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Plateforme iBio

Audrey Dubost

Ingénieur d’études CNRS


  • Activités principales :
    1. Assemblage de génomes
    2. Analyse de diversité (pyroséquençage, miseq)
    3. Analyse RNAseq
    4. Comparaison de génomes
  • Activités secondaires :
    1. Assistante de Prévention référente et assitante de Prévention au bâtiment Mendel
    2. Membre du Conseil de Gestion

Parcours scientifique

  • Ingénieur d’Etudes en Bioinformatique, Laboratoire d’Ecologie Microbienne - Lyon (depuis Janvier 2012)
  • Assistant-Ingénieur en Bioinformatique, INRA Crouel - Clermont-Ferrand (Avril 2011 - Décembre2011)
  • Master de Bioinformatique et Génomique - Université Aix-Marseille II
  • Licence de Génétique - Université Blaise Pascal, Clermont-Ferrand



  • Keshavarz-Tohid, V., Vacheron, J., Dubost, A., Prigent-Combaret, C., Taheri, P., Tarighi, S., et al. (2019). Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov. Systematic And Applied Microbiology. doi:10.1016/j.syapm.2019.04.004
    Résumé : Bacteria of the Pseudomonas putida group are studied for a large panel of properties ranging from plant growth promotion and bioremediation to pathogenicity. To date, most of the classification of individual pseudomonads from this group relies on 16S RNA gene analysis, which is insufficient for accurate taxonomic characterization within bacterial species complexes of the Pseudomonas putida group. Here, a collection of 20 of these bacteria, isolated from various soils, was assessed via multi-locus sequence analysis of rpoD, gyrB and rrs genes. The 20 strains clustered in 7 different clades of the P. putida group. One strain per cluster was sequenced and results were compared to complete genome sequences of type strains of the P. putida group. Phylogenetic analyses, average nucleotide identity data and digital DNA hybridizations, combined to phenotypic characteristics, resulted in the proposition and description of four new species i.e. Pseudomonas alloputida Kh7 T (= LMG 29756 T = CFBP 8484 T) sp. nov., Pseudomonas inefficax JV551A3 T (= DSM108619 T = CFBP 8493 T) sp. nov., Pseudomonas persica RUB6 T (= LMG 29757 T = CFBP 8486 T) sp. nov. and Pseudomonas shirazica VM14 T (= LMG 29953 T = CFBP 8487 T) sp. nov.
    Mots-clés : #3, #ibio, GGDC, group, Pseudomonads genomes.


  • Alonso, L., Creuzé-des-Châtelliers, C., Trabac, T., Dubost, A., Moënne-Loccoz, Y., & Pommier, T. (2018). Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave. Microbiome, 6(1), 216. doi:10.1186/s40168-018-0599-9
    Résumé : The World-famous UNESCO heritage from the Paleolithic human society, Lascaux Cave (France), has endeavored intense microclimatic perturbations, in part due to high touristic pressure. These perturbations have resulted in numerous disturbances of the cave ecosystem, including on its microbial compartment, which resulted in the formation of black stains especially on the rock faces of the passage. We investigated the cave microbiome in this part of Lascaux by sampling three mineral substrates (soil, banks, and inclined planes) on and outside stains to assess current cave microbial assemblage and explore the possibility that pigmented microorganisms involved in stain development occur as microbial consortia.
    Mots-clés : #3, #5, #ibio.

  • Bouffaud, M. - L., Renoud, S., Dubost, A., Moënne-Loccoz, Y., & Muller, D. (2018). 1-Aminocyclopropane-1-carboxylate deaminase producers associated to maize and other Poaceae species. Microbiome, 6(1). doi:10.1186/s40168-018-0503-7
    Mots-clés : #3, #ibio.

  • Guégan, M., Minard, G., Tran, F. H., Tran Van, V., Dubost, A., & Valiente Moro, C. (2018). Short-term impacts of anthropogenic stressors on Aedes albopictus mosquito vector microbiota. Fems Microbiology Ecology. doi:10.1093/femsec/fiy188
    Résumé : Abstract. Recent studies have highlighted the potential role of microbiota in the biology of the Aedes albopictus mosquito vector. This species is highly anthr
    Mots-clés : #7, #ibio.

  • Guyonnet, J. P., Guillemet, M., Dubost, A., Simon, L., Ortet, P., Barakat, M., et al. (2018). Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation. Frontiers In Plant Science, 9. doi:10.3389/fpls.2018.01662
    Résumé : Abstract Plant strategies for soil nutrient uptake have the potential to strongly influence plant-microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterised by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analysed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the root-adhering soil of exploitative species. This increase of microbial activities result probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and soil organic matter degradation via root exudation.
    Mots-clés : #5, #ibio, Active bacterial community, Denitrification, microbial activities, microbiota, Plant nutrient use strategies, rhizosphere, root exudation, Stable isotope probing (SIP).

  • Jacquemond, I., Muggeo, A., Lamblin, G., Tristan, A., Gillet, Y., Bolze, P. A., et al. (2018). Complex ecological interactions of Staphylococcus aureus in tampons during menstruation. Scientific Reports, 8(1), 9942. doi:10.1038/s41598-018-28116-3
    Résumé : Menstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons’ microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.
    Mots-clés : #3, #ibio.

  • Normand, P., Nouioui, I., Pujic, P., Fournier, P., Dubost, A., Schwob, G., et al. (2018). Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa. International Journal Of Systematic And Evolutionary Microbiology, 68(9), 3001-3011. doi:10.1099/ijsem.0.002939
    Mots-clés : #1, #ibio.


  • Doré, J., Kohler, A., Dubost, A., Lindquist, E., Kuo, A., Grigoriev, I. V., et al. (2017). The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation. Environmental Microbiology, 19(3), 1338–1354. doi:10.1111/1462-2920.13670
    Résumé : To clarify the early molecular interaction between ectomycorrhizal partners, we performed a RNA-Seq study of transcriptome reprogramming of the basidiomycete Hebeloma cylindrosporum before symbiotic structure differentiation with Pinus pinaster. Mycorrhiza transcriptome was studied for comparison. By reference to asymbiotic mycelium, 47 and 46 genes were specifically up-regulated over five-fold (p≤0.05) upon rhizosphere colonization and root adhesion respectively. Other 45 were up-regulated throughout the symbiotic interaction, from rhizosphere colonization to differentiated mycorrhizas, whereas 274 were specifically up-regulated in mycorrhizas. Although exoproteome represents 5.6% of H. cylindrosporum proteome, 38.5% of the genes up-regulated upon pre-infectious root colonization encoded extracellular proteins. The proportion decreased to 23.5% in mycorrhizas. At all studied time points, mycorrhiza-induced small secreted proteins (MiSSPs), representing potential effectors, were over-represented among up-regulated genes. This was also the case for carbohydrate-active enzymes (CAZymes). Several CAZymes were up-regulated at all studied stages of the interaction. Consistent with a role in fungal morphogenesis and symbiotic interface differentiation, CAZymes over-expressed before and upon root attachment targeted fungal and both fungal and plant polysaccharides respectively. Different hydrophobins were up-regulated upon early root adhesion, in mycorrhizas or throughout interaction. The functional classification of genes up-regulated only in mycorrhizas pointed to intense metabolic activity and nutritional exchanges. This article is protected by copyright. All rights reserved.
    Mots-clés : #2, #ibio.

  • Galia, W., Leriche, F., Cruveiller, S., Garnier, C., Navratil, V., Dubost, A., et al. (2017). Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat. Bmc Genomics, 18(1), 574. doi:10.1186/s12864-017-3957-2
    Résumé : 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.
    Mots-clés : #6, #ibio.

  • Vacheron, J., Dubost, A., Chapulliot, D., Prigent-Combaret, C., & Muller, D. (2017). Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere. Genome Announcements, 5(15), e00122-17. doi:10.1128/genomeA.00122-17
    Résumé : We report the draft genome sequence of Chryseobacterium sp. JV274. This strain was isolated from the rhizosphere of maize during a greenhouse experiment. JV274 harbors genes involved in flexirubin production (darA and darB genes), bacterial competition (type VI secretion system), and gliding (bacterial motility; type IX secretion system).
    Mots-clés : #3, #4, #ibio.


  • Barbi, F., Prudent, E., Vallon, L., Buée, M., Dubost, A., Legout, A., et al. (2016). Tree species select diverse soil fungal communities expressing different sets of lignocellulolytic enzyme-encoding genes. Soil Biology And Biochemistry, 100, 149-159. doi:10.1016/j.soilbio.2016.06.008
    Résumé : Fungi are the main organisms responsible for plant biomass degradation in soils. While many studies have evaluated the impact of tree species on the taxonomic diversity of soil fungi, very few of them have addressed their functional gene diversity. In the present study, we assessed the impact of tree species, differing with respect to litter quality, and sampling dates on the diversity of four expressed fungal gene-families: one housekeeping gene used as taxonomic marker and three others encoding key enzymes implicated in lignocellulose degradation selected as functional markers. This was performed by the high-throughput sequencing of gene-fragments amplified from forest soil mRNA using fungal specific primers. Messenger RNAs were extracted from 10 soil samples collected over two seasons in plots planted with either the conifer Picea abies or the angiosperm Fagus sylvatica in a common garden experiment. Independently of the gene-family, less than 20% of the fungal transcripts were identified in both forest types. For all four fungal gene-families, variance partitioning identified the tree species and its interaction with the sampling plot as the factors that contributed most to global gene diversity (between 29% and 32%), while the sampling dates accounted for less than 9%. Further analysis of the contribution of soil proprieties revealed that the tree species-generated C/N ratio is the most important factor driving functional gene distribution (between 6% and 29% of the variation explained). Similarly, for each fungal gene family, statistical analyses identified tree species as the main factor responsible for variations in similarity between samples (as estimated by the Bray-Curtis β diversity index). These results highlight that tree species, differing with respect to litter quality, selected different soil fungal communities expressing different set of genes involved in plant organic matter degradation.
    Mots-clés : #2, #ibio, Diversity, Forest soil, Fungal transcripts, High-throughput sequencing, Lignocellulolytic enzymes, Soil organic matter.

  • Simonin, M., Richaume, A., Guyonnet, J. P., Dubost, A., Martins, J. M. F., & Pommier, T. (2016). Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers. Scientific Reports, 6, 33643. doi:10.1038/srep33643
    Mots-clés : #5, #ibio.

  • Vacheron, J., Moënne-Loccoz, Y., Dubost, A., Gonçalves-Martins, M., Muller, D., & Prigent-Combaret, C. (2016). Fluorescent Pseudomonas Strains with only Few Plant-Beneficial Properties Are Favored in the Maize Rhizosphere. Plant Biotic Interactions, 7, 1212. doi:10.3389/fpls.2016.01212
    Résumé : Plant Growth-Promoting Rhizobacteria (PGPR) enhance plant health and growth using a variety of traits. Effective PGPR strains typically exhibit multiple plant-beneficial properties, but whether they are better adapted to the rhizosphere than PGPR strains with fewer plant-beneficial properties is unknown. Here, we tested the hypothesis that strains with higher numbers of plant-beneficial properties would be preferentially selected by plant roots. To this end, the co-occurrence of 18 properties involved in enhanced plant nutrition, plant hormone modulation, or pathogen inhibition was analyzed by molecular and biochemical methods in a collection of maize rhizosphere and bulk soil isolates of fluorescent Pseudomonas. Twelve plant-beneficial properties were found among the 698 isolates. Contrarily to expectation, maize preferentially selected pseudomonads with low numbers of plant-beneficial properties (up to five). This selection was not due to the predominance of strains with specific assortments of these properties, or with specific taxonomic status. Therefore, the occurrence of only few plant-beneficial properties appeared favorable for root colonization by pseudomonads.
    Mots-clés : #3, #cesn, #ibio, fluorescent Pseudomonas, Functional groups, Maize, PGPR, plant-beneficial properties.
    Note Note
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  • Youenou, B., Favre-Bonté, S., Bodilis, J., Brothier, E., Dubost, A., Muller, D., & Nazaret, S. (2015). Comparative genomics of environmental and clinical <i>Stenotrophomonas maltophilia</i> strains with different antibiotic resistance profiles. Genome Biology And Evolution, evv161. doi:10.1093/gbe/evv161
    Mots-clés : #3, #8, #ibio.


  • Barbi, F., Bragalini, C., Vallon, L., Prudent, E., Dubost, A., Fraissinet-Tachet, L., et al. (2014). PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing. Plos One, 9(12), e116264. doi:10.1371/journal.pone.0116264
    Résumé : Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes. This can be tackled by environmental genomic approaches involving the systematic sequencing of key enzyme-coding gene families using soil-extracted RNA as material. Such an approach necessitates the design and evaluation of gene family-specific PCR primers producing sequence fragments compatible with high-throughput sequencing approaches. In the present study, we developed and evaluated PCR primers for the specific amplification of fungal CAZy Glycoside Hydrolase gene families GH5 (subfamily 5) and GH11 encoding endo-β-1,4-glucanases and endo-β-1,4-xylanases respectively as well as Basidiomycota class II peroxidases, corresponding to the CAZy Auxiliary Activity family 2 (AA2), active on lignin. These primers were experimentally validated using DNA extracted from a wide range of Ascomycota and Basidiomycota species including 27 with sequenced genomes. Along with the published primers for Glycoside Hydrolase GH7 encoding enzymes active on cellulose, the newly design primers were shown to be compatible with the Illumina MiSeq sequencing technology. Sequences obtained from RNA extracted from beech or spruce forest soils showed a high diversity and were uniformly distributed in gene trees featuring the global diversity of these gene families. This high-throughput sequencing approach using several degenerate primers constitutes a robust method, which allows the simultaneous characterization of the diversity of different fungal transcripts involved in plant organic matter degradation and may lead to the discovery of complex patterns in gene expression of soil fungal communities.
    Mots-clés : #2, #ibio.

  • Dobrovolskaya, O., Pont, C., Sibout, R., Martinek, P., Badaeva, E., Murat, F., et al. (2014). FRIZZY PANICLE drives supernumerary spikelets in bread wheat (T. aestivum L.). Plant Physiology, pp.114.250043. doi:10.1104/pp.114.250043
    Résumé : Bread wheat inflorescences, or spikes, are characteristically unbranched and normally bear one spikelet per rachis node. Wheat mutants on which supernumerary spikelets (SS) develop are particularly useful resources for work towards understanding the genetic mechanisms underlying wheat inflorescence architecture and, ultimately, yield components. Here, we report the characterization of genetically unrelated mutants leading to the identification of the wheat FRIZZY PANICLE gene, encoding a member of the APETALA2/Ethylene Response Factor (AP2/ERF) transcription factor family, which drives the SS trait in bread wheat. Structural and functional characterization of the three wheat FRIZZY PANICLE homoeologous genes (WFZP) revealed that coding mutations of WFZP-D cause the SS phenotype with the most severe effect when WFZP-D lesions are combined with a frameshift mutation in WFZP-A. We provide WFZP-based resources that may be useful for genetic manipulations with the aim of improving bread wheat yield by increasing grain number.

  • Minard, G., Tran, F. H., Dubost, A., Tran Van, V., Mavingui, P., & Valiente Moro, C. (2014). Pyrosequencing 16S rRNA genes of bacteria associated with wild tiger mosquito Aedes albopictus: a pilot study. Frontiers In Cellular And Infection Microbiology, 4. doi:10.3389/fcimb.2014.00059
    Résumé : The Asian tiger mosquito Aedes (Stegomya) albopictus is an invasive species that has spread across the world in the last two decades, showing a great capacity to adapt to contrasting climates and environments. While demonstrated in many insects, the contribution of bacterial symbionts in Aedes ecology is a challenging aspect that needs to be investigated. Also some bacterial species have already been identified in Ae. albopictus using classical methods, but a more accurate survey of mosquito-associated bacterial diversity is needed to decipher the potential biological functions of bacterial symbionts in mediating or constraining insect adaptation. We surveyed the bacteria associated with field populations of Ae. albopictus from Madagascar by pyrosequencing 16S rRNA gene amplicons. Different aspects of amplicon preparation and sequencing depth were tested to optimize the breadth of bacterial diversity identified. The results revealed that all mosquitoes collected from different sites have a bacterial microbiota dominated by a single taxon, Wolbachia pipientis, which accounted for about 99% of all 92,615 sequences obtained. As Ae. albopictus is known to harbor two Wolbachia strains (wAlbA and wAlbB), a quantitative PCR was used to estimate the relative densities, (i.e., the bacteria-to-host gene ratios) of each strains in individual mosquitoes. Relative densities were between 6.25 × 100.01 and 5.47 × 100.1 for wAlbA and between 2.03 × 100.1 and 1.4 × 101 for wAlbB. Apart from Wolbachia, a total of 31 bacterial taxa were identified at the genus level using different method variations. Diversity index values were low and probably underestimated the true diversity due to the high abundance of Wolbachia sequences vastly outnumbering sequences from other taxa. Further studies should implement alternative strategies to specifically discard from analysis any sequences from Wolbachia, the dominant endosymbiotic bacterium in Ae. albopictus from this area.
    Mots-clés : #7, #ibio.


  • Dibari, B., Murat, F., Dubost, A., Gautier, V., Poncet, C., Lecomte, P., et al. (2012). Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. Bmc Genomics, 13(1), 221. doi:10.1186/1471-2164-13-221
    Résumé : Carotenoids are isoprenoid pigments, essential for photosynthesis and photoprotection in plants. The enzyme phytoene synthase (PSY) plays an essential role in mediating condensation of two geranylgeranyl diphosphate molecules, the first committed step in carotenogenesis. PSY are nuclear enzymes encoded by a small gene family consisting of three paralogous genes (PSY1-3) that have been widely characterized in rice, maize and sorghum. PMID: 22672222
    Mots-clés : Abiotic stress, Carotenoids, Evolution, Intron loss, Phytoene synthase, wheat.

Presentations Orales


  • Vacheron, J., Muller, D., Dubost, A., Moënne-Loccoz, Y., & Prigent-Combaret, C. (2015). PGPR with multiple plant-beneficial functions : The more the better ? Dans . Présenté à Rhizosphère 4, Maastricht - Pays Bas: communication orale.
    Mots-clés : #colloque, #ibio.
  • Vacheron, J., Muller, D., Dubost, A., Moënne-Loccoz, Y., & Prigent-Combaret, C. (2015). Sélection des rhizobactéries phytostimulatrices par la plante : Impact sur la distribution des propriétés phytobénéfiques. Dans . Présenté à Journée de rencontre des doctorants, Ecole doctorale E2M2, Lyon: communication orale.
    Mots-clés : #colloque, #ibio.



  • Simonin, M. (2014). Disturbance of soil nitrogen cycle by titanium dioxide (TiO2) nanoparticles. Dans . BES Lille.
    Mots-clés : #5, #ibio, #poster.


  • Minard, G. (2012). Phylotypage des communautés bactériennes associées au moustique tigre Aedes albopictus. Dans . Journées Scientifiques ARC1.
    Mots-clés : #7, #ibio, #poster.