Data_Sheet_1_High-Throughput Sequencing for Examining Salmonella Prevalence and Pathogen—Microbiota Relationships in Barn Swallows.pdf

Studies in both humans and model organisms suggest that the microbiome may play a significant role in host health, including digestion and immune function. Microbiota can offer protection from exogenous pathogens through colonization resistance, but microbial dysbiosis in the gastrointestinal tract can decrease resistance and is associated with pathogenesis. Little is known about the effects of potential pathogens, such as Salmonella, on the microbiome in wildlife, which are known to play an important role in disease transmission to humans. Culturing techniques have traditionally been used to detect pathogens, but recent studies have utilized high throughput sequencing of the 16S rRNA gene to characterize host-associated microbial communities (i.e., the microbiome) and to detect specific bacteria. Building upon this work, we evaluated the utility of high throughput 16S rRNA gene sequencing for potential bacterial pathogen detection in barn swallows (Hirundo rustica) and used these data to explore relationships between potential pathogens and microbiota. To accomplish this, we first compared the detection of Salmonella spp. in swallows using 16S rRNA data with standard culture techniques. Second, we examined the prevalence of Salmonella using 16S rRNA data and examined the relationship between Salmonella-presence or -absence and individual host factors. Lastly, we evaluated host-associated bacterial diversity and community composition in Salmonella-present vs. -absent birds. Out of 108 samples, we detected Salmonella in six (5.6%) samples based on culture, 25 (23.1%) samples with unrarefied 16S rRNA gene sequencing data, and three (2.8%) samples with both techniques. We found that sex, migratory status, and weight were correlated with Salmonella presence in swallows. In addition, bacterial community composition and diversity differed between birds based on Salmonella status. This study highlights the value of 16S rRNA gene sequencing data for monitoring pathogens in wild birds and investigating the ecology of host microbe-pathogen relationships, data which are important for prediction and mitigation of disease spillover into domestic animals and humans.

研究表明，无论是在人类还是在模式生物中，微生物组可能在宿主健康中扮演着至关重要的角色，包括消化功能和免疫功能。微生物群落可以通过定殖抗性提供对外源病原体的保护，但胃肠道中微生物的失调会降低抵抗力，并与发病机制相关联。关于潜在病原体（如沙门氏菌）对野生动物微生物组的影响知之甚少，而这些病原体在疾病向人类传播中扮演着重要角色。传统的培养技术一直被用于检测病原体，但最近的研究已经开始利用16S rRNA基因的高通量测序来表征宿主相关的微生物群落（即微生物组）以及检测特定细菌。在此基础上，我们评估了高通量16S rRNA基因测序在鹡鸰（Hirundo rustica）中检测潜在细菌病原体的效用，并利用这些数据来探究潜在病原体与微生物群落之间的关系。为此，我们首先比较了使用16S rRNA数据在鹡鸰中检测沙门氏菌（Salmonella spp.）与标准培养技术的检测结果。其次，我们使用16S rRNA数据考察了沙门氏菌的流行情况，并分析了沙门氏菌存在与否与个体宿主因素之间的关系。最后，我们评估了沙门氏菌存在与不存在鸟类中宿主相关细菌的多样性和群落组成。在108个样本中，我们根据培养方法检测到6个（5.6%）样本存在沙门氏菌，25个（23.1%）样本在未稀释的16S rRNA基因测序数据中检测到，以及3个（2.8%）样本在两种技术中均检测到。我们发现性别、迁徙状态和体重与鹡鸰中沙门氏菌的存在相关。此外，基于沙门氏菌状态，鸟类的细菌群落组成和多样性也存在差异。这项研究突出了16S rRNA基因测序数据在监测野生动物病原体和探究宿主微生物-病原体关系生态学方面的价值，这些数据对于预测和减轻疾病传播到家畜和人类具有重要意义。