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Peer-Reviewed Publication
Microbiol Spectr2026;e0030626.July 14, 2026Journal Article

Comparative genomic analysis of Bacteroides fragilis from intestinal and extra-intestinal sites.

Renee E Oles1,2, Marvic Carrillo Terrrazas1, Luke R Loomis1, Simone Zuffa3,4, Maxwell J Neal5, Chia-Yun Hsu1, Adriana Vasquez Ayala1, Caitlin Tribelhorn2, Pedro Belda-Ferre2, Jianshu Zhao2, MacKenzie Bryant2, Jasmine Zemlin3,4, Jocelyn Young6, Parambir S Dulai7,8, William J Sandborn7,9, Mamata Sivagnanam6, David Pride1,9,10,11, Karsten Zengler2,5,9,12, Pieter C Dorrestein3,4,9, Rob Knight2,9,13,14,15,16, Hiutung Chu1,9,17
1Department of Pathology, University of California, San Diego, California, USA.
2Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, California, USA.
3Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA.
4Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA.
5Department of Bioengineering, University of California, San Diego, California, USA.
6Division of Gastroenterology, Hepatology and Nutrition, University of California, San Diego and Rady Children's Hospital, San Diego, California, USA.
7Division of Gastroenterology, University of California, San Diego, California, USA.
8Division of Gastroenterology, Northwestern University, Chicago, Illinois, USA.
9Center for Microbiome Innovation, University of California, San Diego, California, USA.
10Center for Innovative Phage Applications and Therapeutics (IPATH), University of California, San Diego, California, USA.
11Center of Advanced Laboratory Medicine (CALM), University of California, San Diego, California, USA.
12Program in Materials Science and Engineering, University of California, San Diego, California, USA.
13Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, California, USA.
14Department of Computer Science & Engineering, University of California, San Diego, California, USA.
15Halıcıoğlu Data Science Institute, University of California, San Diego, California, USA.
16Hong Kong University of Science and Technology Jockey Club Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, Hong Kong SAR, China.
17Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, California, USA.
PubMed DOI

Abstract

Bacteroides fragilis, a key member of the human gut microbiota, contributes to host health by maintaining intestinal homeostasis. Yet, it is also the most frequently isolated anaerobe in clinical infections. These contrasting roles raise questions about the genetic and ecological factors that explain why this common symbiont is disproportionately linked to infection. We analyzed 813 Division I B.…

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