Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification
Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification
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DOI：
10.1128/aem.71.6.3184-3191.2005
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发表时间：
2005-06-01
影响因子：
4.4
通讯作者：
Field, KG
中科院分区：
文献类型：
--
作者：
Dick, LK;Bernhard, AE;Field, KG
本研究的目的是研究拟杆菌目粪便细菌的寄主分布模式，目的是利用地方性序列作为水生环境中粪便源鉴定的标记。我们分析了8种宿主（人、牛、猪、马、狗、猫、海鸥和麋鹿）粪便中的拟杆菌16S rRNA基因序列。恢复的序列与数据库序列不匹配，表明高水平的未开垦多样性。分析结果显示，8种宿主既有地方性分布，也有世界性分布。反刍动物、猪和马的序列倾向于在系统发育树中形成宿主或宿主群体特定的集群，而人类、狗、猫和海鸥的序列几乎完全聚集在一起。人类、狗、猫和海鸥的许多序列都属于一个包含拟杆菌属栽培物种的大分支。大多数培养的拟杆菌种类与多个宿主的匹配非常密切，因此可能不是粪便来源鉴定的有用目标。一个包含普雷沃氏菌属栽培成员的大分支包括与栽培普雷沃氏菌物种不密切相关的克隆序列。大多数反刍动物序列形成的簇与含有拟杆菌和普氏菌的分支分开。鉴定了猪和马的宿主特异性序列，并用于设计PCR引物来鉴定猪和马的水中粪便污染源。引物成功扩增了目标宿主的粪便dna，而没有扩增其他物种的粪便dna。宿主特有的粪便细菌可能是不同类型消化系统进化的结果。
The purpose of this study was to examine host distribution patterns among fecal bacteria in the order Bacteroidales, with the goal of using endemic sequences as markers for fecal source identification in aquatic environments. We analyzed Bacteroidales 16S rRNA gene sequences from the feces of eight hosts: human, bovine, pig, horse, dog, cat, gull, and elk. Recovered sequences did not match database sequences, indicating high levels of uncultivated diversity. The analysis revealed both endemic and cosmopolitan distributions among the eight hosts. Ruminant, pig, and horse sequences tended to form host- or host group-specific clusters in a phylogenetic tree, while human, dog, cat, and gull sequences clustered together almost exclusively. Many of the human, dog, cat, and gull sequences fell within a large branch containing cultivated species from the genus Bacteroides. Most of the cultivated Bacteroides species had very close matches with multiple hosts and thus may not be useful targets for fecal source identification. A large branch containing cultivated members of the genus Prevotella included cloned sequences that were not closely related to cultivated Prevotella species. Most ruminant sequences formed clusters separate from the branches containing Bacteroides and Prevotella species. Host-specific sequences were identified for pigs and horses and were used to design PCR primers to identify pig and horse sources of fecal pollution in water. The primers successfully amplified fecal DNAs from their target hosts and did not amplify fecal DNAs from other species. Fecal bacteria endemic to the host species may result from evolution in different types of digestive systems.