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

Evolthon: A community endeavor to evolve lab evolution

(2019) Sivan Kaminski Strauss et al.   PLOS BIOLOGY

Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells

(2019) Samuel F. M. Hart et al.   PLOS BIOLOGY

Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community

(2019) Samuel Frederick Mock Hart et al.   eLife

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

Multi-stability and the origin of microbial community types

(2017) Didier Gonze et al.   ISME Journal

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

(2017) Kevin R. Foster et al.   NATURE

Towards a mechanistic foundation of evolutionary theory

(2017) Michael Doebeli et al.   eLife

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

(2017) Babak Momeni et al.   eLife

Public goods and metabolic strategies

(2016) Herwig Bachmann et al.   CURRENT OPINION IN MICROBIOLOGY

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations

(2016) Celia Payen et al.   PLoS Genetics

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Cell-Size Control and Homeostasis in Bacteria

(2015) Sattar Taheri-Araghi et al.   CURRENT BIOLOGY

Levels and limits in artificial selection of communities

(2015) Manuel Blouin et al.   ECOLOGY LETTERS

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Engineering Microbiomes to Improve Plant and Animal Health

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

Acknowledging selection at sub-organismal levels resolves controversy on pro-cooperation mechanisms

(2015) Wenying Shou   eLife

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

(2014) Adrian WR Serohijos et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Selection on soil microbiomes reveals reproducible impacts on plant function

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

Life cycles, fitness decoupling and the evolution of multicellularity

(2014) Katrin Hammerschmidt et al.   NATURE

Genetic drift opposes mutualism during spatial population expansion

(2014) M. J. I. Muller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

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

Availability of public goods shapes the evolution of competing metabolic strategies

(2013) H. Bachmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-Term Dynamics of Adaptation in Asexual Populations

(2013) M. J. Wiser et al.   SCIENCE

Interspecies Interactions Stimulate Diversification of the Streptomyces coelicolor Secreted Metabolome

(2013) M. F. Traxler et al.   mBio

Interspecific bacterial sensing through airborne signals modulates locomotion and drug resistance

(2013) Kwang-sun Kim et al.   Nature Communications

Spatial self-organization favors heterotypic cooperation over cheating

(2013) Babak Momeni et al.   eLife

Strong inter-population cooperation leads to partner intermixing in microbial communities

(2013) Babak Momeni et al.   eLife

The CRISPRs, They Are A-Changin': How Prokaryotes Generate Adaptive Immunity

(2012) Edze R. Westra et al.   Annual Review of Genetics

Adaptation to a new environment allows cooperators to purge cheaters stochastically

(2012) A. J. Waite et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

(2012) Trevor D. Lawley et al.   PLoS Pathogens

Metabolome Profiling Reveals Metabolic Cooperation between Bacillus megaterium and Ketogulonicigenium vulgare during Induced Swarm Motility

(2011) Jian Zhou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Communities as Experimental Units

(2011) Mitch D. Day et al.   BIOSCIENCE

Understanding microbial cooperation

(2011) James A. Damore et al.   JOURNAL OF THEORETICAL BIOLOGY

Economics of membrane occupancy and respiro-fermentation

(2011) K. Zhuang et al.   Molecular Systems Biology

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Escherichia coli Binary Culture Engineered for Direct Fermentation of Hemicellulose to a Biofuel

(2010) H.-D. Shin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1

(2010) J. B. Peris et al.   GENETICS

Rapid evolution of stability and productivity at the origin of a microbial mutualism

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

Enhancing biodegradation of wastewater by microbial consortia with fractional factorial design

(2009) Yuancai Chen et al.   JOURNAL OF HAZARDOUS MATERIALS

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Small RNAs in transcriptional gene silencing and genome defence

(2009) Danesh Moazed   NATURE

Simpson's Paradox in a Synthetic Microbial System

(2009) J. S. Chuang et al.   SCIENCE

Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae

(2008) Gregory I. Lang et al.   GENETICS

Beneficial Fitness Effects Are Not Exponential for Two Viruses

(2008) Darin R. Rokyta et al.   JOURNAL OF MOLECULAR EVOLUTION

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE