摘要
      多种因素影响脊椎动物宿主肠道微生物组的多样性。以前的大多数研究只调查了特定的因素和某些寄主物种或分类群。然而，在更广泛的进化背景下，仍然缺乏对单个因素对肠道微生物多样性的相对贡献的全面评估。在这里，从七个类别的452个宿主物种中收集的2202个肠道细菌群落的16S rRNA基因测序样本被一起分析，以了解广泛影响不同饮食、受威胁状态、圈养状态和栖息地环境因素的宿主脊椎动物肠道微生物组的因素。在野生脊椎动物中，饮食与肠道微生物组α多样性最显著相关，而宿主系统发育和饮食与β多样性显著相关，这与之前的一项研究一致。宿主威胁状态和栖息地环境因素（如地理和气候）也与肠道细菌群落β多样性有关。随后的生态建模揭示了自由放养脊椎动物的随机组装过程和肠道细菌多样性模式之间的强烈关联。此外，对62种圈养脊椎动物和同域人类肠道微生物组的宏基因组分析显示，尽管宿主系统发育、饮食和受威胁状态存在差异，但其多样性和耐药性相似。因此，这些结果表明，圈养减少了宿主系统发育、饮食和受威胁状态对脊椎动物肠道细菌群落多样性的影响。在这些样本中观察到的抗生素耐药基因（ARGs）最多，与对β-内酰胺、氨基糖苷类和四环素的耐药性有关。这些结果还揭示了圈养动物和人类之间ARGs的潜在水平转移，从而共同威胁公共健康和脊椎动物保护。总之，这项研究对脊椎动物肠道微生物群的多样性和耐药性提供了全面的概述。这些综合分析将有助于通过合理控制微生物多样性和减少抗生素使用来指导未来的脊椎动物保护。
Abstract
Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to β-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.

https://www.sciencedirect.com/science/article/abs/pii/S0048969722032752