Effects of hibernation on cecal microbiota in Daurian ground squirrel

doi:10.16829/j.slxb.150622

Abstract

Abstract:

The diversity and composition of gut microbiota in hibernating mammals are affected by seasonal changes and fasting during hibernation. In order to examine the seasonal changes of the cecal microbiota of Daurian ground squirrel (Spermophilus dauricus), we analyzed the diversity, composition, and function of cecal microbiota from six groups of fattening stage (Initial fattening, Rapid fattening, Finished fattening) and hibernation stage (Early hibernation, Late hibernation, Arousal) using 16S rRNA gene high-throughput sequencing technology. In addition, the relationship between physiological characteristics and the composition and function of cecal microbiota was explored by redundancy analysis (RDA). The cecal microbiota was mainly composed of Firmicutes, Bacteroidetes, and Verrucomicrobia. Compared with other periods, the relative abundance of Firmicutes decreased and that of Bacteroidetes and Verrucomicrobia increased in Early hibernation. The Chao1 and ACE indices in Initial fattening, Rapid fattening, and Early hibernation were significantly lower than those in the Arousal, and the Simpson index in Finish fattening was significantly lower than that in Rapid fattening (P < 0.05) calculated by alpha diversity. Significant seasonal clustering of the cecal microbiota was found through the principal coordinate analysis (PCoA) of the weighted and unweighted UniFrac distance matrix. The butanoate metabolism and other metabolic pathways were enriched in fattening stage, and nitrogen metabolism and other related pathways were concentrated in hibernation stage as shown by PICRUSt analysis. The physiological characteristics at different stages were significantly correlated with the composition and function of cecal microbiota. In conclusion, it is indicated that hibernation profoundly affects the diversity and relative abundance of cecal microbiota. The changes in the composition and function of cecal microbiota play an important role in regulating the physiological metabolism, which can help Daurian ground squirrel adapt to seasonal environmental changes.

Key words: Daurian ground squirrel (Spermophilus dauricus), Gut microbiota, Hibernation, High-throughput sequencing

摘要：

冬眠哺乳动物的肠道微生物会发生季节性变化，同时在冬眠期间动物处于禁食状态，对肠道微生物的多样性和组成也产生影响。本研究通过16S rRNA基因高通量测序分析达乌尔黄鼠育肥阶段 (起始育肥期、快速育肥期、育肥完成期) 和冬眠阶段 (冬眠早期、冬眠晚期、出眠期) 共6个时期盲肠菌群的多样性、组成和功能，并通过冗余分析 (RDA) 探究其生理特征与菌群组成和功能之间的关系，揭示达乌尔黄鼠盲肠菌群的季节性变化。菌群组成的分析显示达乌尔黄鼠盲肠菌群主要由厚壁菌门 (Firmicutes)、拟杆菌门 (Bacteroidetes) 和疣微菌门 (Verrucomicrobia) 组成。与其他时期相比，冬眠早期厚壁菌门的相对丰度减少，拟杆菌门和疣微菌门的相对丰度增加。在Alpha多样性中，起始育肥期、快速育肥期和冬眠早期的Chao1和ACE指数显著低于出眠期，育肥完成期的Simpson指数显著低于快速育肥期 (P < 0.05) 。通过加权和非加权的UniFrac距离矩阵的主坐标分析发现盲肠菌群均显示出了明显的季节性聚类。PICRUSt分析中，丁酸代谢等代谢通路在育肥阶段富集，冬眠阶段集中在氮代谢等相关通路中。RDA分析显示达乌尔黄鼠不同时期的生理特征与其盲肠菌群的组成和功能显著相关。本研究表明，冬眠使达乌尔黄鼠盲肠菌群的多样性和相对丰度发生改变，盲肠菌群组成和功能的变化调节了达乌尔黄鼠的生理代谢，使达乌尔黄鼠适应季节性的环境变化。

关键词: 达乌尔黄鼠, 肠道菌群, 冬眠, 高通量测序

CLC Number:

Q938.1

Min MAO, Ming YANG, Xinyu LIU. Effects of hibernation on cecal microbiota in Daurian ground squirrel[J]. ACTA THERIOLOGICA SINICA, 2022, 42(4): 420-431.

毛敏, 杨明, 刘新宇. 冬眠对达乌尔黄鼠盲肠菌群的影响[J]. 兽类学报, 2022, 42(4): 420-431.

Figures/Tables 7

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分组 Group	观察到的OTU数 Observed species	Chao1指数 Chao1 index	ACE指数 ACE index	Shannon指数 Shannon index	Simpson指数 Simpson index
起始育肥期组IF	533.13 ± 23.42^a	588.65 ± 26.17^b	584.73 ± 27.29^b	6.22 ± 0.29^a	0.94 ± 0.02^ab
快速育肥期组RF	531.00 ± 41.45^a	591.35 ± 42.94^b	583.64 ± 42.94^b	6.19 ± 0.29^a	0.93 ± 0.02^b
育肥完成期组FF	585.29 ± 15.33^a	665.68 ± 12.83^ab	647.96 ± 15.07^ab	6.87 ± 0.10^a	0.98 ± 0.00^a
冬眠早期组EH	527.13 ± 35.05^a	603.06 ± 42.69^b	588.95 ± 42.09^b	6.56 ± 0.13^a	0.97 ± 0.00^ab
冬眠晚期组LH	577.00 ± 23.35^a	666.01 ± 29.67^ab	654.41 ± 28.10^ab	6.83 ± 0.11^a	0.98 ± 0.00^ab
出眠期组A	640.38 ± 29.84^a	762.99 ± 37.36^a	752.93 ± 34.15^a	6.78 ± 0.13^a	0.97 ± 0.00^ab

分组 Group	观察到的OTU数 Observed species	Chao1指数 Chao1 index	ACE指数 ACE index	Shannon指数 Shannon index	Simpson指数 Simpson index
起始育肥期组IF	533.13 ± 23.42^a	588.65 ± 26.17^b	584.73 ± 27.29^b	6.22 ± 0.29^a	0.94 ± 0.02^ab
快速育肥期组RF	531.00 ± 41.45^a	591.35 ± 42.94^b	583.64 ± 42.94^b	6.19 ± 0.29^a	0.93 ± 0.02^b
育肥完成期组FF	585.29 ± 15.33^a	665.68 ± 12.83^ab	647.96 ± 15.07^ab	6.87 ± 0.10^a	0.98 ± 0.00^a
冬眠早期组EH	527.13 ± 35.05^a	603.06 ± 42.69^b	588.95 ± 42.09^b	6.56 ± 0.13^a	0.97 ± 0.00^ab
冬眠晚期组LH	577.00 ± 23.35^a	666.01 ± 29.67^ab	654.41 ± 28.10^ab	6.83 ± 0.11^a	0.98 ± 0.00^ab
出眠期组A	640.38 ± 29.84^a	762.99 ± 37.36^a	752.93 ± 34.15^a	6.78 ± 0.13^a	0.97 ± 0.00^ab

类群 Taxa		起始育肥期组IF	快速育肥期组RF	育肥完成期组FF	冬眠早期组EH	冬眠晚期组LH	出眠期组 A
门Phylum	厚壁菌门 Firmicutes	0.7794 ± 0.0236^a	0.7448 ± 0.0291^ab	0.7629 ± 0.0180^ab	0.5783 ± 0.0347^b	0.7519 ± 0.0287^a	0.8225 ± 0.0232^a
	拟杆菌门 Bacteroidetes	0.1863 ± 0.0242^b	0.2207 ± 0.0289^ab	0.2049 ± 0.0167^b	0.3357 ± 0.0255^a	0.1810 ± 0.0300^b	0.1512 ± 0.0254^b
	疣微菌门 Verrucomicrobia	0.0142 ± 0.0042^abc	0.0090 ± 0.0051^bc	0.0079 ± 0.0019^abc	0.0658 ± 0.0274^a	0.0474 ± 0.0126^ab	0.0048 ± 0.0012^c
	Epsilonbacteraeota	0.0000 ± 0.0000^ab	0.0001 ± 0.0001^a	0.0004 ± 0.0003^ab	0.0001 ± 0.0000^ab	0.0000 ± 0.0000^b	0.0000 ± 0.0000^ab
科Family	瘤胃菌科 Ruminococcaceae	0.2395 ± 0.0276^ab	0.1799 ± 0.0217^ab	0.3185 ± 0.0303^a	0.1711 ± 0.0209^b	0.1982 ± 0.0312^ab	0.2261 ± 0.0263^ab
	乳杆菌科 Lactobacillaceae	0.1923 ± 0.0686^a	0.1052 ± 0.0405^a	0.0283 ± 0.0121^ab	0.0009 ± 0.0003^b	0.0009 ± 0.0003^b	0.0471 ± 0.0277^ab
	拟杆菌科 Bacteroidaceae	0.0361 ± 0.0110^b	0.0544 ± 0.0133^ab	0.0477 ± 0.0112^ab	0.1126 ± 0.0144^a	0.0395 ± 0.0156^b	0.0226 ± 0.0053^b
	艾克曼氏菌科 Akkermansiaceae	0.0142 ± 0.0042^abc	0.0090 ± 0.0051^bc	0.0079 ± 0.0019^abc	0.0658 ± 0.0274^a	0.0474 ± 0.0126^ab	0.0048 ± 0.0012^c
	Family 􀃼	0.0242 ± 0.0036^ab	0.0232 ± 0.0019^ab	0.0317 ± 0.0038^a	0.0165 ± 0.0033^b	0.0282 ± 0.0046^ab	0.0271 ± 0.0066^ab
	消化球菌科 Peptococcaceae	0.0047 ± 0.0015^b	0.0019 ± 0.0004^b	0.0052 ± 0.0013^ab	0.0126 ± 0.0040^ab	0.0187 ± 0.0031^a	0.0111 ± 0.0028^ab
	韦荣球菌科 Erysipelotrichaceae	0.0035 ± 0.0009^b	0.0049 ± 0.0013^ab	0.0054 ± 0.0018^ab	0.0093 ± 0.0017^ab	0.0098 ± 0.0009^a	0.0198 ± 0.0072^a
	氨基酸球菌科 Acidaminococcaceae	0.0014 ± 0.0013^ab	0.0205 ± 0.0072^a	0.0078 ± 0.0049^ab	0.0028 ± 0.0028^ab	0.0007 ± 0.0007^b	0.0024 ± 0.0017^ab
属Genus	乳杆菌属 Lactobacillus	0.1923 ± 0.0686^a	0.1052 ± 0.0405^a	0.0283 ± 0.0121^ab	0.0009 ± 0.0003^b	0.0009 ± 0.0003^b	0.0471 ± 0.0277^ab
	拟杆菌属 Bacteroides	0.0361 ± 0.0110^b	0.0544 ± 0.0133^ab	0.0477 ± 0.0112^ab	0.1126 ± 0.0144^a	0.0395 ± 0.0156^b	0.0226 ± 0.0053^b
	Marvinbryantia	0.0137 ± 0.0043^b	0.0159 ± 0.0045^b	0.0203 ± 0.0115^b	0.0583 ± 0.0151^ab	0.0917 ± 0.0132^a	0.0341 ± 0.0082^ab
	［Eubacterium］ coprostanoligenes group	0.0391 ± 0.0103^ab	0.0086 ± 0.0053^b	0.0453 ± 0.0120^a	0.0212 ± 0.0041^ab	0.0252 ± 0.0049^ab	0.0369 ± 0.0108^ab
	艾克曼菌属 Akkermansia	0.0142 ± 0.0042^abc	0.0090 ± 0.0051^bc	0.0079 ± 0.0019^abc	0.0658 ± 0.0274^a	0.0474 ± 0.0126^ab	0.0048 ± 0.0012^c
	瘤胃球菌属1 Ruminococcus 1	0.0321 ± 0.0133^ab	0.0191 ± 0.0073^ab	0.0430 ± 0.0135^a	0.0096 ±0.0052^ab	0.0027 ± 0.0006^b	0.0321 ± 0.0123^a
	脱硫弧菌属 Desulfovibrio	0.0037 ± 0.0016^b	0.0036 ± 0.0010^ab	0.0054 ± 0.0024^ab	0.0105 ±0.0014^a	0.0101 ± 0.0027^ab	0.0053 ± 0.0011^ab

类群 Taxa		起始育肥期组IF	快速育肥期组RF	育肥完成期组FF	冬眠早期组EH	冬眠晚期组LH	出眠期组 A
门Phylum	厚壁菌门 Firmicutes	0.7794 ± 0.0236^a	0.7448 ± 0.0291^ab	0.7629 ± 0.0180^ab	0.5783 ± 0.0347^b	0.7519 ± 0.0287^a	0.8225 ± 0.0232^a
	拟杆菌门 Bacteroidetes	0.1863 ± 0.0242^b	0.2207 ± 0.0289^ab	0.2049 ± 0.0167^b	0.3357 ± 0.0255^a	0.1810 ± 0.0300^b	0.1512 ± 0.0254^b
	疣微菌门 Verrucomicrobia	0.0142 ± 0.0042^abc	0.0090 ± 0.0051^bc	0.0079 ± 0.0019^abc	0.0658 ± 0.0274^a	0.0474 ± 0.0126^ab	0.0048 ± 0.0012^c
	Epsilonbacteraeota	0.0000 ± 0.0000^ab	0.0001 ± 0.0001^a	0.0004 ± 0.0003^ab	0.0001 ± 0.0000^ab	0.0000 ± 0.0000^b	0.0000 ± 0.0000^ab
科Family	瘤胃菌科 Ruminococcaceae	0.2395 ± 0.0276^ab	0.1799 ± 0.0217^ab	0.3185 ± 0.0303^a	0.1711 ± 0.0209^b	0.1982 ± 0.0312^ab	0.2261 ± 0.0263^ab
	乳杆菌科 Lactobacillaceae	0.1923 ± 0.0686^a	0.1052 ± 0.0405^a	0.0283 ± 0.0121^ab	0.0009 ± 0.0003^b	0.0009 ± 0.0003^b	0.0471 ± 0.0277^ab
	拟杆菌科 Bacteroidaceae	0.0361 ± 0.0110^b	0.0544 ± 0.0133^ab	0.0477 ± 0.0112^ab	0.1126 ± 0.0144^a	0.0395 ± 0.0156^b	0.0226 ± 0.0053^b
	艾克曼氏菌科 Akkermansiaceae	0.0142 ± 0.0042^abc	0.0090 ± 0.0051^bc	0.0079 ± 0.0019^abc	0.0658 ± 0.0274^a	0.0474 ± 0.0126^ab	0.0048 ± 0.0012^c
	Family 􀃼	0.0242 ± 0.0036^ab	0.0232 ± 0.0019^ab	0.0317 ± 0.0038^a	0.0165 ± 0.0033^b	0.0282 ± 0.0046^ab	0.0271 ± 0.0066^ab
	消化球菌科 Peptococcaceae	0.0047 ± 0.0015^b	0.0019 ± 0.0004^b	0.0052 ± 0.0013^ab	0.0126 ± 0.0040^ab	0.0187 ± 0.0031^a	0.0111 ± 0.0028^ab
	韦荣球菌科 Erysipelotrichaceae	0.0035 ± 0.0009^b	0.0049 ± 0.0013^ab	0.0054 ± 0.0018^ab	0.0093 ± 0.0017^ab	0.0098 ± 0.0009^a	0.0198 ± 0.0072^a
	氨基酸球菌科 Acidaminococcaceae	0.0014 ± 0.0013^ab	0.0205 ± 0.0072^a	0.0078 ± 0.0049^ab	0.0028 ± 0.0028^ab	0.0007 ± 0.0007^b	0.0024 ± 0.0017^ab
属Genus	乳杆菌属 Lactobacillus	0.1923 ± 0.0686^a	0.1052 ± 0.0405^a	0.0283 ± 0.0121^ab	0.0009 ± 0.0003^b	0.0009 ± 0.0003^b	0.0471 ± 0.0277^ab
	拟杆菌属 Bacteroides	0.0361 ± 0.0110^b	0.0544 ± 0.0133^ab	0.0477 ± 0.0112^ab	0.1126 ± 0.0144^a	0.0395 ± 0.0156^b	0.0226 ± 0.0053^b
	Marvinbryantia	0.0137 ± 0.0043^b	0.0159 ± 0.0045^b	0.0203 ± 0.0115^b	0.0583 ± 0.0151^ab	0.0917 ± 0.0132^a	0.0341 ± 0.0082^ab
	［Eubacterium］ coprostanoligenes group	0.0391 ± 0.0103^ab	0.0086 ± 0.0053^b	0.0453 ± 0.0120^a	0.0212 ± 0.0041^ab	0.0252 ± 0.0049^ab	0.0369 ± 0.0108^ab
	艾克曼菌属 Akkermansia	0.0142 ± 0.0042^abc	0.0090 ± 0.0051^bc	0.0079 ± 0.0019^abc	0.0658 ± 0.0274^a	0.0474 ± 0.0126^ab	0.0048 ± 0.0012^c
	瘤胃球菌属1 Ruminococcus 1	0.0321 ± 0.0133^ab	0.0191 ± 0.0073^ab	0.0430 ± 0.0135^a	0.0096 ±0.0052^ab	0.0027 ± 0.0006^b	0.0321 ± 0.0123^a
	脱硫弧菌属 Desulfovibrio	0.0037 ± 0.0016^b	0.0036 ± 0.0010^ab	0.0054 ± 0.0024^ab	0.0105 ±0.0014^a	0.0101 ± 0.0027^ab	0.0053 ± 0.0011^ab

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