Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys
Donkeys, as single-stomach herbivores, have a complex and diverse microbial community in their digestive tracts. The intestinal bacterial community is crucial for maintaining intestinal homeostasis, as well as the host’s overall nutrition and health. However, research on donkey gut microbes is relat...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1494926/full |
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| author | Yanwei Wang Yanwei Wang Yanwei Wang Tong Hu Tong Hu Kaixuan Liang Kaixuan Liang Shinuo Li Shinuo Li Qiyue Zhang Qiyue Zhang Qiyue Zhang Wenqiang Li Honglei Qu Honglei Qu Boying Dong Haihua Zhang Qiugang Ma Qiugang Ma Ru Jia Shimeng Huang Shimeng Huang |
| author_facet | Yanwei Wang Yanwei Wang Yanwei Wang Tong Hu Tong Hu Kaixuan Liang Kaixuan Liang Shinuo Li Shinuo Li Qiyue Zhang Qiyue Zhang Qiyue Zhang Wenqiang Li Honglei Qu Honglei Qu Boying Dong Haihua Zhang Qiugang Ma Qiugang Ma Ru Jia Shimeng Huang Shimeng Huang |
| author_sort | Yanwei Wang |
| collection | DOAJ |
| description | Donkeys, as single-stomach herbivores, have a complex and diverse microbial community in their digestive tracts. The intestinal bacterial community is crucial for maintaining intestinal homeostasis, as well as the host’s overall nutrition and health. However, research on donkey gut microbes is relatively limited, particularly regarding the microbial colonization patterns in different intestinal segments of adult donkeys. Therefore, this study examined the abundance and function of microbiota across various sites of the intestinal tract (duodenum, jejunum, ileum, cecum, colon) and feces of healthy adult Dezhou male donkeys using 16S rRNA gene sequencing and PICRUSt analysis. The results indicate that donkeys have a rich gut microbial diversity and a large microbial population. No significant differences in the indices of alpha diversity were observed among the donkey’s duodenum, jejunum, ileum, cecum, colon, and feces. A Venn diagram analysis revealed the presence of both unique (Duodenum: 4645; Jejunum: 3586; Ileum: 4904; Cecum: 4253; Colon: 6135; Feces: 4885) and shared (339) ASVs among the different sections. A principal coordinate analysis (PCoA) revealed significant differences (R2 = 0.2076, p < 0.007) across the six intestinal segments of the donkeys. At the phylum level, Firmicutes (63.64%), Bacteroidetes (20.72%), Verrucomicrobiota (9.16%), Patescibacteria (1.95%), Spirochaetota (1.87%), Actinobacteriota (1.13%), and Proteobacteria (0.42%) were the dominant bacteria in all samples. The Wilcoxon rank-sum test revealed significant differences in the proportions of genera among different intestinal segments. Specific genera were significantly enriched in various segments: Lachnospiraceae_UCG-008 and Sphaerochaeta in the duodenum; Christensenellaceae_R-7_group and Bacillus in the jejunum; NK4A214_group and Alloprevotella in the ileum; UCG-005 and Lactobacillus in the cecum; Clostridium_sensu_stricto_1 and Chlamydia in the colon; and Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-004 in the feces. A PICRUSt2 functional prediction analysis indicated that carbohydrate metabolism, prokaryotic cellular communities, antimicrobial drug resistance, immune diseases, membrane transport, signal transduction, and transcription exhibited significant differences among the different intestinal segments. This study provided critical primary data on the differences in donkey gut microbiota and the synergistic effects between gut microbiota and host functions. These findings can be used to assess donkey health status, improve breeding, and develop microbial additives. |
| format | Article |
| id | doaj-art-24ab9fd5edbe4bf696be1d47b573b3c3 |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-24ab9fd5edbe4bf696be1d47b573b3c32025-01-17T06:50:42ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-01-011510.3389/fmicb.2024.14949261494926Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeysYanwei Wang0Yanwei Wang1Yanwei Wang2Tong Hu3Tong Hu4Kaixuan Liang5Kaixuan Liang6Shinuo Li7Shinuo Li8Qiyue Zhang9Qiyue Zhang10Qiyue Zhang11Wenqiang Li12Honglei Qu13Honglei Qu14Boying Dong15Haihua Zhang16Qiugang Ma17Qiugang Ma18Ru Jia19Shimeng Huang20Shimeng Huang21Food Processing and Safety, College of Life Sciences, Shanxi University, Taiyuan, ChinaNational Key Laboratory of Livestock and Poultry Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaLaboratory of Feed Grain Safety and Healthy Poultry Farming, Beijing Jingwa Agricultural Science and Technology Innovation Center, Beijing, ChinaNational Key Laboratory of Livestock and Poultry Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaLaboratory of Feed Grain Safety and Healthy Poultry Farming, Beijing Jingwa Agricultural Science and Technology Innovation Center, Beijing, ChinaNational Key Laboratory of Livestock and Poultry Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaLaboratory of Feed Grain Safety and Healthy Poultry Farming, Beijing Jingwa Agricultural Science and Technology Innovation Center, Beijing, ChinaNational Key Laboratory of Livestock and Poultry Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaLaboratory of Feed Grain Safety and Healthy Poultry Farming, Beijing Jingwa Agricultural Science and Technology Innovation Center, Beijing, ChinaNational Key Laboratory of Livestock and Poultry Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaLaboratory of Feed Grain Safety and Healthy Poultry Farming, Beijing Jingwa Agricultural Science and Technology Innovation Center, Beijing, ChinaCollege of Animal Science and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning, ChinaLaboratory of Feed Grain Safety and Healthy Poultry Farming, Beijing Jingwa Agricultural Science and Technology Innovation Center, Beijing, ChinaNational Key Laboratory of Livestock and Poultry Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaNational Engineering Research Center for Gelatin-Based Traditional Chinese Medicine, Dong-E-E-Jiao Co., Ltd., Liaocheng, ChinaNational Engineering Research Center for Gelatin-Based Traditional Chinese Medicine, Dong-E-E-Jiao Co., Ltd., Liaocheng, ChinaHebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, ChinaNational Key Laboratory of Livestock and Poultry Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaLaboratory of Feed Grain Safety and Healthy Poultry Farming, Beijing Jingwa Agricultural Science and Technology Innovation Center, Beijing, ChinaFood Processing and Safety, College of Life Sciences, Shanxi University, Taiyuan, ChinaNational Key Laboratory of Livestock and Poultry Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, ChinaLaboratory of Feed Grain Safety and Healthy Poultry Farming, Beijing Jingwa Agricultural Science and Technology Innovation Center, Beijing, ChinaDonkeys, as single-stomach herbivores, have a complex and diverse microbial community in their digestive tracts. The intestinal bacterial community is crucial for maintaining intestinal homeostasis, as well as the host’s overall nutrition and health. However, research on donkey gut microbes is relatively limited, particularly regarding the microbial colonization patterns in different intestinal segments of adult donkeys. Therefore, this study examined the abundance and function of microbiota across various sites of the intestinal tract (duodenum, jejunum, ileum, cecum, colon) and feces of healthy adult Dezhou male donkeys using 16S rRNA gene sequencing and PICRUSt analysis. The results indicate that donkeys have a rich gut microbial diversity and a large microbial population. No significant differences in the indices of alpha diversity were observed among the donkey’s duodenum, jejunum, ileum, cecum, colon, and feces. A Venn diagram analysis revealed the presence of both unique (Duodenum: 4645; Jejunum: 3586; Ileum: 4904; Cecum: 4253; Colon: 6135; Feces: 4885) and shared (339) ASVs among the different sections. A principal coordinate analysis (PCoA) revealed significant differences (R2 = 0.2076, p < 0.007) across the six intestinal segments of the donkeys. At the phylum level, Firmicutes (63.64%), Bacteroidetes (20.72%), Verrucomicrobiota (9.16%), Patescibacteria (1.95%), Spirochaetota (1.87%), Actinobacteriota (1.13%), and Proteobacteria (0.42%) were the dominant bacteria in all samples. The Wilcoxon rank-sum test revealed significant differences in the proportions of genera among different intestinal segments. Specific genera were significantly enriched in various segments: Lachnospiraceae_UCG-008 and Sphaerochaeta in the duodenum; Christensenellaceae_R-7_group and Bacillus in the jejunum; NK4A214_group and Alloprevotella in the ileum; UCG-005 and Lactobacillus in the cecum; Clostridium_sensu_stricto_1 and Chlamydia in the colon; and Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-004 in the feces. A PICRUSt2 functional prediction analysis indicated that carbohydrate metabolism, prokaryotic cellular communities, antimicrobial drug resistance, immune diseases, membrane transport, signal transduction, and transcription exhibited significant differences among the different intestinal segments. This study provided critical primary data on the differences in donkey gut microbiota and the synergistic effects between gut microbiota and host functions. These findings can be used to assess donkey health status, improve breeding, and develop microbial additives.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1494926/fulldonkeyintestinespatial variationsmicrobial compositionpredicted functions |
| spellingShingle | Yanwei Wang Yanwei Wang Yanwei Wang Tong Hu Tong Hu Kaixuan Liang Kaixuan Liang Shinuo Li Shinuo Li Qiyue Zhang Qiyue Zhang Qiyue Zhang Wenqiang Li Honglei Qu Honglei Qu Boying Dong Haihua Zhang Qiugang Ma Qiugang Ma Ru Jia Shimeng Huang Shimeng Huang Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys Frontiers in Microbiology donkey intestine spatial variations microbial composition predicted functions |
| title | Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys |
| title_full | Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys |
| title_fullStr | Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys |
| title_full_unstemmed | Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys |
| title_short | Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys |
| title_sort | spatial variations in the microbiota comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys |
| topic | donkey intestine spatial variations microbial composition predicted functions |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1494926/full |
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