Bryson Samuel, Sisson Zachary, Nelson Bradley, Grove Jonas, Reister Emily, Liachko Ivan, Auch Benjamin, Graiziger Carolyn, Khoruts Alexander
Phase Genomics, Seattle, WA, USA.
Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, MN, USA.
Gut Microbes. 2025 Dec;17(1):2559019. doi: 10.1080/19490976.2025.2559019. Epub 2025 Sep 15.
Proximity ligation shotgun metagenomics facilitate the analysis of the relationships between mobile genetic elements, such as plasmids and bacteriophages, and their specific bacterial hosts. We applied this technique to investigate the changes in the fecal microbiome of patients receiving fecal microbiota transplantation (FMT) for recurrent infections (rCDI). FMT was associated with successful engraftment of donor bacteria along with their associated bacteriophages. While fecal microbial diversity increased in all patients, the extent of specific bacterial taxa engraftment varied among individual patients. Interestingly, some donor bacteriophages remained closely linked to their original bacterial hosts, while others expanded their associations across different bacterial taxa. Notably, FMT partially reduced the content of vancomycin resistance and extended-spectrum beta-lactamase genes in the fecal microbiome of rCDI patients.
邻近连接鸟枪法宏基因组学有助于分析移动遗传元件（如质粒和噬菌体）与其特定细菌宿主之间的关系。我们应用这项技术来研究因复发性感染（rCDI）接受粪便微生物群移植（FMT）的患者粪便微生物组的变化。FMT与供体细菌及其相关噬菌体的成功植入有关。虽然所有患者的粪便微生物多样性均增加，但个体患者中特定细菌类群的植入程度有所不同。有趣的是，一些供体噬菌体仍与其原始细菌宿主紧密相连，而其他噬菌体则扩大了它们与不同细菌类群的关联。值得注意的是，FMT部分降低了rCDI患者粪便微生物组中万古霉素抗性和超广谱β-内酰胺酶基因的含量。
