In specialized herbivores retaining a carnivorous digestive tract, such as the giant panda, early-life oral microbiome assembly is crucial for lifelong health, yet remains poorly understood. Here, we longitudinally tracked the saliva and supragingival plaque microbiomes of captive cubs (180 matched samples) from birth to one year using microbiome sequencing and topological cartography. We demonstrate a profound spatial-temporal divergence driven by deterministic succession. Initial plaque colonization exhibited transient priority effects reflecting maternal imprints, rapidly superseded by autogenic niche reconstruction and deep anaerobic maturation. Host ontogeny, notably deciduous tooth eruption, triggered intense microbial exchange, causing significant transient habitat homogenization (peak Mantel correlations at months 6 and 8, p < 0.001). Mature plaque selectively enriched for peptidoglycan biosynthesis and complex carbohydrate degradation, establishing a pre-adaptive metabolic reservoir for the impending high-fiber bamboo diet. Crucially, topological analysis (interaction edges expanded 3.4-fold) revealed that early pioneers evade competitive exclusion by shifting their ecological niche to become inter-module connectors (Pi > 0.62), providing spatial scaffolds for late-arriving climax communities. These findings decipher the deterministic assembly rules of saliva and plaque microbiomes during the extreme milk-to-bamboo dietary transition, advancing our understanding of giant panda adaptive evolution and identifying native keystone targets for preventive veterinary interventions.

Reintroduction programs aim to restore wild populations, yet success is challenged by host microbiome adaptation to natural environments. Here, we characterized the oral microbiota of giant pandas undergoing pre-release training, comparing them to captive and wild conspecifics, to assess training-induced microbial shifts. We found that after one year of reintroduction training, multi-generational captive giant pandas exhibited increased oral microbiome diversity, with community structure, composition, and predicted functions converging toward wild-type profiles. Adaptive changes included reduced relative abundances of Actinobacillus and Bergeyella, and enrichment of Myroides and Psychrobacter. Functionally, these shifts correlated with decreased starch and sucrose, fructose and mannose, and various lipid metabolism pathways, alongside enhanced methane and galactose metabolism which align with the dietary constraints of a singular food source in the wild environment. Our study demonstrates that pre-release training drives oral microbiota convergence toward wild phenotypes, underscoring microbial adaptation as critical for successful captive-to-wild transitions in endangered species.

As common parasites in the wild, ticks significantly limit the population growth of wild giant pandas and hinder the process of reintroducing captive giant pandas into their natural habitats. Research on microbial communities and pathogens in ticks infesting giant pandas is limited, emphasizing the need for a comprehensive investigation. To thoroughly investigate the microbial communities in giant panda-infesting ticks, particularly potential pathogens, we analyzed 246 ticks collected from the ears of wild-living giant pandas using 16S rRNA and metagenomic sequencing. We found that the microbial diversity in female ticks was significantly enriched in summer. The microbial community structure carried by ticks is more significantly influenced by seasonal changes than by sex. Metagenomic results indicated that giant pandas have a higher risk of Coxiella burnetii infection in summer and a higher risk of Anaplasma phagocytophilum, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Rickettsia amblyommatis infections in autumn. Over 90% of the ticks carried pathogens, with 82.54% harboring a single potentially pathogenic symbiont and the remaining 17.46% carrying multiple pathogens, all involving Coxiella burnetii. Using the CARD database, we identified a total of 121 antibiotic resistance genes (ARGs), with 76% exhibiting antibiotic efflux mechanisms. Based on the significantly associated ARGs, we provided antibiotic treatment recommendations for infections potentially caused by pathogenic symbionts. This study provides a clear answer to the potential microbial pathogen risks of ticks infesting giant pandas and offers a framework for tick-borne diseases in reintroduced wild panda populations. IMPORTANCE:Importance: The emergence of tick-borne bacterial diseases poses a serious threat to the population health of wild-living giant pandas. Ticks are obligate hematophagous ectoparasites that survive by feeding on the blood of various animal hosts and spreading pathogens. Although some previous studies have confirmed that wild ticks carried various viruses, the role of wild giant panda-infesting ticks in the bacterial community remains unknown. Here, the identification of the microbial community and antibiotic resistome in giant panda-infesting ticks revealed that most Ixodes ovatus ticks are potentially pathogenic symbionts, including Anaplasma phagocytophilum, Coxiella burnetii, and Rickettsia amblyommatis. Tick-borne disease control also needs to take into account the effects of season, sex, and antibiotic efflux resistance genes. Our findings highlight the contribution of the scientific management of tick-borne diseases in the giant panda population.

The habitats of the Chinese red pandas (Ailurus styani) have been significantly reduced and fragmented in human-dominated landscapes. Scientific habitat assessment, corridor planning, and identification of conservation gaps are essential for ensuring the long-term sustainability of this bamboo-dependent species. To address these issues, we used Ensemble and InVEST models to analyze the distribution and quality of habitats for Chinese red pandas in southwestern China, with a particular emphasis on core habitat connectivity and conservation gaps. Our results indicate that the habitats are not only highly fragmented but also of low quality, with human disturbance and climate change identified as the primary drivers of habitat degradation. Of the total 12,219.5 km2 of suitable habitat, only 47.75 % falls within the boundaries of the Giant Panda National Park. We identified 11 core habitat patches covering a total area of 3,767.7 km2, of which 70.9 % are protected, leaving 1,102.9 km2 as conservation gaps that require urgent protection and restoration efforts. Additionally, we designed 12 cost-effective ecological corridors connecting these core patches, with an average length of 29.1 km, which should be prioritized in future conservation planning. Our findings highlight that the Chinese red pandas in southwestern China survives in a highly fragmented landscape with weak connectivity. This study enhances the accuracy of identifying conservation priority areas and protection gaps, and recommends that the existing Chinese red pandas populations be managed as a regional metapopulation to ensure their long-term survival in human-dominated landscapes.

Understanding physiological adaptations of endangered giant pandas to seasonal changes is critical for improving conservation efforts, yet integrated analyses of blood parameters and feeding strategies remain limited. To decode seasonal adaptation mechanisms, we analyzed 36 monthly blood samples from 3 female pre-released training pandas alongside bamboo components across winter–spring and summer-autumn. Results showed significantly higher lymphocyte counts and urea levels, but lower serum aspartate aminotransferase, serum alkaline phosphatase, glucose and lipase in summer-autumn. Correspondingly, pandas consumed significantly more hemicellulose, crude ash, crude protein and minerals (e.g., potassium, calcium, magnesium, phosphorus, manganese, chromium, copper and zinc) in summer and autumn, while greater intake of starch, lignin, cadmium in winter–spring, reflecting a shift from stems to leaves. Key blood parameters correlated with bamboo component intake. These findings indicate a nutrient-driven strategy favoring anabolic metabolism in resource-rich seasons, providing physiological thresholds for improved conservation and release programs.

IntroductionThe gut microbiota plays a pivotal role in regulating the host's physiological functions and behavior. The coevolutionary relationship between the host and its gut microbiota facilitates adaptation to specific ecological niches. As obligate bamboo feeders, giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus styani) exhibit distinct feeding preferences: the former primarily consumes bamboo stems and leaves, while the latter feeds mainly on bamboo leaves. This study aims to elucidate how these species adapt metabolically to different parts of bamboo via gut microbial activity.MethodsWe employed 16S rRNA gene sequencing to analyze the structure and function of fecal microbial communities in giant pandas (GP) and red pandas (RP).ResultsSignificant differences in gut microbiota composition were observed between the GP and RP groups. Eight core bacterial taxa constituted over 99.97% of the total microbial composition, with the RP group exhibiting higher species richness but lower overall diversity. At the phylum level, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, and Flavobacteria were significantly enriched in the GP group, whereas Firmicutes dominated in the RP group. At the genus level, Sphingomonas, Methylobacterium, Cryomonas, and Terriglobus were more abundant in the GP group, while Streptococcus and Rhizobium were enriched in the RP group. Functional metabolic analysis indicated that lipid and amino acid metabolism pathways were significantly enriched in the GP group, whereas nucleotide and carbohydrate metabolism pathways were prominent in the RP group. Further analysis revealed that Sphingomonas and Methylobacterium in the GP group positively regulated amino acid and lipid metabolism, while Streptococcus in the RP group enhanced nucleotide and carbohydrate metabolism.DiscussionThese findings suggest that the distinct metabolic pathways of the gut microbiota in giant and red pandas have evolved in concert with their dietary strategies, energy acquisition modes, and ecological niche differentiation, forming a highly coordinated adaptive system.

Animals undergo a cognitive process when exposed to novel environments, which plays a crucial role in their ability to identify optimal habitats and support long-term survival. We conducted an initial investigation into the spatial utilization and habitat selection patterns of a femal red panda using GPS collar technology. Our research revealed that the home range and core activity area of the red panda was larger during initial 60 days after release, and markedly decreased thereafter. The red panda's selection of altitude did not align with that of wild individuals until 60 days after release, whereas slope selection may require at least 30 days to stabilize and become consistent with wild individuals' patterns. Our study further revealed that the home range and core activity area of the red panda showed low overlap with the suitable habitat of the wild population during the initial two months; however, this overlap increased significantly, reaching over 90% thereafter. We hypothesize that the red panda may require at least 60 days to acclimate to its new environment after release. Although our study was only based on a single individual, it provides the first evidence of the environmental adaptation process of red panda following released into the wild, thereby establishing a crucial foundation for future conservation and reintroduction initiatives.

Climate change and human activities drive migration, contraction, and expansion of species distribution. The scarcity of data on the distribution dynamics of the Chinese red panda (Ailurus styani) presents a substantial challenge for governments in formulating effective conservation strategies. This study used 11 habitat modeling techniques within the Biomod2 framework to analyze the spatiotemporal change trends in habitat of Chinese red panda in Sichuan Province, China. The results indicate that habitat of the Chinese red panda increase by 35.05 % from 2003 to 2013; however, it decrease by 37.42 % from 2013 to 2023. Further analysis reveal that human activities are the primary driver of habitat loss in 2013-2023, while climatic factors likely contribute to habitat expansion in 2003-2013. Projections under future climate scenarios suggest that the habitat may expand 29.67 % by 2050 and 21.25 % by 2070, reflecting a climate-induced spatial redistribution of habitat. Specifically, future habitat expansion is predominantly projected outside the Giant Panda National Park, at high-altitude regions averaging 2981.4 +/- 284.5 m; in contrast, habitat contraction is concentrated within the park at lower elevations averaging 2117.3 +/- 414.4 m. This shift reflects an adaptive response to cooler and more stable climatic conditions, yet simultaneously intensifies risks of habitat fragmentation and population isolation. These emerging patterns present significant challenges for ecosystem-based conservation and management efforts focused on endangered species. Therefore, we urge immediate actions, including expanding national park networks, reinforcing ecological protection red line designations, enhancing the Natural Forest Protection Program, and implementing integrated ecosystem conservation strategies to mitigate potential adverse impacts.

Despite intensified global efforts in wildlife conservation, livestock grazing remained a critical factor driving habitat changes. The quantitative studies specifically addressing the impact of grazing on the habitat changes of giant (Ailuropoda melanoleuca) and red pandas (Ailurus styani) were notably scarce. To address this knowledge gap, we used grazing data, environmental variables, and animal locations to evaluate the habitat preferences and spatial utilization patterns of giant and red pandas. The research results indicated that the preferred habitat of giant pandas progressively contracted as grazing intensity increased, whereas that of red pandas gradually expanded. However, the habitat suitability index (HSI) for both species declined. Furthermore, the spatial overlap degree in preferred habitats and the contribution of grazing factors in the habitat evaluation model progressively increased as grazing intensity increased. Our research also revealed that livestock was predominantly distributed in the marginal areas with the giant and red pandas. To mitigate grazing disturbance, giant and red pandas exhibited divergent habitat selection patterns. Specifically, red pandas tended to favor lower-altitude areas with steeper terrain under grazing pressure; giant pandas preferred steeper areas regardless of altitude. This study confirmed that grazing was a critical factor influencing the habitat selection of both giant and red pandas. Mitigating grazing pressure through targeted management interventions could significantly reduce this impact, offering a viable strategy for enhancing habitat conservation in the future. Our findings underscored the critical importance for wildlife protection departments in southwestern China to exercise greater caution when formulating and implementing grazing policies.

Adopting unique survival strategies during spring food shortages and simultaneous parturition and nursing is crucial for golden snub-nosed monkeys. Social behaviors, such as altruism within one-male units (OMUs), are decisive for family health, but the role of microbiota in regulating these behaviors remains unknown. We conducted the gut microbiota from members of 10 OMUs using 16S RNA sequencing technology. We found that in adult males, gut microbiota diversity significantly decreased in food shortages and parturition-nursing period. Meanwhile, there was a notable reduction in 12 metabolism-related pathways, including those related to carbohydrates, amino acids, and lipid. The gut microbiota of adult male monkeys shifts from being enriched with the genera Akkermansia in winter to the genera norank Muribaculaceae in spring. This transition alters the pathways for nutrient acquisition, thereby reducing the consumption of stored energy. In contrast, other OMU members (adult females and subadults) did not experience adverse effects on the metabolic functions of their gut microbiota during the food-scarce spring, which is also a critical period for parturition and lactation in adult females. This study elucidates the co-evolution of altruistic behavior and gut microbiota in Sichuan snub-nosed monkeys, insights into the interaction mechanisms between mammalian microbiota and survival strategies.

As apex predators, felids (Felidae) face unresolved phylogenetic controversies due to their recent rapid speciation and remarkable morphological conservatism. Previous studies, often relying on a limited number of genetic markers, were constrained by insufficient data and conflicting phylogenetic signals, leaving these disputes unresolved. Therefore, establishing a robust phylogenetic framework based on larger-scale genomic data is crucial. This study integrated complete mitogenomes from 37 species representing all major felid genera to characterize genomic diversity, selection pressures, and phylogenetic relationships. Results revealed conserved gene content and arrangement patterns but significant intergenic variation in nucleotide composition, with the light-strand encoded ND6 exhibiting pronounced strand-specific bias. Nucleotide diversity was highest in ND4L (Pi = 0.132) and ATP6 (Pi = 0.131), suggesting their utility as novel markers for species delimitation and population studies. Selection pressure analysis indicated strong purifying selection on cytochrome oxidase subunits (e.g., COX1 Ka/Ks = 0.00327) but relaxed constraints on ATP8 (Ka/Ks = 0.12304). Phylogenies reconstructed from the complete 13PCGs + 2rRNAs dataset (showing high congruence between maximum likelihood and Bayesian methods) clearly delineated Felidae into two primary clades (Pantherinae and Felinae), confirming monophyly of all genera and positioning Neofelis nebulosa as the basal lineage within Pantherinae. Crucially, exclusion of ND6 (12PCGs + 2rRNAs) yielded topologies congruent with the complete 13PCGs + 2rRNAs dataset, whereas single-gene or limited multi-gene datasets produced inconsistent trees (particularly at genus-level nodes). This demonstrates that near-complete mitogenomic data (≥12PCGs + 2rRNAs) are essential for reconstructing robust felid phylogenetic frameworks. Our study provides insights into carnivoran mitogenome evolution.

The poor reproductive capacity of giant pandas significantly hinders the development of captive populations, with 80.88% of adult individuals being unable to successfully become pregnant and deliver offspring. The disturbance of vaginal microbiota has been proven to potentially lead to miscarriage, abortion, and stillbirth in mammals. To elucidate the potential relationship between the vaginal microbiota and the reproductive capacity of giant pandas, we performed high-throughput sequencing of vaginal microbiota at the time of fertilization and conducted comparative analyses based on different pregnancy outcomes. We found that the microbial diversity in the delivery (D) group exceeded that in the non-delivery (ND) group and the vaginal microbial community structure was statistically different between the two groups. The vaginal microbiota in the delivery pandas consisted of unclassified Pseudomonadaceae which was gradually replaced by the Escherichia-Shigella type of vaginal microbiota in the ND group. A function predictions analysis showed that infectious disease, glycan biosynthesis, and metabolism were significantly enriched in the ND group. Additionally, an analysis of the microbial community phenotypic categories indicated that the ND group exhibited a significantly higher abundance of Gram-negative bacteria, facultative anaerobes, potential pathogens, and stress-tolerant species compared to the D group, predominantly driven by the elevated abundance of Escherichia-Shigella. Escherichia-Shigella can be used within LDA and ROC analyses to diagnostically distinguish the vaginal microflora associated with bad pregnancy outcomes during estrus. Our results will help to identify potential pathogens causing reproductive tract diseases, reduce the number of reproductive tract disease infections in pandas, and increase the birth rate of giant pandas in conservation breeding programs.

Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.

To achieve reproduction, male solitary mammals need to locate females using chemical communication with high levels of precision. In the case of giant pandas, the total estrus period of females was usually 15 days each year, however, successful mating activity is finished within 3 days from respective home range. The mating pattern of giant pandas, where multiple males compete for each female requires females employ efficient systems to communicate their estrus phases. To verifying whether the scent secretions of giant pandas changes by gender and estrus progression, the microbiota and compounds in 29 anogenital gland samples from 14 individuals during estrus were analyzed by 16S rRNA sequencing and GC-MS. We show that the microbiota communities covary by gender with 4 particular compounds of scent secretions. Among 597 genera, 34 were identified as biomarkers that could be used to distinguish between different estrus phases. By bacterial-compounds co-analysis, 3 fatty ester acids and squalene compounds covaried with the development of estrus in the bacterial communities of female giant pandas. This study helps clarify how a large, solitary mammal expresses accurate information to improve the likelihood of successful reproduction by changing the composition of microbiota and odor compounds of anogenital glands during estrus.

Tick infestations have been reported as one of the factors threatening the health of giant pandas, but studies of viral pathogens carried by ticks feeding on the blood of giant pandas are limited. To assess whether blood-sucking ticks of giant pandas can carry viral pathogens and if so, whether the viruses in ticks are associated with those previously detected in giant panda hosts, we determined the viromes of ticks detached from giant pandas in a field stocking area in Sichuan Province, southwest China. Using viral metagenomics we identified 32 viral species in ticks, half of which (including anellovirus [n = 9], circovirus [n = 3], and gemycircularvirus [n = 4]) showed homology to viruses carried by giant pandas and their associated host species (such as red pandas and mosquitoes) in the same living domain. Remarkably, several viruses in this study phylogenetically assigned as bunyavirus, hepe-like virus, and circovirus were detected with relatively high abundance, but whether these newly identified tick-associated viruses can replicate in ticks and then transmit to host animals during a blood meal will require further investigation. These findings further expand our understanding of the role of giant panda-infesting ticks in the local ecosystem, especially related to viral acquisition and transmission, and lay a foundation to assess the risk for giant panda exposure to tick-borne viruses. IMPORTANCE Ticks rank only second to mosquitoes as blood-feeding arthropods, capable of spreading pathogens (including viruses, bacteria, and parasites) to hosts during a blood meal. To better understand the relationship between viruses carried by ticks and viruses that have been reported in giant pandas, it is necessary to analyze the viromes of giant panda-parasitic blood-sucking ticks. This study collected 421 ticks on the body surface of giant pandas in Sichuan Province, China. We characterized the extensive genetic diversity of viruses harbored by these ticks and reported frequent communication of viruses between giant pandas and their ticks. While most of the virome discovered here are nonpathogenic viruses from giant pandas and potentially tick-specific viruses, we revealed some possible tick-borne viruses, represented by novel bunyaviruses. This research contributes to the literature because currently there are few studies on the virome of giant pandainfesting ticks.

Ticks rank second in the world as vectors of disease. Tick infestation is one of the factors threatening the health and survival of giant pandas. Here, we describe the mitogenomes of Ixodes acutitarsus and Ixodes ovatus parasitizing giant pandas, and perform comparative and phylogenetic genomic analyses on the newly sequenced and other available mitogenomes of hard ticks. All six newly determined mitogenomes contain a typical gene component and share an ancient Arthropoda gene arrangement pattern. Our study suggests that I. ovatus is a species complex with high genetic divergence, indicating that different clades of I. ovatus represent distinct species. Comparative mitogenomic analyses show that the average A + T content of Ixodidae mitogenomes is 78.08%, their GC-skews are strongly negative, while AT-skews fluctuate around 0. A large number of microsatellites are detected in Ixodidae mitogenomes, and the main microsatellite motifs are mononucleotide A and trinucleotide AAT. We summarize five gene arrangement types, and identify the trnY-COX1-trnS1-COX2-trnK-ATP8-ATP6-COX3-trnG fragment is the most conserved region, whereas the region near the control region is the rearrangement hotspot in Ixodidae mitogenomes. The phylogenetic trees based on 15 genes provide a very convincing relationship (Ixodes + (Robertsicus + ((Bothriocroton + Haemaphysalis) + (Amblyomma + (Dermacentor + (Rhipicentor + (Hyalomma + Rhipicephalus))))))) with very strong supports. Remarkably, Archaeocroton sphenodonti is embedded in the Haemaphysalis clade with strong supports, resulting in paraphyly of the Haemaphysalis genus, so in-depth morphological and molecular studies are essential to determine the taxonomic status of A. sphenodonti and its closely related species. Our results provide new insights into the molecular phylogeny and evolution of hard ticks, as well as basic data for population genetics assessment and efficient surveillance and control for the giant panda-infesting ticks.

基于大熊猫Ailuropoda melanoleuca野外分布数据及环境变量,利用MaxEnt模型对岷山山系南端的大熊猫适宜栖息地分布进行了预测及分析.结果 显示:研究区域内有大熊猫适宜栖息地330.9 km2,占研究区域内保护区总面积的23.2％;并且龙溪虹口-白水河-九顶山一线的大熊猫的栖息地存在一定的破碎化现象.建议继续加强对大熊猫栖息地的保护,减少人为干扰,促进大熊猫栖息地的恢复,增进各相邻保护区间的沟通交流、数据分享,更准确掌握、了解该区域大熊猫的动态.