The paper predicts the structure and function of all proteins in uropathogenic E. coli UTI89 using computational methods and identifies novel host-microbe and microbe-phage interaction pathways.

bioRxiv · Jun 16, 2026 · PreprintMicrobiology

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities

Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson, Thomas Abeel, Ashlee M. Earl

StrainGE identifies low-abundance microbial strains from metagenomic data with higher sensitivity and resolution than existing tools.

Genome biology · Mar 7, 2022Peer-reviewedBioinformatics

Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature

Christopher R. Brydges, Oliver Fiehn, Helen S. Mayberg, Henry L. Schreiber, Siamak Mahmoudian Dehkordi, Sudeepa Bhattacharyya, Jungho Cha, Ki Sueng Choi, W. Edward Craighead, Ranga Rama Krishnan, Augustus John Rush, Boadie Waid Dunlop, Rima F Kaddurah-Daouk, Brenda W.J.H. Penninx, Elizabeth Binder, , Piero Rinaldo

The paper links indoxyl sulfate, a gut microbiome-derived metabolite, to anxiety symptoms and specific brain connectivity patterns in patients with depression.

Scientific Reports · Oct 25, 2021Peer-reviewedNeuroscience