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1. Metagenomic shotgun sequencing of blood to identify bacteria and viruses in leukemic febrile neutropenia

Author: Prakhar Vijayvargiya, Adeline Feri, Mathilde Mairey, Cécile Rouillon, Patricio R. Jeraldo, Zerelda Esquer Garrigos, Matthew J. Thoendel, Kerryl E. Greenwood-Quaintance, M. Rizwan Sohail, Priya Sampathkumar, Megan T. Spychalla, A. K. Stewart, Mrinal M. Patnaik, Aaron J. Tande, Stéphane Cruveiller, Irene Hannet, Pascale Beurdeley, and Robin Patel
Subjects: Medicine, Science
Abstract: Despite diagnostic advances in microbiology, the etiology of neutropenic fever remains elusive in most cases. In this study, we evaluated the utility of a metagenomic shotgun sequencing based assay for detection of bacteria and viruses in blood samples of patients with febrile neutropenia. We prospectively enrolled 20 acute leukemia patients and obtained blood from these patients at three time points: 1) anytime from onset of neutropenia until before development of neutropenic fever, 2) within 24 hours of onset of neutropenic fever, 3) 5–7 days after onset of neutropenic fever. Blood samples underwent sample preparation, sequencing and analysis using the iDTECT® Dx Blood v1® platform (PathoQuest, Paris, France). Clinically relevant viruses or bacteria were detected in three cases each by metagenomic shotgun sequencing and blood cultures, albeit with no concordance between the two. Further optimization of sample preparation methods and sequencing platforms is needed before widespread adoption of this technology into clinical practice.
Published: 2022

2. Correction: PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Author: Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise, Eduardo P. C. Rocha, and David Vallenet
Subjects: Biology (General), QH301-705.5
Published: 2021

3. PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.

Author: Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise, Eduardo P C Rocha, and David Vallenet
Subjects: Biology (General), QH301-705.5
Abstract: The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don't account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN.
Published: 2020
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4. Modulation of Quorum Sensing as an Adaptation to Nodule Cell Infection during Experimental Evolution of Legume Symbionts

Author: Mingxing Tang, Olivier Bouchez, Stéphane Cruveiller, Catherine Masson-Boivin, and Delphine Capela
Subjects: symbiosis, rhizobium, experimental evolution, infection, quorum sensing, regulation, Microbiology, QR1-502
Abstract: ABSTRACT Over millions of years, changes have occurred in regulatory circuitries in response to genome reorganization and/or persistent changes in environmental conditions. How bacteria optimize regulatory circuitries is crucial to understand bacterial adaptation. Here, we analyzed the experimental evolution of the plant pathogen Ralstonia solanacearum into legume symbionts after the transfer of a natural plasmid encoding the essential mutualistic genes. We showed that the Phc quorum sensing system required for the virulence of the ancestral bacterium was reconfigured to improve intracellular infection of root nodules induced by evolved Ralstonia. A single mutation in either the PhcB autoinducer synthase or the PhcQ regulator of the sensory cascade tuned the kinetics of activation of the central regulator PhcA in response to cell density so that the minimal stimulatory concentration of autoinducers needed for a given response was increased. Yet, a change in the expression of a PhcA target gene was observed in infection threads progressing in root hairs, suggesting early programming for the late accommodation of bacteria in nodule cells. Moreover, this delayed switch to the quorum sensing mode decreased the pathogenicity of the ancestral strain, illustrating the functional plasticity of regulatory systems and showing how a small modulation in signal response can produce drastic changes in bacterial lifestyle. IMPORTANCE Rhizobia are soil bacteria from unrelated genera able to form a mutualistic relationship with legumes. Bacteria induce the formation of root nodules, invade nodule cells, and fix nitrogen to the benefit of the plant. Rhizobial lineages emerged from the horizontal transfer of essential symbiotic genes followed by genome remodeling to activate and/or optimize the acquired symbiotic potential. This evolutionary scenario was replayed in a laboratory evolution experiment in which the plant pathogen Ralstonia solanacearum successively evolved the capacities to nodulate Mimosa pudica and poorly invade, then massively invade, nodule cells. In some lines, the improvement of intracellular infection was achieved by mutations modulating a quorum sensing regulatory system of the ancestral strain. This modulation that affects the activity of a central regulator during the earliest stages of symbiosis has a huge impact on late stages of symbiosis. This work showed that regulatory rewiring is the main driver of this pathogeny-symbiosis transition.
Published: 2020
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5. Parallels between experimental and natural evolution of legume symbionts

Author: Camille Clerissi, Marie Touchon, Delphine Capela, Mingxing Tang, Stéphane Cruveiller, Clémence Genthon, Céline Lopez-Roques, Matthew A. Parker, Lionel Moulin, Catherine Masson-Boivin, and Eduardo P. C. Rocha
Subjects: Science
Abstract: It is unclear if experimental evolution is a good model for natural processes. Here, Clerissi et al. find parallels between the evolution of symbiosis in rhizobia after horizontal transfer of a plasmid over 10 million years ago and experimentally evolved symbionts.
Published: 2018
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6. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation

Author: Evelyne Krin, Sebastian Aguilar Pierlé, Odile Sismeiro, Bernd Jagla, Marie-Agnès Dillies, Hugo Varet, Oihane Irazoki, Susana Campoy, Zoé Rouy, Stéphane Cruveiller, Claudine Médigue, Jean-Yves Coppée, and Didier Mazel
Subjects: SOS response, DNA repair, Transcriptome, ncRNA, nrdA, nrdB, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. Results Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5’UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369–1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. Conclusions We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria.
Published: 2018
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7. Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat

Author: Wessam Galia, Francoise Leriche, Stéphane Cruveiller, Cindy Garnier, Vincent Navratil, Audrey Dubost, Stéphanie Blanquet-Diot, and Delphine Thevenot-Sergentet
Subjects: RNA-Seq, EHEC, Ground beef, Natural microbiota, 16S metagenomics analysis, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef. Results Based on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota’s inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota. Conclusion In the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses.
Published: 2017
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8. Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic Acids

Author: Justine Cheval, Erika Muth, Gaëlle Gonzalez, Muriel Coulpier, Pascale Beurdeley, Stéphane Cruveiller, and Marc Eloit
Subjects: 4-thiouridine, RNA-seq, Vero, biologicals, high-throughput sequencing, metagenomics, Microbiology, QR1-502
Abstract: ABSTRACT The use of high-throughput sequencing (HTS) to identify viruses in biologicals differs from current molecular approaches, since its use enables an unbiased approach to detection without the need to design specific primers to preamplify target sequences. Its broad range of detection and analytical sensitivity make it an important tool to ensure that biologicals are free from adventitious viruses. Similar to other molecular methods, however, identification of viral sequences in cells by HTS does not prove viral infection, since this could reflect carryover of inert viral sequences from reagents or other sources or the presence of transcriptionally inactive cellular sequences. Due to the broad range of detection associated with HTS, the above can potentially be perceived as a drawback for the testing of pharmaceutical biological products using this method. In order to avoid the identification of inert viral sequences, we present a methodology based on metabolic RNA labeling and sequencing, which enables the specific identification of newly synthesized viral RNAs in infected cells, resulting in the ability to unambiguously distinguish active infection by DNA or RNA viruses from inert nucleic acids. In the present study, we report the ability to differentiate Vero cells acutely infected by a single-stranded positive-sense RNA virus (tick-borne encephalitis virus) from cells which have been in contact with nonreplicating virus particles. Additionally, we also found a laboratory contamination by the squirrel monkey retrovirus of our Vero cell line, which was derived from an Old World (African green) monkey, a type of contamination which until now has been identified only in cells derived from primates from the New World. IMPORTANCE The use of high-throughput sequencing (HTS) to identify viral contamination of biological products is extremely sensitive and provides a broad range of detection. Nevertheless, viral sequences identified can also be inert. Examples include contamination resulting from reagents or the presence of inactivated viruses in animal-derived components of the cell culture medium. We therefore developed a method that relies on the sequencing of newly synthesized RNAs, an unequivocal sign of the presence of a transcriptionally active virus. This improvement in the specificity of viral testing increases the acceptability of HTS as a standard test for cells used in manufacturing biologicals and in biotherapies.
Published: 2019
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9. Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium

Author: Pauline Chaignaud, Bruno Maucourt, Marion Weiman, Adriana Alberti, Steffen Kolb, Stéphane Cruveiller, Stéphane Vuilleumier, and Françoise Bringel
Subjects: dehalogenation, chloromethane, dichloromethane, GEI, genomic island, genome adaptation, Microbiology, QR1-502
Abstract: Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains. In terms of gene content, adaptation toward dehalogenation appears limited, strains CM4 and DM4 sharing between 75 and 85% of their genome with other strains of M. extorquens. Transcript abundance in cultures of strain CM4 grown with chloromethane and of strain DM4 grown with dichloromethane was compared to growth with methanol as a reference C1 growth substrate. Previously identified strain-specific dehalogenase-encoding genes were the most transcribed with chlorinated methanes, alongside other genes encoded by genomic islands (GEIs) and plasmids involved in growth with chlorinated compounds as carbon and energy source. None of the 163 genes shared by strains CM4 and DM4 but not by other strains of M. extorquens showed higher transcript abundance in cells grown with chlorinated methanes. Among the several thousand genes of the M. extorquens core genome, 12 genes were only differentially abundant in either strain CM4 or strain DM4. Of these, 2 genes of known function were detected, for the membrane-bound proton translocating pyrophosphatase HppA and the housekeeping molecular chaperone protein DegP. This indicates that the adaptive response common to chloromethane and dichloromethane is limited at the transcriptional level, and involves aspects of the general stress response as well as of a dehalogenation-specific response to intracellular hydrochloric acid production. Core genes only differentially abundant in either strain CM4 or strain DM4 total 13 and 58 CDS, respectively. Taken together, the obtained results suggest different transcriptional responses of chloromethane- and dichloromethane-degrading M. extorquens strains to dehalogenative metabolism, and substrate- and pathway-specific modes of growth optimization with chlorinated methanes.
Published: 2017
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10. DNA Adenine Methyltransferase (Dam) Overexpression Impairs Photorhabdus luminescens Motility and Virulence

Author: Amaury Payelleville, Anne Lanois, Marie Gislard, Emeric Dubois, David Roche, Stéphane Cruveiller, Alain Givaudan, and Julien Brillard
Subjects: entomopathogenic bacterium, MTase, insect, pathogenicity, flagellar genes, RNA-seq, Microbiology, QR1-502
Abstract: Dam, the most described bacterial DNA-methyltransferase, is widespread in gamma-proteobacteria. Dam DNA methylation can play a role in various genes expression and is involved in pathogenicity of several bacterial species. The purpose of this study was to determine the role played by the dam ortholog identified in the entomopathogenic bacterium Photorhabdus luminescens. Complementation assays of an Escherichia coli dam mutant showed the restoration of the DNA methylation state of the parental strain. Overexpression of dam in P. luminescens did not impair growth ability in vitro. In contrast, compared to a control strain harboring an empty plasmid, a significant decrease in motility was observed in the dam-overexpressing strain. A transcriptome analysis revealed the differential expression of 208 genes between the two strains. In particular, the downregulation of flagellar genes was observed in the dam-overexpressing strain. In the closely related bacterium Xenorhabdus nematophila, dam overexpression also impaired motility. In addition, the dam-overexpressing P. luminescens strain showed a delayed virulence compared to that of the control strain after injection in larvae of the lepidopteran Spodoptera littoralis. These results reveal that Dam plays a major role during P. luminescens insect infection.
Published: 2017
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11. In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum

Author: Florent Ailloud, Tiffany M. Lowe, Isabelle Robène, Stéphane Cruveiller, Caitilyn Allen, and Philippe Prior
Subjects: Ralstonia solanacearum, Transcriptomics, Host adaptation, Medicine, Biology (General), QH301-705.5
Abstract: Background. Ralstonia solanacearum is an economically important plant pathogen with an unusually large host range. The Moko (banana) and NPB (not pathogenic to banana) strain groups are closely related but are adapted to distinct hosts. Previous comparative genomics studies uncovered very few differences that could account for the host range difference between these pathotypes. To better understand the basis of this host specificity, we used RNAseq to profile the transcriptomes of an R. solanacearum Moko strain and an NPB strain under in vitro and in planta conditions.Results. RNAs were sequenced from bacteria grown in rich and minimal media, and from bacteria extracted from mid-stage infected tomato, banana and melon plants. We computed differential expression between each pair of conditions to identify constitutive and host-specific gene expression differences between Moko and NPB. We found that type III secreted effectors were globally up-regulated upon plant cell contact in the NPB strain compared with the Moko strain. Genes encoding siderophore biosynthesis and nitrogen assimilation genes were highly up-regulated in the NPB strain during melon pathogenesis, while denitrification genes were up-regulated in the Moko strain during banana pathogenesis. The relatively lower expression of oxidases and the denitrification pathway during banana pathogenesis suggests that R. solanacearum experiences higher oxygen levels in banana pseudostems than in tomato or melon xylem.Conclusions. This study provides the first report of differential gene expression associated with host range variation. Despite minimal genomic divergence, the pathogenesis of Moko and NPB strains is characterized by striking differences in expression of virulence- and metabolism-related genes.
Published: 2016
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12. Author Correction: Parallels between experimental and natural evolution of legume symbionts

Author: Camille Clerissi, Marie Touchon, Delphine Capela, Mingxing Tang, Stéphane Cruveiller, Clémence Genthon, Céline Lopez-Roques, Matthew A. Parker, Lionel Moulin, Catherine Masson-Boivin, and Eduardo P. C. Rocha
Subjects: Science
Abstract: Clémence Genthon and Céline Lopez-Roques, who performed sequencing, were inadvertently omitted from the author list. This has now been corrected in the PDF and HTML versions of the Article.
Published: 2018
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13. Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli

Author: Colin Raeside, Joël Gaffé, Daniel E. Deatherage, Olivier Tenaillon, Adam M. Briska, Ryan N. Ptashkin, Stéphane Cruveiller, Claudine Médigue, Richard E. Lenski, Jeffrey E. Barrick, and Dominique Schneider
Subjects: Microbiology, QR1-502
Abstract: ABSTRACT Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement events were detected, including 82 deletions, 19 inversions, and 9 duplications, with lineages having between 5 and 20 events. In three populations, successive rearrangements impacted particular regions. In five populations, rearrangements affected over a third of the chromosome. Most rearrangements involved recombination between insertion sequence (IS) elements, illustrating their importance in mediating genome plasticity. Two lines of evidence suggest that at least some of these rearrangements conferred higher fitness. First, parallel changes were observed across the independent populations, with ~65% of the rearrangements affecting the same loci in at least two populations. For example, the ribose-utilization operon and the manB-cpsG region were deleted in 12 and 10 populations, respectively, suggesting positive selection, and this inference was previously confirmed for the former case. Second, optical maps from clones sampled over time from one population showed that most rearrangements occurred early in the experiment, when fitness was increasing most rapidly. However, some rearrangements likely occur at high frequency and may have simply hitchhiked to fixation. In any case, large-scale rearrangements clearly influenced genomic evolution in these populations. IMPORTANCE Bacterial chromosomes are dynamic structures shaped by long histories of evolution. Among genomic changes, large-scale DNA rearrangements can have important effects on the presence, order, and expression of genes. Whole-genome sequencing that relies on short DNA reads cannot identify all large-scale rearrangements. Therefore, deciphering changes in the overall organization of genomes requires alternative methods, such as optical mapping. We analyzed the longest-running microbial evolution experiment (more than 25 years of evolution in the laboratory) by optical mapping, genome sequencing, and PCR analyses. We found multiple large genome rearrangements in all 12 independently evolving populations. In most cases, it is unclear whether these changes were beneficial themselves or, alternatively, hitchhiked to fixation with other beneficial mutations. In any case, many genome rearrangements accumulated over decades of evolution, providing these populations with genetic plasticity reminiscent of that observed in some pathogenic bacteria.
Published: 2014
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14. Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer.

Author: Philippe Remigi, Delphine Capela, Camille Clerissi, Léna Tasse, Rachel Torchet, Olivier Bouchez, Jacques Batut, Stéphane Cruveiller, Eduardo P C Rocha, and Catherine Masson-Boivin
Subjects: Biology (General), QH301-705.5
Abstract: Horizontal gene transfer (HGT) is an important mode of adaptation and diversification of prokaryotes and eukaryotes and a major event underlying the emergence of bacterial pathogens and mutualists. Yet it remains unclear how complex phenotypic traits such as the ability to fix nitrogen with legumes have successfully spread over large phylogenetic distances. Here we show, using experimental evolution coupled with whole genome sequencing, that co-transfer of imuABC error-prone DNA polymerase genes with key symbiotic genes accelerates the evolution of a soil bacterium into a legume symbiont. Following introduction of the symbiotic plasmid of Cupriavidus taiwanensis, the Mimosa symbiont, into pathogenic Ralstonia solanacearum we challenged transconjugants to become Mimosa symbionts through serial plant-bacteria co-cultures. We demonstrate that a mutagenesis imuABC cassette encoded on the C. taiwanensis symbiotic plasmid triggered a transient hypermutability stage in R. solanacearum transconjugants that occurred before the cells entered the plant. The generated burst in genetic diversity accelerated symbiotic adaptation of the recipient genome under plant selection pressure, presumably by improving the exploration of the fitness landscape. Finally, we show that plasmid imuABC cassettes are over-represented in rhizobial lineages harboring symbiotic plasmids. Our findings shed light on a mechanism that may have facilitated the dissemination of symbiotic competency among α- and β-proteobacteria in natura and provide evidence for the positive role of environment-induced mutagenesis in the acquisition of a complex lifestyle trait. We speculate that co-transfer of complex phenotypic traits with mutagenesis determinants might frequently enhance the ecological success of HGT.
Published: 2014
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15. Molecular and evolutionary bases of within-patient genotypic and phenotypic diversity in Escherichia coli extraintestinal infections.

Author: Maxime Levert, Oana Zamfir, Olivier Clermont, Odile Bouvet, Sylvain Lespinats, Marie Claire Hipeaux, Catherine Branger, Bertrand Picard, Claude Saint-Ruf, Françoise Norel, Thierry Balliau, Michel Zivy, Hervé Le Nagard, Stéphane Cruveiller, Béatrice Chane-Woon-Ming, Susanna Nilsson, Ivana Gudelj, Katherine Phan, Thomas Ferenci, Olivier Tenaillon, and Erick Denamur
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: Although polymicrobial infections, caused by combinations of viruses, bacteria, fungi and parasites, are being recognised with increasing frequency, little is known about the occurrence of within-species diversity in bacterial infections and the molecular and evolutionary bases of this diversity. We used multiple approaches to study the genomic and phenotypic diversity among 226 Escherichia coli isolates from deep and closed visceral infections occurring in 19 patients. We observed genomic variability among isolates from the same site within 11 patients. This diversity was of two types, as patients were infected either by several distinct E. coli clones (4 patients) or by members of a single clone that exhibit micro-heterogeneity (11 patients); both types of diversity were present in 4 patients. A surprisingly wide continuum of antibiotic resistance, outer membrane permeability, growth rate, stress resistance, red dry and rough morphotype characteristics and virulence properties were present within the isolates of single clones in 8 of the 11 patients showing genomic micro-heterogeneity. Many of the observed phenotypic differences within clones affected the trade-off between self-preservation and nutritional competence (SPANC). We showed in 3 patients that this phenotypic variability was associated with distinct levels of RpoS in co-existing isolates. Genome mutational analysis and global proteomic comparisons in isolates from a patient revealed a star-like relationship of changes amongst clonally diverging isolates. A mathematical model demonstrated that multiple genotypes with distinct RpoS levels can co-exist as a result of the SPANC trade-off. In the cases involving infection by a single clone, we present several lines of evidence to suggest diversification during the infectious process rather than an infection by multiple isolates exhibiting a micro-heterogeneity. Our results suggest that bacteria are subject to trade-offs during an infectious process and that the observed diversity resembled results obtained in experimental evolution studies. Whatever the mechanisms leading to diversity, our results have strong medical implications in terms of the need for more extensive isolate testing before deciding on antibiotic therapies.
Published: 2010
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16. Structure, function, and evolution of the Thiomonas spp. genome.

Author: Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean-Yves Coppée, Michael Chandler, Violaine Bonnefoy, Céline Brochier-Armanet, Mohamed Barakat, Valérie Barbe, Fabienne Battaglia-Brunet, Odile Bruneel, Christopher G Bryan, Jessica Cleiss-Arnold, Stéphane Cruveiller, Mathieu Erhardt, Audrey Heinrich-Salmeron, Florence Hommais, Catherine Joulian, Evelyne Krin, Aurélie Lieutaud, Didier Lièvremont, Caroline Michel, Daniel Muller, Philippe Ortet, Caroline Proux, Patricia Siguier, David Roche, Zoé Rouy, Grégory Salvignol, Djamila Slyemi, Emmanuel Talla, Stéphanie Weiss, Jean Weissenbach, Claudine Médigue, and Philippe N Bertin
Subjects: Genetics, QH426-470
Abstract: Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live.
Published: 2010
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17. Experimental evolution of a plant pathogen into a legume symbiont.

Author: Marta Marchetti, Delphine Capela, Michelle Glew, Stéphane Cruveiller, Béatrice Chane-Woon-Ming, Carine Gris, Ton Timmers, Véréna Poinsot, Luz B Gilbert, Philipp Heeb, Claudine Médigue, Jacques Batut, and Catherine Masson-Boivin
Subjects: Biology (General), QH301-705.5
Abstract: Rhizobia are phylogenetically disparate alpha- and beta-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen in symbiosis with legumes. Ample evidence indicates that horizontal transfer of symbiotic plasmids/islands has played a crucial role in rhizobia evolution. However, adaptive mechanisms that allow the recipient genomes to express symbiotic traits are unknown. Here, we report on the experimental evolution of a pathogenic Ralstonia solanacearum chimera carrying the symbiotic plasmid of the rhizobium Cupriavidus taiwanensis into Mimosa nodulating and infecting symbionts. Two types of adaptive mutations in the hrpG-controlled virulence pathway of R. solanacearum were identified that are crucial for the transition from pathogenicity towards mutualism. Inactivation of the hrcV structural gene of the type III secretion system allowed nodulation and early infection to take place, whereas inactivation of the master virulence regulator hrpG allowed intracellular infection of nodule cells. Our findings predict that natural selection of adaptive changes in the legume environment following horizontal transfer has been a major driving force in rhizobia evolution and diversification and show the potential of experimental evolution to decipher the mechanisms leading to symbiosis.
Published: 2010
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18. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Author: Marie Touchon, Claire Hoede, Olivier Tenaillon, Valérie Barbe, Simon Baeriswyl, Philippe Bidet, Edouard Bingen, Stéphane Bonacorsi, Christiane Bouchier, Odile Bouvet, Alexandra Calteau, Hélène Chiapello, Olivier Clermont, Stéphane Cruveiller, Antoine Danchin, Médéric Diard, Carole Dossat, Meriem El Karoui, Eric Frapy, Louis Garry, Jean Marc Ghigo, Anne Marie Gilles, James Johnson, Chantal Le Bouguénec, Mathilde Lescat, Sophie Mangenot, Vanessa Martinez-Jéhanne, Ivan Matic, Xavier Nassif, Sophie Oztas, Marie Agnès Petit, Christophe Pichon, Zoé Rouy, Claude Saint Ruf, Dominique Schneider, Jérôme Tourret, Benoit Vacherie, David Vallenet, Claudine Médigue, Eduardo P C Rocha, and Erick Denamur
Subjects: Genetics, QH426-470
Abstract: The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.
Published: 2009
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19. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

Author: Stéphane Vuilleumier, Ludmila Chistoserdova, Ming-Chun Lee, Françoise Bringel, Aurélie Lajus, Yang Zhou, Benjamin Gourion, Valérie Barbe, Jean Chang, Stéphane Cruveiller, Carole Dossat, Will Gillett, Christelle Gruffaz, Eric Haugen, Edith Hourcade, Ruth Levy, Sophie Mangenot, Emilie Muller, Thierry Nadalig, Marco Pagni, Christian Penny, Rémi Peyraud, David G Robinson, David Roche, Zoé Rouy, Channakhone Saenampechek, Grégory Salvignol, David Vallenet, Zaining Wu, Christopher J Marx, Julia A Vorholt, Maynard V Olson, Rajinder Kaul, Jean Weissenbach, Claudine Médigue, and Mary E Lidstrom
Subjects: Medicine, Science
Abstract: BACKGROUND:Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. METHODOLOGY/PRINCIPAL FINDINGS:The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid). CONCLUSION/SIGNIFICANCE:These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.
Published: 2009
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20. Comparative analysis of Acinetobacters: three genomes for three lifestyles.

Author: David Vallenet, Patrice Nordmann, Valérie Barbe, Laurent Poirel, Sophie Mangenot, Elodie Bataille, Carole Dossat, Shahinaz Gas, Annett Kreimeyer, Patricia Lenoble, Sophie Oztas, Julie Poulain, Béatrice Segurens, Catherine Robert, Chantal Abergel, Jean-Michel Claverie, Didier Raoult, Claudine Médigue, Jean Weissenbach, and Stéphane Cruveiller
Subjects: Medicine, Science
Abstract: Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.
Published: 2008
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21. A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

Author: Daniel Muller, Claudine Médigue, Sandrine Koechler, Valérie Barbe, Mohamed Barakat, Emmanuel Talla, Violaine Bonnefoy, Evelyne Krin, Florence Arsène-Ploetze, Christine Carapito, Michael Chandler, Benoît Cournoyer, Stéphane Cruveiller, Caroline Dossat, Simon Duval, Michael Heymann, Emmanuelle Leize, Aurélie Lieutaud, Didier Lièvremont, Yuko Makita, Sophie Mangenot, Wolfgang Nitschke, Philippe Ortet, Nicolas Perdrial, Barbara Schoepp, Patricia Siguier, Diliana D Simeonova, Zoé Rouy, Béatrice Segurens, Evelyne Turlin, David Vallenet, Alain Van Dorsselaer, Stéphanie Weiss, Jean Weissenbach, Marie-Claire Lett, Antoine Danchin, and Philippe N Bertin
Subjects: Genetics, QH426-470
Abstract: Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the beta-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.
Published: 2007
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22. High-Throughput Sequencing (HTS) of newly synthetized RNAs enables one shot detection and identification of live mycoplasmas and differentiation from inert nucleic acids

Author: Stéphane Cruveiller, Edwige Gros, Marc Eloit, Florence Tardy, Fabienne Archer, Alexandra Bobet-Erny, Adélie Colin, Angélique Champavère, Pascale Beurdeley, Céline Desbrousses, PathoQuest, Infections Virales et Pathologie Comparée - UMR 754 (IVPC), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mycoplasmoses des Ruminants - UMR (MYCO), and Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Bioengineering, RNA-Seq, Biologicals, Biology, medicine.disease_cause, Immunofluorescence, Applied Microbiology and Biotechnology, 4-Thiouridine, DNA sequencing, 03 medical and health sciences, Mycoplasma, 0302 clinical medicine, Sterility, medicine, Humans, High throughput sequencing, 030212 general & internal medicine, Acholeplasma laidlawii, Pharmacology, Biological Products, Microbial Viability, General Immunology and Microbiology, medicine.diagnostic_test, Sequence Analysis, RNA, High-Throughput Nucleotide Sequencing, RNA, General Medicine, RNA, Bacterial, 030104 developmental biology, Biochemistry, A549 Cells, Metagenomics, Nucleic acid, Identification (biology), Drug Contamination, Biotechnology
Abstract: International audience; Mycoplasma contamination threatens both the safety of biologics produced in cell substrates as well as the quality of scientific results based on cell-culture observations. Methods currently used to detect contamination of cells include culture, enzymatic activity, immunofluorescence and PCR but suffer from some limitations. High throughput sequencing (HTS) can be used to identify microbes like mycoplasmas in biologics since it enables an unbiased approach to detection without the need to design specific primers to pre-amplify target sequences but it does not enable the confirmation of microbial infection since this could reflect carryover of inert sequences. In order to unambiguously differentiate the presence of live or dead mycoplasmas in biological products, the present method was developed based on metabolic RNA labelling of newly synthetized mycoplasmal RNAs. HTS of labelled RNA detected A549 cell infection with Acholeplasma laidlawii in a manner similar to both PCR and culture and demonstrated that this technique can unambiguously identify bacterial species and differentiates infected cells from cells exposed to a high inoculum of heat-inactivated mycoplasmas. This method therefore combines the advantage of culture (that detects only live microorganisms) with those of molecular tests (rapidity) together with a very broad range of bacterial detection and identification.
Published: 2020
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23. Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria

Author: Christopher T. Lefèvre, Caroline L. Monteil, Béatrice Alonso, Denis S. Grouzdev, Zoé Rouy, Stéphane Cruveiller, David Pignol, Nicolas Ginet, Guy Perrière, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Microbiologie Environnementale et Moléculaire (MEM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), ANR-18-CE31-0003,SIGMAG,SIGNATURE DES MAGNETITES PRODUITES PAR LES BACTERIES MAGNETOTACTIQUES : PERSPECTIVES CHIMIQUES ET ISOTOPIQUES(2018), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Gene Transfer, Horizontal, Magnetotactic bacteria, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Article, 03 medical and health sciences, Phylogenetics, Gram-Negative Bacteria, Magnetotaxis, Magnetospirillum, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Alphaproteobacteria, 030304 developmental biology, 0303 health sciences, Experimental evolution, Bacteria, biology, 030306 microbiology, Clonal interference, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], biology.organism_classification, Evolutionary biology, Parallel evolution, Adaptation
Abstract: Under the same selection pressures, two genetically divergent populations may evolve in parallel toward the same adaptive solutions. Here, we hypothesized that magnetotaxis (i.e., magnetically guided chemotaxis) represents a key adaptation to micro-oxic habitats in aquatic sediments and that its parallel evolution homogenized the phenotypes of two evolutionary divergent clusters of freshwater spirilla. All magnetotactic bacteria affiliated to the Magnetospirillum genus (Alphaproteobacteria class) biomineralize the same magnetic particle chains and share highly similar physiological and ultrastructural features. We looked for the processes that could have contributed at shaping such an evolutionary pattern by reconciling species and gene trees using newly sequenced genomes of Magnetospirillum related bacteria. We showed that repeated horizontal gene transfers and homologous recombination of entire operons contributed to the parallel evolution of magnetotaxis. We propose that such processes could represent a more parsimonious and rapid solution for adaptation compared with independent and repeated de novo mutations, especially in the case of traits as complex as magnetotaxis involving tens of interacting proteins. Besides strengthening the idea about the importance of such a function in micro-oxic habitats, these results reinforce previous observations in experimental evolution suggesting that gene flow could alleviate clonal interference and speed up adaptation under some circumstances.
Published: 2020
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24. PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Author: Adelme Bazin, Stéphane Cruveiller, Claudine Médigue, David Vallenet, Guillaume Gautreau, Rémi Planel, Eduardo P. C. Rocha, Mathieu Gachet, Amandine Perrin, Mathieu Dubois, Christophe Ambroise, Alexandra Calteau, Catherine Matias, Laura Burlot, Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Laboratoire de Probabilités, Statistique et Modélisation (LPSM (UMR_8001)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), ED 515 - Complexité du vivant, Laboratoire de Probabilités, Statistiques et Modélisations (LPSM (UMR_8001)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), This research was supported in part by the IRTELIS and Phare PhD programs of the French Alternative Energies and Atomic Energy Commission (CEA) for GG and AB respectively, the French Government 'Investissements d’Avenir' programs (namely FRANCE GENOMIQUE [ANR-10-INBS-09-08], the INSTITUT FRANÇAIS DE BIOINFORMATIQUE [ANR-11-INBS-0013], and the Agence Nationale de la Recherche [Projet ANR-16-CE12-29 for EPCR])., We acknowledge Alexandre Renaux and Jonathan Mercier for their preliminary insights on pangenome graphs. We thank Mélanie Buy for drawing the PPanGGOLiN logo. Finally, we thank Guilhem Royer, Valentin Sabatet, Johan Rollin, Mohammed-Amin Madoui, Tom Delmont, Nicolas Pons and Pierre Peterlongo for all their advice along this work., Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Collège doctoral [Sorbonne universités]
Subjects: Computer science, [SDV]Life Sciences [q-bio], 01 natural sciences, Genome, 010104 statistics & probability, Database and Informatics Methods, Biology (General), Genome Evolution, Genomic organization, Data Management, 0303 health sciences, Markov random field, Applied Mathematics, Simulation and Modeling, Genomics, Genomic Databases, Physical Sciences, Engineering and Technology, Synthetic Biology, Algorithms, Research Article, Computer and Information Sciences, QH301-705.5, Computational biology, Research and Analysis Methods, Molecular Evolution, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Gene family, 0101 mathematics, Gene, Genome size, 030304 developmental biology, Taxonomy, Comparative genomics, Evolutionary Biology, Bacteria, Correction, Biology and Life Sciences, Computational Biology, 15. Life on land, Comparative Genomics, Synthetic Genomics, Genome Analysis, Biological Databases, Multivariate Analysis, Genome dynamics, Genome, Bacterial, Software, Mathematics
Abstract: The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don’t account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN., Author summary Microorganisms have the greatest biodiversity and evolutionary history on earth. At the genomic level, it is reflected by a highly variable gene content even among organisms from the same species which explains the ability of microbes to be pathogenic or to grow in specific environments. We developed a new method called PPanGGOLiN which accurately represents the genomic diversity of a species (i.e. its pangenome) using a compact graph structure. Based on this pangenome graph, we classify genes by a statistical method according to their occurrence in the genomes. This method allowed us to build pangenomes even for uncultivated species at an unprecedented scale. We applied our method on all available genomes in databanks in order to depict the overall diversity of hundreds of species. Overall, our work enables microbiologists to explore and visualize pangenomes alike a subway map.
Published: 2020
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25. MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

Author: Johan Rollin, Mathieu Gachet, Adrien Josso, Rémi Planel, Guillaume Gautreau, Hugo Pereira, David Roche, Alexandra Calteau, Jordan Langlois, Zoé Rouy, Claudine Médigue, David Vallenet, Stéphane Cruveiller, Aurélie Lajus, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Service d'Ecologie Sociale, CP 231, Universite´ Libre de Bruxelles, Boulevard du Triomphe, 1050 Brussels, Belgium, Université libre de Bruxelles (ULB), Représenter, Inventer la Réalité, du Romantisme au XXIe siècle (RIRRA 21), Université Paul-Valéry - Montpellier 3 (UPVM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE)
Subjects: 0301 basic medicine, Paper, Computer science, Data management, Context (language use), Bacterial genome size, Computational biology, comparative genomics, Genome, 03 medical and health sciences, Annotation, transcriptomics, User-Computer Interface, microbial genome annotation system, Computer Graphics, Relevance (information retrieval), Molecular Biology, ComputingMilieux_MISCELLANEOUS, variant detection, Comparative genomics, Microbiological Phenomena, Internet, 030102 biochemistry & molecular biology, business.industry, Computational Biology, Molecular Sequence Annotation, Genome project, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Genome, Microbial, 030104 developmental biology, ComputingMethodologies_PATTERNRECOGNITION, metabolic networks, Database Management Systems, business, gene function curation, Databases, Chemical, Metabolic Networks and Pathways, Software, Information Systems
Abstract: The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources.
Published: 2017
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26. The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-β-Lactamase-Producing Strains of Escherichia coli

Author: Typhaine Billard-Pomares, Catherine Branger, Olivier Clermont, Claudine Médigue, Valérie Barbe, Guilhem Royer, Bertrand Picard, Stéphane Cruveiller, Dominique Pognard, Jeremy Glodt, Fatma Magdoud, David Roche, Bénédicte Condamine, Odile Rigal, Sara Dion, Miguel Castellanos, Stéphanie Fouteau, and Erick Denamur
Subjects: Operon, Hydrolases, Virulence, Microbial Sensitivity Tests, Biology, medicine.disease_cause, beta-Lactamases, Microbiology, Epidemiology and Surveillance, 03 medical and health sciences, Mice, Plasmid, medicine, Escherichia coli, Animals, Humans, Pharmacology (medical), Insertion sequence, Arginine deiminase, Escherichia coli Infections, Phylogeny, 030304 developmental biology, Pharmacology, 0303 health sciences, Strain (chemistry), 030306 microbiology, biology.organism_classification, Infectious Diseases, England, Urinary Tract Infections, bacteria, France, Bacteria, Plasmids
Abstract: We previously identified an operon involved in an arginine deiminase (ADI) pathway (arc operon) on a CTX-M-producing plasmid from an O102-ST405 strain of Escherichia coli. As the ADI pathway was shown to be involved in the virulence of various Gram-positive bacteria, we tested whether the ADI pathway could be involved in the epidemiological success of extended-spectrum-␤-lactamase (ESBL)-producing E. coli strains. We studied two collections of human E. coli isolated in France (n ϭ 493) and England (n ϭ 1,509) and show that the prevalence of the arc operon (i) is higher in ESBL-producing strains (12.1%) than in nonproducers (2.5%), (ii) is higher in CTX-M-producing strains (16%) than in other ESBL producers (3.5%), and (iii) increased over time in ESBL-producing strains from 0% before 2000 to 43.3% in 2011 to 2012. The arc operon, found in strains from various phylogenetic backgrounds, is carried by IncF plasmids (85%) or chromosomes (15%) in regions framed by numerous insertion sequences, indicating multiple arrivals. Competition experiments showed that the arc operon enhances fitness of the strain in vitro in ly-sogeny broth with arginine. In vivo competition experiments showed that the arc operon is advantageous for the strain in a mouse model of urinary tract infection (UTI), whereas it is a burden in a mouse model of intestinal colonization. In summary , we have identified a trait linked to CTX-M-producing strains that is responsible for a trade-off between two main E. coli lifestyles, UTI and gut commensalism. This trait alone cannot explain the wide spread of ESBLs in E. coli but merits epidemiological surveillance.
Published: 2019

27. Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic Acids

Author: Marc Eloit, Erika Muth, Gaelle Gonzalez, Muriel Coulpier, Stéphane Cruveiller, Justine Cheval, Pascale Beurdeley, PathoQuest, Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), École nationale vétérinaire - Alfort (ENVA), Université Paris-Est (UPE), Découverte de pathogènes – Pathogen discovery, Institut Pasteur [Paris], Pathoquest, Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), École nationale vétérinaire d'Alfort (ENVA), and Institut Pasteur [Paris] (IP)
Subjects: squirrel monkey retrovirus, tick-borne encephalitis virus, viruses, lcsh:QR1-502, Microbiology, DNA sequencing, Virus, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Chlorocebus aethiops, Animals, Molecular Biology, Vero Cells, 030304 developmental biology, 0303 health sciences, metagenomics, biology, Applied and Environmental Science, 030302 biochemistry & molecular biology, RNA, Computational Biology, High-Throughput Nucleotide Sequencing, high-throughput sequencing, RNA virus, Cell Differentiation, DNA Contamination, biology.organism_classification, Virology, QR1-502, Vero, virus safety, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, biologicals, Cell culture, 4-thiouridine, DNA, Viral, Viruses, Nucleic acid, Vero cell, RNA, Viral, RNA-seq, DNA, Research Article
Abstract: The use of high-throughput sequencing (HTS) to identify viral contamination of biological products is extremely sensitive and provides a broad range of detection. Nevertheless, viral sequences identified can also be inert. Examples include contamination resulting from reagents or the presence of inactivated viruses in animal-derived components of the cell culture medium. We therefore developed a method that relies on the sequencing of newly synthesized RNAs, an unequivocal sign of the presence of a transcriptionally active virus. This improvement in the specificity of viral testing increases the acceptability of HTS as a standard test for cells used in manufacturing biologicals and in biotherapies., The use of high-throughput sequencing (HTS) to identify viruses in biologicals differs from current molecular approaches, since its use enables an unbiased approach to detection without the need to design specific primers to preamplify target sequences. Its broad range of detection and analytical sensitivity make it an important tool to ensure that biologicals are free from adventitious viruses. Similar to other molecular methods, however, identification of viral sequences in cells by HTS does not prove viral infection, since this could reflect carryover of inert viral sequences from reagents or other sources or the presence of transcriptionally inactive cellular sequences. Due to the broad range of detection associated with HTS, the above can potentially be perceived as a drawback for the testing of pharmaceutical biological products using this method. In order to avoid the identification of inert viral sequences, we present a methodology based on metabolic RNA labeling and sequencing, which enables the specific identification of newly synthesized viral RNAs in infected cells, resulting in the ability to unambiguously distinguish active infection by DNA or RNA viruses from inert nucleic acids. In the present study, we report the ability to differentiate Vero cells acutely infected by a single-stranded positive-sense RNA virus (tick-borne encephalitis virus) from cells which have been in contact with nonreplicating virus particles. Additionally, we also found a laboratory contamination by the squirrel monkey retrovirus of our Vero cell line, which was derived from an Old World (African green) monkey, a type of contamination which until now has been identified only in cells derived from primates from the New World. IMPORTANCE The use of high-throughput sequencing (HTS) to identify viral contamination of biological products is extremely sensitive and provides a broad range of detection. Nevertheless, viral sequences identified can also be inert. Examples include contamination resulting from reagents or the presence of inactivated viruses in animal-derived components of the cell culture medium. We therefore developed a method that relies on the sequencing of newly synthesized RNAs, an unequivocal sign of the presence of a transcriptionally active virus. This improvement in the specificity of viral testing increases the acceptability of HTS as a standard test for cells used in manufacturing biologicals and in biotherapies.
Published: 2019
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28. Complete genome sequence of Bradyrhizobium sp. Strain ORS3257, an efficient nitrogen-fixing bacterium isolated from cowpea in Senegal

Author: Eric Giraud, Elisabeth Navarro, Tatiana Krasova Wade, Daniel Gargani, Albin Teulet, Djamel Gully, Joël Fardoux, Marc Neyra, Antoine Le Quéré, Stéphane Cruveiller, Institut de recherche pour le développement (IRD [Sénégal]), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Agence Nationale de la Recherche : ANR-VMCS-2008, ANR-16-CE20-0013, ANR-08-VULN-0007,PEPS,Peru Ecosystem Projection Scenarios(2008), Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Milieux aquatiques, écologie et pollutions (UR MALY), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)
Subjects: Fixation de l'azote, F40 - Écologie végétale, F60 - Physiologie et biochimie végétale, Symbiose, Biology, Genome, Bradyrhizobium, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Immunology and Microbiology (miscellaneous), Symbiosis, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Bactérie fixatrice de l'azote, Molecular Biology, Gene, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Vegetal Biology, Génome, Strain (chemistry), 030306 microbiology, Aeschynomene, food and beverages, biology.organism_classification, Aeschynomène, Nitrogen fixation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biologie végétale, Vigna unguiculata
Abstract: International audience; Here, we report the complete genome sequence of Bradyrhizobium sp. strain ORS3257, which forms efficient symbioses with cowpea, peanut, or groundnut. These genomic data will be useful to identify genes associated with symbiotic performance and host compatibility on several legumes, including Aeschynomene species , with which a Nod-independent type III secretion system (T3SS)-dependent sym-biosis can be established.
Published: 2019
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29. MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

Author: Stéphane Cruveiller, Zoé Rouy, Claude Scarpelli, David Roche, David Vallenet, Jonathan Mercier, Alexandre Renaux, Claudine Médigue, Johan Rollin, Adrien Josso, Mathieu Gachet, Alexandra Calteau, Aurélie Lajus, Informatics and Applied Informatics, and Faculty of Sciences and Bioengineering Sciences
Subjects: 0301 basic medicine, Data management, 030106 microbiology, Context (language use), Biology, Polymorphism, Single Nucleotide, Genome, Evolution, Molecular, 03 medical and health sciences, Consistency (database systems), Annotation, Databases, Genetic, Genetics, Database Issue, Metabolomics, Biological data, Ecology, business.industry, Microbiota, Computational Biology, Genome project, Data science, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Metagenomics, Multigene Family, Metabolome, Metagenome, business, Software
Abstract: The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations.
Published: 2016
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30. Experimental evolution of rhizobia may lead to either extra- or intracellular symbiotic adaptation depending on the selection regime

Author: Stéphane Cruveiller, Carine Gris, Delphine Capela, Alain Jauneau, Catherine Masson-Boivin, Camille Clerissi, Marta Marchetti, Yasmine Yousfi, Olivier Bouchez, Eduardo P. C. Rocha, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UPS - Fédération de Recherches Agrobiosciences, Interaction, Biodiversity Plateforme d'Imagerie, Centre National de la Recherche Scientifique (CNRS), French National Research Agency : ANR-12-ADAP-0014-01, French Laboratory of Excellence project 'TULIP' : ANR-10-LABX-41, ANR-11-IDEX-0002-02, France Genomique National Infrastructure : ANR-10-INBS-09, ANR-12-ADAP-0014,SHAPE,Design de nouveaux rhizobia par évolution expérimentale: vers une compréhension de l'adaptation des bactéries à l'environnement plante(2012), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 281605,EC:FP7:ERC,ERC-2011-StG_20101109,EVOMOBILOME(2012), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), ANR-11-IDEX-0002-02/10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2011), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0301 basic medicine, Mimosa, Root nodule, [SDV]Life Sciences [q-bio], 030106 microbiology, extracellular, adaptation, rhizobia, Plant Root Nodulation, Plant Roots, Rhizobia, rhizobium, 03 medical and health sciences, Symbiosis, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, experimental evolution, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Experimental evolution, biology, Cupriavidus taiwanensis, Cupriavidus, infection cellulaire, fungi, 15. Life on land, évolution expérimentale, biology.organism_classification, Adaptation, Physiological, Biological Evolution, intracellular, Phenotype, symbiosis, Eukariota, 030104 developmental biology, Evolutionary biology, Ralstonia solanacearum, Adaptation, Plasmids
Abstract: Special Issue: Microbial Local Adaptation; Experimental evolution is a powerful approach to study the process of adaptation to new environments, including the colonization of eukaryotic hosts. Facultative endosymbionts, including pathogens and mutualists, face changing and spatially structured environments during the symbiotic process, which impose diverse selection pressures. Here, we provide evidence that different selection regimes, involving different times spent in the plant environment, can result in either intra- or extracellular symbiotic adaptations. In previous work, we introduced the symbiotic plasmid of Cupriavidus taiwanensis, the rhizobial symbiont of Mimosa pudica, into the phytopathogen Ralstonia solanacearum and selected three variants able to form root nodules on M. pudica, two (CBM212 and CBM349) being able to rudimentarily infect nodule cells and the third one (CBM356) only capable of extracellular infection of nodules. Each nodulating ancestor was further challenged to evolve using serial ex planta-in planta cycles of either 21 (three short-cycle lineages) or 42 days (three long-cycle lineages). In this study, we compared the phenotype of the 18 final evolved clones. Evolution through short and long cycles resulted in similar adaptive paths on lineages deriving from the two intracellularly infectious ancestors, CBM212 and CBM349. In contrast, only short cycles allowed a stable acquisition of intracellular infection in lineages deriving from the extracellularly infecting ancestor, CBM356. Long cycles, instead, favoured improvement of extracellular infection. Our work highlights the importance of the selection regime in shaping desired traits during host-mediated selection experiments.
Published: 2016
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31. The revisited genome ofPseudomonas putidaKT2440 enlightens its value as a robust metabolicchassis

Author: Antoine Danchin, David Vallenet, Jörn Petersen, Claire M. Fraser, Claudine Médigue, Hans-Peter Klenk, Zoé Rouy, Agnieszka Sekowska, Stéphane Cruveiller, Víctor de Lorenzo, Pablo I. Nikel, Maria Jose Lopez-Sanchez, Eugeni Belda, Ruben G. A. van Heck, Anne Morgat, Valérie Barbe, and Vitor A. P. Martins dos Santos
Subjects: 0301 basic medicine, Genetics, Whole genome sequencing, Rhizosphere, Systems biology, Strain (biology), 030106 microbiology, Biology, biology.organism_classification, Microbiology, Genome, Pseudomonas putida, 03 medical and health sciences, 030104 developmental biology, Gene, Ecology, Evolution, Behavior and Systematics, Bacteria
Abstract: Summary By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., 2002) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data—let alone metabolic modeling and other nowadays common systems biology approaches—allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state-of-the-art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein-coding genes and re-annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology.
Published: 2016
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32. Author Correction: Parallels between experimental and natural evolution of legume symbionts

Author: Céline Lopez-Roques, Mingxing Tang, Lionel Moulin, Delphine Capela, Clémence Genthon, Camille Clerissi, Eduardo P. C. Rocha, Catherine Masson-Boivin, Matthew A. Parker, Marie Touchon, and Stéphane Cruveiller
Subjects: Genome evolution, History, Mimosa, Gene Transfer, Horizontal, Science, General Physics and Astronomy, 02 engineering and technology, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Natural (music), Gene Regulatory Networks, lcsh:Science, Author Correction, Symbiosis, Parallels, 030304 developmental biology, Comparative genomics, 0303 health sciences, Experimental evolution, Multidisciplinary, Cupriavidus, Genetic Variation, Fabaceae, General Chemistry, 021001 nanoscience & nanotechnology, Adaptation, Physiological, Evolutionary biology, Genes, Bacterial, Mutation, Ralstonia solanacearum, lcsh:Q, Directed Molecular Evolution, 0210 nano-technology, Plasmids
Abstract: The emergence of symbiotic interactions has been studied using population genomics in nature and experimental evolution in the laboratory, but the parallels between these processes remain unknown. Here we compare the emergence of rhizobia after the horizontal transfer of a symbiotic plasmid in natural populations of Cupriavidus taiwanensis, over 10 MY ago, with the experimental evolution of symbiotic Ralstonia solanacearum for a few hundred generations. In spite of major differences in terms of time span, environment, genetic background, and phenotypic achievement, both processes resulted in rapid genetic diversification dominated by purifying selection. We observe no adaptation in the plasmid carrying the genes responsible for the ecological transition. Instead, adaptation was associated with positive selection in a set of genes that led to the co-option of the same quorum-sensing system in both processes. Our results provide evidence for similarities in experimental and natural evolutionary transitions and highlight the potential of comparisons between both processes to understand symbiogenesis.
Published: 2018

33. Parallels between experimental and natural evolution of legume symbionts

Author: Eduardo P. C. Rocha, Camille Clerissi, Stéphane Cruveiller, Clémence Genthon, Mingxing Tang, Lionel Moulin, Catherine Masson-Boivin, Matthew A. Parker, Marie Touchon, Delphine Capela, Céline Lopez-Roques, Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génétique des génomes - Genetics of Genomes (UMR 3525), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Binghamton University [SUNY], State University of New York (SUNY), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), French National Research Agency : ANR-12-ADAP-0014-01, ANR-16-CE20-0011-01, the 'Laboratoire d'Excellence (LABEX)' TULIP : ANR-10-LABX-41, France Genomique National infrastructure - 'Investissement d'avenir' program : ANR-10-INBS-09, ANR-12-ADAP-0014,SHAPE,Design de nouveaux rhizobia par évolution expérimentale: vers une compréhension de l'adaptation des bactéries à l'environnement plante(2012), ANR-16-CE20-0011,REPLAY,Rejouer l'évolution des rhizobia: vers un cadre conceptuel et pratique pour le design de nouveaux symbiotes fixateurs(2016), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Génétique des génomes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ANR-11-IDEX-0002-02/10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2011), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0301 basic medicine, Genome evolution, Symbiogenesis, Science, [SDV]Life Sciences [q-bio], 030106 microbiology, General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, Article, Rhizobia, Population genomics, 03 medical and health sciences, Negative selection, lcsh:Science, 030304 developmental biology, Comparative genomics, 0303 health sciences, Experimental evolution, Multidisciplinary, biology, 030306 microbiology, Cupriavidus taiwanensis, General Chemistry, biology.organism_classification, 030104 developmental biology, Evolutionary biology, Horizontal gene transfer, lcsh:Q, Adaptation, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: The emergence of symbiotic interactions has been studied using population genomics in nature and experimental evolution in the laboratory, but the parallels between these processes remain unknown. Here we compare the emergence of rhizobia after the horizontal transfer of a symbiotic plasmid in natural populations of Cupriavidus taiwanensis, over 10 MY ago, with the experimental evolution of symbiotic Ralstonia solanacearum for a few hundred generations. In spite of major differences in terms of time span, environment, genetic background, and phenotypic achievement, both processes resulted in rapid genetic diversification dominated by purifying selection. We observe no adaptation in the plasmid carrying the genes responsible for the ecological transition. Instead, adaptation was associated with positive selection in a set of genes that led to the co-option of the same quorum-sensing system in both processes. Our results provide evidence for similarities in experimental and natural evolutionary transitions and highlight the potential of comparisons between both processes to understand symbiogenesis., It is unclear if experimental evolution is a good model for natural processes. Here, Clerissi et al. find parallels between the evolution of symbiosis in rhizobia after horizontal transfer of a plasmid over 10 million years ago and experimentally evolved symbionts.
Published: 2018
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34. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation

Author: Jean-Yves Coppée, Bernd Jagla, Zoé Rouy, Hugo Varet, Didier Mazel, Claudine Médigue, Oihane Irazoki, Evelyne Krin, Stéphane Cruveiller, Sebastian Aguilar Pierlé, Odile Sismeiro, Susana Campoy, Marie-Agnès Dillies, Plasticité du Génome Bactérien - Bacterial Genome Plasticity (PGB), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris] (IP), Universitat Autònoma de Barcelona (UAB), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), This study was funded by the Institut Pasteur, the Centre National de la Recherche Scientifique (CNRS-UMR3525), the French National Research Agency (ANR-2012-Blanc SVSE3-DynamINT), the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant n°ANR-10-LABX-62-IBEID), the Spanish the Ministerio de Economía y Competitividad (BIO2016–77011-R), Generalitat de Catalunya (2014SGR 572), and the European Union Seventh Framework Programme (FP7-HEALTH-2011-single-stage) 'Evolution and Transfer of Antibiotic Resistance' (EvoTAR). The Transcriptome and EpiGenome Platform is a member of the France Génomique consortium (ANR10-NBS-09-08)., ANR-12-BSV3-0015,DynamINT,Recombination des cassettes d'intégron: dynamique in vivo et in vitro(2012), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 282004,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,EVOTAR(2011), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: NcRNA, 0301 basic medicine, SOS response, lcsh:QH426-470, lcsh:Biotechnology, [SDV]Life Sciences [q-bio], Mitomycin, genetic processes, 030106 microbiology, DNA repair, Biology, medicine.disease_cause, Regulon, Transcriptome, 03 medical and health sciences, SOS Response (Genetics), lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, medicine, SOS Response, Genetics, Vibrio cholerae, Gene, Gene Expression Profiling, Promoter, biochemical phenomena, metabolism, and nutrition, ncRNA, nrdB, nrdA, lcsh:Genetics, enzymes and coenzymes (carbohydrates), Phenotype, bacteria, Repressor lexA, Transcription Initiation Site, NrdB, 5' Untranslated Regions, NrdA, Research Article, Biotechnology
Abstract: Background The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. Results Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5’UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369–1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. Conclusions We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria. Electronic supplementary material The online version of this article (10.1186/s12864-018-4716-8) contains supplementary material, which is available to authorized users.
Published: 2018
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35. Synonymous Genetic Variation in Natural Isolates ofEscherichia coliDoes Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment

Author: Stéphane Cruveiller, Jeffrey E. Barrick, Richard E. Lenski, Rohan Maddamsetti, Philip J. Hatcher, and Claudine Médigue
Subjects: Silent mutation, Mutation rate, mutation rate, Genomics, Biology, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Effective population size, Genetic variation, Escherichia coli, Genetics, experimental evolution, Selection, Genetic, Molecular Biology, Gene, Phylogeny, Silent Mutation, Discoveries, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Experimental evolution, Genetic Variation, Biological Evolution, Horizontal gene transfer, effective population size, 030217 neurology & neurosurgery
Abstract: Synonymous genetic differences vary by more than 20-fold among genes in natural isolates of Escherichia coli. One hypothesis to explain this heterogeneity is that genes with high levels of synonymous variation mutate at higher rates than genes with low synonymous variation. If so, then one would expect to observe similar mutational patterns in evolution experiments. In fact, however, the pattern of synonymous substitutions in a long-term evolution experiment with E. coli does not support this hypothesis. In particular, the extent of synonymous variation across genes in that experiment does not reflect the variation observed in natural isolates of E. coli. Instead, gene length alone predicts with high accuracy the prevalence of synonymous changes in the experimental populations. We hypothesize that patterns of synonymous variation in natural E. coli populations are instead caused by differences across genomic regions in their effective population size that, in turn, reflect different histories of recombination, horizontal gene transfer, selection, and population structure.
Published: 2015
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36. Complete Genome Sequence of

Author: Djamel, Gully, Albin, Teulet, Nicolas, Busset, Nico, Nouwen, Joël, Fardoux, Zoe, Rouy, David, Vallenet, Stéphane, Cruveiller, and Eric, Giraud
Subjects: food and beverages, Prokaryotes, biochemical phenomena, metabolism, and nutrition
Abstract: Here, we report the complete genome sequence of Bradyrhizobium sp. strain ORS285, which is able to nodulate Aeschynomene legumes using two distinct strategies that differ in the requirement of Nod factors. The genome sequence information of this strain will help understanding of the different mechanisms of interaction of rhizobia with legumes.
Published: 2017

37. The genomic and transcriptomic basis of the potential of Lactobacillus plantarum A6 to improve the nutritional quality of a cereal based fermented food

Author: Williams Turpin, Marion Weiman, Aurélie Lajus, Stéphane Cruveiller, Christèle Humblot, and Jean-Pierre Guyot
Subjects: 0301 basic medicine, Pennisetum, 030106 microbiology, Genomics, Biology, Carbohydrate metabolism, Microbiology, Genome, DNA sequencing, Transcriptome, 03 medical and health sciences, Lactobacillus, Gene, food and beverages, High-Throughput Nucleotide Sequencing, General Medicine, biology.organism_classification, 030104 developmental biology, Biochemistry, Food Microbiology, Carbohydrate Metabolism, Fermented Foods, Edible Grain, Nutritive Value, Lactobacillus plantarum, Genome, Bacterial, Food Science
Abstract: The objective of this work was to investigate the nutritional potential of Lactobacillus plantarum A6 in a food matrix using next generation sequencing. To this end, we characterized the genome of the A6 strain for a complete overview of its potential. We then compared its transcriptome when grown in a food matrix made from pearl millet to and its transcriptome when cultivated in a laboratory medium. Genomic comparison of the strain L. plantarum A6 with the strains WCFS1, ST-III, JDM1 and ATCC14917 led to the identification of five regions of genomic plasticity. More specifically, 362 coding sequences, mostly annotated as coding for proteins of unknown functions, were specific to L. plantarum A6. A total of 1201 genes were significantly differentially expressed in laboratory medium and food matrix. Among them, 821 genes were up-regulated in the food matrix compared to the laboratory medium, representing 23% of whole genomic objects. In the laboratory medium, the expression of 380 genes, representing 11% of the all genomic objects was at least double than in the food matrix. Genes encoding important functions for the nutritional quality of the food were identified. Considering its efficiency as an amylolytic strain, we investigated all genes involved in carbohydrate metabolism, paying particular attention to starch metabolism. An extracellular alpha amylase, a neopullulanase and maltodextrin transporters were identified, all of which were highly expressed in the food matrix. In addition, genes involved in alpha-galactoside metabolism were identified but only two of them were induced in food matrix than in laboratory medium. This may be because alpha galactosides were already eliminated during soaking. Different biosynthetic pathways involved in the synthesis of vitamin B (folate, riboflavin, and cobalamin) were identified. They allowed the identification of a potential of vitamin synthesis, which should be confirmed through biochemical analysis in further work. Surprisingly, some genes involved in metabolism and bioaccessibility of iron were identified. They were related directly to the use of transport of iron, or indirectly to metabolism of polyphenols, responsible of iron chelation in the food. The combination of genomics and transcriptomics not only revealed previously undocumented nutritional properties of L. plantarum A6, but also documented the behaviour of this bacterium in food.
Published: 2017

38. An antimicrobial peptide-resistant minor subpopulation of Photorhabdus luminescens is responsible for virulence

Author: Emeric Dubois, Sylvie Pagès, Anne Lanois, Julien Brillard, Maurine Bonabaud, Annabelle Mouammine, Sophie Gaudriault, Alain Givaudan, David Roche, Grégory Jubelin, Ludovic Legrand, Stéphane Cruveiller, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] ( DGIMI ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ), Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, GenomiX, Institut de Génomique Fonctionnelle, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Génomique Fonctionnelle ( IGF ), Centre National de la Recherche Scientifique ( CNRS ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Montpellier 1 ( UM1 ) -Université de Montpellier ( UM ), Centre Interlangues - Texte, Image, Langage ( TIL ), Université de Bourgogne ( UB ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Sécurité et Qualité des Produits d'Origine Végétale ( SQPOV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Avignon et des Pays de Vaucluse ( UAPV ), Ecologie microbienne des insectes et interactions hôte-pathogène ( EMIP ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), INRA 2011_1333_03 2015_1333, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Insecta, Operon, [SDV]Life Sciences [q-bio], [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, 030106 microbiology, Population, salmonella, Virulence, Drug resistance, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, peptide antimicrobien, Article, Bacterial genetics, Microbiology, 03 medical and health sciences, inhomogeneity, Disk Diffusion Antimicrobial Tests, Photorhabdus luminescens, Drug Resistance, Bacterial, Gene Order, hétérogénéité, Animals, education, ComputingMilieux_MISCELLANEOUS, photorhabdus luminescens, bactérie, education.field_of_study, Multidisciplinary, biology, Gene Expression Profiling, Enterobacteriaceae Infections, biology.organism_classification, bacterium, 030104 developmental biology, Regulon, Gene Expression Regulation, Genes, Bacterial, Mutation, Photorhabdus, Antimicrobial Cationic Peptides
Abstract: Some of the bacterial cells in isogenic populations behave differently from others. We describe here how a new type of phenotypic heterogeneity relating to resistance to cationic antimicrobial peptides (CAMPs) is determinant for the pathogenic infection process of the entomopathogenic bacterium Photorhabdus luminescens. We demonstrate that the resistant subpopulation, which accounts for only 0.5% of the wild-type population, causes septicemia in insects. Bacterial heterogeneity is driven by the PhoPQ two-component regulatory system and expression of pbgPE, an operon encoding proteins involved in lipopolysaccharide (LPS) modifications. We also report the characterization of a core regulon controlled by the DNA-binding PhoP protein, which governs virulence in P. luminescens. Comparative RNAseq analysis revealed an upregulation of marker genes for resistance, virulence and bacterial antagonism in the pre-existing resistant subpopulation, suggesting a greater ability to infect insect prey and to survive in cadavers. Finally, we suggest that the infection process of P. luminescens is based on a bet-hedging strategy to cope with the diverse environmental conditions experienced during the lifecycle.
Published: 2017
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39. Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria

Author: Laurence, Blanchard, Philippe, Guérin, David, Roche, Stéphane, Cruveiller, David, Pignol, David, Vallenet, Jean, Armengaud, and Arjan, de Groot
Subjects: Genetic Variation, Gene Expression Regulation, Bacterial, zinc peptidase, Regulon, transcriptional repressor, Repressor Proteins, transcriptomics, proteomics, Bacterial Proteins, Stress, Physiological, Metalloproteases, population characteristics, bacteria, Deinococcus, gene regulation, Original Research
Abstract: The extreme radiation resistance of Deinococcus bacteria requires the radiation‐stimulated cleavage of protein DdrO by a specific metalloprotease called IrrE. DdrO is the repressor of a predicted radiation/desiccation response (RDR) regulon, composed of radiation‐induced genes having a conserved DNA motif (RDRM) in their promoter regions. Here, we showed that addition of zinc ions to purified apo‐IrrE, and short exposure of Deinococcus cells to zinc ions, resulted in cleavage of DdrO in vitro and in vivo, respectively. Binding of IrrE to RDRM‐containing DNA or interaction of IrrE with DNA‐bound DdrO was not observed. The data are in line with IrrE being a zinc peptidase, and indicate that increased zinc availability, caused by oxidative stress, triggers the in vivo cleavage of DdrO unbound to DNA. Transcriptomics and proteomics of Deinococcus deserti confirmed the IrrE‐dependent regulation of predicted RDR regulon genes and also revealed additional members of this regulon. Comparative analysis showed that the RDR regulon is largely well conserved in Deinococcus species, but also showed diversity in the regulon composition. Notably, several RDR genes with an important role in radiation resistance in Deinococcus radiodurans, for example pprA, are not conserved in some other radiation‐resistant Deinococcus species.
Published: 2017

40. Characterization of a P1-Like Bacteriophage Carrying an SHV-2 Extended-Spectrum β-Lactamase from an Escherichia coli Strain

Author: Jean-Yves Bouet, Valérie Barbe, Catherine Branger, Marie Elise Jacquet, Stéphanie Fouteau, Typhaine Billard-Pomares, Miguel Castellanos, Stéphane Cruveiller, Claudine Médigue, Erick Denamur, Jorge Blanco, Olivier Clermont, and David Roche
Subjects: Operon, Molecular Sequence Data, Biology, medicine.disease_cause, beta-Lactamases, Epidemiology and Surveillance, Microbiology, Bacteriophage, Plasmid, Escherichia coli, medicine, Humans, Pharmacology (medical), Gene, Escherichia coli Infections, Prophage, Pharmacology, Genetics, Base Sequence, Chromosomes, Artificial, P1 Bacteriophage, Sequence Analysis, DNA, biology.organism_classification, Infectious Diseases, Lytic cycle, Mobile genetic elements
Abstract: P1 bacteriophages lysogenize bacteria as independent plasmid-like elements. We describe here a P1-like bacteriophage, RCS47, carrying a bla SHV-2 gene, isolated from a clinical strain of Escherichia coli from phylogroup B1, and we report the prevalence of P1-like prophages in natural E. coli isolates. We found that 70% of the sequence of RCS47, a 115-kb circular molecule, was common to the reference P1 bacteriophage under GenBank accession no. AF234172.1 , with the shared sequences being 99% identical. RCS47 had acquired two main foreign DNA fragments: a 9,636-bp fragment mobilized by two IS 26 elements containing a bla SHV-2 gene, and an 8,544-bp fragment mobilized by two IS 5 elements containing an operon encoding a dimethyl sulfoxide reductase. The reference P1 prophage plasmid replication gene belonged to the IncY incompatibility group, whereas that of RCS47 was from an unknown group. The lytic capacity of RCS47 and bla SHV-2 gene transduction, through the lysogenization of RCS47 in the recipient E. coli strains, were not demonstrated. The prevalence of P1-like prophages in various animal and human E. coli strain collections, as determined by the PCR detection of repL , the lytic replication gene, was 12.6%. No differences in the prevalences of these prophages were found between extended-spectrum β-lactamase (ESBL)-producing and non-ESBL-producing strains ( P = 0.69), but this prevalence was lower in phylogroup B2 than in the other phylogroups ( P = 0.008), suggesting epistatic interactions between P1 family phages and the genetic background of E. coli strains. P1-like phages are part of the mobile elements that carry antibiotic resistance. The high prevalence of P1-like prophages suggests their role may be underestimated.
Published: 2014
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41. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

Author: Wafa Frigui, Fadel Sayes, Camille Locht, Gregory Salvignol, Varun Khanna, Eve Willery, Danielle Walker, Anne-Sophie Debrie, Philip Supply, Michael Marceau, Timothy P. Stinear, Alessandro Cascioferro, Roland Brosch, Sylvain Brisse, Michael A. Quail, Stephen D. Bentley, Michel Fabre, Sophie Mangenot, Laurence Fiette, Claudine Médigue, Stéphane Cruveiller, Carine Rouanet, Claude Leclerc, Alexandre Pawlik, Julien Tap, Torsten Seemann, Laleh Majlessi, Christiane Bouchier, Roxane Simeone, Laurence Ma, David Roche, Cecile Parmentier, Valérie Barbe, Mickael Orgeur, Julian Parkhill, Eva C. Boritsch, Alexis Criscuolo, Maria-Cristina Gutierrez, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Pathogénomique mycobactérienne intégrée, Institut Pasteur [Paris] (IP), Régulation Immunitaire et Vaccinologie, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Histopathologie humaine et Modèles animaux, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), HIA Percy, Mécanismes moléculaires de la pathogénie microbienne, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Wellcome Trust Sanger Institute [Cambridge], Génomique (Plate-Forme) - Genomics Platform, Victorian Bioinformatics Consortium [Clayton], Monash University [Clayton], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Mécanismes moléculaires de la pathogenèse bactérienne, Département Infection et Epidémiologie - Department of Infection and Epidemiology, University of Melbourne, The work was supported in part by the Institut Pasteur (PTR 314 and PTR 383), European Community's Framework Programme 7 grant 260872, Wellcome Trust grant 098051 and Genoscope collaborative grant 114., European Project: 260872,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,MM4TB(2011), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)
Subjects: MESH: Sequence Analysis, DNA, MESH: Mycobacterium tuberculosis, Tuberculosis, MESH: Spleen, [SDV]Life Sciences [q-bio], MESH: Mice, Inbred BALB C, Virulence, Genomics, MESH: Virulence, MESH: Base Sequence, MESH: Genome, Bacterial, Genome, DNA sequencing, Mycobacterium tuberculosis, 03 medical and health sciences, Genetic variation, Genetics, medicine, MESH: Species Specificity, MESH: Animals, MESH: Lung, MESH: Mice, 030304 developmental biology, 0303 health sciences, MESH: Molecular Sequence Data, biology, 030306 microbiology, MESH: Adaptation, Biological, MESH: Genomics, MESH: Polymorphism, Single Nucleotide, biology.organism_classification, medicine.disease, MESH: Cluster Analysis, 3. Good health, MESH: Inverted Repeat Sequences, Mycobacterium
Abstract: International audience; Global spread and limited genetic variation are hallmarks of M. tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa. Here, we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4-5× coverage), 454/Roche (13-18× coverage) and/or Illumina DNA sequencing (45-105× coverage). We show that STB isolates are highly recombinogenic and evolutionarily early branching, with larger genome sizes, higher rates of genetic variation, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse infection experiments showed that STB strains are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms, and we provide insights into the molecular events involved.
Published: 2013
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42. Tempo and mode of genome evolution in a 50,000-generation experiment

Author: Aurko Dasgupta, Richard E. Lenski, Jeffrey E. Barrick, Sébastien Wielgoss, Noah Ribeck, Claudine Médigue, Jeffrey L. Blanchard, Gabriel C. Wu, Stéphane Cruveiller, Daniel E. Deatherage, Dominique Schneider, Olivier Tenaillon, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC), Department of Microbiology, University of Massachusetts [Amherst] (UMass Amherst), University of Massachusetts System (UMASS)-University of Massachusetts System (UMASS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0301 basic medicine, Nonsynonymous substitution, Genome evolution, Mutation rate, Time Factors, Lineage (genetic), 030106 microbiology, Biology, Genome, Article, Evolution, Molecular, 03 medical and health sciences, Intergenic region, Mutation Rate, Reproduction, Asexual, Escherichia coli, Selection, Genetic, Phylogeny, Selection (genetic algorithm), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Experimental evolution, Multidisciplinary, Natural selection, Models, Genetic, 030306 microbiology, Escherichia coli Proteins, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 030104 developmental biology, Genes, Bacterial, Genetic Loci, Evolutionary biology, Adaptation, Genome, Bacterial, Neutral mutation
Abstract: Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. Here we analysed 264 complete genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The populations that retained the ancestral mutation rate support a model in which most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to mutation-accumulation lines evolved under a bottlenecking regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions and deletions are overrepresented in the long-term populations, further supporting the inference that most mutations that reached high frequency were favoured by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.
Published: 2016
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43. Draft Genome Sequence of Campylobacter jejuni Bf, an Atypical Strain Able To Grow under Aerobiosis

Author: Stéphane Cruveiller, Nabila Haddad, Monique Zagorec, Vicky Bronnec, Mathieu Hernould, Odile Tresse, UMR 1014 SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), LUNAM Université [Nantes Angers Le Mans], Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), SECurité des ALIments et Microbiologie, and Institut National de la Recherche Agronomique (INRA)-École nationale d'ingénieurs des techniques des industries agricoles et alimentaires (ENITIAA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)
Subjects: 0301 basic medicine, Whole genome sequencing, biology, Strain (chemistry), [SDV]Life Sciences [q-bio], Campylobacteriosis, medicine.disease, biology.organism_classification, Campylobacter jejuni, campylobacter jejuni, Microbiology, séquence du génome, 03 medical and health sciences, 030104 developmental biology, aérobiose, Genetics, medicine, Prokaryotes, Molecular Biology
Abstract: In this study, we describe the draft genome sequence of a Campylobacter jejuni clinical isolate issued from a French patient suffering from severe campylobacteriosis. This atypical strain is characterized by an unusual resistance to oxygen and the ability to grow under an aerobic atmosphere, a characteristic as-of-yet unique to this species.
Published: 2016
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44. Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria

Author: Mickaël Le Gac, Antonia Suau, Dominique Schneider, Claudine Médigue, Stéphane Cruveiller, Jessica Plucain, Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Génomique et évolution des microorganismes, Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Département Dyneco Pelagos, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Unité Dyneco, Laboratoire Pelagos, Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire d'Ecologie Pélagique (PELAGOS), and Dynamiques des Écosystèmes Côtiers (DYNECO)
Subjects: 0106 biological sciences, 0301 basic medicine, Entomology, Experimental evolution, Escherichia coli, Adaptation, Historical contingency, Epistasis, Population, Biology, Environment, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, 03 medical and health sciences, Gene–environment interaction, education, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Genetics, education.field_of_study, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Replicate, Adaptation, Physiological, 030104 developmental biology, Phenotype, Evolutionary biology, Gene-Environment Interaction, Contingency, Genome, Bacterial, Research Article
Abstract: Background The impact of historical contingency, i.e. the past evolutionary history of a population, on further adaptation is mostly unknown at both the phenotypic and genomic levels. We addressed this question using a two-step evolution experiment. First, replicate populations of Escherichia coli were propagated in four different environmental conditions for 1000 generations. Then, all replicate populations were transferred and propagated for further 1000 generations to a single new environment. Results Using this two-step experimental evolution strategy, we investigated, at both the phenotypic and genomic levels, whether and how adaptation in the initial historical environments impacted evolutionary trajectories in a new environment. We showed that both the growth rate and fitness of the evolved populations obtained after the second step of evolution were contingent upon past evolutionary history. In contrast however, the genes that were modified during the second step of evolution were independent from the previous history of the populations. Conclusions Our work suggests that historical contingency affects phenotypic adaptation to a new environment. This was however not reflected at the genomic level implying complex relationships between environmental factors and the genotype-to-phenotype map., BMC Evolutionary Biology, 16, ISSN:1471-2148
Published: 2016
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45. Adhesion, biofilm formation, and genomic features of Campylobacter jejuni Bf, an atypical strain able to grow under aerobic conditions

Author: Vicky Bronnec, Agnès Bouju, Stéphane Cruveiller, Ramila Rodrigues, Monique Zagorec, Katerina Demnerova, Odile Tresse, Hana Turoňová, Nabila Haddad, UMR 1014 SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-SECurité des ALIments et Microbiologie (SECALIM), Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Institute of Chemical Technology, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Consortium National de Recherche en Génomique (CNRG), UMR 1014 SECALIM, Ecole Nationale Vétérinaire Agroalimentaire et de l'Alimentation Nantes Atlantique (ONIRIS), Institut National de la Recherche Agronomique (INRA), SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-École nationale d'ingénieurs des techniques des industries agricoles et alimentaires (ENITIAA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), and Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)
Subjects: 0301 basic medicine, Microbiology (medical), genome sequence, [SDV]Life Sciences [q-bio], 030106 microbiology, Campylobacteriosis, medicine.disease_cause, confocal microscopy, Microbiology, Campylobacter jejuni, Genome, biofilm, 03 medical and health sciences, medicine, oxidative stress, Gene, Pathogen, Original Research, 2. Zero hunger, Mutation, food borne pathogen, biology, Strain (chemistry), Biofilm, biology.organism_classification, medicine.disease, 13. Climate action
Abstract: Campylobacter jejuni is the leading cause of bacterial enteritis in Europe. Human campylobacteriosis cases are frequently associated to the consumption of contaminated poultry meat. To survive under environmental conditions encountered along the food chain, i.e., from poultry digestive tract its natural reservoir to the consumer’s plate, this pathogen has developed adaptation mechanisms. Among those, biofilm lifestyle has been suggested as a strategy to survive in the food environment and under atmospheric conditions. Recently, the clinical isolate C. jejuni Bf has been shown to survive and grow under aerobic conditions, a property that may help this strain to better survive along the food chain. The aim of this study was to evaluate the adhesion capacity of C. jejuni Bf and its ability to develop a biofilm. C. jejuni Bf can adhere to abiotic surfaces and to human epithelial cells, and can develop biofilm under both microaerobiosis and aerobiosis. These two conditions have no influence on this strain, unlike results obtained with the reference strain C. jejuni 81-176, which harbors only planktonic cells under aerobic conditions. Compared to 81-176, the biofilm of C. jejuni Bf is more homogenous and cell motility at the bottom of biofilm was not modified whatever the atmosphere used. C. jejuni Bf whole genome sequence did not reveal any gene unique to this strain, suggesting that its unusual property does not result from acquisition of new genetic material. Nevertheless some genetic particularities seem to be shared only between Bf and few others strains. Among the main features of C. jejuni Bf genome we noticed (i) a complete type VI secretion system important in pathogenicity and environmental adaptation; (ii) a mutation in the oorD gene involved in oxygen metabolism; and (iii) the presence of an uncommon insertion of a 72 amino acid coding sequence upstream from dnaK, which is involved in stress resistance. Therefore, the atypical behavior of this strain under aerobic atmosphere may result from the combination of insertions and mutations. In addition, the comparison of mRNA transcript levels of several genes targeted through genome analysis suggests the modification of regulatory processes in this strain.
Published: 2016
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46. In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum

Author: Tiffany M. Lowe, Stéphane Cruveiller, Isabelle Robène, Caitilyn Allen, Philippe Prior, Florent Ailloud, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Laboratoire de santé des végétaux (LSV Angers), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Department of Plant Pathology, University of Wisconsin-Madison, Commissariat Energie Atom & Energie Alternat, Lab Anal Bioinformat Genom & Metab, Evry, France, Partenaires INRAE, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UAR 0865 Paris Réunion, Institut National de la Recherche Agronomique (INRA)-Direction des Ressources Humaines (DRH)-Paris Réunion (PARIS REUNION), European Union (ERDF), Conseil Regional de La Reunion, French Agence Nationale de la Recherche, CIRAD, ANSES [11-237/BSL], NIH National Research Service Award [T32 GM07215], Agriculture and Food Research Initiative Competitive Grant from the USDA National Institute of Food and Agriculture [2015-67011-22799], Prior, Philippe, Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and CNRS, CNRS, UMR 8030, Genom Metab, Evry, France
Subjects: 0301 basic medicine, Identification, Phylogénie, [SDV]Life Sciences [q-bio], Denitrification pathway, lcsh:Medicine, Medical and Health Sciences, Expression des gènes, 2.2 Factors relating to the physical environment, Aetiology, Pathotype, 2. Zero hunger, Ralstonia solanacearum, Virulence, Strain (chemistry), General Neuroscience, food and beverages, General Medicine, Genomics, Biological Sciences, Transcriptomics, Host adaptation, General Agricultural and Biological Sciences, Infection, Plante hôte, Pouvoir pathogène, 030106 microbiology, Biology, Séquence d'ARN, Microbiology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Métabolisme, Genetics, Adaptation, Gene, H20 - Maladies des plantes, Génie génétique, Comparative genomics, Transcription génique, Host (biology), transcriptomique, lcsh:R, Musa, biology.organism_classification, Gène, U30 - Méthodes de recherche
Abstract: Background.Ralstonia solanacearumis an economically important plant pathogen with an unusually large host range. The Moko (banana) and NPB (not pathogenic to banana) strain groups are closely related but are adapted to distinct hosts. Previous comparative genomics studies uncovered very few differences that could account for the host range difference between these pathotypes. To better understand the basis of this host specificity, we used RNAseq to profile the transcriptomes of anR. solanacearumMoko strain and an NPB strain underin vitroandin plantaconditions.Results.RNAs were sequenced from bacteria grown in rich and minimal media, and from bacteria extracted from mid-stage infected tomato, banana and melon plants. We computed differential expression between each pair of conditions to identify constitutive and host-specific gene expression differences between Moko and NPB. We found that type III secreted effectors were globally up-regulated upon plant cell contact in the NPB strain compared with the Moko strain. Genes encoding siderophore biosynthesis and nitrogen assimilation genes were highly up-regulated in the NPB strain during melon pathogenesis, while denitrification genes were up-regulated in the Moko strain during banana pathogenesis. The relatively lower expression of oxidases and the denitrification pathway during banana pathogenesis suggests thatR. solanacearumexperiences higher oxygen levels in banana pseudostems than in tomato or melon xylem.Conclusions.This study provides the first report of differential gene expression associated with host range variation. Despite minimal genomic divergence, the pathogenesis of Moko and NPB strains is characterized by striking differences in expression of virulence- and metabolism-related genes.
Published: 2016
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47. Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

Author: Valérie Barbe, Jonathan L. Gordon, Aline Escalon, Olivier Pruvost, Pierre Lefeuvre, Stéphane Cruveiller, and Lionel Gagnevin
Subjects: Phylogénie, Évolution, Xanthomonas campestris citri, Gene islands, Genome, Xanthomonas citri, Plant pathogen, Pathotype, Phylogeny, Recombination, Genetic, 2. Zero hunger, Genetics, 0303 health sciences, Gene presence/absence, Genome, Plant, Research Article, Biotechnology, Plante hôte, Genome evolution, Xanthomonas, Pouvoir pathogène, Biology, Polymorphism, Single Nucleotide, Host Specificity, Evolution, Molecular, 03 medical and health sciences, stomatognathic system, Phylogenetics, Pathotype evolution, Pathogenicity, Adaptation, H20 - Maladies des plantes, 030304 developmental biology, Génie génétique, Comparative genomics, Génome, Bacterial disease, 030306 microbiology, Host (biology), Sequence Analysis, DNA, Host range determination, biology.organism_classification, Recombination, Recombinaison, Gène, Carte génétique, Metagenomics, Ancestral character estimation
Abstract: Background The identification of factors involved in the host range definition and evolution is a pivotal challenge in the goal to predict and prevent the emergence of plant bacterial disease. To trace the evolution and find molecular differences between three pathotypes of Xanthomonas citri pv. citri that may explain their distinctive host ranges, 42 strains of X. citri pv. citri and one outgroup strain, Xanthomonas citri pv. bilvae were sequenced and compared. Results The strains from each pathotype form monophyletic clades, with a short branch shared by the Aw and A pathotypes. Pathotype-specific recombination was detected in seven regions of the alignment. Using Ancestral Character Estimation, 426 SNPs were mapped to the four branches at the base of the A, A*, Aw and A/Aw clades. Several genes containing pathotype-specific nonsynonymous mutations have functions related to pathogenicity. The A pathotype is enriched for SNP-containing genes involved in defense mechanisms, while A* is significantly depleted for genes that are involved in transcription. The pathotypes differ by four gene islands that largely coincide with regions of recombination and include genes with a role in virulence. Both A* and Aw are missing genes involved in defense mechanisms. In contrast to a recent study, we find that there are an extremely small number of pathotype-specific gene presences and absences. Conclusions The three pathotypes of X. citri pv. citri that differ in their host ranges largely show genomic differences related to recombination, horizontal gene transfer and single nucleotide polymorphism. We detail the phylogenetic relationship of the pathotypes and provide a set of candidate genes involved in pathotype-specific evolutionary events that could explain to the differences in host range and pathogenicity between them. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2310-x) contains supplementary material, which is available to authorized users.
Published: 2015
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48. Chemical Evolution of a Bacterium’s Genome

Author: Philippe Marlière, Julien Patrouix, Volker Döring, Piet Herdewijn, Sabine Tricot, Stéphane Cruveiller, Madeleine Bouzon, and Rupert Mutzel
Subjects: General Medicine
Published: 2011
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49. Chemical Evolution of a Bacterium’s Genome

Author: Piet Herdewijn, Philippe Marlière, Julien Patrouix, Rupert Mutzel, Madeleine Bouzon, Sabine Tricot, Stéphane Cruveiller, and Volker Döring
Subjects: DNA, Bacterial, chemistry.chemical_classification, Growth medium, education.field_of_study, Evolution, Chemical, Bacteria, Population, Uracil, General Chemistry, Molecular biology, Catalysis, Thymine, Evolution, Molecular, chemistry.chemical_compound, chemistry, Biochemistry, Escherichia coli, Nucleic acid, Nucleoside triphosphate, Nucleotide, education, Genome, Bacterial, DNA
Abstract: We set out to develop a generic technology for evolving the chemical constitution of microbial populations by using the simplest possible algorithm. Extant living cells polymerize a restricted set of nucleic acid precursors, namely, four nucleoside triphosphates (UTP, CTP, ATP, GTP) and four deoxynucleoside triphosphates (dTTP, dCTP, dATP, dGTP). Synthetic analogues, such as 5-halogenopyrimidines, 7-deazapurines, and 8-azapurines, are known to partially replace canonical bases in cellular RNA and DNA, yet were never demonstrated to sustain unlimited self-reproduction of an organism through complete genome or transcriptome substitution. A hamster cell line serially adapted to grow in the presence of bromodeoxyuridine, while dTMP synthesis was inhibited with aminopterin, has been reported to harbor DNA highly enriched in bromouracil over thymine. However, the significance of these findings could not be ascertained owing to the absence of a direct physical measurement of the base composition of the DNA and the absence of an assay of thymidylate biosynthesis, as well as the likely presence of metabolic components, such as nucleotides in the complex growth medium of the cells. Only certain DNA viruses are known to have undergone full transliteration of a canonical base through the biosynthesis of a noncanonical nucleoside triphosphate, for example, hydroxymethylcytosine in the T4 bacteriophage, presumably to counteract the restriction enzymes of their bacterial hosts. When Weiss and coworkers attempted to substitute thymine in the DNA of Escherichia coli with uracil, over 90% replacement was reached, but further growth was prevented. Genome-scale transliteration has apparently not evolved in any known living cell, possibly owing to a chemical barrier that natural biodiversity cannot overcome. Our experimental plan consisted of the combination of tight metabolic selection with the long-term automated cultivation of fast-growing asexual bacterial populations to change a canonical DNA base for a chemical ersatz. The cultivation setup was elaborated from the GM3 fluidic format (Figure 1), which features the cyclic transfer of the culture between twin growth chambers that alternately undergo sterilization. This cycle ensures that no internal surface of the device is spared from transient periodic cleansing with a sterilizing agent (5m sodium hydroxide), and therefore that no cultivated variant can escape dilution and selection for faster growth through the formation of biofilms. The active elimination of biofilms (wall growth) has proved critical for reprogramming and improving the metabolism of microbial populations. The GM3 cultivation device was connected to two nutrient reservoirs of different composition: a relaxing medium R that contains the canonical nutrient and a stressing medium S that contains the ersatz nutrient. Liquid pulses of defined volume are sent at regular intervals of time from these reservoirs to the culture, which is kept at a constant volume. Depending upon the state of the adapting cells, as measured by turbidity recording of the population density, the culture periodically receives a pulse of fixed volume of either medium R (if the population density falls below a fixed threshold) or medium S (if the density is higher than or equal to the threshold). Successive pulses thus renew the culture at a fixed dilution rate with a nutrient-medium flow whose composition varies with respect to the growth response of the population in such a way that the lowest tolerable concentration of canonical nutrient is automatically maintained over passing generations. We designate this mode of operation as the conditional pulse-feed regime. It qualifies as a simplified and generalized version of a method pioneered by Oliver. Mutations that confer a lower requirement for the canonical nutrient or a higher survival rate under starvation are expected to accumulate in the genome of the adapting population. No attempt was made to implement a finer regulation of differential nutrient supply than the coarse-grained control by medium-switch pulse feed described above. We thus relied on the robustness of biochemical machineries and their evolution to dampen oscillations. [*] Dr. P. Marli re Heurisko USA Inc., Delaware (USA)
Published: 2011
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50. The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

Author: Eugeni, Belda, Ruben G A, van Heck, Maria, José Lopez-Sanchez, Stéphane, Cruveiller, Valérie, Barbe, Claire, Fraser, Hans-Peter, Klenk, Jörn, Petersen, Anne, Morgat, Pablo I, Nikel, David, Vallenet, Zoé, Rouy, Agnieszka, Sekowska, Vitor A P, Martins Dos Santos, Víctor, de Lorenzo, Antoine, Danchin, and Claudine, Médigue
Subjects: Bacterial Proteins, Nitrogen, Pseudomonas putida, Genomics, Carbon, Genome, Bacterial
Abstract: By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data-let alone metabolic modeling and other nowadays common systems biology approaches-allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state-of-the-art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein-coding genes and re-annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology.
Published: 2015

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