Controlling the human microbiome

SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection

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

Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers

(2022) Melissa Dsouza et al.   Cell Host & Microbe

Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics

(2022) Mayank Baranwal et al.   eLife

Design, construction, and in vivo augmentation of a complex gut microbiome

(2022) Alice G. Cheng et al.   CELL

Multi-kingdom ecological drivers of microbiota assembly in preterm infants

(2021) Chitong Rao et al.   NATURE

Data-driven control of complex networks

(2021) Giacomo Baggio et al.   Nature Communications

Challenges in benchmarking metagenomic profilers

(2021) Zheng Sun et al.   NATURE METHODS

Microbiome Structure and Function in Woodchip Bioreactors for Nitrate Removal in Agricultural Drainage Water

(2021) Arnaud Jéglot et al.   Frontiers in Microbiology

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

(2021) Ilija Dukovski et al.   Nature Protocols

A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns

(2020) Robert Marsland et al.   Scientific Reports

The Community Simulator: A Python package for microbial ecology

(2020) Robert Marsland et al.   PLoS One

AI Feynman: A physics-inspired method for symbolic regression

(2020) Silviu-Marian Udrescu et al.   Science Advances

Dissimilarity–Overlap analysis of replicate enrichment communities

(2020) Jean C. C. Vila et al.   ISME Journal

An ecological framework to understand the efficacy of fecal microbiota transplantation

(2020) Yandong Xiao et al.   Nature Communications

Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour

(2020) Sílvia F. Henriques et al.   Nature Communications

Macroecological laws describe variation and diversity in microbial communities

(2020) Jacopo Grilli   Nature Communications

Deciphering functional redundancy in the human microbiome

(2020) Liang Tian et al.   Nature Communications

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

(2019) Robert Marsland et al.   PLoS Computational Biology

A theoretical framework for controlling complex microbial communities

(2019) Marco Tulio Angulo et al.   Nature Communications

Microbial coexistence through chemical-mediated interactions

(2019) Lori Niehaus et al.   Nature Communications

Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

(2019) David B Bernstein et al.   eLife

Revealing Complex Ecological Dynamics via Symbolic Regression

(2019) Yize Chen et al.   BIOESSAYS

Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species–species modelling

(2019) J. D. Brunner et al.   Journal of the Royal Society Interface

Synthetic ecology of the human gut microbiota

(2019) Gino Vrancken et al.   NATURE REVIEWS MICROBIOLOGY

Donor Screening for Fecal Microbiota Transplantation

(2019) Zain Kassam et al.   NEW ENGLAND JOURNAL OF MEDICINE

Multistability and regime shifts in microbial communities explained by competition for essential nutrients

(2019) Veronika Dubinkina et al.   eLife

Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community

(2019) Harry Mickalide et al.   Cell Systems

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

Multiple stable states in microbial communities explained by the stable marriage problem

(2018) Akshit Goyal et al.   ISME Journal

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Role of priority effects in the early-life assembly of the gut microbiota

(2018) Daniel Sprockett et al.   Nature Reviews Gastroenterology & Hepatology

Computer-guided design of optimal microbial consortia for immune system modulation

(2018) Richard R Stein et al.   eLife

Signatures of ecological processes in microbial community time series

(2018) Karoline Faust et al.   Microbiome

Stability of the human faecal microbiome in a cohort of adult men

(2018) Raaj S. Mehta et al.   Nature Microbiology

Ecological suicide in microbes

(2018) Christoph Ratzke et al.   Nature Ecology & Evolution

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

You are what you eat: diet, health and the gut microbiota

(2018) Niv Zmora et al.   Nature Reviews Gastroenterology & Hepatology

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract

(2018) Isabel F. Escapa et al.   mSystems

Multi-stability and the origin of microbial community types

(2017) Didier Gonze et al.   ISME Journal

Fundamental limitations of network reconstruction from temporal data

(2017) Marco Tulio Angulo et al.   Journal of the Royal Society Interface

The resilience of the intestinal microbiota influences health and disease

(2017) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Mapping the ecological networks of microbial communities

(2017) Yandong Xiao et al.   Nature Communications

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

(2017) Eugen Bauer et al.   PLoS Computational Biology

Two dynamic regimes in the human gut microbiome

(2017) Sean M. Gibbons et al.   PLoS Computational Biology

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

(2017) Babak Momeni et al.   eLife

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

(2017) Joanne B. Emerson et al.   Microbiome

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

Community structure follows simple assembly rules in microbial microcosms

(2017) Jonathan Friedman et al.   Nature Ecology & Evolution

Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons

(2016) Hong-Tai Cao et al.   BIOESSAYS

Temporal Stability of the Human Skin Microbiome

(2016) Julia Oh et al.   CELL

Gleaning Insights from Fecal Microbiota Transplantation and Probiotic Studies for the Rational Design of Combination Microbial Therapies

(2016) Lauren E. Hudson et al.   CLINICAL MICROBIOLOGY REVIEWS

The steady-state assumption in oscillating and growing systems

(2016) Alexandra-M. Reimers et al.   JOURNAL OF THEORETICAL BIOLOGY

Universality of human microbial dynamics

(2016) Amir Bashan et al.   NATURE

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Advancing microbial sciences by individual-based modelling

(2016) Ferdi L. Hellweger et al.   NATURE REVIEWS MICROBIOLOGY

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance

(2016) Andrés Moya et al.   TRENDS IN MICROBIOLOGY

High-order species interactions shape ecosystem diversity

(2016) Eyal Bairey et al.   Nature Communications

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface

(2016) Pranjul Shah et al.   Nature Communications

Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism

(2016) Tim A. Hoek et al.   PLOS BIOLOGY

On the Origins and Control of Community Types in the Human Microbiome

(2016) Travis E. Gibson et al.   PLoS Computational Biology

Faecal microbiota transplantation is promising but not a panacea

(2016) Michael J. Sadowsky et al.   Nature Microbiology

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

Systematic Review: Adverse Events of Fecal Microbiota Transplantation

(2016) Sinan Wang et al.   PLoS One

Controlling the false discovery rate via knockoffs

(2015) Rina Foygel Barber et al.   ANNALS OF STATISTICS

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

Transient dynamics of competitive exclusion in microbial communities

(2015) Stilianos Louca et al.   ENVIRONMENTAL MICROBIOLOGY

Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling

(2015) Hao Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Weight Gain After Fecal Microbiota Transplantation

(2015) N. Alang et al.   Open Forum Infectious Diseases

Fecal Microbiota Transplant for Relapsing Clostridium difficile Infection Using a Frozen Inoculum From Unrelated Donors: A Randomized, Open-Label, Controlled Pilot Study

(2014) Ilan Youngster et al.   CLINICAL INFECTIOUS DISEASES

Fecal microbiota transplantation as therapy for inflammatory bowel disease: A systematic review and meta-analysis

(2014) Ruben J. Colman et al.   Journal of Crohns & Colitis

Towards Predictive Models of the Human Gut Microbiome

(2014) Vanni Bucci et al.   JOURNAL OF MOLECULAR BIOLOGY

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Target control of complex networks

(2014) Jianxi Gao et al.   Nature Communications

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Fecal Microbiota Transplantation: Long-Term Safety Issues

(2013) Wael El-Matary   AMERICAN JOURNAL OF GASTROENTEROLOGY

Fecal Microbiota Transplantation for Clostridium difficile Infection: Systematic Review and Meta-Analysis

(2013) Zain Kassam et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

An overview of fecal microbiota transplantation: techniques, indications, and outcomes

(2013) Lawrence J. Brandt et al.   GASTROINTESTINAL ENDOSCOPY

Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context

(2013) J. Iranzo et al.   JOURNAL OF BACTERIOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mathematical modeling of primary succession of murine intestinal microbiota

(2013) S. Marino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Fecal microbiota transplantation

(2012) Olga C. Aroniadis et al.   CURRENT OPINION IN GASTROENTEROLOGY

Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure

(2012) Manuel Ferrer et al.   ENVIRONMENTAL MICROBIOLOGY

A framework for human microbiome research

(2012)   NATURE

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Detecting Causality in Complex Ecosystems

(2012) G. Sugihara et al.   SCIENCE

Microbiota-Targeted Therapies: An Ecological Perspective

(2012) K. P. Lemon et al.   Science Translational Medicine

Temporal Dynamics of the Human Vaginal Microbiota

(2012) P. Gajer et al.   Science Translational Medicine

Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota

(2012) Vanni Bucci et al.   PLoS Computational Biology

Fecal microbiota transplantation in relapsing Clostridium difficile infection

(2012) Faith Rohlke et al.   Therapeutic Advances in Gastroenterology

The Evolution of Bacteriocin Production in Bacterial Biofilms

(2011) Vanni Bucci et al.   AMERICAN NATURALIST

iDynoMiCS: next-generation individual-based modelling of biofilms

(2011) Laurent A. Lardon et al.   ENVIRONMENTAL MICROBIOLOGY

Controllability of complex networks

(2011) Yang-Yu Liu et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Fecal microbiota transplantation and emerging applications

(2011) Thomas J. Borody et al.   Nature Reviews Gastroenterology & Hepatology

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Distilling Free-Form Natural Laws from Experimental Data

(2009) Michael Schmidt et al.   SCIENCE

A bunch of tiny individuals—Individual-based modeling for microbes

(2008) Ferdi L. Hellweger et al.   ECOLOGICAL MODELLING

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques

(2008) Rudolf Amann et al.   NATURE REVIEWS MICROBIOLOGY

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA