FIG 1 .

Fecal microbiota transplantation (FMT) to treat ulcerative colitis. (A) Diagram of the treatment regimens. Patient 1 received 30 rounds of FMT, patient 2 received 25, and patient 3 received 22. All patients were in remission (gray-shaded boxes) while receiving the FMT course and remained in remission for more than 11 weeks following their last FMT. However, all three eventually experienced a relapse requiring immunotherapy. Administration of mesalamine, given orally or through a rectal enema, was allowed during the trial, depending on the clinical disease activity. Three samples (indicated as triangles) were taken from each patient: one before the beginning of the FMT course (pre), the second after the 13th FMT (during), and the third 2 to 3 weeks after finishing the FMT course (post). (B) Bacterial lineages in the samples studied. Bacterial taxonomic representation and abundance were characterized by sequencing of 16S rRNA gene tags. Details are described in reference 15. (C) Viral families detected in the samples studied, assessed by alignment of reads to a curated database of viral sequences (18). (D) Gene types inferred from analysis of the VLP contigs. VLP contigs were analyzed for open reading frames (ORFs), and then ORFs were annotated using the CDD. The output was interpreted using custom annotation relating Pfam domains to viral gene functions. Gene types identified are summarized at the right in the figure. The percentages of classified phage ORFs from the four donor samples, patient 1, patient 2, and patient 3 were 8.9%, 7.1%, 3.8%, and 9.5%, respectively.