ArticleNature microbiology2021
Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes.
Article in Nature microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 95 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
95 citing papers in PubMed, 136 citations in OpenAlex.
- 15-strain live biotherapeutic product or same donor fecal microbiota transplant for recurrent Clostridioides difficile infection: a randomized phase 1b trial.Nature medicine · 2026Trial
- Microbiome compositional changes and clonal engraftment in a phase 3 trial of fecal microbiota, live-jslm for recurrentGut microbes · 2025Trial
- Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.Nature communications · 2025Trial
- Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement.Science translational medicine · 2023Trial
- Fecal microbiota transplantation reverses insulin resistance in type 2 diabetes: A randomized, controlled, prospective study.Frontiers in cellular and infection microbiology · 2022Trial
- Species- and strain-level assessment usingGut microbesTrial
- Why probiotics fail: gut niche tension as the missing variable?Gut microbes · 2026Review
- Temporal dynamics of gut biosynthetic gene clusters link persistent colonization and engraftment in fecal microbiota transplantation.Gut microbes · 2026Article
- Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.Gut microbes · 2026Article
- Combining genotoxic gut bacterial strains increases tumor burden and accelerates onset in a germ-free mouse model of colon carcinogenesis.Cell reports · 2026Article
- Article
- Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.Cell host & microbe · 2026Article
- An Integrated Dataset of Clinical and Microbial Profiles for Fecal Microbiota Transplantation.Scientific data · 2026Article
- ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.bioRxiv : the preprint server for biology · 2026Article
- Fecal microbiota transplantation in chronic liver disease: Current and future state of the art.Hepatology communications · 2026Review
- Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.Microorganisms · 2026Review
- The Gut-Brain-Immune Axis in Glioma: Emerging Mechanisms and Therapeutic Opportunities.Cellular and molecular neurobiology · 2026Review
- Potential influence of gut microbiota on the process of hypertriglyceridemia-aggravated acute pancreatitis.World journal of gastroenterology · 2026Review
- Route of fecal microbiota transplantation delivery determined the dynamics and predictability of donor microbe colonization.Animal microbiome · 2025Article
- Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
13 authors at 2 institutions in 1 country.
Funding
Abstract
Fecal microbiota transplantation (FMT) has been successfully applied to treat recurrent Clostridium difficile infection in humans, but a precise method to measure which bacterial strains stably engraft in recipients and evaluate their association with clinical outcomes is lacking. We assembled a collection of >1,000 different bacterial strains that were cultured from the fecal samples of 22 FMT donors and recipients. Using our strain collection combined with metagenomic sequencing data from the same samples, we developed a statistical approach named Strainer for the detection and tracking of bacterial strains from metagenomic sequencing data. We applied Strainer to evaluate a cohort of 13 FMT longitudinal clinical interventions and detected stable engraftment of 71% of donor microbiota strains in recipients up to 5 years post-FMT. We found that 80% of recipient gut bacterial strains pre-FMT were eliminated by FMT and that post-FMT the strains present persisted up to 5 years later, together with environmentally acquired strains. Quantification of donor bacterial strain engraftment in recipients independently explained (precision 100%, recall 95%) the clinical outcomes (relapse or success) after initial and repeat FMT. We report a compendium of bacterial species and strains that consistently engraft in recipients over time that could be used in defined live biotherapeutic products as an alternative to FMT. Our analytical framework and Strainer can be applied to systematically evaluate either FMT or defined live bacterial therapeutic studies by quantification of strain engraftment in recipients.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.