NPJ Biofilms Microbiomes. 2023 Aug 3;9(1):54. doi: 10.1038/s41522-023-00421-4.

Qinglong Wu ^1 2, Prapaporn Boonma ^1 2 3, Shyam Badu ^1 2, Nazli Yalcinkaya ^1 2, Sik Yu So ^1 2, Kevin W Garey ⁴, Kent Williams ⁵, L Eugene Arnold ⁶, Robert J Shulman ⁷, Richard Kellermayer ⁷, Tor C Savidge ^8 9

Author information

¹Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.

²Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA.

³Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.

⁴Department of Pharmacy Practice and Translational Research, College of Pharmacy, University of Houston, Houston, TX, USA.

⁵Department of Pediatrics, Ohio State University & Nationwide Children's Hospital, Columbus, OH, USA.

⁶Department of Psychiatry and Behavioral Health, Ohio State University, Columbus, OH, USA.

⁷Department of Pediatrics, Baylor College of Medicine & Texas Children's Hospital, Houston, TX, USA.

⁸Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA. Tor.Savidge@bcm.edu.

⁹Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TX, USA. Tor.Savidge@bcm.edu.

Abstract

Fecal microbiota transplantation (FMT) has proven to be an effective treatment for recurrent Clostridioides difficile infection (rCDI) in both adult and pediatric patients. However, as microbiome development is a critical factor in children, it remains unclear whether adult fecal donors can provide age-appropriate functional restoration in pediatric patients. To address this issue, we conducted an integrated systems approach and found that concordant donor strain engraftment, along with metabolite restoration, are associated with FMT outcomes in both adult and pediatric rCDI patients. Although functional restoration after FMT is not strain-specific, specialized metabolic functions are retained in pediatric patients when adult fecal donors are used. Furthermore, we demonstrated broad utility of high-resolution variant-calling by linking probiotic-strain engraftment with improved gastrointestinal symptoms in adults with irritable bowel syndrome and in children with autism spectrum disorder. Our findings emphasize the importance of strain-level identification when assessing the efficacy of probiotics and microbiota-based therapeutics.