Yuan Michael L, Dean Samantha H, Longo Ana V, Rothermel Betsie B, Tuberville Tracey D, Zamudio Kelly R
Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA; Archbold Biological Station, Venus, FL, 33960, USA.
Mol Ecol. 2015 May;24(10):2521-36. doi: 10.1111/mec.13169. Epub 2015 Apr 20.
Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut-fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we characterized the faecal microbial community of a population of gopher tortoises (Gopherus polyphemus) and examined how age, genetic diversity, spatial structure and kinship influence differences among individuals. We recovered phylotypes associated with known cellulolytic function, including candidate phylum Termite Group 3, suggesting their importance for gopher tortoise digestion. Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine-scale spatial structure, inbreeding, degree of relatedness and possibly ontogeny shaped patterns of diversity in faecal microbiomes of gopher tortoises. Our findings corroborate widespread convergence of faecal-associated microbes based on gut morphology and diet and demonstrate the role of spatial and demographic structure in driving differentiation of gut microbiota in natural populations.
食草脊椎动物依靠复杂的互利共生肠道细菌群落来促进纤维素和半纤维素的消化。在系统发育上多样的哺乳动物群体中，肠道微生物通常基于饮食和肠道形态而趋同。然而，对于食草性后肠发酵爬行动物的微生物群落知之甚少。在这里，我们研究个体水平的因素如何可能限制专性食草爬行动物肠道微生物的组成。我们使用多重16S rRNA基因测序，对一群地鼠龟（Gopherus polyphemus）的粪便微生物群落进行了表征，并研究了年龄、遗传多样性、空间结构和亲属关系如何影响个体间的差异。我们鉴定出了与已知纤维素分解功能相关的系统发育型，包括候选门白蚁群3，这表明它们对地鼠龟消化的重要性。虽然宿主遗传结构并不能解释微生物组成和群落结构的变化，但我们发现精细尺度的空间结构、近亲繁殖、亲缘程度以及可能的个体发育塑造了地鼠龟粪便微生物群的多样性模式。我们的研究结果证实了基于肠道形态和饮食的粪便相关微生物的广泛趋同，并证明了空间和种群结构在推动自然种群中肠道微生物群分化方面的作用。
