I. Gordo

Massive lateral gene transfer under strain coexistence in the gut

The paper studies how two distinct E. coli strains coexist in the mouse gut and finds strain-specific evolutionary modes and significant lateral gene transfer.

Shared evolutionary path in social microbiomes

The paper assesses how host-to-host bacterial transmission affects E. coli evolution in mice, finding a daily transmission rate of 7% and similar evolutionary dynamics among co-housed mice.

Epistasis decreases with increasing antibiotic pressure but not temperature

The paper quantifies genotype-by-genotype-by-environment interactions in E. coli under varying antibiotic and temperature conditions, finding that epistasis decreases with higher antibiotic pressure but not temperature.

Two modes of evolution shape bacterial strain diversity in the gut for thousands of generations

This study shows that two evolutionary modes shape bacterial strain diversity in the gut over thousands of generations, with diversifying selection leading to ecotype coexistence and directional selection causing selective sweeps.

Gut melange a trois: fluctuating selection modulated by microbiota, host immune system, and antibiotics

The paper shows fluctuating selection on an iscR allele in E. coli in the mouse gut, influenced by antibiotics, microbiota, and the immune system.

Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution

This study estimates the mutation rate of SARS-CoV-2 during experimental evolution and identifies genome-wide mutation patterns and mutator emergence.

Epigenetic switching outcompetes genetic mutations during adaptation to fluctuating environments

This study shows that epigenetic switching provides a fitness advantage over genetic mutations in fluctuating environments, with coexistence possible under constant pressure at high switching rates.

Molecular signatures of resource competition: clonal interference favors ecological diversification and can lead to incipient speciation

This study shows that clonal interference in large populations promotes ecological diversification and can lead to speciation, while smaller populations experience diversification through mutation accumulation.

DNA breaks-mediated cost reveals RNase HI as a new target for selectively eliminating antibiotic resistance

The paper shows that targeting RNase HI, which degrades R-loops causing DNA breaks, increases the fitness cost of antibiotic resistance and can eliminate resistant bacteria.

Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate

This study shows that a natural Bacillus subtilis isolate rapidly loses social traits during domestication in a lab environment due to mutations in the DegU gene within a week.

Dysbiosis personalizes fitness effect of antibiotic resistance in the mammalian gut

The study shows that the fitness effect of antibiotic resistance mutations varies between hosts, shaped by the gut microbiota, and predicts host-specific evolution of resistance.

Low Mutational Load Allows for High Mutation Rate Variation in Gut Commensal Bacteria

The paper tracks long-term evolution of gut commensal E. coli in mice, finding high mutation rate variation and identifying molecular causes of hypermutator emergence and coexistence.

Sex overrides mutation in Escherichia coli colonizing the gut

The paper shows that phages drive rapid evolution in the gut by promoting horizontal gene transfer and genetic diversity in E. coli.

Rampant Reverse Evolution towards Specialization in Commensal Bacteria Colonizing the Gut

This study shows reverse evolution in gut bacteria, where a lost phenotype reappears through genetic changes, leading to coexisting generalist and specialist strains influenced by diet.