圈养腹泻和健康林麝粪便菌群差异分析

doi:10.16431/j.cnki.1671-7236.2025.08.029

摘要/Abstract

摘要： 【目的】对比分析圈养条件下腹泻和健康林麝粪便菌群组成和多样性差异，找出具有显著差异的生物标志菌群，为防治林麝腹泻提供参考。【方法】利用Illumina NovaSeq 6000平台对腹泻(D组，n=10)和健康(H组，n=10)林麝粪便菌群总DNA中16S rRNA基因V3-V4区测序，分析D和H组林麝粪便在菌群组成、多样性、标志菌群和功能之间的差异。【结果】 Alpha多样性分析结果显示，D组林麝粪便中菌群的ACE和Chao1指数显著高于H组(P＜0.05)，Simpson和Shannon指数低于H组，其中Simpson指数差异显著(P＜0.05)；Beta多样性分析结果显示，D和H组间的菌群群落结构存在显著差异(R²＝0.55，P＝0.001)；门水平上，厚壁菌门(Firmicutes)是2组的共有优势菌门，差异菌门包括拟杆菌门(Bacteroidota)、变形菌门(Proteobacteria)和放线菌门(Actinobacteriota)。属水平上，瘤胃菌科UCG 005属(Ruminococcaceae_UCG_005)是2组的共有优势菌属，差异菌属包括不动杆菌属(Acinetobacter)、拟杆菌属(Bacteroides)和理研菌科RC9属(Rikenellaceae_RC9_gut_group)；D组有奥尔森菌属(Olsenella)等23个标志菌群，H组有理研菌科RC9属等15个标志菌群；基于PICRUSt2功能预测发现，与H组相比，D组膜转运、氨基酸运输与代谢、内分泌与代谢疾病等功能丰度显著增加(P＜0.05)，而次级代谢物的合成、细胞增殖与凋亡、免疫防御等显著下降(P＜0.05)。【结论】腹泻会显著改变林麝肠道菌群组成、菌群多样性和功能丰度，肠道中不动杆菌属、奥尔森菌属和理研菌科RC9属等菌群的丰度是判断林麝肠道健康状态的特征标志菌群。

关键词: 林麝; 腹泻; 粪便菌群; 多样性

Abstract: 【Objective】 This study aimed to comparatively analyze the differences in the composition and diversity of fecal flora between diarrheal and healthy forest musk deer under captive conditions,and identify the biomarker flora with significant differences,so as to provide a reference for the prevention and treatment of diarrhea in forest musk deer. 【Method】 Illumina NovaSeq 6000 platform was used to sequence the V3-V4 region of 16S rRNA gene in the total DNA of fecal flora of diarrhea (group D,n=10) and healthy (group H,n=10) forest musk deer,and the differences between groups D and H in the composition,diversity,biomarker flora and functions of the flora were analyzed. 【Result】 Alpha diversity analysis results showed that ACE and Chao1 indices of fecal microfiota of forest musk deer in group D were significantly higher than those of group H (P＜0.05),while the Simpson and Shannon indices were lower than those of group H,with a significant difference in the Simpson index between the two groups (P＜0.05).The results of Beta diversity showed that there was a significant difference in the community structure of flora between groups D and H (R²＝0.55，P＝0.001).The results showed that at phylum level,Firmicutes was the dominant phylum in both groups.The differential phyla included Bacteroidota,Proteobacteria and Actinobacteriota.At genus level,Ruminococcaceae_UCG_005 emerged as the common dominant genus in both groups,while the differential genera included Acinetobacter,Bacteroides and Rikenellaceae_RC9_gut_group.Group D contained 23 marker microbiota such as Olsenella,and group H had 15 marker microbiota such as Rikenellaceae_RC9_gut_group.Based on PICRUSt2 function prediction,it was found that compared with group H,group D was significantly increased in membrane transport,amino acid transport and metabolism,endocrine and metabolic diseases (P＜0.05),and significantly decreased in the biosynthesis of other secondary metabolites,cell growth and death,defense mechanisms (P＜0.05). 【Conclusion】 Diarrhea could significantly change the composition,diversity and functional abundance of the intestinal flora of forest musk deer.The abundance of Acinetobacter,Olsenella and Rikenellaceae_RC9_gut_group in the gut were characteristic markers of the intestinal health of forest musk deer.

Key words: forest musk deer; diarrhea; fecal microbita; diversity

中图分类号:

S865.4^＋1

张杰, 郑雪莉, 姜艳芬, 王洪永, 乔美萍, 唐清山, 卜书海. 圈养腹泻和健康林麝粪便菌群差异分析[J]. 中国畜牧兽医, 2025, 52(8): 3810-3819.

ZHANG Jie, ZHENG Xueli, JIANG Yanfen, WANG Hongyong, QIAO Meiping, TANG Qingshan, BU Shuhai. Analysis of the Differences in Fecal Microbiota Between Diarrheic and Healthy Captive Forest Musk Deer[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(8): 3810-3819.

参考文献

[1] 魏辅文，杨奇森，吴毅，等.中国兽类分类与分布[M].北京：科学出版社，2022. WEI F W,YANG Q S,WU Y,et al.Taxonomy and Distribution of Mammals in China[M].Beijing:Science Press,2022.(in Chinese)
[2] 王永奇，孟秀祥.陕西省林麝驯养分布、种群动态及疾病发生[J].生态学杂志，2014，33(10):2720-2726. WANG Y Q,MENG X X.The current status and disease occurrence of captive forest musk deer (Moschus berezovskii) in Shaanxi province[J].Chinese Journal of Ecology,2014,33(10):2720-2726.(in Chinese)
[3] CHEN S Y,LUO S Y,YAN C.Gut microbiota implications for health and welfare in farm animals:A review[J].Animals,2021,12(1):93.
[4] 许珂，卜书海，梁宗锁，等.林麝研究进展[J].黑龙江畜牧兽医，2014，7:147-150. XU K,BU S H,LIANG Z S,et al.Research progress in forest musk deer[J].Heilongjiang Animal Science and Veterinary Medicine,2014,7:147-150.(in Chinese)
[5] LI Y M,HU X L,YANG S,et al.Comparison between the fecal bacterial microbiota of healthy and diarrheic captive musk deer[J].Frontiers in Microbiology,2018,2(9):300.
[6] 赵贵军，封孝兰，朱吉彬，等.成年与未成年圈养林麝粪便菌群多样性的比较[J].兽类学报，2019，39(3):266-275. ZHAO G J,FENG X L,ZHU J B,et al.Comparative analysis of fecal microbiota of captive musk deer in juvenile and adult[J].Acte Theriologica Sinica,2019,39(3):266-275.(in Chinese)
[7] LI Y M,HU X L,YANG S,et al.Comparative analysis of the gut microbiota composition between captive and wild forest musk deer[J].Frontiers in Microbiology,2017,8:1705.
[8] 江峰，宋鹏飞，张婧捷，等.不同养殖场林麝肠道微生物组成和功能的差异[J].兽类学报，2023，43(2):129-140. JIANG F,SONG P F,ZHANG J J,et al.Comparative analysis of gut microbial composition and functions of forest musk deer in different breeding centres[J].Acte Theriologica Sinica,2023,43(2):129-140.(in Chinese)
[9] 刘旭.林麝复合微生态制剂对育成林麝几种免疫相关因子及肠道菌群的影响[D].成都：四川农业大学，2020. LIU X.Effects of compound probiotics on the immunerelated factors and gut microbiota of growing forest musk deer[D].Chengdu:Sichuan Agricultural University,2020.(in Chinese)
[10] 伍林红.林麝源益生菌的效用评价及微胶囊的制备[D].杨凌：西北农林科技大学，2023. WU L H.Efficacy evaluation of probiotics from Moschus berezovskii and preparation of microcapsules[D].Yangling:Northwest A&F University,2023.(in Chinese)
[11] HAO Z,DING X D,WANG J.Effects of gut bacteria and their metabolites on gut health of animals[J].Advances in Applied Microbiology,2024,127:223-252.
[12] JIANG X T,PENG X,DENG G H,et al.Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland[J].Microbial Ecology,2013,66(1):96-104.
[13] GUO W,REN K,NING R,et al.Fecal microbiota transplantation provides new insight into wildlife conservation[J].Global Ecology and Conservation,2020,24:e01234.
[14] PÉREZ B V E,ALTEMANN E,TUDISCO R,et al.Editorial:Recent advances and perspectives on the gastrointestinal microbiota of small ruminants[J].Frontiers in Microbiology,2024,15:1473958.
[15] CUI S W,GUO S H,ZHAO Q M,et al.Alterations of microbiota and metabolites in the feces of calves with diarrhea associated with Rotavirus and Coronavirus infections[J].Frontiersin Microbiology,2023,14:1159637.
[16] HE Z Y,MA Y L,YANG S R,et al.Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia coli infection[J].Microbiome,2022,10(1):79.
[17] 赵清梅，崔省委，郭仕辉，等.腹泻犊牛粪便菌群及粪便代谢物的变化特征分析[J].中国畜牧兽医，2024，51(9):4092-4105. ZHAO Q H,CUI S W,GUO S H,et al.Characteristics of microbiota and metabolites in feces of calves with diarrhea[J].China Animal Husbandry & Veterinary Medicine,2024,51(9):4092-4105.(in Chinese)
[18] ZHU H L,ZHAO X W,HAN R W,et al.Changes in bacterial community and expression of genes involved in intestinal innate immunity in the jejunum of newborn lambs during the first 24 hours of life[J].Journal of Dairy Science,2021,104(8):9263-9275.
[19] 苏日娜.原麝全基因组学及肠道菌群多样性和基因功能分析研究[D].呼和浩特：内蒙古农业大学，2022. SU R N.Study on the whole genome sequencing of Siberian musk deer and analysis of gut microbiome diversity and gene function[D].Hohhot:Inner Mongolia Agricultural University,2022.(in Chinese)
[20] 杜欣颖，夏介英，李东晓，等.健康与腹泻林麝肠道菌群的多态性[J].中国微生态学杂志，2021，33(7):745-751. DU X Y,XIA J Y,LI D X,et al.Polymorphism of fecal microbiota of healthy vs diarrhea musk deer[J].Chinese Journal of Microecology,2021,33(7):745-751.(in Chinese)
[21] JIANG F,SONG P F,WANG H J,et al.Comparative analysis of gut microbial composition and potential functions in captive forest and Alpine musk deer[J].Applied Microbiology and Biotechnology,2022,106(3):1325-1339.
[22] JIANG C X,HOU X L,GAO X N,et al.The 16S rDNA high-throughput sequencing correlation analysis of milk and gut microbial communities in mastitis Holstein cows[J].BMC Microbiology,2023,23(1):180.
[23] 马友记，陈鹏飞，马青，等.不同运动量对滩羊瘤胃菌群多样性的影响[J].畜牧兽医学报，2023，54(8):3393-3405. MA Y J,CHEN P F,MA Q,et al.Effects of different exercise amounts on rumen microflora diversity of Tan sheep[J].Acta Veterinaria et Zootechnica Sinica,2023,54(8):3393-3405.(in Chinese)
[24] WAITE D W,TAYLOR M W.Characterizing the avian gut microbiota:Membership,driving influences,and potential function[J].Frontiers in Microbiology,2014,5:223.
[25] SHIN N R,WHON T W,BAE J W.Proteobacteria:Microbial signature of dysbiosis in gut microbiota[J].Trends in Biotechnology,2015,33(9):496-503.
[26] COSTA M C,ARROYO L G,ALLEN-VERCOE E,et al.Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene[J].PLoS One,2017,7(7):e41484.
[27] HALIM J,CARR R A,FLIORENT R,et al.Combinations of antibiotics effective against extensively- and pandrug-resistant Acinetobacter baumannii patient isolates[J].Microorganisms,2024,12(7):1353.
[28] PAOLA F N,LUISA M D.Editorial on the research topic of the special issue "current status of acinetobacter infections"[J].Pathogens,2023,12(2):219.
[29] 何森，曹新芳，郑雪莉，等.宏基因组测序分析野生林麝瘤胃、小肠和大肠微生物组成和抗生素抗性基因[J].动物营养学报，2021，33(1):484-493. HE S,CAO X F,ZHENG X L,et al.Composition of microbiota antibiotic resistance genes in rumen,small intestine and large intestine of wild forest musk deer analyzed by metagenomic sequencing[J].Chinese Journal of Animal Nutrition,2021,33(1):484-493.(in Chinese)
[30] 王小琪.青藏高原动物肠道微生物数据挖掘与生物标记物筛选研究[D].合肥：中国科学技术大学，2022. WANG X Q.Data mining and biomarker screening of animal intestinal micobiota in the Qinhai-Tibetan plateau[D].Hefei:University of Science and Technology of China,2022.(in Chinese)
[31] 张玉莹，刘书杰，冯宇哲，等.基于16S rRNA测序分析正常与腹泻牦牛犊牛粪便细菌区系组成[J].中国畜牧兽医，2021，48(9):3293-3302. ZHANG Y Y,LIU S J,FENG Y Z,et al.Bacterial flora composition of normal and diarrhea yak calves based on 16S rRNA sequencing[J].China Animal Husbandry & Veterinary Medicine,2021,48(9):3293-3302.(in Chinese)