摘要
出身背景
了解偏远地区野生动物的自然微生物组和耐药性对于监测人类在环境中的足迹，包括抗菌药物的使用（AU）是必要的。海洋鬣蜥是加拉帕戈斯群岛的特有物种，在那里它们受到人为因素的高度影响，这些因素会改变它们的微生物群以及它们的抗微生物基因（ARGs）的丰度和多样性。因此，本研究旨在应用独立于培养的方法来表征从无人岛Rabida（n = 8） 和费尔南迪纳（Cabo Douglas，n = 30; 埃斯皮诺萨角，n = 30). 通过SmartChip RT-PCR、16S rRNA和宏基因组下一代测序（mNGS）分析海洋鬣蜥的新鲜粪便，以确定其微生物组、微生物代谢途径、抗性组、移动性组和病毒群。
后果
尽管生态位存在差异，但海洋鬣蜥的肠道微生物组组成是高度保守的，这三个地方共有86%的分类群。然而，位点特异性差异主要在抗性组、移动性组、病毒组和代谢途径组成中发现，这突出表明在每个位置都存在诱导微生物适应的因素。功能性肠道微生物组分析揭示了它在维生素、辅因子、蛋白质生成氨基酸、碳水化合物、核苷和核苷酸、脂肪酸、脂质和其他海洋鬣蜥所需化合物的生物合成和降解中的作用。细菌ARG的总体丰度相对较低（0.006%）；然而，在鬣蜥的肠道宏基因组中发现了编码对22种药物类别耐药的基因。携带ARG的重叠群和共现网络分析表明，共生细菌是ARG的主要宿主。沙门氏菌、弧菌和克雷伯氏菌等具有公共卫生意义的Taxas也携带与MGE相关的多药耐药性基因，这些基因可以通过水平基因转移影响ARGs的传播。
结论
海洋鬣蜥依靠肠道微生物组通过共生关系生物合成和降解几种化合物。在微生物辅助基因库（即ARGs、MGE和毒力）和代谢途径中证明了生态位特异性适应，但在微生物组组成中没有。独立于文化的方法概述了来自偏远岛屿的加拉帕戈斯海洋鬣蜥中存在多种抗性成分。海洋鬣蜥中AR病原体的存在引发了人们对原始地区抗微生物威胁分散的担忧，强调野生动物是识别非盟影响的前哨物种。
Abstract
Background
Understanding the natural microbiome and resistome of wildlife from remote places is necessary to monitor the human footprint on the environment including antimicrobial use (AU). Marine iguanas are endemic species from the Galapagos Islands where they are highly affected by anthropogenic factors that can alter their microbiota as well as their abundance and diversity of antimicrobial-resistant genes (ARGs). Thus, this study aims to apply culture-independent approaches to characterize the marine iguana’s gut metagenomic composition of samples collected from the uninhabited islands Rabida (n = 8) and Fernandina (Cabo Douglas, n = 30; Punta Espinoza, n = 30). Fresh feces from marine iguanas were analyzed through SmartChip RT-PCR, 16S rRNA, and metagenomic next-generation sequencing (mNGS) to identify their microbiome, microbial-metabolic pathways, resistome, mobilome, and virulome.

Results
The marine iguana’s gut microbiome composition was highly conserved despite differences in ecological niches, where 86% of taxa were shared in the three locations. However, site-specific differences were mainly identified in resistome, mobilome, virulorome, and metabolic pathway composition, highlighting the existence of factors that induce microbial adaptations in each location. Functional gut microbiome analyses revealed its role in the biosynthesis and degradation of vitamins, cofactors, proteinogenic amino acids, carbohydrates, nucleosides and nucleotides, fatty acids, lipids, and other compounds necessary for the marine iguanas. The overall bacterial ARG abundance was relatively low (0.006%); nevertheless, the presence of genes encoding resistance to 22 drug classes was identified in the iguana’s gut metagenome. ARG-carrying contig and co-occurrence network analyses revealed that commensal bacteria are the main hosts of ARGs. Taxa of public health interest such as Salmonella, Vibrio, and Klebsiella also carried multidrug-resistance genes associated with MGEs which can influence the dissemination of ARGs through horizontal gene transfer.

Conclusion
Marine iguanas depend on the gut microbiome for the biosynthesis and degradation of several compounds through a symbiotic relationship. Niche-specific adaptations were evidenced in the pool of microbial accessory genes (i.e., ARGs, MGEs, and virulence) and metabolic pathways, but not in the microbiome composition. Culture-independent approaches outlined the presence of a diverse resistome composition in the Galapagos marine iguanas from remote islands. The presence of AR pathogens in marine iguanas raises concerns about the dispersion of microbial-resistant threats in pristine areas, highlighting wildlife as sentinel species to identify the impact of AU.

https://link.springer.com/article/10.1186/s42523-022-00218-4