兽类学报 ›› 2022, Vol. 42 ›› Issue (5): 519-530.DOI: 10.16829/j.slxb.150721
张良志1,2, 唐显江1,3, 任世恩1,3, 赵雅琪1,3, 张堰铭1,2()
收稿日期:
2022-08-02
接受日期:
2022-08-22
出版日期:
2022-09-30
发布日期:
2022-09-21
通讯作者:
张堰铭
作者简介:
张良志 (1981- ),女,副研究员,主要从事分子生态学研究.
基金资助:
Liangzhi ZHANG1,2, Xianjiang TANG1,3, Shien Ren1,3, Yaqi ZHAO1,3, Yanming ZHANG1,2()
Received:
2022-08-02
Accepted:
2022-08-22
Online:
2022-09-30
Published:
2022-09-21
Contact:
Yanming ZHANG
摘要:
群落生态构建过程是近年来微生物群落生态学的研究热点。室内饲养可引起肠道菌群的剧烈变化,这种改变是否会影响群落的构建过程,一直未见报道。本文以高原鼠兔 (Ochotona curzoniae) 为对象,采用16S rRNA测序技术,探讨室内饲养和野生高原鼠兔肠道微生物群落在结构、功能以及群落构建过程等方面的差异。结果表明,在繁殖季节,室内饲养组的群落多样性指数和均匀度指数均显著低于野外组;群落丰度指数和群落覆盖度指数在非繁殖季节显著高于繁殖季节。拟杆菌门 (Bacteroidetes) 在室内饲养组显著富集,而厚壁菌门 (Firmicute) 和浮霉菌门 (Planctomycetes) 在野外组显著富集;在野外组,Epsilonbacteraeota和软壁菌门 (Tenericutes) 在繁殖季节显著富集。菌群功能分析显示,室内饲养组与野生组在细胞通讯和心血管疾病通路存在显著差异;野外组繁殖季节与非繁殖季节肠道菌群功能在氨基酸代谢、碳水化合物代谢和脂质代谢等通路存在显著差异。中性模型拟合结果表明,室内饲养明显降低了菌群构建的随机过程。野外组生理状态也会降低菌群构建的随机性。本研究证明室内饲养和宿主生理状态均会对高原鼠兔肠道菌群组成及群落构建产生影响,此结果为实现高原鼠兔室内繁殖提供了新的理论基础。
中图分类号:
张良志, 唐显江, 任世恩, 赵雅琪, 张堰铭. 室内饲养对高原鼠兔肠道微生物群落构建过程的影响[J]. 兽类学报, 2022, 42(5): 519-530.
Liangzhi ZHANG, Xianjiang TANG, Shien Ren, Yaqi ZHAO, Yanming ZHANG. Effects of captivity on the assembly process of microbiota communities of plateau pikas[J]. ACTA THERIOLOGICA SINICA, 2022, 42(5): 519-530.
图1 不同组间高原鼠兔肠道微生物alpha多样性指数差异. a:Sobs指数;b:Ace指数;c:Chao指数;d:Coverage 指数;e:Shannon指数;f: Shannoneven指数
Fig. 1 Differences in alpha diversity of the gut microbiota among three plateau pika groups. a: Sobs index; b: Ace index; c: Chao index; d: Coverage index; e: Shannon index; f: Shannoneven index
图2 不同组间高原鼠兔肠道微生物结构变化. a:依据不加权UniFrac 距离的PCoA;b:依据加权UniFrac 距离的PCoA
Fig. 2 The structure of the gut microbiota among different plateau pika groups. a: PCoA based on unweighted UniFrac distances; b: PCoA based on weighted UniFrac distances
图3 不同组间高原鼠兔肠道微生物组成分析. a:门水平组成;b:科水平组成.
Fig. 3 Differences in taxonomic compositions of the gut microbiota among different plateau pika groups. a: phylum level; b: family level
OTU ID | Cap_Apr | Wild_Apr | Wild_Jan |
---|---|---|---|
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes | 0.339 225 | 0.641 988 | 0.659 580 |
d__Bacteria; k__norank_d__Bacteria; p__Bacteroidetes | 0.558 989 | 0.225 796 | 0.252 759 |
d__Bacteria; k__norank_d__Bacteria; p__Epsilonbacteraeota | 0.028 674 | 0.063 268 | 0.012 728 |
d__Bacteria; k__norank_d__Bacteria; p__Spirochaetes | 0.031 141 | 0.021 820 | 0.019 720 |
d__Bacteria; k__norank_d__Bacteria; p__Verrucomicrobia | 0.010 711 | 0.009 175 | 0.015 093 |
d__Bacteria; k__norank_d__Bacteria; p__Proteobacteria | 0.006 001 | 0.011 293 | 0.015 427 |
d__Bacteria; k__norank_d__Bacteria; p__unclassified_k__norank_d__Bacteria | 0.018 309 | 0.005 707 | 0.006 724 |
Others | 0.006 950 | 0.020 953 | 0.017 969 |
表1 高原鼠兔肠道菌群门水平相对丰度
Table 1 The percentage of the bacteria in phylum level of plateau pika
OTU ID | Cap_Apr | Wild_Apr | Wild_Jan |
---|---|---|---|
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes | 0.339 225 | 0.641 988 | 0.659 580 |
d__Bacteria; k__norank_d__Bacteria; p__Bacteroidetes | 0.558 989 | 0.225 796 | 0.252 759 |
d__Bacteria; k__norank_d__Bacteria; p__Epsilonbacteraeota | 0.028 674 | 0.063 268 | 0.012 728 |
d__Bacteria; k__norank_d__Bacteria; p__Spirochaetes | 0.031 141 | 0.021 820 | 0.019 720 |
d__Bacteria; k__norank_d__Bacteria; p__Verrucomicrobia | 0.010 711 | 0.009 175 | 0.015 093 |
d__Bacteria; k__norank_d__Bacteria; p__Proteobacteria | 0.006 001 | 0.011 293 | 0.015 427 |
d__Bacteria; k__norank_d__Bacteria; p__unclassified_k__norank_d__Bacteria | 0.018 309 | 0.005 707 | 0.006 724 |
Others | 0.006 950 | 0.020 953 | 0.017 969 |
OTU ID | Cap_Apr | Wild_Apr | Wild_Jan |
---|---|---|---|
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae | 0.165 574 | 0.302 052 | 0.350 869 |
d__Bacteria; k__norank_d__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales;f__Muribaculaceae | 0.412 680 | 0.104 957 | 0.088 984 |
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae | 0.081 744 | 0.211 662 | 0.192 503 |
d__Bacteria; k__norank_d__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales;f__Prevotellaceae | 0.089 237 | 0.050 616 | 0.102 269 |
d__Bacteria; k__norank_d__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Rikenellaceae | 0.040 646 | 0.057 848 | 0.050 388 |
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Christensenellaceae | 0.023 953 | 0.034 994 | 0.042 735 |
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiales_vadinBB60_group | 0.017 045 | 0.051 833 | 0.031 483 |
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Erysipelotrichia; o__Erysipelotrichales; f__Erysipelotrichaceae | 0.028 851 | 0.027 822 | 0.026 446 |
d__Bacteria; k__norank_d__Bacteria; p__Epsilonbacteraeota; c__Campylobacteria; o__Campylobacterales; f__Campylobacteraceae | 0.023 531 | 0.057 268 | 0.011 288 |
d__Bacteria; k__norank_d__Bacteria; p__Spirochaetes; c__Spirochaetia; o__Spirochaetales;f__Spirochaetaceae | 0.031 141 | 0.021 820 | 0.019 720 |
Others | 0.030 931 | 0.054 559 | 0.052 066 |
表2 高原鼠兔肠道菌群科水平相对丰度
Table 2 The percentage of the bacteria in family level of plateau pika
OTU ID | Cap_Apr | Wild_Apr | Wild_Jan |
---|---|---|---|
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae | 0.165 574 | 0.302 052 | 0.350 869 |
d__Bacteria; k__norank_d__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales;f__Muribaculaceae | 0.412 680 | 0.104 957 | 0.088 984 |
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae | 0.081 744 | 0.211 662 | 0.192 503 |
d__Bacteria; k__norank_d__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales;f__Prevotellaceae | 0.089 237 | 0.050 616 | 0.102 269 |
d__Bacteria; k__norank_d__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Rikenellaceae | 0.040 646 | 0.057 848 | 0.050 388 |
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Christensenellaceae | 0.023 953 | 0.034 994 | 0.042 735 |
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiales_vadinBB60_group | 0.017 045 | 0.051 833 | 0.031 483 |
d__Bacteria; k__norank_d__Bacteria; p__Firmicutes; c__Erysipelotrichia; o__Erysipelotrichales; f__Erysipelotrichaceae | 0.028 851 | 0.027 822 | 0.026 446 |
d__Bacteria; k__norank_d__Bacteria; p__Epsilonbacteraeota; c__Campylobacteria; o__Campylobacterales; f__Campylobacteraceae | 0.023 531 | 0.057 268 | 0.011 288 |
d__Bacteria; k__norank_d__Bacteria; p__Spirochaetes; c__Spirochaetia; o__Spirochaetales;f__Spirochaetaceae | 0.031 141 | 0.021 820 | 0.019 720 |
Others | 0.030 931 | 0.054 559 | 0.052 066 |
图4 不同组间高原鼠兔肠道微生物相对丰度的差异. a, b, c:门水平的组间两两比较;d, e, f:科水平组间两两比较 (LEfSe, LDA > 4, P < 0.05)
Fig. 4 Taxonomic alterations of the gut microbiota in different plateau pika groups. Pairwise comparisons of Cap_Apr vs. Wild_Apr; Cap_Apr vs. Wild_Jan; Wild_Apr vs. Wild_Jan in phylum level ( a, b, c) and in family level (d, e, f) by the linear discriminant analysis effect size (LEfSe) method (LDA > 4, P < 0.05)
图5 不同组间高原鼠兔肠道微生物菌群功能差异分析. Level 3 水平的KEEG分析,a:Cap_Apr和 Wild_Apr 比较结果;b:Cap_Apr和Wild_Jan 比较结果;c:Wild_Apr 和Wild_Jan比较结果, 使用welch t-test检验
Fig. 5 Functional variations of the gut microbiota in different plateau pika groups. Level 3 KEGG pathways were differentially represented between the Cap_Apr vs. Wild_Apr (a), Cap_Apr vs. Wild_Jan (b), Wild_Apr vs. Wild_Jan (c). Differences were assessed by the Welch t-test and are denoted as the corrected P-value
图6 不同组间高原鼠兔肠道微生物菌群构建过程分析. a:Cap_Apr;b:Wild_Apr;c:Wild_Jan
Fig. 6 Assembly process of microbiota communities in different groups of plateau pikas. Predicted occurrence frequencies for Cap_Apr (a), Wild_Apr (b) and Wild_Jan (c)
成分 Content | 比例 Percentage(%) |
---|---|
水分 Water | 7.8 |
粗蛋白 Crude protein | 16.6 |
粗脂肪 Crude fat | 3.1 |
粗纤维 Crude fiber | 12.2 |
粗灰分 Crude ash | 8.5 |
无氮浸出物 Nnitrogen-free extract | 52.8 |
表3 饲养高原鼠兔饲料成分表
Table 3 The content of the artificial diets of captive plateau pikas
成分 Content | 比例 Percentage(%) |
---|---|
水分 Water | 7.8 |
粗蛋白 Crude protein | 16.6 |
粗脂肪 Crude fat | 3.1 |
粗纤维 Crude fiber | 12.2 |
粗灰分 Crude ash | 8.5 |
无氮浸出物 Nnitrogen-free extract | 52.8 |
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