Comparative Analysis of Gut Microbiota Changes in Père David's Deer Populations in Beijing Milu Park and Shishou, Hubei Province in China

Zhang, Meishan; Shi, Minghui; Fan, Mengyuan; Xu, Sheng‐Quan; Li, Yimeng; Zhang, Tianxiang; Cha, Muha; Liu, Yang; Guo, Xiaobing; Chen, Qi; Li, Yi-Ping; Zhang, Shumiao; Hu, Defu; Liu, Shuqiang

doi:10.3389/fmicb.2018.01258

Cited by 25 publications

(46 citation statements)

References 23 publications

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“…However, Père David’s deer remains a significant conservation concern in China. Mass die-offs of deer have occurred suddenly in some protected areas, which have been suggested to be related to infections of the gastrointestinal tract (Qiu et al, 2014; Bahrndorff et al, 2016; Yang et al, 2016; Zhang et al, 2018). Therefore, future conservation and management decisions require more focus and data on the health, welfare, and quality of Père David’s deer.…”

Section: Introductionmentioning

confidence: 99%

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

Sun

Liu

et al. 2019

Front. Microbiol.

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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.

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Section: Introductionmentioning

confidence: 99%

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

Sun

Liu

et al. 2019

Front. Microbiol.

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“…4) is a graphical representation that uses a system of colored gradients to represent the size of values in a data matrix, and the cluster data are also expressed in heatmap according to species or the abundance similarity of samples [20]. In order to reflect the similarities and differences between multiple sample communities, high-abundance and low-abundance species are clustered by color gradient and similarity [21]. Based on the species composition and relative abundance of each sample, a heatmap analysis was performed to extract the species at each taxonomic level [21].…”

Section: Comparison Of Core Intestinal Microbiota In Sturgeons From Tmentioning

confidence: 99%

“…In order to reflect the similarities and differences between multiple sample communities, high-abundance and low-abundance species are clustered by color gradient and similarity [21]. Based on the species composition and relative abundance of each sample, a heatmap analysis was performed to extract the species at each taxonomic level [21].…”

Section: Comparison Of Core Intestinal Microbiota In Sturgeons From Tmentioning

confidence: 99%

“…Mapping was achieved using R language tools, and a heatmap cluster analysis was performed at the levels of the phylum, class, order, family, genus, and species, respectively [21]. The result was found in Fig.…”

Section: Comparison Of Core Intestinal Microbiota In Sturgeons From Tmentioning

confidence: 99%

“…Alpha diversity indices mainly include Chao1, Observed_species, Shannon, PD_whole_tree, and Good's coverage, which can response to the richness and diversity of a single sample species [21]. The Chao1 index measures the richness of species (i.e., the number of species), whereas the Shannon index measure the diversity of species [21]. Observed_species shows the number of OTU was observed with the increase of sequencing depth.…”

Section: Alpha Diversity Analysis Of Microbial Communities In Sturgeomentioning

confidence: 99%

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Comparative study on the effects of different feeding habits and diets on intestinal microbiota in Acipenser baeri Brandt and Huso huso

Xing

et al. 2019

Preprint

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Background: Siberian sturgeon ( Acipenser baeri Brandt) and Beluga sturgeon ( Huso huso ) are two important commercial fish in China, and the feeding habits of them are very different. Diets and feeding habits are two significant factors to affect the gastrointestinal microbiota in ﬁsh. The intestinal microbiota has been reported to play a key role in nutrition and immunity. However, it is rarely reported about the relationship between the intestinal microbiota and feeding habits/diets on different Acipenseridae fish. This study is to comparative analysis of gut microbial community in Siberian sturgeon and Beluga sturgeon fed with the same diet/Beluga sturgeon fed with different diets in order to determine the effects of different feeding habits/diets on the fish intestinal microbiota. Results: According to the experimental objectives, BL and BH groups were Beluga sturgeon ( Huso huso ) fed with low fishmeal diet and high fishmeal diet, respectively. SH group represented Siberian sturgeon ( Acipenser baeri Brandt) fed with the same diet as BH group. After 16 weeks feeding trial, the intestinal microbiota was examined by 16S rRNA high-throughput sequencing technology. On the phylum level, Proteobacteria and Bacteroidetes were signiﬁcantly higher in BL group than BH group, and Cyanobacteria showed the opposite trend. Compared with BH group, Proteobacteria and Firmicutes were signiﬁcantly increased in SH group, whereas Cyanobacteria were clearly decreased. At the genus level, Pseudomonas and Citrobacter in BL group were signiﬁcantly higher comparing with BH group, while Bacillus , Luteibacter , Staphylococcus and Oceanobacillus was lower in BH group than SH group. Conclusions: Alpha and beta diversities indicated that the intestinal microﬂora were significant difference between Siberian sturgeon and Beluga sturgeon when they fed with the same diet. Meanwhile, Beluga sturgeon fed with low fishmeal diet can increase the species diversity of intestinal microbiota than it fed with high fishmeal diet. Therefore, feeding habits clearly affected the gastrointestinal microbiota of sturgeons. Moreover, the impact of changes in food on the gut microbiota of sturgeons should be taken into consideration during the process of sturgeon aquaculture.

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Marked variations in gut microbial diversity, functions, and disease risk between wild and captive alpine musk deer

Jiang

Song

Liu

et al. 2023

Appl Microbiol Biotechnol

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Maintaining a healthy status is crucial for the successful captive breeding of endangered alpine musk deer (Moschus chrysogaster, AMD), and captive breeding programs are beneficial to the ex-situ conservation and wild population recovery of this species. Meanwhile, the gut microbiota is essential for host health, survival, and environmental adaptation. However, changes in feeding environment and food can affect the composition and function of gut microbiota in musk deer, ultimately impacting their health and adaptation. Therefore, regulating the health status of wild and captive AMD through a non-invasive method that targets gut microbiota is a promising approach. Here, 16S rRNA gene sequencing was employed to reveal the composition and functional variations between wild (N = 23) and captive (N = 25) AMD populations. The results indicated that the gut microbiota of wild AMD exhibited significantly higher alpha diversity (P < 0.001) and greater abundance of the phylum Firmicutes, as well as several dominant genera, including UCG-005, Christensenellaceae R7 group, Monoglobus, Ruminococcus, and Roseburia (P < 0.05), compared to captive AMD. These findings suggest that the wild AMD may possess more effective nutrient absorption and utilization, a more stable intestinal microecology, and better adaption to the complex natural environment. The captive individuals displayed higher metabolic functions with an increased abundance of the phylum Bacteroidetes and certain dominant genera, including Bacteroides, Rikenellaceae RC9 gut group, NK4A214 group, and Alistipes (P < 0.05), which contributed to the metabolic activities of various nutrients. Furthermore, captive AMD showed a higher level of 11 potential opportunistic pathogens and a greater enrichment of disease-related functions compared to wild AMD, indicating that wild musk deer have a lower risk of intestinal diseases and more stable intestinal structure in comparison to captive populations. These findings can serve as a valuable theoretical foundation for promoting the healthy breeding of musk deer and as a guide for evaluating the health of wild-released and reintroduced musk deer in the future. Key points • Wild and captive AMD exhibit contrasting gut microbial diversity and certain functions. • With higher diversity, certain bacteria aid wild AMD’s adaptation to complex habitats. • Higher potential pathogens and functions increase disease risk in captive AMD.

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Comparative Analysis of Gut Microbiota Changes in Père David's Deer Populations in Beijing Milu Park and Shishou, Hubei Province in China

Cited by 25 publications

References 23 publications

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

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

Comparative study on the effects of different feeding habits and diets on intestinal microbiota in Acipenser baeri Brandt and Huso huso

Marked variations in gut microbial diversity, functions, and disease risk between wild and captive alpine musk deer

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