hongjuan, ZHU Hanyi, ZHANG Zhibin

2026, 46(5):  705-719.  DOI: 10.16829/j.slxb.151156

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The norway rat (Rattus norvegicus) and the Asian house rat (Rattus tanezumi) are closely related species inhabiting the tropical region of Hainan. Microhabitat segregation is considered an important mechanism for their coexistence. The gut microbiota plays a crucial role in regulating host physiological functions and in adaptation to environmental changes. Therefore, comparing the differences in gut microbial composition and functions between the two closely related species in the same habitat is conducive to elucidating their coexistence mechanisms from a physiological perspective. To accurately identify species, this study combined morphological indicators and the COI gene DNA barcoding to distinguish two rodent species. The gut microbial community structure and its functional characteristics were analyzed using high-throughput sequencing of 16S rDNA was used to analyze the gut microbial community structure and functional characteristics of the two rat species. The results showed that among 34 rats identified by COI gene sequencing, 27 were R. norvegicus and 7 R. tanezumi. Significant differences were observed in alpha diversity (Shannon index) and beta diversity of gut microbiota between the two species, while no significant differences were found between individuals of different sexes within the same species. Differences in the composition of gut microbiota at the phylum, family, and genus levels, as well as functional predictions, revealed unique ecological adaptations of each species. Specifically, R. norvegicus exhibited higher abundances of Pseudomonadota, Lactobacillaceae, and Lactobacillus, reflecting an omnivorous tendency. In contrast, the ratio of Bacillota to Bacteroidota in the R. tanezumi was higher, and the abundance of fiber-degrading bacteria, such as Muribaculaceae and Lachnospiraceae, also increased. Additionally, the carbon metabolism and biosynthesis of amino acids pathways were enriched in R. tanezumi, indicating a stronger herbivorous tendency. This study demonstrates that there is a significant difference in the structure and function of gut microbiota between R. norvegicus and R. tanezumi, suggesting divergences in their dietary preferences and ecological adaptation strategies. This study proposes that differences in intestinal microbiota, together with the synergistic effects of microhabitat segregation, reduce interspecific competition and promote sympatric coexistence, thereby providing a new perspective for understanding the coexistence mechanisms of closely related rodent species in tropical regions.

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The effect of food preference on energy metabolism and gut microbiota in lactating striped hamsters

DU Yajie, ZHAO Zhen, ZHANG Kaiyuan, CAO Jing, ZHAO Zhijun

2026, 46(5):  720-733.  DOI: 10.16829/j.slxb.151095

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Food diversity and seasonal variation in food quality are key environmental challenges for wild small mammals. Lactation represents one of the most energy-demanding life-history stages, during which dietary preferences are critical for meeting maternal energy needs and ensuring reproductive success. Using energy budget analysis and 16S rRNA gene sequencing, we examined the impacts of high-protein, high-fat, and high-fiber diets during lactation on energy intake, reproductive output, and gut microbiota in striped hamsters (Cricetulus barabensis). The hamsters showed a significant preference for high-fat food, which accounted for 59. 8% of total intake in the non-reproductive period and rose to 78. 1% during lactation. In contrast, control, high-protein, and high-fiber foods comprised only 8. 4%, 3. 3%, and 10. 1% of intake, respectively. Lactating females exhibited significantly increased food intake and resting metabolic rate compared to the non-reproductive period. However, their maximum intake of each food type did not exceed that of the control group. Females on high-protein or high-fiber diets showed significantly lower lactation output and offspring body weights than those in the control and high-fat groups. Digestive system weight increased significantly during lactation. In the high-fiber group, both large intestine and cecum weights were significantly higher than in other groups. At the phylum level, Firmicutes and Bacteroidetes dominated the gut microbiota. Compared to the control group, the highprotein group had decreased Firmicutes and increased Bacteroidetes abundance. The alpha diversity (ASVs number, Chao1 index and Shannon index) was significantly decreased in the hamsters fed with high-fiber and high-protein diet, while it was not significantly changed in the hamsters fed with high-fat food diet and those fed with various types of food. These findings suggest that lactating striped hamsters exhibit strong dietary preferences. The higher specific dynamic action of high-protein food may explain their lower intake. Digestive system plasticity may also reach a limit, constraining dietary choices. The hamsters that were fed a high-fiber and high-protein diets failed to meet the energy needs of their offspring despite increasing their own energy intake, which was partly due to the significant decrease in milk energy output. These changes may be related to a significant decrease in the alpha diversity of the gut microbiota. Seasonal changes in food availability play a key role in shaping reproductive strategies in wild small mammals, and exclusive reliance on high-protein or high-fiber diets may compromise maternal reproductive performance.

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Gut microbiota structure and function in Sorex caecutiens across different seasons within the same region

XUE Qiyuan, CAI He, ZHANG Yifei, GAO Yi, GUO Qiuying, ZHANG Zhihui, JIN Zhimin, ZHANG Junsheng, LIU Zhu

2026, 46(5):  734-743.  DOI: 10.16829/j.slxb.151122

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The gut microbiota is closely related to the host’s behavior, health, and development, and is influenced by a variety of factors such as season, diet, and environment. To explore the differences in the gut microbiota of Sorex caecutiens in different seasons, we collected samples from 33 S. caecutiens individuals in summer, autumn, and winter (Divided into summer group, autumn group, and winter group), and performed high-throughput sequencing of the 16S rRNA gene on their gut contents. After species annotation of the sequencing results, the species composition, α-diversity, β-diversity, inter-group differences, and functions of the gut microbiota were analyzed. The results showed that there were no significant differences in the Simpson and Chao1 indices of the gut microbiota of S. caecutiens in the three seasons, while the Shannon index of the winter group was significantly higher than that of the other two seasons (P < 0. 05). The β-diversity analysis results indicated that there were differences in the gut microbiota structure of S. caecutiens in the three seasons (P < 0. 01). At the phylum level, the dominant phylum in summer and autumn were Firmicutes (52. 39%, 53. 21%) and Campylobacterota (23. 42%, 21. 41%), while in winter, the dominant phylum were Proteobacteria (41. 15%) and Campylobacterota (29. 27%). At the genus level, the dominant genus in summer and autumn were Mycoplasma (23. 42%, 41. 22%) and Helicobacter (21. 94%, 21. 41%), while in winter, the dominant genus was Helicobacter (29. 27%). LEfSe analysis revealed that Firmicutes, Verrucomicrobiota, and Desulfobacterota were enriched in autumn, while Proteobacteria, Actinobacteriota, and Bacteroidota were enriched in winter. The functional analysis results showed that metabolism was the dominant function in all three groups (relative abundance > 75%), and the functional abundance of genetic information processing in the gut microbiota of S. caecutiens in autumn was significantly higher than that in the other two seasons (P < 0. 05). Through the analysis of the gut microbiota in the three seasons, we gained a preliminary understanding of the composition and function of the gut microbiota of S. caecutiens, which changes with the seasons to adapt to the different feeding habits.

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Analysis of structural and functional differences in the gut microbiota between juvenile and adult captive giant pandas in the Qinling region

WANG Binpeng, ZHANG Danhui, YANG Zhimei, PAN Yueting, LUO Xiaobin, MO Ran, ZAN Linsen, WANG Xiaoyu, MEI Chugang

2026, 46(5):  744-758.  DOI: 10.16829/j.slxb.151162

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This study investigated structural and functional differences in the gut microbiota of juvenile and adult captive giant pandas (Ailuropoda melanoleuca) in Qinling using metagenomic sequencing, with the aim of characterizing microbial adaptation to age-related dietary shifts and informing the development of targeted probiotics to support digestion and nutritional health. Fecal samples were collected from three juveniles (2 4 months old) and three adults (62 63 months old) at the Qinling Giant Panda Research Center. After sequencing, we conducted taxonomic profiling, diversity analyses, and functional annotation of the fecal microbiome. In total, 424 716 776 high-quality reads were generated, yielding 318 605 non-redundant genes. Alpha-diversity analyses showed that adults had significantly higher richness (Chao1 and ACE) but significantly lower diversity (Shannon and Simpson) than juveniles (P < 0. 01), suggesting a community with more taxa but greater dominance by a few lineages in adults. Beta-diversity analyses revealed a clear separation in microbial community structure between the two age groups. At the genus level, Lactobacillus predominated in juveniles, whereas Escherichia and Streptococcus were predominant in adults. Notably, several low-abundance bacteria with potential lignocellulose-degrading capacity (e. g., Bacillus licheniformis, Geobacillus galactosidasius, and Thermoclostridium stercorarium) were detected exclusively in adults. Functional annotation indicated that CAZy families (GT4, GH43, and GH73) and functions related to carbohydrate metabolism, amino acid metabolism, translation, lipid metabolism，and ribosome biogenesis were significantly enriched in juveniles compared with adults (P < 0. 05). Overall, this metagenomic analysis delineates distinct gut microbial features of juvenile and adult captive giant pandas and highlights candidate taxa potentially involved in lignocellulose degradation, providing a basis for precision probiotic development and gut-health management in this species.

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Analysis of intestinal flora diversity and the isolation and identification of pathogenic bacteria in diseased Yangtze finless porpoise

WANG Runping, MEI Zhigang, RAO Rongcheng, MIN Jialing, WEI Lili, DAI Yingen

2026, 46(5):  759-772.  DOI: 10.16829/j.slxb.151076

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In order to explore the causative agents and potential control measures for skin ulcers in the Yangtze finless porpoise (Neophocaena asiaeorientalis), as well as to scientifically evaluate its intestinal microbiota composition. A comprehensive postmortem analysis was conducted on a diseased deceased individual, including tissue necropsy, histopathological examination, intestinal flora composition assessment, pathogen isolation and identification, and antimicrobial susceptibility testing. The findings reveal that the Yangtze finless porpoise is emaciated, exhibiting multiple ulcers on its body surface. Necropsy further showed congested internal organs and the presence of ascites. In terms of the intestinal flora of the Yangtze finless porpoise revealed, at the phylum level, the relative abundance of Proteobacteria in the rectum is significantly higher than that in the foregut (P =0. 000 3) and hindgut (P =0. 000 4). At the genus level, Enterococcus was significantly more abundant in the foregut than that in the hind gut (P < 0. 000 1) and rectum (P < 0. 000 1), whereas Fusobacterium showed significantly higher relative abundance in the hindgut compared to the rectum (P = 0. 015 8). Additionally, a potential pathogen strain P2 was isolated from the skin lesions and identified as Aeromonas hydrophila through 16S rDNA sequencing. Antimicrobial susceptibility testing indicated that strain A. hydrophila P2 was highly sensitive to eight antibiotics, moderately sensitive to four antibiotics, and resistant to eighteen antibiotics. Collectively, these findings suggest that the Yangtze finless porpoise, is experiencing stress due to significant habitat changes during the dry season, which adversely affects its immune function. This stress leads to infection by A. hydrophila P2, which likely triggered skin inflammation and ulceration, subsequently affecting multiple internal organs, including the kidneys and intestines. Ultimately, feeding disorders contribute to severe body depletion, leading to death. This study provides important references data for the development of preventive measures against bacterial diseases in the Yangtze finless porpoise.