Olivier Tenaillon
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View article: High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli
High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli Open
Genetic exchange is a cornerstone of evolutionary biology and genomics, driving adaptation and enabling the identification of genetic determinants underlying phenotypic traits. In Escherichia coli , horizontal gene transfer via conjugation…
View article: Evidence for Neolithic acquisition of the high pathogenic island by <i>Escherichia coli</i> followed by recent selection
Evidence for Neolithic acquisition of the high pathogenic island by <i>Escherichia coli</i> followed by recent selection Open
Many genetic elements involved in virulence and pathogenicity have been identified in commensal bacteria that are also opportunistic pathogens, but how these elements evolve is less well known. Understanding the evolutionary history of vir…
View article: The evolution of robustness and fragility during long-term bacterial adaptation
The evolution of robustness and fragility during long-term bacterial adaptation Open
Theory predicts that well-adapted populations may evolve mechanisms to counteract the inevitable influx of deleterious mutations. While mutational robustness can be directly selected in the laboratory, evidence for its spontaneous evolutio…
View article: Evaluation of phenotypic and genotypic methods for detecting KPC variants
Evaluation of phenotypic and genotypic methods for detecting KPC variants Open
Klebsiella pneumoniae carbapenemases (KPCs) have spread and diversified extensively. To date, 242 clinical variants have been identified and harbor different hydrolytic capacities, thereby interfering with rapid diagnostic tests. The accur…
View article: High-Throughput Conjugation Reveals Strain Specific Recombination Patterns Enabling Precise Trait Mapping in Escherichia coli
High-Throughput Conjugation Reveals Strain Specific Recombination Patterns Enabling Precise Trait Mapping in Escherichia coli Open
Genetic exchange is a cornerstone of evolutionary biology and genomics, driving adaptation and enabling the identification of genetic determinants underlying phenotypic traits. In Escherichia coli , horizontal gene transfer via conjugation…
View article: The evolution of robustness and fragility during long-term bacterial adaptation
The evolution of robustness and fragility during long-term bacterial adaptation Open
Most mutations affecting fitness are harmful, and their inevitable occurrence reduces mean population fitness. Theory predicts that well-adapted populations may evolve mechanisms to minimize this deleterious load. Direct selection to incre…
View article: <i>In vitro</i> microbiota model recapitulates and predicts individualised sensitivity to dietary emulsifier
<i>In vitro</i> microbiota model recapitulates and predicts individualised sensitivity to dietary emulsifier Open
Background Non-absorbed dietary emulsifiers, including carboxymethylcellulose (CMC), directly disturb intestinal microbiota, thereby promoting chronic intestinal inflammation in mice. A randomised controlled-feeding study (Functional Resea…
View article: Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases
Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases Open
Background Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted and targeted phen…
View article: Changing fitness effects of mutations through long-term bacterial evolution
Changing fitness effects of mutations through long-term bacterial evolution Open
The distribution of fitness effects of new mutations shapes evolution, but it is challenging to observe how it changes as organisms adapt. Using Escherichia coli lineages spanning 50,000 generations of evolution, we quantify the fitness ef…
View article: Deep mutational scanning of RNA polymerase
Deep mutational scanning of RNA polymerase Open
RNA polymerase deep mutational scanning data accompanying the manuscript titled: Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs
View article: Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs
Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs Open
RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple traits involving trade-offs such as growth versus maintenance. Laboratory evolution has revealed that mutations in RNAP subunits, including RpoB, are f…
View article: Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs
Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs Open
RNA polymerase deep mutational scanning data accompanying the manuscript titled: Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs
View article: Deep mutational scanning of RNA polymerase
Deep mutational scanning of RNA polymerase Open
RNA polymerase deep mutational scanning data accompanying the manuscript titled: Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs
View article: Deep mutational scanning of RNA polymerase
Deep mutational scanning of RNA polymerase Open
RNA polymerase deep mutational scanning data accompanying the manuscript titled: Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs
View article: Predicting the effect of mutations to investigate recent events of selection across 60,472 <i>Escherichia coli</i> strains
Predicting the effect of mutations to investigate recent events of selection across 60,472 <i>Escherichia coli</i> strains Open
Microbial genomics studies focusing on the dynamics of selection have often used a small number of distant genomes. As a result, they could only analyze mutations that had become fixed during the divergence between species. However, thousa…
View article: Flexibility in Aphid Endosymbiosis: Dual Symbioses Have Evolved Anew at Least Six Times
Flexibility in Aphid Endosymbiosis: Dual Symbioses Have Evolved Anew at Least Six Times Open
A recommendation of: Alejandro Manzano-Marín, Armelle Coeur d'acier, Anne-Laure Clamens, Corinne Cruaud, Valérie Barbe, Emmanuelle Jousselin Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional …
View article: Perturbation and resilience of the gut microbiome up to three months after β-lactams exposure in healthy volunteers suggest an important role of endogenous β-lactamases
Perturbation and resilience of the gut microbiome up to three months after β-lactams exposure in healthy volunteers suggest an important role of endogenous β-lactamases Open
Background Antibiotics notoriously perturb the gut microbiota. We used untargeted and targeted phenotypic and genotypic approaches to study faecal samples collected up to 90 days following a 3-day course of intravenous β-lactam antibiotics…
View article: Data Carpentry Genomics Curriculum Example Data
Data Carpentry Genomics Curriculum Example Data Open
p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 16.0px 'Andale Mono'; color: #29f914; background-color: #000000} span.s1 {font-variant-ligatures: no-common-ligatures} These files are intended for use with the Data Carpentry Genomics curriculu…
View article: Towards evolutionary predictions: Current promises and challenges
Towards evolutionary predictions: Current promises and challenges Open
Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicin…
View article: Klebsiella pneumoniae Carbapenemase Variants Resistant to Ceftazidime-Avibactam: an Evolutionary Overview
Klebsiella pneumoniae Carbapenemase Variants Resistant to Ceftazidime-Avibactam: an Evolutionary Overview Open
First variants of the Klebsiella pneumoniae carbapenemase (KPC), KPC-2 and KPC-3, have encountered a worldwide success, particularly in K. pneumoniae isolates. These beta-lactamases conferred resistance to most beta-lactams including carba…
View article: The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France
The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France Open
Escherichia coli is an opportunistic pathogen with the greatest burden of antibiotic resistance, one of the main causes of bacterial infections and an increasing concern in an aging population. Deciphering the evolutionary dynamics of viru…
View article: Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes
Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes Open
Characterizing the effect of mutations is key to understand the evolution of protein sequences and to separate neutral amino-acid changes from deleterious ones. Epistatic interactions between residues can lead to a context dependence of mu…
View article: MiniBioReactor Array (MBRA) <i>in vitro</i> gut model: a reliable system to study microbiota-dependent response to antibiotic treatment
MiniBioReactor Array (MBRA) <i>in vitro</i> gut model: a reliable system to study microbiota-dependent response to antibiotic treatment Open
Background Antimicrobial drugs are mostly studied for their impact on emergence of bacterial antibiotic resistance, but their impact on the gut microbiota is also of tremendous interest. In vitro gut models are important tools to study suc…
View article: A Microbiota-Dependent Response to Anticancer Treatment in an In Vitro Human Microbiota Model: A Pilot Study With Hydroxycarbamide and Daunorubicin
A Microbiota-Dependent Response to Anticancer Treatment in an In Vitro Human Microbiota Model: A Pilot Study With Hydroxycarbamide and Daunorubicin Open
Background Anticancer drug efficacy is linked to the gut microbiota’s composition, and there is a dire need to better understand these interactions for personalized medicine. In vitro microbiota models are promising tools for studies requi…
View article: Modeling the bacterial dynamics in the gut microbiota following an antibiotic‐induced perturbation
Modeling the bacterial dynamics in the gut microbiota following an antibiotic‐induced perturbation Open
Recent studies have highlighted the importance of ecological interactions in dysbiosis of gut microbiota, but few focused on their role in antibiotic‐induced perturbations. We used the data from the CEREMI trial in which 22 healthy volunte…
View article: Predictability shifts from local to global rules during bacterial adaptation
Predictability shifts from local to global rules during bacterial adaptation Open
The distribution of fitness effects of new mutations is central to predicting adaptive evolution, but observing how it changes as organisms adapt is challenging. Here we use saturated, genome-wide insertion libraries to quantify how the fi…
View article: Local and Global Protein Interactions Contribute to Residue Entrenchment in Beta-Lactamase TEM-1
Local and Global Protein Interactions Contribute to Residue Entrenchment in Beta-Lactamase TEM-1 Open
Due to their rapid evolution and their impact on healthcare, beta-lactamases, protein degrading beta-lactam antibiotics, are used as generic models of protein evolution. Therefore, we investigated the mutation effects in two distant beta-l…
View article: rRNA operon multiplicity as a bacterial genome stability insurance policy
rRNA operon multiplicity as a bacterial genome stability insurance policy Open
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View article: rRNA operon multiplicity as a bacterial genome stability insurance policy
rRNA operon multiplicity as a bacterial genome stability insurance policy Open
Quick growth restart after upon encountering favourable environmental conditions is a major fitness contributor in natural environment. It is widely assumed that the time required to restart growth after nutritional upshift is determined b…
View article: Local and Global Protein Interactions Contribute to Residue Entrenchment in Beta-Lactamase TEM-1
Local and Global Protein Interactions Contribute to Residue Entrenchment in Beta-Lactamase TEM-1 Open
Due to their rapid evolution and their impact on health care, be-ta-lactamases, protein degrading beta-lactam antibiotics, are used as generic model of protein evolution. Therefore, we investigated the mutation effects in two distant beta-…