David's Deer Research Articles

Increased incidences of cervical ribs in deer indicate extinction risk

Mammals as a rule have seven cervical vertebrae, a number which remains remarkably conserved. Occasional deviations of this number are usually due to the presence of cervical ribs on the seventh vertebra, indicating a homeotic transformation from a cervical rib-less vertebra into a thoracic rib-bearing vertebra. These transformations are often associated with major congenital abnormalities or pediatric cancers (pleiotropic effects) that are, at least in humans, strongly selected against. Based on data from Late Pleistocene mammoths (Mammuthus primigenius) and woolly rhinoceroses (Coelodonta antiquitatis) from the North Sea, we hypothesized that high incidences of cervical ribs in declining populations are due to inbreeding and/or adverse conditions impacting early pregnancies. In this study, we investigated the incidence of cervical ribs in an extinct Late Pleistocene megaherbivore, giant deer (Megaloceros giganteus) from Ireland and in the extant highly inbred Père David deer (Elaphurus davidianus) and in twenty other extant species. We show that the incidence of cervical ribs is exceptionally high in both the Irish giant deer and the Père David deer and much higher than in extant outbred deer. Our data support the hypothesis that inbreeding and genetic drift increase the frequencies of maladaptive alleles in populations at risk of extinction. The high incidence of cervical ribs indicates a vulnerable condition, which may have contributed to the extinction of megaherbivore species in the Late Pleistocene. We argue that cervical rib frequency may be a good proxy for extinction risk in inbred populations.

Seasonal covariations of diet-gut microbiota in the adaptation of the newly reintroduced Père David's deer (Elaphurus davidianus) to the northern habitat

Milu (Père David's deer, Elaphurus davidianus), once extinct in the wild, was one of the few indigenous large herbivores of the wetland ecosystem in China. The reintroduction of milu in northern China has just started and is expected to restore not only that species, but also the ecosystem. To acquire insights into the adaptive process of the milu population first rewilded in the northern habitat and provide knowledge for the on-going and future reintroduction attempts, we used DNA metabarcoding to analyze the diets and gut microbiota of those milu in the first year after releasing. The results showed strong seasonality in both diet and gut microbiota. Significant higher dietary diversity was detected in in autumn than summer and winter. Woody dietary components increased continuously from summer to winter. A significant correspondence was found between the dietary and microbial diversities. Enrichment of metabolic pathways involved in lipid and amino acid metabolism was identified in summer, and of those involved in carbohydrate and glycan metabolism was identified in winter. Pathways related to metabolism of certain amino acid were differently abundant in the breeding season. The study indicated the contribution of foraging and gut microbial seasonality to the overwintering, reproduction and environmental adaption of the reintroduced milu. The enrichment of opportunistic pathogen Treponema and lower microbial diversity indicated higher health risk in winter, and thus disease prevention measures were suggested. Pre- and post-release food evaluation and monitoring was recommended to ensure food sufficiency in the reintroductions.

Impact of Environmental Food Intake on the Gut Microbiota of Endangered Père David's Deer: Primary Evidence for Population Reintroduction.

Reintroduction has been successful in re-establishing several endangered wild animals in their historical habitats, including Père David's deer (Elaphurus davidianus). Continuous monitoring of reintroduced individuals is essential for improving the sustainability of ex situ conservation efforts. Despite an increased recognition of the significance of the gut microbiome for animal health, the correlation between diet and the gut microbiome in E. davidianus is unclear. In this study, 15 fresh fecal samples of E. davidianus were collected from Tianjin Qilihai Wetland and the association between dietary and gut microbiota composition was evaluated. Microscopic observations showed that Nymphoides peltata [relative density (RD = 0.3514), Phragmites australis (RD = 0.2662), Setaria viridis (RD = 0.1211), and Typha orientalis (RD = 0.1085) were the main dietary plants in the fecal samples. High-throughput 16S rRNA sequencing showed a predominance of the phyla Firmicutes and Proteobacteria and the genus Psychrobacillus (26.53%) in the gut microbiota. The RD of N. peltata was significantly positively correlated with the abundance of Firmicutes (p = 0.005) and the genus UCG-005 (p = 0.024). This study indicates a close association between food digestion and nutrient intake, providing basic monitoring data for the full reintroduction and recovery of wild E. davidianus.

Diet analysis of Père David's deer (Elaphurus davidianus) based on stable isotope analysis

Supplemental feed for free‐ranging deer is often advocated by managers to compensate for winter survival. However, providing extra food has great costs so it is important to know how essential supplemental feed is for deer populations. In our study, supplemental feed is supplied year round for free‐ranging Père David's deer Elaphurus davidianus since early 2019 to help them survive food shortages in the Jiangsu Dafeng Milu National Nature Reserve. To understand use of supplemental feed, we quantified the biomass contributions of C3 plants, C4 plants and supplemental feed consumed by free‐ranging deer by assessing their faecal carbon and nitrogen stable isotope values in May, July, October and December. The diet–faeces trophic shift of deer was assessed using semi‐captive animals. Faeces in both areas were collected and faecal δ13C values revealed more variable diets of free‐ranging deer than semi‐captive deer in different months. MixSIAR model showed that C4 plants contributed greatly to deer diet biomass (75.1, 82, 64.3, 79.4%, respectively in May, July, October and December) compared with C3 plants and supplemental feed. We suggest that managers should consider the efficiency of long‐term supplemental feed and consider the selection of C3 and C4 plants during restoration.

Discovery of Elaphuri Davidiani Cornu-specific peptide biomarkers by peptidomics analysis-based method.

Elaphuri Davidiani Cornu (EDC) is the antler of the male Père David's deer, which has been reported to have multiple biological activities, and its use as a traditional Chinese medicine (TCM) in China has been known for thousands of years. However, EDC is difficult to distinguish from other related species-derived antlers in powder or extract form in TCM clinic use, such as Cervus elaphus Cornu (CEC) and Cervus nippon Cornu (CNC), both derived from Cervidae and easily confused with EDC. In this study, a strategy using peptidomics combined with mathematics set analysis was used to identify EDC-specific peptide biomarkers, and four specific peptide biomarkers (Pep-E1-E4) were identified and validated. Pep-E1, Pep-E3, and Pep-E4 could be exclusively detected in EDC samples, with relative peak areas of 0.298±0.060, 0.039±0.015, and 0.037±0.008, whereas Pep-E2 showed relative peak area of 0.516±0.101 in EDC, 0.132±0.026 in CEC, and 0.136±0.047 in CNC samples, respectively. These four peptides are applicable to distinguish EDC from CEC and CNC, which is of great significance for the quality control of EDC.

Feeding, mating and animal wellbeing: new insights from phylogenetic comparative methods.

Feeding, mating and animal wellbeing: new insights from phylogenetic comparative methods.

Diet composition and selection of Père David's deer in Hubei Shishou Milu National Nature Reserve, China.

Hubei Shishou Milu National Nature Reserve is an ideal place to restore the wild population of Père David's deer (Elaphurus davidianus). Understanding foraging ecology and diet composition is essential for assessing population development or establishing long-term effective conservation measures for endangered species. However, little is known about the diet composition of Père David's deer and its diet selection mechanism. In this study, we used stable isotope technology to investigate the diet composition of Père David's deer according to various tissues (i.e., fur, muscle, liver, heart, and feces) and seasons, and evaluated the correlation between the nutrient composition of plants and diet composition. Bayesian isotope analysis showed that the autumn and winter diet estimated by fur and fecal samples indicated a diet dominated by C3 grasses (42.7%-57.2%, mean), while the summer diet estimated by muscle and liver samples was dominated by C3 forbs (30.9%-41.6%, mean). The Pearson correlation test indicated that the contribution of winter diet composition reflected by fur and fecal samples was associated with correlations with crude protein (r=.666, p < .01) and soluble sugars (r=.695, p <.01). The results indicated that crude protein and soluble sugars were important factors influencing the winter diet selection of Père David's deer. In the context of the current reintroduction facing many challenges, such as habitat fragmentation, wetland degradation, and human disturbance, comprehensively evaluating the diet selection mechanism of Père David's deer under different resource specificities and temporal changes should be considered in the future.

Effects of David Deer Grazing on Soil Bacterial and Fungal Communities in an Eastern Coastal Wetland of China

The grazing activity of animals has a significant role on the environmental modification of land. In the coastal wetlands of eastern China, long-term David deer (Elaphurus davidianus) grazing has caused the degradation of various ecological elements in the area. Still, few studies have been reported concerning the effects of David deer grazing on the soil microorganisms of their habitats. We analyzed the community structure of soil bacteria and fungi in an area of continuous annual grazing and another area without traces of David deer grazing so as to learn about the effects of deer grazing on the soil microbial community structure in a spatial instead of temporal way, in preparation for improving the environment for deer survival. David deer grazing drastically changed the physicochemical characteristics of the soil, accelerating the alkalinization process and inhibiting the buildup of nutrients. There were differences in the microbial community structure between the grazed and the control areas, with bacteria predominating. The control had a higher level of bacterial and fungal alpha-diversity than the grazed area. The makeup of the soil’s microbial community was also influenced, except for the dominant microbial at the phylum level. In addition to the establishment of numerous complex fungal functional types, David deer grazing increased the number of bacterial functional types linked to the carbon cycle. The impacts of soil pH and urease activity on bacterial and fungi populations were highlighted using the redundancy analysis. This study demonstrates that David deer grazing changes and complicates microbial functional kinds of composition, as well as modifies the composition of the soil’s microbial community, improving the soil nutrient cycling process, mainly the carbon element.

Antler tine homologies and cervid systematics: A review of past and present controversies with special emphasis on Elaphurus davidianus.

Antlers are the most conspicuous trait of cervids and have been used in the past to establish a classification of their fossil and living representatives. Since the availability of molecular data, morphological characters have generally become less important for phylogenetic reconstructions. In recent years, however, the appreciation of morphological characters has increased, and they are now more frequently used in addition to molecular data to reconstruct the evolutionary history of cervids. A persistent challenge when using antler traits in deer systematics is finding a consensus on the homology of structures. Here, we review early and recent attempts to homologize antler structures and objections to this approach, compare and evaluate recent advances on antler homologies, and critically discuss these different views in order to offer a basis for further scientific exchange on the topic. We further present some developmental aspects of antler branching patterns and discuss their potential for reconstructing cervid systematics. The use of heterogeneous data for reconstructing phylogenies has resulted in partly conflicting hypotheses on the systematic position of certain cervid species, on which we also elaborate here. We address current discussions on the use of different molecular markers in cervid systematics and the question whether antler morphology and molecular data can provide a consistent picture on the evolutionary history of cervids. In this context, special attention is given to the antler morphology and the systematic position of the enigmatic Pere David's deer (Elaphurus davidianus).

Identification and genetic characterization of Blastocystis subtypes in Père David's deer (Elaphurus davidianus) from Shishou, China.

Blastocystis is a protozoan parasite frequently reported in the gastrointestinal tract of humans and animals, with a global distribution. No information on the infections of Blastocystis in Père David's deer (Elaphurus davidianus, PDD) is available. In this study, a total of 128 fecal samples collected in the National Nature Reserve of Shishou, Hubei Province of China, were used to determine the occurrence and subtypes of Blastocystis in PDD. Amplification of the SSU rDNA gene confirmed the common presence of Blastocystis infection, with an observed prevalence of 56.3% (72/128). Through nucleotide sequencing and phylogenetic analysis, five known subtypes, which consisted of one zoonotic subtype (ST10) and four ruminant-specifical subtypes (ST21, ST23, ST25, and ST26), were identified in this study. This represents a high degree genetic diversity of parasites within the host. Of the 72 PCR-positive samples, ruminant-specific subtypes were the most frequently observed, with ST21 being the most prevalent subtype (56.9.7%, 41/72). This is the first report characterizing the molecular subtypes of Blastocystis in PDD. The findings demonstrate a broad diversity and zoonotic potential of Blastocystis in PDD. Further study of the transmission potential between wildlife and humans or domestic animals in the region is required.

Père David's Deer (Elaphurus davidianus) in China: Population Dynamics and Challenges

The reintroduction of rare and endangered species is one of the most important approaches to conservation and ecosystem restoration, but it has still proven to be an adventurous undertaking and most reintroduction programmes fail, so successful demonstrations are needed. Père David's deer (Elaphurus davidianus, Milu in Chinese) could be considered one of conservation's great success stories, as this species' path on the road to extinction has been reversed by a combination of ex-situ conservation and successful re-introduction in China. The species had been consigned to an imperial hunting ground when the last Chinese herds were exterminated during the fall of the Qing Dynasty (1644–1912). Fortunately, a few of the last remaining individuals were sent to European zoos. From these animals, a herd was bred on the 14th Duke of Bedford's estate, Woburn Abbey, and between 1985 and 1987, and 38 Milu were donated back to China for re-introduction in Beijing Milu Park (BMP), the former imperial hunting ground. An additional 39 deer were released at Dafeng National Nature Reserve (DFNNR), Jiangsu Province in 1986. In both of these safe and protected locations, the Milu thrived allowing for over 700 Milu to be sent to a further 82 sites throughout the species' original Chinese range over the last 36 years. As a result, the Milu population totaled 9136 by 2021, with 2855 individuals now living back in the wild; while another 5681 individuals inhabit the DFNNR, and 186 reside in BMP. Wild Milu, however, still face significant conservation challenges. The population lacks genetic diversity, leading to severe inbreeding depression and carrying multiple risks, such as high miscarriage rates, a reduced lifespan, and susceptibility to disease. Environmental constraints such as pollution and habitat fragmentation further result in small, fragmented wild populations. Moreover, the species currently lacks a national level conservation master plan, the associated coordinated monitoring platforms, and breeding plans for China's captive populations. Finally, there is now a lack of international cooperation in the conservation of this species. We therefore call for both a national-level conservation master plan in China and international cooperation to develop a shared database and germplasm databank covering Milu across all countries with ex-situ populations, as crucial steps for securing the long-term conservation of Milu and preventing it from ever becoming “extinct in the wild” again.

麋鹿沧桑命运与未来保护展望

麋鹿作为中国特有的鹿科动物，经历129年的保护努力，种群数量恢复到10000多头。因近亲繁殖严重，表面上看已无灭绝危险，但仍存在巨大隐忧。通过对麋鹿种群变迁、灭绝、重引入、恢复现状及四大种群（乌邦寺、南海子、大丰、石首野化种群）的发展趋势进行追踪分析，探究近千年来困扰麋鹿种群发展壮大的多重因素，提出种群保护与栖息地保护并重、强化疫病监测等保护对策，为麋鹿及其它大型陆生濒危哺乳动物突破种群发展瓶颈提供借鉴。;Père David's deer (Elaphurus davidianus), a unique species of deer in China, the population has recovered to more than 10000 in the world after more than 100 years of efforts. It seems that there is no danger of extinction due to the high levels of inbreeding in the population of Père David's deer, but there are still huge concerns. By analyzing the changes, extinction, and recovery of the population of Père David's deer and the development trend of four major populations (Woburn Abbey, Nanhaizi, Dafeng and Shishou), this paper explored the multiple factors that have been disturbing the development and expansion of the population of Père David's deer in the past thousand years. The protection measures, such as placing equal emphasis on population protection and habitat protection and strengthening disease monitoring, were put forward to provide reference for Père David's deer and other large terrestrial endangered mammals to break through the bottleneck of population development.

The primary visual cortex of Cetartiodactyls: organization, cytoarchitectonics and comparison with perissodactyls and primates

Cetartiodactyls include terrestrial and marine species, all generally endowed with a comparatively lateral position of their eyes and a relatively limited binocular field of vision. To this day, our understanding of the visual system in mammals beyond the few studied animal models remains limited. In the present study, we examined the primary visual cortex of Cetartiodactyls that live on land (sheep, Père David deer, giraffe); in the sea (bottlenose dolphin, Risso’s dolphin, long-finned pilot whale, Cuvier’s beaked whale, sperm whale and fin whale); or in an amphibious environment (hippopotamus). We also sampled and studied the visual cortex of the horse (a closely related perissodactyl) and two primates (chimpanzee and pig-tailed macaque) for comparison. Our histochemical and immunohistochemical results indicate that the visual cortex of Cetartiodactyls is characterized by a peculiar organization, structure, and complexity of the cortical column. We noted a general lesser lamination compared to simians, with diminished density, and an apparent simplification of the intra- and extra-columnar connections. The presence and distribution of calcium-binding proteins indicated a notable absence of parvalbumin in water species and a strong reduction of layer 4, usually enlarged in the striated cortex, seemingly replaced by a more diffuse distribution in neighboring layers. Consequently, thalamo-cortical inputs are apparently directed to the higher layers of the column. Computer analyses and statistical evaluation of the data confirmed the results and indicated a substantial correlation between eye placement and cortical structure, with a markedly segregated pattern in cetaceans compared to other mammals. Furthermore, cetacean species showed several types of cortical lamination which may reflect differences in function, possibly related to depth of foraging and consequent progressive disappearance of light, and increased importance of echolocation.

EVALUATION OF PASSIVE TRANSFER IN NINE SPECIES OF CERVIDAE

The reliability of packed cell volumes (PCV), total solids (TS), blood glucose (BG), γ-glutamyl transferase (GGT), and glutaraldehyde test in determining passive transfer of colostral immunoglobulins was investigated in nine species of cervids: axis deer (Axis axis), hog deer (Axis porcinus), sika deer (Cervus nippon), tufted deer (Elaphodus cephalophus), Père David's deer (Elaphurus davidianus), pudu (Pudu puda), sambar deer (Rusa unicolor), barasinga deer (Rucervus duvaucelli), and Eld's deer (Rucervus eldii). Individually the parameters evaluated were significant though imperfect predictors of passive transfer status in cervids. Interpreted collectively as a panel along with neonate condition, these tests were clinically helpful in diagnosing failure of passive transfer (FPT). Collectively interpreting test results as a panel along with clinical assessment of the animal is recommended. Some species-specific variations in TS, GGT, and glutaraldehyde test results were identified.

Quantifying the Long-Term Expansion and Dieback of Spartina Alterniflora Using Google Earth Engine and Object-Based Hierarchical Random Forest Classification

The overwhelming spread of Spartina alterniflora (S. alterniflora) (smooth cordgrass) over recent decades has put many native plant communities and coastal environments at risk. Therefore, long-term monitoring of S. alterniflora dynamics is necessary to better understand and manage the invasion of the species. However, it is difficult to map Spartina saltmarshes in China on an annual or multiyear epoch basis. To address this issue, we developed a classification approach integrating Google Earth Engine (GEE) and object-based hierarchical random forest (RF) classification, and we applied this approach to quantify the expansion and dieback of S. alterniflora at Dafeng Milu National Nature Reserve, Jiangsu, China during 1993–2020. Results showed that the area of S. alterniflora expanded from 24.48 ha in 1993 to 1564.96 ha in 2010. However, after ecological hydrological engineering and an increase in Elaphures davidianus (Pere David's deer) numbers in 2011, the S. alterniflora area decreased significantly to 944.28 ha in 2020. During 2011–2020, the S. alterniflora area decreased substantially at a rate of 67 ha per year and by 86% in one area studied in Dafeng Milu National Nature Reserve. In 2020, the 944.28 ha of S. alterniflora in the reserve was mainly distributed in mudflats by the sea. Overall, these results show that it is feasible to identify S. alterniflora using the GEE platform and object-based hierarchical RF classification; moreover, this approach could improve understanding and management of this invasion species.

Widespread Prevalence of Plasmid-Mediated Colistin Resistance Gene mcr-1 in Escherichia coli from Père David's Deer in China.

Père David's deer (Elaphurus davidianus or milu) is an endangered species, and the prevalence of antimicrobial resistance (AMR) such as mcr-1-positive strains among them has been unknown. In this study, we aimed to investigate the genomic characterizations of mcr-1-positive strains and provide insight into the dissemination of AMR in nature reserve settings. Sixty-seven mcr-1-positive Escherichia coli isolates from 97 fecal samples were identified by PCR and found resistant to colistin. The prevalence of β-lactam resistance was very high, and there were 64 mcr-1-positive isolates containing β-lactamase genes. Transconjugants of 66 mcr-1-positive isolates were acquired through conjugation experiments. PCR-based replicon typing (PBRT) showed that 44 strains harbored IncI2 mcr-1-bearing plasmids, eight strains harbored IncX4 mcr-1-carrying plasmids, and 14 strains harbored IncHI2 mcr-1-positive plasmids. Notably, mcr-1 was located in the chromosome of LD27-1. Clonal dissemination and horizontal dissemination of mcr-1 by plasmids coexist. We first report the prevalence of plasmid-mediated mcr-1 in E. coli from Père David's deer in China. mcr-1-bearing IncI2 plasmid was the most frequent plasmid type, and the first IncI2 plasmid harboring both blaCTX-M-132 and mcr-1 is characterized here. Our results support the implication of Père David's deer as a potential reservoir for MCR-1-producing E. coliIMPORTANCE The mcr-1 gene is widely reported around the world and has been identified on various plasmids with different replicon types. Resistance to the last-line antibiotic colistin mediated by mcr-1 still represents a threat to global public health. Père David's deer is a highly endangered species originating in China, and many deer are currently being raised in captivity for gradual reintroduction to the wild. If this species carries AMR bacteria, it will pose a potential threat to the environment. Therefore, research on the dissemination of mcr-1-positive E. coli from Père David's deer is of great significance. This is the first study to investigate the microbiological and genomic surveillance of MCR-1-producing bacteria colonized among Père David's deer in China, and we uncovered a high prevalence of MCR-1-producing E. coli The importance of constant surveillance for AMR bacteria in nature reserve settings is emphasized.

Methylenecyclopropylglycine and hypoglycin A intoxication in three Pére David's Deers (Elaphurus davidianus) with atypical myopathy.

BackgroundHypoglycin A (HGA) and methylenecyclopropylglycine (MCPrG) from seeds/seedlings of Sycamore maple (SM, Acer pseudoplatanus) causes atypical myopathy (AM) in horses. AM was not known to occur in wild ruminants until several fatalities in milus (Elaphurus davidianus) following the ingestion of HGA in SM seeds. However, a role for MCPrG has not previously been evaluated.ObjectivesTo test the hypothesis that MCPrG is also a major factor in AM in milus, three milus (M1, M2, M3) from the Zoo Dresden (aged 7–11 years, 2 females and 1 male, in good nutritional condition) that developed AM were studied.MethodsSerum, urine and methanol extracts from the liver, kidney, rumen digesta and faeces were analysed by ultrahigh‐performance liquid chromatography‐tandem mass spectrometry for HGA, MCPrG and for conjugates of carnitine (C) and glycine (G): Methylenecyclopropylacetyl (MCPA)‐G, MCPA‐C, Methylenecyclopropylformyl (MCPF)‐G, MCPF‐C, butyryl‐C and isobutyryl‐C.ResultsHGA in serum was high (M2 480 nmol/L; M3 460 nmol/L), but MCPrG was not. HGA and MCPrG were found in rumen and faeces extracts, and MCPrG was also identified in the liver. Metabolites of HGA and MCPrG were high in serum, urine and liver, but not in the rumen or faeces.ConclusionsThis study shows that MCPrG is involved in the pathophysiology of AM in milus. The metabolism of MCPrG is considered to be faster because, after ingestion, the specific metabolites appear highly concentrated in the serum. The high toxin concentration in the liver suggests that a possible transfer into products for human consumption may pose a risk.

Seroprevalence of Toxoplasma gondii infection in the endangered Père David's deer (Elaphurus davidianus) in China

Père David's deer (Elaphurus davidianus) is an emblematic endangered species and regarded as a national treasure, toxoplasmosis is a serious zoonotic parasitic disease for wild animals. Little is known about the prevalence of antibodies to this parasite in Père David's deer. In this study, sera from 43 wild Père David's deer, from Dafeng nature reserve China were tested for antibodies to Toxoplasma gondii by MAT. The investigation showed that antibodies to toxoplasma were detected in 8 of 43 (18.60%, 95% CI 6.97–30.24) samples. Seroprevalence ranged from 15.00% to 21.74% between the different genders, but the difference was not significant according to SPSS analysis (P > 0.05). This report of seroprevalence of antibodies to T. gondii in Père David's deer provides basic data of T. gondii infection data, which is important for controlling and preventing toxoplasmosis in Père David's deer.

Biological characteristics and genetic evolutionary analysis of emerging pathogenic Bacillus cereus isolated from Père David's deer (Elaphurus davidianus)

Bacillus cereus (B. cereus) is widely distributed in the environment. It is one of the most common opportunistic food-borne pathogens associated with food poisoning, not only being majorly reported to cause fatal infections of the gastrointestinal tract, but also responsible for abdominal distress and vomiting. The current study was undertaken to evaluate the biological characteristics and the genetic evolution of B. cereus isolated from infected organs of dead Elaphurus davidianus (E. davidianus). B. cereus was characterized through antibiotic sensitivity tests, mouse lethality assay, whole genome sequencing analysis, and genome annotation. The results revealed that the isolated B. cereus strain was highly resistant to rifampicin, lincomycin, sulfamethoxazole, erythromycin, and ampicillin, with a high pathogenicity phenotype. KEGG annotation revealed that “metabolic pathways” had the largest number of unigenes, followed by “biosynthesis of secondary metabolites” and “biosynthesis of antibiotics”. GO analysis resulted in 8039 unigenes categorized. Meanwhile, 54,779 unigenes were annotated and grouped into 23 categories based on COG functional classifications. Moreover, one gene (codY) was found to be related to the host in conformity with the analysis done on PHI-base. Other tests led to the identification of 16 B. cereus virulence factor genes and five resistance types, with potential resistance against bacitracin, penicillin, and fosfomycin. We isolated a highly drug-resistant and pathogenic B. cereus strain from E. davidianus, showing that a variety of antimicrobial drugs should be avoided in clinical treatments. Furthermore, to the best of our knowledge, this is the first study to report whole genome sequencing of a emergence of food-borne B. cereus strain isolated from E. davidianus deer; it will be helpful to extensively investigate the genetic and molecular mechanisms of drug resistance and pathogenesis about B. cereus in both humans and animals.

Analysis of the Gut Microbiome of Wild and Captive Père David's Deer.

Père David’s deer (Elaphurus davidianus or milu) is a highly endangered species originating from China, and many deer are currently being raised in captivity for gradual re-introduction to the wild. Wild and captive deer currently live in the same region but have vastly different diets. In this study, we used 16S rRNA high-throughput sequencing to identify the healthy core microbiome in the gut of wild and captive Père David’s deer and investigate how dietary factors influence the gut microbiome by comparing their differences. A core shared gut microbiome was identified in healthy Père David’s deer, which was similar to that of other ruminants, mainly comprising the phyla Firmicutes and Bacteroidetes. There were no differences in the richness or diversity of the gut microbiome between the wild and captive deer. However, PCA and ANOSIM demonstrated clear differences in the microbial community structure between the captive and wild deer, which mainly manifested as changes in the relative abundance of 39 bacterial genera. As the majority of these genera were not dominant in the deer gut, no significant difference was detected in functional modules related to the microbiome between the two groups. Therefore, the difference in dietary factors does not appear to affect the healthy core gut microbiome between captive and wild Père David’s deer, suggesting strong co-evolution and the possibility of re-establishment in the wild. These data could guide future applications of population management in Père David’s deer conservation.