作者
Andrew Brantley Hall, Moran Yassour, Jenny Sauk, Ashley Garner, Xiaofang Jiang, Timothy Arthur, Georgia K Lagoudas, Tommi Vatanen, Nadine Fornelos, Robin Wilson, Madeline Bertha, Melissa Cohen, John Garber, Hamed Khalili, Dirk Gevers, Ashwin N Ananthakrishnan, Subra Kugathasan, Eric S Lander, Paul Blainey, Hera Vlamakis, Ramnik J Xavier, Curtis Huttenhower
发表日期
2017/12
期刊
Genome medicine
卷号
9
页码范围
1-12
出版商
BioMed Central
简介
Background
Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes.
Methods
We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn.
Results
We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of …
学术搜索中的文章
AB Hall, M Yassour, J Sauk, A Garner, X Jiang, T Arthur… - Genome medicine, 2017