Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes.
Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes.
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DOI：
10.1128/msystems.00016-18
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发表时间：
2018-05
期刊：
影响因子：
6.4
通讯作者：
Dantas G
中科院分区：
文献类型：
--
作者：
Tsukayama P;Boolchandani M;Patel S;Pehrsson EC;Gibson MK;Chiou KL;Jolly CJ;Rogers J;Phillips-Conroy JE;Dantas G
抗生素暴露导致脊椎动物宿主微生物群落的组成和功能发生急性和持续的变化。然而，在抗生素广泛应用于临床和农业实践之前，人们对这些社区的状况知之甚少。我们描述了野生和圈养狒狒种群的粪便微生物群和抗生素耐药性，以了解人类暴露的影响，并了解灵长类动物微生物群在抗生素时代可能发生的变化。我们使用非培养和生物信息学方法来鉴定野生和圈养狒狒肠道中的功能性抗性基因，并表明与野生狒狒组相比，暴露于人类与微生物群组成和抗性组扩展的变化相关。我们的研究结果表明，与人类接触相关的圈养和生活方式的变化可能会导致灵长类动物肠道群落生态的显着变化。环境微生物具有数百万年的抗生素生产能力，跨越了人类和其他脊椎动物的进化。然而，在过去的世纪中，抗生素在临床和农业实践中的工业规模使用已经导致这些药剂暴露于人类和环境微生物群的显著增加。这种扰动预计将改变微生物群落的生态，并促进抗生素抗性（AR）基因的进化和转移。我们研究了野生和圈养狒狒种群，以了解暴露于人类和人类活动的影响（例如，抗生素疗法）对灵长类动物粪便微生物群的组成和其共同携带的抗疟药基因（“耐药基因组”）的影响。使用一种不依赖于培养的宏基因组方法，我们在野生和圈养狒狒群体的肠道微生物群中鉴定了功能性抗生素耐药基因，并发现微生物群结构和耐药基因在栖息地和生活方式中存在显著差异。我们的研究结果支持这样的观点，即抗生素耐药性是肠道微生物群落的一个古老特征，与人类共享栖息地可能对灵长类动物微生物群的结构和功能产生重要影响。重要性抗生素暴露导致脊椎动物宿主相关微生物群落的组成和功能发生急性和持续的变化。然而，在抗生素广泛应用于临床和农业实践之前，人们对这些社区的状况知之甚少。我们描述了野生和圈养狒狒种群的粪便微生物群和抗生素耐药性，以了解人类暴露的影响，并了解灵长类动物微生物群在抗生素时代可能发生的变化。我们使用非培养和生物信息学方法来鉴定野生和圈养狒狒肠道中的功能性抗性基因，并表明与野生狒狒组相比，暴露于人类与微生物群组成和抗性组扩展的变化相关。我们的研究结果表明，与人类接触相关的圈养和生活方式的变化可能会导致灵长类动物肠道群落生态的显着变化。
Antibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the effect of human exposure and to understand how the primate microbiota may have been altered during the antibiotic era. We used culture-independent and bioinformatics methods to identify functional resistance genes in the guts of wild and captive baboons and show that exposure to humans is associated with changes in microbiota composition and resistome expansion compared to wild baboon groups. Our results suggest that captivity and lifestyle changes associated with human contact can lead to marked changes in the ecology of primate gut communities. Environmental microbes have harbored the capacity for antibiotic production for millions of years, spanning the evolution of humans and other vertebrates. However, the industrial-scale use of antibiotics in clinical and agricultural practice over the past century has led to a substantial increase in exposure of these agents to human and environmental microbiota. This perturbation is predicted to alter the ecology of microbial communities and to promote the evolution and transfer of antibiotic resistance (AR) genes. We studied wild and captive baboon populations to understand the effects of exposure to humans and human activities (e.g., antibiotic therapy) on the composition of the primate fecal microbiota and the antibiotic-resistant genes that it collectively harbors (the “resistome”). Using a culture-independent metagenomic approach, we identified functional antibiotic resistance genes in the gut microbiota of wild and captive baboon groups and saw marked variation in microbiota architecture and resistomes across habitats and lifeways. Our results support the view that antibiotic resistance is an ancient feature of gut microbial communities and that sharing habitats with humans may have important effects on the structure and function of the primate microbiota. IMPORTANCE Antibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the effect of human exposure and to understand how the primate microbiota may have been altered during the antibiotic era. We used culture-independent and bioinformatics methods to identify functional resistance genes in the guts of wild and captive baboons and show that exposure to humans is associated with changes in microbiota composition and resistome expansion compared to wild baboon groups. Our results suggest that captivity and lifestyle changes associated with human contact can lead to marked changes in the ecology of primate gut communities.