Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies
Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies
复制标题
五种同域沙漠啮齿动物的肠道微生物生态学与草食性和食虫性喂养策略的关系
DOI：
10.1093/icb/icac045
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发表时间：
2022
影响因子：
2.6
通讯作者：
Hedayati, Stefanie
中科院分区：
文献类型：
--
作者：
Kohl, Kevin D.;Dieppa-Colón, Etan;Goyco-Blas, José;Peralta-Martínez, Karen;Scafidi, Luke;Shah, Sarth;Zawacki, Emma;Barts, Nick;Ahn, Young;Hedayati, Stefanie
哺乳动物的肠道微生物群落为宿主提供了许多好处。然而，鉴于微生物组领域最近的发展，我们仍然缺乏对跨物种构建这些群落的各种生态和进化因素的透彻了解。元生物编码是一种强大的技术，它允许同时研究多个微生物生态学问题。在这里，我们使用DNA代谢编码技术、预测性元基因组学和依赖于培养的技术来研究从同一环境中收集的几种啮齿动物的肠道微生物群落，这些啮齿动物采用不同的自然摄食策略[肉食性口袋鼠(Chaetdipus Penicillatus)；肉食性袋鼠(Dipodomys Merriami)；草食性林木动物(Neotoma Albigula)；杂食性仙人掌鼠(Permyscus Eremicus)；以及食虫性蚱蜢鼠(Onychomys Torridus)]。特别令人感兴趣的是，由于草食和食虫饮食中分别含有大量的不可消化纤维和几丁质外骨骼，啮齿动物的肠道微生物群落发生了变化。我们发现，草食性林木动物拥有最大的微生物多样性。食草动物口袋鼠和袋鼠的基因丰度最高，与纤维消化相关的基因预测丰度最高，这表明这些物种对种子纤维含量的潜在适应能力，以及由于它们体型较小而对消化的限制。食虫蝗虫小鼠在其微生物群成员中表现出最大的个体间差异，也表现出最高的甲壳素降解基因的预测丰度。基于培养的方法鉴定了178个微生物分离物(主要是芽孢杆菌和肠球菌)，其中一些能够降解纤维素和甲壳素。我们观察到几个菌株水平的多样性在这些分离株之间的代谢能力，在某种程度上突显了限制和隐藏的多样性潜在的DNA元编码技术。然而，这些方法提供了同时研究几个问题的能力，从而增强了我们对肠道微生物生态学的理解。
The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus); and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genusRuminococcusand highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarilyBacillusandEnterococcus), with some capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.