title: Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
abstract: Fecal microbiota transplantation (FMT) has shown efficacy in treating recurrent Clostridium difficile infection and is increasingly being applied to other gastrointestinal disorders, yet the fate of native and introduced microbial strains remains largely unknown. To quantify the extent of donor microbiota colonization, we monitored strain populations in fecal samples from a recent FMT study on metabolic syndrome patients using single-nucleotide variants in metagenomes. We found extensive coexistence of donor and recipient strains, persisting 3 months after treatment. Colonization success was greater for conspecific strains than for new species, the latter falling within fluctuation levels observed in healthy individuals over a similar time frame. Furthermore, same-donor recipients displayed varying degrees of microbiota transfer, indicating individual patterns of microbiome resistance and donor-recipient compatibilities.
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 Sydney, Australia.
authors.forename: Simone S
authors.initials: SS
authors.lastname: Li
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Ana
authors.initials: A
authors.lastname: Zhu
authors.affiliation: Genomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Benes
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Paul I
authors.initials: PI
authors.lastname: Costea
authors.affiliation: Genomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Rajna
authors.initials: R
authors.lastname: Hercog
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Hildebrand
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.affiliation: Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, Netherlands. Diabetes Center, Vrije University Medical Center, 1018 HV Amsterdam, Netherlands. Wallenberg Laboratory, University of Gothenburg, 41345 Gothenburg, Sweden.
authors.forename: Max
authors.initials: M
authors.lastname: Nieuwdorp
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland. Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.
authors.forename: Jarkko
authors.initials: J
authors.lastname: Salojärvi
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany.
authors.forename: Anita Y
authors.initials: AY
authors.lastname: Voigt
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Zeller
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. bork@embl.de willem.devos@wur.nl sunagawa@embl.de.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland. Laboratory of Microbiology, Wageningen University, 6703 HB Wageningen, Netherlands. Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, 00014 Helsinki, Finland. bork@embl.de willem.devos@wur.nl sunagawa@embl.de.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany. Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany. Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany. bork@embl.de willem.devos@wur.nl sunagawa@embl.de.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D001419:Bacteria / Q000145:classification / Q000302:isolation & purification; D003015:Clostridium Infections / Q000382:microbiology / Q000628:therapy*; D000069467:Fecal Microbiota Transplantation; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome / Q000502:physiology*; D006801:Humans; D013559:Symbiosis; D014019:Tissue Donors; D014184:Transplantation, Homologous