|Table of Contents|

Diversity and community structure of gut microbiomes of captive giant pandas in different regions(PDF)

Chinese Journal of Applied & Environmental Biology[ISSN:1006-687X/CN:51-1482/Q]

Issue:
2021 05
Page:
1218-1225
Research Field:
Articles
Publishing date:

Info

Title:
Diversity and community structure of gut microbiomes of captive giant pandas in different regions
Author(s):
WANG Xin1 LI Caiwu2 JIN Lei1 ZHAO Lingling3 DENG Wenwen2 LI Ti2 XIONG Yuewu2 ZHANG Guiquan2 LI Guo2 HE Yongguo2 WU Daifu2 ZHANG Hemin2 HUANG Yan2? & ZOU Likou1?
1 College of Resources, Sichuan Agricultural University, Chengdu 611130, China 2 Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda (CCRCGP), Dujiangyan 611830, China 3 Nanjing Hongshan Forest Zoo, Nanjing 210028, China
Keywords:
giant panda captive high-throughput sequencing technology gut microbiome diversity
CLC:
-
PACS:
DOI:
10.19675/j.cnki.1006-687x.2020.06072
DocumentCode:

Abstract:
The gut microbiota of giant pandas are varied, with the age and living environment of the animals being important factors affecting the composition of their intestinal microbiota. This study investigated the regional differences therein by examining the structure and composition of bacteria from 74 giant pandas from different regions using high-throughput sequencing technology. The results showed that the most dominant phyla in the giant panda microbiota were Proteobacteria (61.95%) and Firmicutes (29.08%). At the genus level, the bacteria consisted mainly of Escherichia (24.92%), Pseudomonas (21.60%), Streptococcus (9.33%), Clostridium (9.58%), and Sphingobacterium (6.74%). When the giant pandas at the China Conservation and Research Center for the Giant Panda were transferred to other cities or regions, the core bacterial species–such as Escherichia, Pseudomonas, Streptococcus, and Clostridium remained present, although it appears that there were changes in their abundance and unique flora were also developed. There was no significant difference (P > 0.05) in the alpha diversity of sub-adult giant panda gut microbiomes; however, the gut microbiomes of sub-adult giant pandas in the Baoding and Guangzhou groups were significantly different (P < 0.05) based on beta diversity. The community diversity of the adult giant panda gut microbiomes in the Hetaoping and Shanghai groups was significantly different (P < 0.05) based on alpha diversity, while there was no significant difference among all adult giant pandas based on beta diversity (P >0.05). A similar gut bacterial community was found in giant pandas that ate the same kind of bamboo but otherwise were from widely different regions. Overall, geographical environments could probably affect the intestinal microbiota of captive giant pandas. Feeding these animals different kinds of bamboo has become one of the major factors causing a difference to develop in the intestinal microbial structure of captive giant pandas from different regions.

References

1 宗雪, 崔国发, 袁婧. 基于条件价值法的大熊猫(Ailuropoda melanoleuca)存在价值评估[J]. 生态学报, 2008, 28 (5): 2090-2098 [Zong X, Cui GF, Yuan J. Contingent valuation of the existent economic of giant panda (Ailuropoda melanoleuca) [J]. Acta Ecol Sin, 2008, 28 (5): 2090-2098]
2 Meng QK, Miao F, Zhen J, Huang Y, Wang XY, Peng Y. Impact of earthquake-induced landslide on the habitat suitability of giant panda in Wolong, China [J]. J Mount Sci, 2016, 13 (10): 1789-1805
3 鲍楠, 刘成君, 张和民, 李德生. 大熊猫肠道微生态的研究进展[J]. 畜牧与兽医, 2005, 37 (4): 57-59 [Bao N, Liu CJ, Zhang HM, Li DS. Advances in intestinal microecology of giant panda [J]. Anim Husb Veter Med, 2005, 37 (4): 57-59]
4 张泽钧, 张陕宁, 魏辅文, 王鸿加, 李明, 胡锦矗. 移地与圈养大熊猫野外放归的探讨[J]. 兽类学报, 2006, 26 (3): 292-299 [Zhang ZJ, Zhang SN, Wei FW, Wang HJ, Li M, Hu JC. Translocation and discussion on reintroduction of captive giant panda [J]. Acta Ther Sin, 2006, 26 (3): 292-299]
5 鲍楠, 刘成君, 谭志, 张和民, 李德生. 野外放归大熊猫肠道菌群变化的研究[J]. 畜牧与兽医, 2005, 37 (8): 10-13 [Bao N, Liu CJ, Tan Z, Zhang HM, Li DS. Changes of intestinal microflora in the giant panda returned to wild [J]. Anim Husb Veter Med, 2005, 37 (8): 10-13]
6 Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo CW, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ. The treatment-naive microbiome in new-onset Crohn’s disease [J]. Cell Host Micr, 2014, 15 (3): 382-392
7 孙飞龙, 刘敬贤, 席丹, 王万云, 高更更, 冯宁, 杨水云. 大熊猫肠道疾病致病菌[J]. 经济动物学报, 2002, 6 (2): 20-23 [Sun LF, Liu JX, Xi D, Wang WY, Gao GG, Feng N, Yang SY. Pathogens of intestinal diseases in giant panda [J]. J Econ Anim, 2002, 6 (2): 20-23]
8 Mueller S, Saunier K, Hanisch C, Norin E, Alm L, Midtvedt T, Cresci A, Silvi S, Orpianesi C, Verdenelli MC. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study[J]. Appl Environ Microb, 2006, 72 (2): 1027-1033
9 郭壮. 应用焦磷酸测序技术对不同人群肠道微生物群落结构的研究[D]. 无锡: 江南大学, 2013 [Guo Z. Study on the structure of gut microbiota in different ethnic groups by pyrosequencing [D]. Wuxi: Jiangnan University, 2013]
10 叶莉, 吴芳, 王昱佳, 郑珺文, 白杰英. 中国不同地区恒河猴肠道菌群的微生物组学特性分析[C]//中国畜牧兽医学会动物传染病学分会第十六次学术研讨会. 中国畜牧兽医学会动物传染病学分会第十六次学术研讨会论文集. 济南: 中国畜牧兽医学会, 2015: 324 [Ye L, Wu F, Wang YJ, Zheng JW, Bai JY. Analysis of the microbiome characteristics of the intestinal flora of rhesus monkeys in different regions of China[C]//The 16th Symposium of the Animal Infectious Diseases Branch of the Chinese Society of Animal Husbandry and Veterinary Medicine. Proceedings of the 16th Symposium of the Chinese Society of Animal Husbandry and Veterinary Medicine. Jinan: Chinese Society of Animal Husbandry and Veterinary Medicine, 2015: 324]
11 尹业师, 王欣. 影响实验小鼠肠道菌群的多因素比较研究[J]. 实验动物科学, 2012, 29 (4): 12-18 [Yin YS, Wang X. Comparative study for factors that affect microbiota colonization in experimental mice [J]. Labor Anim Sci, 2012, 29 (4): 12-18]
12 Zhao S, Li C, Li G, Yang S, Zhou Y, He Y, Wu D, Zhou Y, Zeng W, Li T. Comparative analysis of gut microbiota among the male, female and pregnant giant pandas (Ailuropoda Melanoleuca) [J]. Open Life Sci, 2019, 14: 288-298
13 李果, 王鑫, 李才武, 周应敏, 吴代福, 黄炎, 张和民, 邹立扣. 圈养老年大熊猫肠道内菌群结构研究[J]. 黑龙江畜牧兽医, 2019 (8):160-164, 185-186[ Li G, Wang X, Li CW, Zhou YM, Wu DF, Huang Y, Zhang HM, Zou LK. Study on intestinal flora structure of captive aged giant panda [J]. Heilongjiang Anim Sci Veter Med, 2019 (8): 160-164, 185-186]
14 刘燕, 王曦, 刘学锋, 李林海, 郑常明, 夏茂华, 张成林. 北京动物园3只亚成体大熊猫粪便菌群比较分析[J]. 野生动物学报, 2018, 39 (1): 19-23 [Liu Y, Wang X, Liu XF, Li LH, Zheng CM, Xia MH, Zou CL. Fecal bacteria diversity of three sub-adult giant panda of the Beijing Zoo [J]. Chin J Wildl, 2018, 39 (1): 19-23]
15 何永果, 晋蕾, 李果, 李才武, 李蓓, 李伟, 张亚辉, 胡正泉, 黄炎, 张和民, 邹立扣. 基于高通量测序技术研究成年大熊猫肠道菌群[J]. 应用与环境生物学报, 2017, 23 (5): 771-777 [He YG, Jin L, Li G, Li CW, Li B, Li W, Zhang YH, Hu ZQ, Huang Y, Zhang HM, Zou Likou. Gut microbiome of adult giant pandas based on high-throughput sequencing technology [J]. Chin J Appl Environ Biol, 2017, 23 (5): 771-777]
16 Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform [J]. Microbiome, 2014, 2 (1): 6-6
17 Mago? T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies [J]. Bioinformatics, 2011, 27 (21): 2957-2963
18 Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads [J]. Nat Methods, 2013, 10 (10): 996-998
19 Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection [J]. Bioinformatics, 2011, 27 (16): 2194-2200
20 Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput [J]. Nucleic Acids Res, 2004, 32 (5): 1792-1797
21 王岚. 不同年龄段圈养大熊猫肠道微生物群落多样性的研究[D]. 南充: 西华师范大学, 2019 [Wang L. The diversity of capative giant panda gut microbiome viewed across age [D]. Nanchong: China West Normal University, 2019]
22 王晓燕. 成年与老年大熊猫肠道菌群16S rDNA-RFLP技术分析[D]. 雅安: 四川农业大学, 2013 [Wang XY. Analysis the intestinal flora of adult and elderly panda by 16S rDNA-RFLP technology [D]. Ya’an: Sichuan Agriculture University, 2013]
23 王燚. 基于ERIC-PCR和16S rDNA-RFLP技术对亚成体大熊猫肠道菌群结构的研究[D]. 雅安: 四川农业大学, 2011 [Wang Y. Estimation of giant panda’s intestinal flora structure in intestine based on 16S rDNA-RFLP technologies [D]. Ya’an: Sichuan Agriculture University, 2011]
24 王晓艳, 袁听, 廖虹, 罗永久, 何延美, 王承东, 刘小敏, 吴虹林, 彭广能. 圈养老年大熊猫肠道菌群16S rDNA克隆文库的建立[J]. 中国畜牧兽医, 2015, 42 (6): 1402-1408 [Wang XY, Yuan T, Liao H, Luo YJ, He YM, Wang CD, Liu XM, Wu HL, Peng GN. Construction of the 16S rDNA clone library of intestinal flora of captive elderly giant panda [J]. Anim Husb Vet Med, 2015, 42 (6): 1402-1408]
25 Tun HM, Mauroo NF, Yuen CS, Ho JC, Wong MT, Leung FC. Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca) [J]. PLoS ONE, 2014, 9 (1): e79902
26 晋蕾, 邓晴, 李才武, 邓雯文, 杨盛智, 周宇, 曾文, 冯莉, 张和民, 何永果, 邹立扣. 幼年大熊猫断奶前后肠道微生物与血清生化及代谢物的变化[J]. 应用与环境生物学报, 2019, 25 (6): 1477-1485 [Jin L, Deng Q, Li CW, Deng WW, Yang SZ, Zhou Y, Zeng W, Feng L, Zhang HM, He YG, Zou LK. Variations in gut microbiota and the biochemical characteristics of serum and serum metabolites before and after cub giant panda weaning [J]. Chin J Appl Environ Biol, 2019, 25 (6): 1477-1485]
27 Guo M, Chen J, Li Q, Fu Y, Fan G, Ma J, Peng L, Zeng L, Chen J, Wang Y. Dynamics of gut microbiome in giant panda cubs reveal transitional microbes and pathways in early life [J]. Front Microbiol, 2018, 9: 3138
28 Yang S, Gao X, Meng J, Zhang A, Zhou Y, Long M, Li B, Deng W, Jin L, Zhao S. Metagenomic analysis of bacteria, fungi, bacteriophages, and helminths in the gut of giant pandas [J]. Front microbiol, 2018, 9: 1717
29 Oyeleke SB. Isolation and characterization of cellulose hydrolysing microorganism from the rumen of ruminants [J]. Afr J Biotechnol, 2008, 7 (10):1503-1504
30 Williams CL, Dill-Mcfarland KA, Vandewege MW, Sparks DL, Willard ST, Kouba AJ, Suen G, Brown AE. Dietary shifts may trigger dysbiosis and mucous stools in giant pandas (Ailuropoda melanoleuca) [J]. Front microbiol, 2016, 7: 661-661
31 Zhu L, Wu Q, Dai J, Zhang S, Wei F. Evidence of cellulose metabolism by the giant panda gut microbiome [J]. PNAS, 2011, 108 (43): 17714-17719
32 Lambiase A, Rossano F, Del Pezzo M, Raia V, Sepe A, De Gregorio F, Catania M R. Sphingobacterium respiratory tract infection in patients with cystic fibrosis [J]. BMC Res Notes, 2009, 2: 262
33 Cheng JF, Guo JX, Bian YN, Chen ZL, Li CL, Li XD, Li YH. Sphingobacterium athyrii sp. nov., a cellulose- and xylan-degrading bacterium isolated from a decaying fern (Athyrium wallichianum Ching) [J]. Int J Syst Evol Microbiol, 2019, 69 (3): 752-760
34 Pernas-Pardavila H, Vallejo-Alonso AM, Novo-Veleiro I, De La Cruz DN, González-Quintela A. Sphingobacterium multivorum: An Atypical Bacterium in an Atypical Place [J]. Eur Eur J Case Rep Intern Med, 2019, 6 (9): 001214
35 詹明晔, 付小花, 张姝, 张鑫, 杨海迪, 俞锦华, 王爱善, 王磊. 不同地区成体大熊猫肠道微生物结构差异性及其与纤维素消化能力的相关性[J]. 应用与环境生物学报, 2019, 25 (3): 736-742 [Zhan MY, Fu XH, Zhang S, Zhang X, Yang HD, Yu JH, Wang AS, Wang L. Differences of the intestinal microbial structure of adult giant panda in different regions and its correlation with the digestibility of cellulose [J]. Chin J Appl Environ Biol, 2019, 25 (3): 736-742]
36 叶志勇, 吕文其, 刘新华, 姜文球, 权洙浣, 金银规, 李昌雨. 大熊猫小肠结肠炎耶尔森氏菌感染及治疗[J]. 中国兽医杂志, 1998 (8): 11 [Ye ZY, Lü WQ, Liu XH, Jiang WQ, Quan ZH, Jin YG, Li CY. Treatment and infection of Yersinia in enterocolitis of Panda [J]. Chin J Anim Sci, 1998 (8): 11]
37 Li K, Dan Z, Gesang L, Wang H, Zhou Y, Du Y, Ren Y, Shi Y, Nie Y. Comparative analysis of gut microbiota of native tibetan and han populations living at different altitudes [J]. PloS ONE, 2016, 11 (5): e0155863
38 Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Gaskins HR, Stumpf RM, Yildirim S, Torralba M, Gillis M, Wilson BA, Nelson KE, White BA, Leigh SR. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes [J]. ISME J, 2013, 7 (7): 1344-1353
39 Barelli C, Albanese D, Donati C, Pindo M, Dallago C, Rovero F, Cavalieri D, Tuohy KM, Hauffe HC, De Filippo C. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation [J]. Sci Rep, 2015, 5: 14862
40 Chevalier C, Stojanovi? O, Colin DJ, Suarez-Zamorano N, Tarallo V, Veyrat-Durebex C, Rigo D, Fabbiano S, Stevanovi? A, Hagemann S, Montet X, Seimbille Y, Zamboni N, Hapfelmeier S, Trajkovski M. Gut microbiota orchestrates energy homeostasis during cold [J]. Cell, 2015, 163 (6): 1360-1374
41 Zhao J, Yao Y, Li D, Xu H, Wu J, Wen A, Xie M, Ni Q, Zhang M, Peng G, Xu H. Characterization of the gut microbiota in six geographical populations of Chinese rhesus macaques (Macaca mulatta), implying an adaptation to high-altitude environment [J]. Microb Ecol, 2018, 76 (2): 565-577
42 Jin L, Wu D, Li C, Zhang A, Xiong Y, Wei R, Zhang G, Yang S, Deng W, Li T. Bamboo nutrients and microbiome affect gut microbiome of giant panda [J]. Symbiosis, 2020, 80 (3): 293-304

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