Multi-omics analysis reveals the genetic and environmental factors in shaping the gut resistome of a keystone rodent species.

IF 8 2区 生物学 Q1 BIOLOGY Science China Life Sciences Pub Date : 2024-11-01 Epub Date: 2024-08-30 DOI:10.1007/s11427-024-2679-3
Guoliang Li, Dong Zhu, Chaoyuan Cheng, Haiyan Chu, Fuwen Wei, Zhibin Zhang
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Abstract

Understanding the emergence and spread of antibiotic resistance genes (ARGs) in wildlife is critical for the health of humans and animals from a "One Health" perspective. The gut microbiota serve as a reservoir for ARGs; however, it remains poorly understood how environmental and host genetic factors influence ARGs by affecting the gut microbiota. To elucidate this, we analyzed whole-genome resequencing data from 79 individuals of Brandt's vole in two geographic locations with different antibiotics usage, together with metabolomic data and shotgun sequencing data. A high diversity of ARGs (851 subtypes) was observed in vole's gut, with a large variation in ARG composition between individuals from Xilingol and Hulunbuir in China. The diversity and composition of ARGs were strongly correlated with variations in gut microbiota community structure. Genome-wide association studies revealed that 803 loci were significantly associated (P<5.05×10-9) with 31 bacterial species, and bipartite networks identified 906 bacterial species-ARGs associations. Structural equation modeling analysis showed that host genetic factors, air temperature, and presence of pollutants (Bisphenol A) significantly affected gut microbiota community structure, which eventually regulated the diversity of ARGs. The present study advances our understanding of the complex host-environment interactions that underlie the spread of ARGs in the natural environments.

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多组学分析揭示了形成一种关键啮齿动物肠道抗性组的遗传和环境因素。
从 "一体健康 "的角度来看,了解野生动物抗生素耐药基因(ARGs)的出现和传播对人类和动物的健康至关重要。肠道微生物群是 ARGs 的储存库;然而,人们对环境和宿主遗传因素如何通过影响肠道微生物群来影响 ARGs 仍然知之甚少。为了弄清这个问题,我们分析了两个使用不同抗生素的地区的79只布氏田鼠的全基因组重测序数据,以及代谢组数据和枪式测序数据。在布氏田鼠肠道中观察到 ARGs 的高度多样性(851 个亚型),来自中国锡林郭勒和呼伦贝尔的布氏田鼠个体之间 ARGs 的组成差异很大。ARGs的多样性和组成与肠道微生物群落结构的变化密切相关。全基因组关联研究发现,803个基因位点与31种细菌有显著关联(P-9),双方位网络发现906种细菌与ARGs有关联。结构方程建模分析表明,宿主遗传因素、气温和污染物(双酚 A)的存在对肠道微生物群落结构有明显影响,最终调节了 ARGs 的多样性。本研究加深了我们对宿主与环境之间复杂的相互作用的理解,这种相互作用是 ARGs 在自然环境中传播的基础。
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来源期刊
CiteScore
15.10
自引率
8.80%
发文量
2907
审稿时长
3.2 months
期刊介绍: Science China Life Sciences is a scholarly journal co-sponsored by the Chinese Academy of Sciences and the National Natural Science Foundation of China, and it is published by Science China Press. The journal is dedicated to publishing high-quality, original research findings in both basic and applied life science research.
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