title: Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations.
abstract: Fecal microbiota transplantation is a compelling treatment for recurrent Clostridium difficile infections, with potential applications against other diseases associated with changes in gut microbiota. But variability in fecal bacterial communities-believed to be the therapeutic agent-can complicate or undermine treatment efficacy. To understand the effects of transplant preparation methods on living fecal microbial communities, we applied a DNA-sequencing method (PMA-seq) that uses propidium monoazide (PMA) to differentiate between living and dead fecal microbes, and we created an analysis pipeline to identify individual bacteria that change in abundance between samples. We found that oxygen exposure degraded fecal bacterial communities, whereas freeze-thaw cycles and lag time between donor defecation and transplant preparation had much smaller effects. Notably, the abundance of Faecalibacterium prausnitzii-an anti-inflammatory commensal bacterium whose absence is linked to inflammatory bowel disease-decreased with oxygen exposure. Our results indicate that some current practices for preparing microbiota transplant material adversely affect living fecal microbial content and highlight PMA-seq as a valuable tool to inform best practices and evaluate the suitability of clinical fecal material.
authors.affiliation: Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.|Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
authors.forename: Nathaniel D
authors.initials: ND
authors.lastname: Chu
authors.affiliation: Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.|OpenBiome, Medford, Massachusetts, United States of America.|Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
authors.forename: Mark B
authors.initials: MB
authors.lastname: Smith
authors.affiliation: Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
authors.forename: Allison R
authors.initials: AR
authors.lastname: Perrotta
authors.affiliation: Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.|OpenBiome, Medford, Massachusetts, United States of America.
authors.forename: Zain
authors.initials: Z
authors.lastname: Kassam
authors.affiliation: Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.|OpenBiome, Medford, Massachusetts, United States of America.|Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
mesh_terms: D016360:Clostridioides difficile; D004761:Enterocolitis, Pseudomembranous / Q000382:microbiology / Q000628:therapy*; D000069467:Fecal Microbiota Transplantation / Q000379:methods*; D005243:Feces / Q000382:microbiology*; D041981:Gastrointestinal Tract / Q000382:microbiology; D006801:Humans; D064307:Microbiota