Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach.
Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach.
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DOI：
10.3389/fmicb.2021.697553
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发表时间：
2021
影响因子：
5.2
通讯作者：
Gourmelon M
中科院分区：
文献类型：
--
作者：
Boukerb AM;Noël C;Quenot E;Cadiou B;Chevé J;Quintric L;Cormier A;Dantan L;Gourmelon M
沿海地区的粪便污染令人高度关注，因为它影响到洗澡和贝类捕捞活动。野生水鸟在可检测污染的整体信号中不可忽视。然而，对野生水鸟肠道微生物群的研究主要集中在迁徙轨迹和进食对其形状的影响，很少有研究将其与其他来源进行比较，并开发基于定量PCR（qPCR）的微生物源跟踪（MST）标记来检测此类污染。因此，通过使用16 S rRNA扩增子高通量测序，本研究的目的是（i）探索和比较来自野生水鸟的粪便细菌群落（即，6科15种，n = 275个样品）的家禽，牛，猪，和污水处理厂的流入/流出物（n = 150个样品）和（ii）开发新的MST标记的水鸟。野生水鸟和其他四个群体之间观察到显着差异。我们从高变V3-V4区域鉴定了7，349个扩增子序列变体（ASV）。厚壁菌门和变形菌门以及较小程度的放线菌门和拟杆菌门普遍存在，而梭杆菌门和Epsilonbacteraeota主要存在于野生水鸟中。在非度量多维尺度（NMDS）排序的样本聚类表明，由组聚类形状，具有较高的多样性在野生水鸟。此外，根据鸟类和/或动物物种和科，细菌群落的结构是不同的（分别为Adonis R2 = 0.13，p = 10-4，Adonis R2 = 0.11，p = 10-4）。微生物组组成分析（ANCOM）表明，野生水鸟组与其他类群的差异在于存在来自梭杆菌科（W = 566）和肠球菌科（W = 565）的序列，分别对应于鲸杆菌属（W = 1427）和猫球菌属（W = 1427）。总之，我们的研究结果表明，一些水鸟成员呈现出不同的粪便微生物组，允许设计qPCR MST标记。例如，已经开发了与天鹅和牡蛎相关的标记（分别命名为Swan_2和Oyscab）。此外，在我们的数据集中检测到携带与鸟粪相关的潜在人类病原体的细菌属，包括肠道病原体，即，弓形杆菌属、梭菌属、螺杆菌属和弯曲杆菌属，以及环境病原体，即，伯克霍尔德菌和假单胞菌。未来涉及其他野生动物宿主的研究可能会改善肠道微生物组研究和MST标记物的开发，有助于缓解未知的粪便污染源。
Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible in the overall signal of the detectable pollution. Yet, studies on wild waterbirds’ gut microbiota focus on migratory trajectories and feeding impact on their shape, rare studies address their comparison to other sources and develop quantitative PCR (qPCR)-based Microbial Source Tracking (MST) markers to detect such pollution. Thus, by using 16S rRNA amplicon high-throughput sequencing, the aims of this study were (i) to explore and compare fecal bacterial communities from wild waterbirds (i.e., six families and 15 species, n = 275 samples) to that of poultry, cattle, pigs, and influent/effluent of wastewater treatment plants (n = 150 samples) and (ii) to develop new MST markers for waterbirds. Significant differences were observed between wild waterbirds and the four other groups. We identified 7,349 Amplicon Sequence Variants (ASVs) from the hypervariable V3–V4 region. Firmicutes and Proteobacteria and, in a lesser extent, Actinobacteria and Bacteroidetes were ubiquitous while Fusobacteria and Epsilonbacteraeota were mainly present in wild waterbirds. The clustering of samples in non-metric multidimensional scaling (NMDS) ordination indicated a by-group clustering shape, with a high diversity within wild waterbirds. In addition, the structure of the bacterial communities was distinct according to bird and/or animal species and families (Adonis R2 = 0.13, p = 10–4, Adonis R2 = 0.11, p = 10–4, respectively). The Analysis of Composition of Microbiomes (ANCOM) showed that the wild waterbird group differed from the others by the significant presence of sequences from Fusobacteriaceae (W = 566) and Enterococcaceae (W = 565) families, corresponding to the Cetobacterium (W = 1427) and Catellicoccus (W = 1427) genera, respectively. Altogether, our results suggest that some waterbird members present distinct fecal microbiomes allowing the design of qPCR MST markers. For instance, a swan- and an oystercatcher-associated markers (named Swan_2 and Oyscab, respectively) have been developed. Moreover, bacterial genera harboring potential human pathogens associated to bird droppings were detected in our dataset, including enteric pathogens, i.e., Arcobacter, Clostridium, Helicobacter, and Campylobacter, and environmental pathogens, i.e., Burkholderia and Pseudomonas. Future studies involving other wildlife hosts may improve gut microbiome studies and MST marker development, helping mitigation of yet unknown fecal pollution sources.
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影响因子：
15.5
作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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