Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

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(2022) Paul Feuerstadt et al.   NEW ENGLAND JOURNAL OF MEDICINE

Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis

(2022) Byron J. Smith et al.   Scientific Reports

inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

(2021) Matthew R. Olm et al.   NATURE BIOTECHNOLOGY

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

(2021) Francesco Asnicar et al.   NATURE MEDICINE

Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients

(2021) Diwakar Davar et al.   SCIENCE

Strain inheritance and neonatal gut microbiota development: A meta-analysis

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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity

(2021) Brooke C. Wilson et al.   Microbiome

Prevotella diversity, niches and interactions with the human host

(2021) Adrian Tett et al.   NATURE REVIEWS MICROBIOLOGY

Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes

(2021) Varun Aggarwala et al.   Nature Microbiology

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(2020) Pauli Virtanen et al.   NATURE METHODS

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Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

(2020) Francesco Asnicar et al.   Nature Communications

Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

(2020) Edoardo Pasolli et al.   Nature Communications

Oral Capsulized Fecal Microbiota Transplantation for Eradication of Carbapenemase-producing Enterobacteriaceae Colonization With a Metagenomic Perspective

(2020) Haggai Bar-Yoseph et al.   CLINICAL INFECTIOUS DISEASES

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(2020) Thea Van Rossum et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic Characterization of Gut Microbiota of Carriers of Extended-Spectrum Beta-Lactamase or Carbapenemase-Producing Enterobacteriaceae Following Treatment with Oral Antibiotics and Fecal Microbiota Transplantation: Results from a Multicenter Randomized Trial

(2020) Stefano Leo et al.   Microorganisms

Shiga toxin-producing E. coli transmission via fecal microbiota transplant

(2020) Caroline Zellmer et al.   CLINICAL INFECTIOUS DISEASES

Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn’s Disease

(2020) Lingjia Kong et al.   GASTROENTEROLOGY

Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma

(2020) Gianluca Ianiro et al.   Nature Communications

Effects of fecal microbiota transplantation in subjects with irritable bowel syndrome are mirrored by changes in gut microbiome

(2020) Rasmus Goll et al.   Gut Microbes

Fecal Microbiota Transplant in Two Ulcerative Colitis Pediatric Cases: Gut Microbiota and Clinical Course Correlations

(2020) Andrea Quagliariello et al.   Microorganisms

Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients

(2020) Erez N. Baruch et al.   SCIENCE

The Efficacy of Fecal Microbiota Transplantation for Children With Tourette Syndrome: A Preliminary Study

(2020) Hui-Jun Zhao et al.   Frontiers in Psychiatry

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

The Mediterranean Diet: From an Environment-Driven Food Culture to an Emerging Medical Prescription

(2019) Cristina-Mihaela Lăcătușu et al.   International Journal of Environmental Research and Public Health

Systematic review with meta-analysis: efficacy of faecal microbiota transplantation for the treatment of irritable bowel syndrome

(2019) Gianluca Ianiro et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram‐staining properties

(2019) Chris M. Rands et al.   ENVIRONMENTAL MICROBIOLOGY

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study

(2019) Matthias Willmann et al.   BMC BIOLOGY

International consensus conference on stool banking for faecal microbiota transplantation in clinical practice

(2019) Giovanni Cammarota et al.   GUT

Fecal transplant in children with Clostridioides difficile gives sustained reduction in antimicrobial resistance and potential pathogen burden

(2019) Suchitra K Hourigan et al.   Open Forum Infectious Diseases

Incidence of Bloodstream Infections, Length of Hospital Stay, and Survival in Patients With Recurrent Clostridioides difficile Infection Treated With Fecal Microbiota Transplantation or Antibiotics

(2019) Gianluca Ianiro et al.   ANNALS OF INTERNAL MEDICINE

Human transmission of Blastocystis by Fecal Microbiota Transplantation without development of gastrointestinal symptoms in recipients

(2019) Elisabeth M Terveer et al.   CLINICAL INFECTIOUS DISEASES

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

(2018) Christopher S. Smillie et al.   Cell Host & Microbe

Efficacy of different faecal microbiota transplantation protocols for Clostridium difficile infection: A systematic review and meta-analysis

(2018) Gianluca Ianiro et al.   United European Gastroenterology Journal

On the Road to Strain-Resolved Comparative Metagenomics

(2018) Nicola Segata   mSystems

Population-level analysis ofBlastocystissubtype prevalence and variation in the human gut microbiota

(2018) Raul Y Tito et al.   GUT

Case series of successful treatment with fecal microbiota transplant (FMT) oral capsules mixed from multiple donors even in patients previously treated with FMT enemas for recurrent Clostridium difficile infection

(2018) Mahtab Chehri et al.   MEDICINE

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens

(2017) Sohn Kim et al.   IMMUNOLOGICAL REVIEWS

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome

(2017) Francesco Beghini et al.   ISME Journal

iRECIST: guidelines for response criteria for use in trials testing immunotherapeutics

(2017) Lesley Seymour et al.   LANCET ONCOLOGY

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Accessible, curated metagenomic data through ExperimentHub

(2017) Edoardo Pasolli et al.   NATURE METHODS

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients

(2017) Eli L. Moss et al.   PLoS One

Strain profiling and epidemiology of bacterial species from metagenomic sequencing

(2017) Davide Albanese et al.   Nature Communications

Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile

(2017) Ranjit Kumar et al.   npj Biofilms and Microbiomes

Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohnʼs Disease

(2016) Byron P. Vaughn et al.   INFLAMMATORY BOWEL DISEASES

Different immunological responses to early-life antibiotic exposure affecting autoimmune diabetes development in NOD mice

(2016) Youjia Hu et al.   JOURNAL OF AUTOIMMUNITY

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(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

(2016) Aaron Weimann et al.   mSystems

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(2015) Dinghua Li et al.   BIOINFORMATICS

Antimicrobial resistance: A global emerging threat to public health systems

(2015) Maurizio Ferri et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

(2015) Paul Moayyedi et al.   GASTROENTEROLOGY

Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis

(2015) Noortje G. Rossen et al.   GASTROENTEROLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohnʼs Disease

(2015) David L. Suskind et al.   INFLAMMATORY BOWEL DISEASES

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis

(2015) Christopher J. Damman et al.   PLoS One

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

The microbial eukaryoteBlastocystisis a prevalent and diverse member of the healthy human gut microbiota

(2014) Pauline D. Scanlan et al.   FEMS MICROBIOLOGY ECOLOGY

Clinical and Microbiological Characteristics of Eggerthella lenta Bacteremia

(2014) B. J. Gardiner et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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(2012) Catherine A. Lozupone et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome

(2010) Hedvig E. Jakobsson et al.   PLoS One

Decreased Diversity of the Fecal Microbiome in RecurrentClostridium difficile–Associated Diarrhea

(2008) Ju Young Chang et al.   JOURNAL OF INFECTIOUS DISEASES