Shifts in the temperature-sensitive periods for spring phenology in European beech and pedunculate oak clones across latitudes and over recent decades.

2 months 2 weeks ago
Wenden, B. ; Mariadassou, M. ; Chmielewski, F.-M. ; Vitasse, Y.
Global Change Biology, 2019
Spring phenology of temperate trees has advanced worldwide in response to global warming. However, increasing temperatures may not necessarily lead to further phenological advance, especially in the warmer latitudes because of insufficient chilling and/or shorter daylength. Determining the start of the forcing phase, i.e. when buds are able to respond to warmer temperatures in spring, is therefore crucial to predict how phenology will change in the future. In this study, we used 4,056 leaf-out date observations during the period 1969-2017 for clones of European beech (Fagus sylvatica L.) and pedunculate oak (Quercus robur L.) planted in 63 sites covering a large latitudinal gradient (from Portugal ~ 41°N to Norway ~ 63°N) at the International Phenological Gardens in order to (i) evaluate how the sensitivity periods to forcing and chilling have changed with climate warming, and (ii) test whether consistent patterns occur along biogeographical gradients, i.e. from colder to warmer environments. Partial Least Squares regressions suggest that the length of the forcing period has been extended over the recent decades with climate warming in the colder latitudes but has been shortened in the warmer latitudes for both species, with a more pronounced shift for beech. We attribute the lengthening of the forcing period in the colder latitudes to earlier opportunities with temperatures that can promote bud development. In contrast, at warmer or oceanic climates, the beginning of the forcing period has been delayed, possibly due to insufficient chilling. However, in spite of a later beginning of the forcing period, spring phenology has continued to advance at these areas due to a faster satisfaction of heat requirements induced by climate warming. Overall, our results support that ongoing climate warming will have different effects on the spring phenology of forest trees across latitudes due to the interactions between chilling and forcing requirements and photoperiod.

Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

2 months 3 weeks ago
Vila Nova, M. ; Durimel, K. ; La, K. ; Felten, A. ; Bessieres, P. ; Mistou, M.-Y. ; Mariadassou, M. ; Radomski, N.
BMC Genomics, 2019, 20 (1)
Pièces jointes : 2019_VilaNova_BMC GENOMICS.pdf
Background: Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv) . Results: Based on a genome dataset including Salmonella serovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively. Conclusions: Our results suggest that the genetic and metabolic determinants of Salmonella adaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.

Effect of sodium chloride reduction or partial substitution with potassium chloride on the microbiological, biochemical and sensory characteristics of semi-hard and soft cheeses

3 months 2 weeks ago
DUGAT-BONY, E. ; Bonnarme, P. ; Fraud, S. ; Catellote, J. ; Sarthou, A.-S. ; LOUX, V. ; Rué, O. ; Bel ; Chuzeville ; Hélinck, S.
Food Research International, 2019, 125 : 108643.
Sodium reduction in the human diet is currently one of the main concerns for public health agencies and, consequently, has become a challenge for the food industries. In this study, the impact of reduced sodium chloride content (20%) or its partial substitution with potassium chloride in soft (“Camembert”-type) and semi-hard (“Reblochon”-type) cheeses was evaluated. Analyses included physicochemical and biochemical composition, microbial counts, 16S rRNA gene metabarcoding and metatranscriptomic analysis, volatile aroma compounds and sensory analysis. Regarding soft cheeses, the salt content of cheeses affected proteolysis at 21 days of ripening. RNA sequencing revealed that the relative activity of G. candidum increased, whereas that of P. camemberti decreased in reduced salt cheeses in comparison to the controls. Higher global intensity of odor and taste was observed in cheeses with reduced salt content, consistent with higher levels of alcohol and ester components. Regarding semi-hard cheeses, modifications of salt content did not significantly affect either their biochemical parameters and sensory characteristics or their technological microbial composition at day 21 of ripening. Finally, no impact of salt content was observed on the growth of the spoiler Yarrowia lipolytica in soft cheeses. In contrast, reducing salt content increased spoiler growth in semi-hard cheeses, as highlighted by a greater development of Pseudomonas that led to an increase in cheese proteolysis and lipolysis. In conclusion, the effect of reducing salt content is highly dependent on the cheese type. This factor should thus be taken into account by the dairy industry when the reduction of salt content is being considered. Moreover, the quality of raw products, in particular, the level of spoiler microorganisms, must be controlled before use during dairy processes.

Guide pratique à destination des biologistes, bioinformaticiens et statisticiens qui souhaitent s’initier aux analyses métabarcoding

4 months 2 weeks ago
Falentin, H. ; Auer, L. ; Mariadassou, M. ; Pascal, G. ; Rué, O. ; Dugat-Bony, E. ; Delbes, C. ; Nicolas, A. ; RIFA, E. ; Mondy, S. ; Le Boulch, M. ; Cauquil, L. ; Hernandez Raquet, G. ; Terrat, S. ; Abraham, A.-L.
Cahier des Techniques de l'INRA, 2019, 2019 (97) : 1-23.
Pièces jointes : article
Les méthodes d’analyse métabarcoding (également appelées métagénomique ciblée ou amplicon) sont de plus en plus utilisées pour étudier la diversité des espèces présentes dans un écosystème (micro organismes, plantes, animaux). Le principe consiste à extraire l’ADN d’un échantillon environnemental puis à amplifier par PCR un fragment cible à l’aide d’un couple d’amorces prédéfini. Ces produits PCR, après ajouts de barcodes (oligonucléotides uniques pour chaque échantillon) et adaptateurs de séquençage, sont ensuite séquencés. Après le séquençage, les séquences sont triées par échantillon grâce aux barcodes puis assignées à des taxons par comparaison avec des séquences de référence. Beaucoup de méthodes et outils d’analyse ont été développés pour obtenir une vision la plus précise possible des écosystèmes étudiés. Les techniques de préparation puis d’analyse des échantillons dépendent de l’écosystème, des questions auxquelles on souhaite répondre et de la technologie de séquençage utilisée. Nous proposons des conseils issus de nos expériences, discussions et lectures bibliographiques afin de guider les lecteurs depuis la planification expérimentale jusqu’à l’analyse des données, en détaillant les points de vigilance à chaque étape.

Bioinformatics tools and workflow to select blood biomarkers for early cancer diagnosis: an application to pancreatic cancer

5 months ago
Vandenbrouck, Y. ; Christiany, D. ; Combes, F. ; Loux, V. ; Brun, V.
Proteomics, 2019, 19 (21-22)
Secretome proteomics for the discovery of cancer biomarkers holds great potential to improve early cancer diagnosis. In this context, a knowledge‐based approach relying on mechanistic criteria related to the type of cancer should help to identify candidates from available “omics” information. Numerous bioinformatics tools, databases and “omics” datasets are available, but are often widely disseminated. In addition biomedical researchers with little programming experience or no in‐house bioinformatics support can find these tools difficult to access and use. With the aim of accelerating the discovery process for novel biomarkers, we have developed a set of tools we made available via a Galaxy‐based instance thereby providing a centralized access to a unified framework to assist end‐users biologists. These tools we implemented proceed by a step‐by‐step strategy to mine transcriptomics and proteomics databases for information relating to tissue‐specificity, allow the selection of proteins that are part of the secretome, and combine this information with proteomics datasets to rank the most promising candidate biomarkers for early cancer diagnosis. Using pancreatic cancer as a case study, this strategy produced a list of 24 candidate biomarkers suitable for experimental assessment by MS‐based proteomics. Among these proteins, three (SYCN, REG1B and PRSS2) were previously reported as circulating candidate biomarkers of pancreatic cancer. Further refinement of this list allowed us to prioritize 14 candidate biomarkers along with their associated proteotypic peptides for further investigation, using targeted MS‐based proteomics. The bioinformatics tools and the workflow implementing this strategy for the selection of candidate biomarkers are freely accessible at for researchers who wish to reuse them in their own quests for biomarker discovery.

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis

6 months 1 week ago
Lejal, E. ; Estrada-Peña, A. ; Marsot, M. ; Cosson, J.-F. ; Rué, O. ; Mariadassou, M. ; Midoux, C. ; Vayssier-Taussat, M. ; Pollet, T.
BioRxiv, 2019 : 1-22.
The developmentof high throughput sequencing (HTS) technologies has substantially improvedanalysis of bacterial community diversity, composition,and functions. Over the last decade, HTS has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g. individual tick samples, these contaminants may represent a large part of the obtained sequences,and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess theproportion of contaminantsequences resulting from thesesteps. We analyzed the microbiota of individual Ixodesricinusticksbyincluding several categories of controls throughout the analytical process:crushing, DNA extraction,and DNA amplification Results Controls yielded a significant number of sequences (1,126 to 13,198 mean sequences,depending onthe control category). Some operational taxonomic units (OTUs)detected in these controls belong to genera reported in previous tick microbiota studies. Inthis study, these OTUs accounted for 50.9% of the total number of sequences inour samples, and wereconsidered contaminants. Contamination levels (i.e. the percentage of sequences belonging to OTUs identified as contaminants) variedwith tick stage and gender: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rateslower than 20%. Contamination mainly correspondedto OTUs detected in crushing and DNA extraction controls, highlighting the importance of carefully controlling these steps. -Conclusion Here,we showed that contaminant OTUs from extraction and amplification stepscan represent more than half the total sequence yield in sequencing runs,and lead to unreliable results when characterizing tick microbial communities.We thus strongly advise the routine use of blanks and negative controls in tick microbiota studies, and more generally in studies involving low biomass

Gut bacteria are critical for optimal muscle function: a potential link with glucose homeostasis

7 months ago
Nay, K. ; Jollet, M. ; Goustard, B. ; Baati, N. ; Vernus, B. ; Pontones , M. ; Lefeuvre-Orfila, L. ; Bendavid, C. ; Rué, O. ; Mariadassou, M. ; Bonnieu, A. ; Ollendorff, V. ; Lepage, P. ; Derbré , F. ; Ramonatxo, C.
American Journal of Physiology. Endocrinology and Metabolism, 2019, 317 (1) : E158-E171.
Gut microbiota is involved in the development of several chronic diseases, including diabetes, obesity and cancer, through its interactions with the host organs. It has been suggested that the cross-talk between gut microbiota and skeletal muscle plays a role in different pathological conditions, such as intestinal chronic inflammation and cachexia. However, it remains unclear whether gut microbiota directly influences skeletal muscle function. In this work, we studied the impact of gut microbiota modulation on mice skeletal muscle function and investigated the underlying mechanisms. We determined the consequences of gut microbiota depletion after treatment with a mixture of broad spectrum antibiotics for 21 days and after 10-days natural reseeding. We found that in gut microbiota-depleted mice, running endurance was decreased, as well as the extensor digitorum longus muscle fatigue index in an ex vivocontractile test. Importantly, the muscle endurance capacity was efficiently normalized by natural reseeding. Theseendurance changes werenot relatedto variationin muscle mass, fiber typology or mitochondrial function. However, several pertinent glucose metabolism markers such as ileum gene expression of short fatty acidchain and glucose transporters,Gpr41and Sglt1and muscle glycogen level, paralleled the muscle endurance changes observed after ATB treatment and reseeding. As glycogen is a key energetic substrate for prolonged exercise, modulating itsmuscle availability via gut microbiota represents one potent mechanism that can contribute to the gut microbiota/skeletal muscle axis. Taken together, our results strongly support the hypothesis that gut bacteria are required for host optimal skeletal muscle function.

Identification of hanks-type kinase PknB-specific targets in the Streptococcus thermophilus phosphoproteome

7 months 2 weeks ago
Henry, C. ; Haller, L. ; Blein-Nicolas, M. ; Zivy, M. ; Canette, A. ; Verbrugghe, M. ; Mézange, C. ; Boulay, M. ; Gardan, R. ; Samson, S. ; Martin, V. ; André Leroux, G. ; Monnet, V.
Frontiers in Microbiology, 2019, 10 : 1329.
Pièces jointes : 2019_Henry_Front Microbiol.pdf
Protein phosphorylation especially on serine/threonine/tyrosine residues are frequent in many bacteria. This post-translational modification has been associated with pathogenicity and virulence in various species. However, only few data have been produced so far on generally recognized as safe bacteria used in food fermentations. A family of kinases known as Hanks-type kinases is suspected to be responsible for, at least, a part of these phosphorylations in eukaryotes as in bacteria. The objective of our work was to establish the first phosphoproteome of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy fermentations in order to identified the proteins and pathways tagged by Ser/Thr/Tyr phosphorylations. In addition, we have evaluated the role in this process of the only Hanks-type kinase encoded in the S. thermophilus genome. We have constructed a mutant defective for the Hanks type kinase in S. thermophilus and established the proteomes and phosphoproteomes of the wild type and the mutant strains. To do that, we have enriched our samples in phosphopeptides with titane beads and used dimethyl tags to compare phosphopeptide abundances. Peptides and phosphopeptides were analyzed on a last generation LC-MS/MS system. We have identified and quantified 891 proteins representing half of the theoretical proteome. Among these proteins, 106 contained phosphorylated peptides. Various functional groups of proteins (amino acid, carbon and nucleotide metabolism, translation, cell cycle, stress response, …) were found phosphorylated. The phosphoproteome was only weakly reduced in the Hanks-type kinase mutant indicating that this enzyme is only one of the players in the phosphorylation process. The proteins that are modified by the Hanks-type kinase mainly belong to the divisome.

Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism

8 months 1 week ago
Zhang, X. ; Grosfeld, A. ; Williams ; Vasiliauskas, D. ; Barretto, S. ; Smith, L. ; Mariadassou, M. ; Philippe, C. ; Devime, F. ; Melchior, C. ; Gourcerol, G. ; Dourmap, N. ; Lapaque, N. ; Larraufie, P. ; Blottière, H. ; Herberden, C. ; Gerard, P. ; Rehfeld, J. F. ; Ferraris, R. P. ; Fritton, J. C. ; Ellero-Simatos, S. ; Douard, V.
FASEB Journal, 2019
Current fructose consumption levels often overwhelm the intestinal capacity to absorb fructose. We investigated the impact of fructose malabsorption on intestinal endocrine function and addressed the role of the microbiota in this process. To answer this question, a mouse model of moderate fructose malabsorption [ketohexokinase mutant (KHK)-/-] and wild-type (WT) littermate mice were used and received a 20%-fructose (KHK-F and WT-F) or 20%-glucose diet. Cholecystokinin (Cck) mRNA and protein expression in the ileum and cecum, as well as preproglucagon (Gcg) and neurotensin (Nts) mRNA expression in the cecum, increased in KHK-F mice. In KHK-F mice, triple-label immunohistochemistry showed major up-regulation of CCK in enteroendocrine cells (EECs) that were glucagon-like peptide-1 (GLP-1)+/Peptide YY (PYY-) in the ileum and colon and GLP-1-/PYY- in the cecum. The cecal microbiota composition was drastically modified in the KHK-F in association with an increase in glucose, propionate, succinate, and lactate concentrations. Antibiotic treatment abolished fructose malabsorption-dependent induction of cecal Cck mRNA expression and, in mouse GLUTag and human NCI-H716 cells, Cck mRNA expression levels increased in response to propionate, both suggesting a microbiota-dependent process. Fructose reaching the lower intestine can modify the composition and metabolism of the microbiota, thereby stimulating the production of CCK from the EECs possibly in response to propionate.-Zhang, X., Grosfeld, A., Williams, E., Vasiliauskas, D., Barretto, S., Smith, L., Mariadassou, M., Philippe, C., Devime, F., Melchior, C., Gourcerol, G., Dourmap, N., Lapaque, N., Larraufie, P., Blottière, H. M., Herberden, C., Gerard, P., Rehfeld, J. F., Ferraris, R. P., Fritton, J. C., Ellero-Simatos, S., Douard, V. Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism.

Complete genome sequence of the industrial fast-acidifying strain Streptococcus thermophilus N4L

10 months 4 weeks ago
Proust, L. ; Loux, V. ; Martin, V. ; Magnabosco, C. ; Pedersen, M. ; Monnet, V. ; Juillard, V.
Microbiology Resource Announcements, 2018, 7 (8)
Pièces jointes : 2018_Proust_Microbiology Resource Announcements.pdf
Streptococcus thermophilus is one of the most used dairy starters for the production of yogurt and cheese. We report here the complete genome sequence of the industrial strain S. thermophilus N4L, which is used in dairy technology for its fast-acidifying phenotype.

Variational inference for probabilistic Poisson PCA

1 year 2 months ago
Chiquet, J. ; Mariadassou, M. ; Robin, S.
Annals of Applied Statistics, 2018, 12 (4) : 2674-2698.
Many application domains such as ecology or genomics have to deal with multivariate non Gaussian observations. A typical example is the joint observation of the respective abundances of a set of species in a series of sites, aiming to understand the co-variations between these species. The Gaussian setting provides a canonical way to model such dependencies, but does not apply in general. We consider here the multivariate exponential family framework for which we introduce a generic model with multivariate Gaussian latent variables. We show that approximate maximum likelihood inference can be achieved via a variational algorithm for which gradient descent easily applies. We show that this setting enables us to account for covariates and offsets. We then focus on the case of the Poisson-lognormal model in the context of community ecology. We demonstrate the efficiency of our algorithm on microbial ecology datasets. We illustrate the importance of accounting for the effects of covariates to better understand interactions between species.

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

1 year 4 months ago
Poirier, S. ; Rué, O. ; Peguilhan, R. ; Coeuret, G. ; Zagorec, M. ; Champomier-Verges, M.-C. ; Loux, V. ; Chaillou, S.
Plos One, 2018, 13 (9)
Pièces jointes : Poirier_Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing A comparative analysis with 16S rDNA V3-V4 amplicon sequencing.pdf
Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.

Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater

1 year 4 months ago
Delforno, T. P. ; Macedo, T. Z. ; Midoux, C. ; Lacerda ; Rué, O. ; Mariadassou, M. ; Loux, V. ; Varesche ; Bouchez ; Bize ; Oliveira
Science of the Total Environment, 2019, 2019 (649) : 482-494.
Three distinct biological reactors fed with synthetic medium (UASB_Control), synthetic medium and linear alkylbenzene sulfonate (LAS; UASB_SL), and real laundry wastewater (UASB_LW) were compared using a metatranscriptomic approach to determine putative bioindicator genes and taxonomies associated to all steps of anaerobic LAS biodegradation pathway. A homemade bioinformatics pipeline combined with an R workflow was developed to perform the RNAseq data analysis. UASB_SL and UASB_LWshowed similar values of LAS biological degradation (~47%) and removal (53–55%). Rarefaction analysis revealed that 1–2million readswere sufficient to access the whole functional capacity. In the first step of LAS biodegradation pathway, fumarate reductase subunit C was detected and taxonomically assigned to the genus Syntrophobacter (0.002% - UASB_SL; 0.0015% - UASB_LW; not detected - UASB_Control). In the second step, many enzymes related to beta-oxidation were observed and most of them with low relative abundance in UASB Control and taxonomically related with Smithella, Acinetobacter and Syntrophorhabdus. For the ring cleavage step, the abundance of 6 OCH CoA hydrolase putative genewas ten times higher in UASB_SL and UASB_LWwhen compared to UASB_Control, and assigned to Desulfomonile and Syntrophorhabdus. Finally, the adenylylsulfate reductase, taxonomically related with Desulfovibrio and Desulfomonile, was observed in the desulfonation step with the highest relative abundance in UASB_LW.

Oak genome reveals facets of long lifespan

1 year 8 months ago
Plomion, C. ; Aury, J.-M. ; Amselem, J. ; Leroy, T. ; Murat, F. ; Duplessis, S. ; Faye, S. ; Francillonne, N. ; Labadie ; Le Provost, G. ; Lesur Kupin, I. ; Bartholome, J. ; Faivre-Rampant, P. ; Kohler, A. ; Leplé, J.-C. ; Chantret, N. ; Chen, J. ; Dievart, A. ; Alaeitabar, T. ; Barbe ; Belser ; Berges, H. ; Bodenes, C. ; Bogeat-Triboulot, M.-B. ; Bouffaud, M.-L. ; Brachi, B. ; Chancerel, E. ; Cohen, D. ; Couloux ; Da Silva ; Dossat ; Ehrenmann, F. ; Gaspin, C. ; Grima-Pettenati, J. ; Guichoux, E. ; Hecker, A. ; Herrmann, S. ; Hugueney, P. ; Hummel, I. ; Klopp, C. ; Lalanne, C. ; Lascoux, M. ; Lasserre, E. ; Lemainque ; Desprez-Loustau, M. L. ; Luyten, I. ; Madoui ; Mangenot ; Marchal, C. ; Maumus, F. ; Mercier ; Michotey, C. ; Panaud ; Picault ; Rouhier, N. ; Rué, O. ; Rustenholz, C. ; Salin, F. ; Soler, M. ; Tarkka, M. ; Velt, A. ; Zanne, A. E. ; Martin, F. ; Wincker, P. ; Quesneville, H. ; Kremer, A. ; Salse, J.
Nature Plants, 2018, 4 (7) : 440-452.
Pièces jointes : Publis18-agap-014_plomion_oak.pdf
Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes

1 year 8 months ago
Loux, V. ; Coeuret, G. ; Zagorec, M. ; Champomier-Verges, M.-C. ; Chaillou, S.
Genome Announcements, 2018, 6 (16) : 3 p.
Pièces jointes : Genome Announc.-2018-Loux-.pdf
We present here the complete and draft genome sequences of nine Lactobacillus sakei strains, selected from the entire range of clonal complexes from the three known lineages of the species. The strains were chosen to provide a wide view of pangenomic and plasmidic diversity for this important foodborne species.

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes

1 year 9 months ago
Cornuault, J. ; Petit, M. A. ; Mariadassou, M. ; De Jesus Benevides, L. ; Moncaut, E. ; Langella, P. ; Sokol, H. ; De Paepe, M.
Microbiome, 2018, 6 (1) : 14 p.
Pièces jointes : 2018_Cornuault_Microbiome.pdf
Background: Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases. Methods: We identified 18 prophages in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage clades, and annotated the genome of the type phage of each clade. For two of the phages, we studied prophage induction in vitro and in vivo in mice. Finally, we aligned reads from already published viral metagenomic data onto the newly identified phages. Results: We show that each phage clade represents a novel viral genus and that a surprisingly large fraction of them (10 of the 18 phages) codes for a diversity-generating retroelement, which could contribute to their adaptation to the digestive tract environment. We obtained either experimental or in silico evidence of activity for at least one member of each genus. In addition, four of these phages are either significantly more prevalent or more abundant in stools of IBD patients than in those of healthy controls. Conclusion: Since IBD patients generally have less F. prausnitzii in their microbiota than healthy controls, the higher prevalence or abundance of some of its phages may indicate that they are activated during disease. This in turn suggests that phages could trigger or aggravate F. prausnitzii depletion in patients. Our results show that prophage detection in sequenced strains of the microbiota can usefully complement viral metagenomic studies.

Genomic diversity and evolution of the fish pathogen flavobacterium psychrophilum

1 year 10 months ago
Duchaud, E. ; Rochat, T. ; Habib, C. ; Barbier, P. ; Loux, V. ; Guerin, C. ; Dalsgaard, I. ; Madsen, L. ; Nilsen, H. ; Sundell, K. ; Wiklund, T. ; Strepparava, N. ; Wahli, T. ; Caburlotto, G. ; Manfrin, A. ; Wiens, G. D. ; Fujiwara-Nagata, E. ; Avendano-Herrera, R. ; Bernardet, J. F. ; Nicolas, P.
Frontiers in Microbiology, 2018, 9 : 1-20.
Pièces jointes : Frontiers in Microbiology.pdf
Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout (Oncorhynchus mykiss) worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with similar to 0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for similar to 80% of the genes in each genome. The pan-genome seems nevertheless "open" according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to similar to 4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to similar to 13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of tools for the genetic manipulation of F. psychrophilum, a particular attention was also paid to plasmids. Their extraction and sequencing to completion revealed plasmid diversity that remained hidden to classical plasmid profiling due to size similarities.

Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue

1 year 11 months ago
El Kafsi, H. ; Loux, V. ; Mariadassou, M. ; Blin, C. ; Chiapello, H. ; Abraham, A.-L. ; Maguin, E. ; Van De Guchte, M.
Scientific Reports, 2017, 7
Pièces jointes : srep44331.pdf
The first Lactobacillus delbrueckii ssp. bulgaricus genome sequence revealed the presence of a very large inverted repeat (IR), a DNA sequence arrangement which thus far seemed inconceivable in a non-manipulated circular bacterial chromosome, at the replication terminus. This intriguing observation prompted us to investigate if similar IRs could be found in other bacteria. IRs with sizes varying from 38 to 76 kbp were found at the replication terminus of all 5 L. delbrueckii ssp. bulgaricus chromosomes analysed, but in none of 1373 other chromosomes. They represent the first naturally occurring very large IRs detected in circular bacterial genomes. A comparison of the L. bulgaricus replication terminus regions and the corresponding regions without IR in 5 L. delbrueckii ssp. lactis genomes leads us to propose a model for the formation and evolution of the IRs. The DNA sequence data are consistent with a novel model of chromosome rescue after premature replication termination or irreversible chromosome damage near the replication terminus, involving mechanisms analogous to those proposed in the formation of very large IRs in human cancer cells. We postulate that the L. delbrueckii ssp. bulgaricus-specific IRs in different strains derive from a single ancestral IR of at least 93 kbp.

FROGS: Find, Rapidly, OTUs with Galaxy Solution

2 years ago
Escudie, F. ; Auer, L. ; Bernard, M. ; Mariadassou, M. ; Cauquil, L. ; Vidal, K. ; Maman Haddad, S. ; Hernandez-Raquet, G. ; Combes, S. ; Pascal, G.
Bioinformatics, 2018, 34 (8) : 1287-1294.
Motivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.