{"doi":"10.1038/s41598-021-84152-6","title":"Lower endoscopic delivery of freeze-dried intestinal microbiota results in more rapid and efficient engraftment than oral administration","abstract":"<jats:title>Abstract</jats:title><jats:p>Fecal microbiota transplantation (FMT) is a highly effective treatment for recurrent <jats:italic>Clostridioides difficile</jats:italic> infection (rCDI). However, standardization of FMT products is essential for its broad implementation into clinical practice. We have developed an oral preparation of freeze-dried, encapsulated microbiota, which is ~ 80% clinically effective, but results in delayed engraftment of donor bacteria relative to administration via colonoscopy. Our objective was to measure the engraftment potential of freeze-dried microbiota without the complexity of variables associated with oral administration. We compared engraftment of identical preparations and doses of freeze-dried microbiota following colonoscopic (9 patients) versus oral administration (18 patients). Microbiota were characterized by sequencing of the 16S rRNA gene, and engraftment was determined using the SourceTracker algorithm. Oligotyping analysis was done to provide high-resolution patterns of microbiota engraftment. Colonoscopic FMT was associated with greater levels of donor engraftment within days following the procedure (ANOVA <jats:italic>P</jats:italic> = 0.035) and specific increases in the relative abundances of donor <jats:italic>Lachnospiraceae</jats:italic>, <jats:italic>Bacteroidaceae</jats:italic>, and <jats:italic>Porphyromonadaceae</jats:italic> (<jats:italic>P</jats:italic> ≤ 0.033). Lower relative abundances of <jats:italic>Bacteroidaceae</jats:italic>, <jats:italic>Lachnospiraceae</jats:italic>, and <jats:italic>Ruminococcaceae</jats:italic> families were associated with clinical failures. These results suggest that further optimization of oral capsule FMT may improve its engraftment efficiency and clinical efficacy.</jats:p>","journal":"Scientific Reports","year":2021,"id":613534,"datarank":0.4943755299006494,"base_score":3.295836866004329,"endowment":3.295836866004329,"self_citation_contribution":0.4943755299006494,"citation_network_contribution":0.0,"self_endowment_contribution":0.4943755299006494,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":26,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":4,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":861932,"name":"Hossam Halaweish","orcid":"0009-0006-6507-4758","position":1,"is_corresponding":false},{"id":1580671,"name":"Carolyn Graiziger","orcid":null,"position":2,"is_corresponding":false},{"id":463345,"name":"Matthew J. 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Sadowsky","orcid":null,"position":9,"is_corresponding":false},{"id":320937,"name":"Alexander Khoruts","orcid":"0000-0002-3205-3188","position":10,"is_corresponding":false},{"id":653447,"name":"Christopher Staley","orcid":"0000-0002-2309-0083","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Lower endoscopic delivery of freeze-dried intestinal microbiota results in more rapid and efficient engraftment than oral administration","abstract":"<jats:title>Abstract</jats:title><jats:p>Fecal microbiota transplantation (FMT) is a highly effective treatment for recurrent <jats:italic>Clostridioides difficile</jats:italic> infection (rCDI). However, standardization of FMT products is essential for its broad implementation into clinical practice. We have developed an oral preparation of freeze-dried, encapsulated microbiota, which is ~ 80% clinically effective, but results in delayed engraftment of donor bacteria relative to administration via colonoscopy. Our objective was to measure the engraftment potential of freeze-dried microbiota without the complexity of variables associated with oral administration. We compared engraftment of identical preparations and doses of freeze-dried microbiota following colonoscopic (9 patients) versus oral administration (18 patients). Microbiota were characterized by sequencing of the 16S rRNA gene, and engraftment was determined using the SourceTracker algorithm. Oligotyping analysis was done to provide high-resolution patterns of microbiota engraftment. Colonoscopic FMT was associated with greater levels of donor engraftment within days following the procedure (ANOVA <jats:italic>P</jats:italic> = 0.035) and specific increases in the relative abundances of donor <jats:italic>Lachnospiraceae</jats:italic>, <jats:italic>Bacteroidaceae</jats:italic>, and <jats:italic>Porphyromonadaceae</jats:italic> (<jats:italic>P</jats:italic> ≤ 0.033). Lower relative abundances of <jats:italic>Bacteroidaceae</jats:italic>, <jats:italic>Lachnospiraceae</jats:italic>, and <jats:italic>Ruminococcaceae</jats:italic> families were associated with clinical failures. These results suggest that further optimization of oral capsule FMT may improve its engraftment efficiency and clinical efficacy.</jats:p>","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":4,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"33633264","pmcid":"PMC7907225","openalex_id":null,"authors":[],"funders":[{"funder_name":"Hubbard Broadcasting Foundation","grant_id":"","title":null},{"funder_name":"University of Minnesota Academic Health Center","grant_id":"","title":null},{"funder_name":"Frank J Maslowski and Eleanor A Maslowski Charitable Trust","grant_id":"","title":null},{"funder_name":"Achieving Cures Together","grant_id":"","title":null}],"total_grants":4,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.nature.com/articles/s41598-021-84152-6.pdf","host_type":"publisher"},{"url":"https://www.nature.com/articles/s41598-021-84152-6","host_type":"publisher"},{"url":"https://doaj.org/article/ada7bfb87fa644a88ca2f400ae09159f","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7907225","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC7907225","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC7907225?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":[],"mesh_terms":["Humans","Clostridium Infections","Disease Susceptibility","Freeze Drying","Treatment Outcome","Biodiversity","Aged","Aged, 80 and over","Middle Aged","Disease Management","Female","Male","Metagenome","Metagenomics","Gastrointestinal Microbiome","Fecal Microbiota Transplantation","Transanal Endoscopic Microsurgery"],"keywords":[],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.24709056.v1","title":"Additional file 1 of Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24709056","title":"Additional file 1 of Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24709144.v1","title":"Additional file 2 of Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics","publisher":"figshare","resource_type":"Dataset"},{"doi":"10.6084/m9.figshare.24709144","title":"Additional file 2 of Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics","publisher":"figshare","resource_type":"Dataset"}],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T08:26:59.300213Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}