Engineering complex communities by directed evolution

Designing Synthetic Microbial Consortia for Biofuel Production

(2020) Yujia Jiang et al.   TRENDS IN BIOTECHNOLOGY

Bacterial adaptation is constrained in complex communities

(2020) Thomas Scheuerl et al.   Nature Communications

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

(2020) Robert Marsland et al.   Scientific Reports

Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures

(2020) Dingrong Kang et al.   Frontiers in Microbiology

Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells

(2020) See-Yeun Ting et al.   Cell Host & Microbe

The Community Simulator: A Python package for microbial ecology

(2020) Robert Marsland et al.   PLoS One

Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity

(2020) Guilhem Doulcier et al.   eLife

Effects of microbial evolution dominate those of experimental host-mediated indirect selection

(2020) Jigyasa Arora et al.   PeerJ

Artificially selecting bacterial communities using propagule strategies*

(2020) Chang‐Yu Chang et al.   EVOLUTION

Higher-Order Interactions Dampen Pairwise Competition in the Zebrafish Gut Microbiome

(2020) Deepika Sundarraman et al.   mBio

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

(2019) Alan R. Pacheco 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

Toxicity drives facilitation between 4 bacterial species

(2019) Philippe Piccardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulations reveal challenges to artificial community selection and possible strategies for success

(2019) Li Xie et al.   PLOS BIOLOGY

Understanding microbial community dynamics to improve optimal microbiome selection

(2019) Robyn J. Wright et al.   Microbiome

Microbial community design: methods, applications, and opportunities

(2019) Alexander Eng et al.   CURRENT OPINION IN BIOTECHNOLOGY

Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation

(2019) Sean P. Gilmore et al.   ACS Synthetic Biology

Artificially selecting microbial communities: If we can breed dogs, why not microbiomes?

(2019) Flor I. Arias-Sánchez et al.   PLOS BIOLOGY

Innovation by Evolution: Bringing New Chemistry to Life (Nobel Lecture)

(2019) Frances H. Arnold   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Effect of the Reproduction Method in an Artificial Selection Experiment at the Community Level

(2019) Tiffany Raynaud et al.   Frontiers in Ecology and Evolution

Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere

(2019) Michael D. Jochum et al.   PLoS One

High-order interactions distort the functional landscape of microbial consortia

(2019) Alicia Sanchez-Gorostiaga et al.   PLOS BIOLOGY

Defining Higher-Order Interactions in Synthetic Ecology: Lessons from Physics and Quantitative Genetics

(2019) Alvaro Sanchez   Cell Systems

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

(2019) Harry Mickalide et al.   Cell Systems

Statistical physics of community ecology: a cavity solution to MacArthur’s consumer resource model

(2018) Madhu Advani et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation

(2018) Pilar Eliana Puentes-Téllez et al.   MICROBIAL ECOLOGY

Deciphering microbial interactions in synthetic human gut microbiome communities

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

An exclusive metabolic niche enables strain engraftment in the gut microbiota

(2018) Elizabeth Stanley Shepherd et al.   NATURE

Design of synthetic bacterial communities for predictable plant phenotypes

(2018) Sur Herrera Paredes et al.   PLOS BIOLOGY

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

(2018) Richard R Stein et al.   eLife

Enrichment and characterization of an environmental microbial consortium displaying efficient keratinolytic activity

(2018) Dingrong Kang et al.   BIORESOURCE TECHNOLOGY

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Anaerobic lignocellulolytic microbial consortium derived from termite gut: enrichment, lignocellulose degradation and community dynamics

(2018) Adèle Lazuka et al.   Biotechnology for Biofuels

Microbiome interactions shape host fitness

(2018) Alison L. Gould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A macroecological theory of microbial biodiversity

(2017) William R. Shoemaker et al.   Nature Ecology & Evolution

Community structure follows simple assembly rules in microbial microcosms

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

Different inocula produce distinctive microbial consortia with similar lignocellulose degradation capacity

(2016) Larisa Cortes-Tolalpa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

High-Order Interactions between Species Strongly Influence the Activity of Microbial Communities

(2016) Xiaokan Guo et al.   BIOPHYSICAL JOURNAL

Cultivated Sub-Populations of Soil Microbiomes Retain Early Flowering Plant Trait

(2016) Kevin Panke-Buisse et al.   MICROBIAL ECOLOGY

Manipulating Bacterial Communities by in situ Microbiome Engineering

(2016) Ravi U. Sheth et al.   TRENDS IN GENETICS

The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community

(2016) Xiaokan Guo et al.   PLoS Computational Biology

Microbial Community Coalescence for Microbiome Engineering

(2016) Matthias C. Rillig et al.   Frontiers in Microbiology

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

(2016) Jaejoon Jung et al.   Scientific Reports

Levels and limits in artificial selection of communities

(2015) Manuel Blouin et al.   ECOLOGY LETTERS

Ecological communities by design

(2015) J. K. Fredrickson   SCIENCE

Engineering Microbiomes to Improve Plant and Animal Health

(2015) U.G. Mueller et al.   TRENDS IN MICROBIOLOGY

Ecological perspectives on synthetic biology: insights from microbial population biology

(2015) Ana E. Escalante et al.   Frontiers in Microbiology

Human Gut Microbes Use Multiple Transporters to Distinguish Vitamin B12 Analogs and Compete in the Gut

(2014) Patrick H. Degnan et al.   Cell Host & Microbe

Vitamin B 12 as a Modulator of Gut Microbial Ecology

(2014) Patrick H. Degnan et al.   Cell Metabolism

Selection on soil microbiomes reveals reproducible impacts on plant function

(2014) Kevin Panke-Buisse et al.   ISME Journal

Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

(2014) J. J. Faith et al.   Science Translational Medicine

Unconventional approaches to isolation and enrichment of functional microbial consortium – A review

(2013) Duu-Jong Lee et al.   BIORESOURCE TECHNOLOGY

The social structure of microbial community involved in colonization resistance

(2013) Xuesong He et al.   ISME Journal

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

(2013) Jeremy J. Minty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biohydrogen from cellulosic feedstock: Dilution-to-stimulation approach

(2012) Kuo-Ling Ho et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

Microbiota-Targeted Therapies: An Ecological Perspective

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

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Microbial Communities as Experimental Units

(2011) Mitch D. Day et al.   BIOSCIENCE

Evolution in metacommunities

(2011) C. J. Goodnight   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Function-specific response to depletion of microbial diversity

(2010) Hannes Peter et al.   ISME Journal

Characterization of two diesel fuel degrading microbial consortia enriched from a non acclimated, complex source of microorganisms

(2010) Giulio Zanaroli et al.   Microbial Cell Factories

Directed enzyme evolution: climbing fitness peaks one amino acid at a time

(2009) Cara A Tracewell et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Enhanced biofilm formation and 3-chlorobenzoate degrading activity by the bacterial consortium ofBurkholderiasp. NK8 andPseudomonas aeruginosaPAO1

(2009) S. Yoshida et al.   JOURNAL OF APPLIED MICROBIOLOGY

In the light of directed evolution: Pathways of adaptive protein evolution

(2009) J. D. Bloom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Response to Goldman and Brown: Making sense of microbial consortia using ecology and evolution

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY

Making sense of microbial consortia using ecology and evolution

(2008) Robert P. Goldman et al.   TRENDS IN BIOTECHNOLOGY