Lindner Blake G, Choudhury Rakin A, Pinamang Princess, Bingham Lilia, D'Amico Isabelle, Hatt Janet K, Konstantinidis Konstantinos T, Graham Katherine E
School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
Environ Sci Technol Lett. 2024 Aug 7;11(9):931-939. doi: 10.1021/acs.estlett.4c00233. eCollection 2024 Sep 10.
Advancements within fecal source tracking (FST) studies are complicated by a lack of knowledge regarding the genetic content and distribution of fecally shed microbial populations. To address this gap, we performed a systematic literature review and curated a large collection of genomes (n = 26,018) representing fecally shed prokaryotic species across broad and narrow source categories commonly implicated in FST studies of recreational waters (i.e., cats, dogs, cows, seagulls, chickens, pigs, birds, ruminants, human feces, and wastewater). We find that across these sources the total number of prokaryotic genomes recovered from materials meeting our initial inclusion criteria varied substantially across fecal sources: from none in seagulls to 9,085 in pigs. We examined genome sequences recovered from these metagenomic and isolation-based studies extensively via comparative genomic approaches to characterize trends across source categories and produce a finalized genome database for each source category which is available online (n = 12,730). On average, 81% of the genomes representing species-level populations occur only within a single source. Using fecal slurries to test the performance of each source database, we report read capture rates that vary with fecal source alpha diversity and database size. We expect this resource to be useful to FST-related objectives, One Health research, and sanitation efforts globally.
粪便源追踪（FST）研究的进展因对粪便中微生物种群的遗传内容和分布缺乏了解而变得复杂。为了填补这一空白，我们进行了系统的文献综述，并精心整理了大量基因组（n = 26,018），这些基因组代表了在娱乐用水FST研究中通常涉及的广泛和狭窄来源类别中粪便排出的原核生物物种（即猫、狗、牛、海鸥、鸡、猪、鸟类、反刍动物、人类粪便和废水）。我们发现，在这些来源中，从符合我们初始纳入标准的材料中回收的原核生物基因组总数在不同粪便来源之间差异很大：从海鸥中没有到猪中有9,085个。我们通过比较基因组方法广泛检查了从这些宏基因组和基于分离的研究中回收的基因组序列，以表征不同来源类别的趋势，并为每个来源类别生成一个最终的基因组数据库，该数据库可在线获取（n = 12,730）。平均而言，代表物种水平种群的基因组中有81%仅出现在单一来源中。使用粪便浆液测试每个来源数据库的性能，我们报告了随粪便来源α多样性和数据库大小而变化的读取捕获率。我们预计这一资源将对全球与FST相关的目标、“同一健康”研究和卫生工作有用。
