The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia

Bacterial species rarely work together

(2022) Jacob D. Palmer et al.   SCIENCE

A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients

(2022) Jinyuan Yan et al.   Scientific Data

Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia

(2022) Lucie Bernard-Raichon et al.   Nature Communications

Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae

(2022) Ana Djukovic et al.   Nature Communications

5-Aminosalicylic Acid Ameliorates Colitis and Checks Dysbiotic Escherichia coli Expansion by Activating PPAR-γ Signaling in the Intestinal Epithelium

(2021) Stephanie A. Cevallos et al.   mBio

Initialization is critical for preserving global data structure in both t-SNE and UMAP

(2021) Dmitry Kobak et al.   NATURE BIOTECHNOLOGY

Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients

(2021) Chen Liao et al.   Scientific Data

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner

(2021) Emmanuel Montassier et al.   Nature Microbiology

Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition

(2021) Lisa Osbelt et al.   Cell Host & Microbe

Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data

(2021) George Armstrong et al.   mSystems

Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents

(2020) Jens Walter et al.   CELL

Compositional flux within the intestinal microbiota and risk for bloodstream infection with gram-negative bacteria

(2020) Igor Stoma et al.   CLINICAL INFECTIOUS DISEASES

High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis

(2020) Bing Zhai et al.   NATURE MEDICINE

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation

(2020) Jonathan U. Peled et al.   NEW ENGLAND JOURNAL OF MEDICINE

Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages

(2020) Benjamin A. Siranosian et al.   Nature Communications

Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition

(2020) Rita A. Oliveira et al.   Nature Microbiology

Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation

(2020) Rachael B. Chanin et al.   Cell Host & Microbe

The gut microbiota is associated with immune cell dynamics in humans

(2020) Jonas Schluter et al.   NATURE

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

(2019) Abigail J. Johnson et al.   Cell Host & Microbe

Antibiotic-induced shifts in fecal microbiota density and composition during hematopoietic stem cell transplantation

(2019) Sejal Morjaria et al.   INFECTION AND IMMUNITY

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

(2019) Dongwan D. Kang et al.   PeerJ

High heterogeneity of multidrug-resistant Enterobacteriaceae fecal levels in hospitalized patients is partially driven by intravenous beta-lactams.

(2019) Ana Djukovic et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bacteria Use Collective Behavior to Generate Diverse Combat Strategies

(2018) Despoina A.I. Mavridou et al.   CURRENT BIOLOGY

Stereotypic Immune System Development in Newborn Children

(2018) Axel Olin et al.   CELL

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Precision identification of diverse bloodstream pathogens in the gut microbiome

(2018) Fiona B. Tamburini et al.   NATURE MEDICINE

Dietary sugar silences a colonization factor in a mammalian gut symbiont

(2018) Guy E. Townsend et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Colonocyte metabolism shapes the gut microbiota

(2018) Yael Litvak et al.   SCIENCE

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

Antibiotic-mediated modification of the intestinal microbiome in allogeneic hematopoietic stem cell transplantation

(2016) J Whangbo et al.   BONE MARROW TRANSPLANTATION

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella

(2016) Fabian Rivera-Chávez et al.   Cell Host & Microbe

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

The human microbiome in hematopoiesis and hematologic disorders

(2015) V. E. Manzo et al.   BLOOD

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

The dynamic microbiome

(2014) Georg K. Gerber   FEBS LETTERS

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Intestinal Microbiota Containing Barnesiella Species Cures Vancomycin-Resistant Enterococcus faecium Colonization

(2013) Carles Ubeda et al.   INFECTION AND IMMUNITY

Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis

(2013) Lionel Rigottier-Gois   ISME Journal

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation

(2012) Ying Taur et al.   CLINICAL INFECTIOUS DISEASES

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

(2010) Carles Ubeda et al.   JOURNAL OF CLINICAL INVESTIGATION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glycogen and Maltose Utilization by Escherichia coli O157:H7 in the Mouse Intestine

(2008) S. A. Jones et al.   INFECTION AND IMMUNITY