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Plateforme iBio

Danis Abrouk


  • Responsable Informatique Ecologie Microbienne Lyon
  • Responsable Informatique CRB
  • CSSI



  • 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.

  • Lecomte, S. M., Achouak, W., Abrouk, D., Heulin, T., Nesme, X., & Haichar, F. Z. (2018). Diversifying Anaerobic Respiration Strategies to Compete in the Rhizosphere. Frontiers In Environmental Science, 6. doi:10.3389/fenvs.2018.00139
    Résumé : The rhizosphere is the interface between plant roots and soil where intense, varied interactions between plants and microbes influence plants’ health and growth through their influence on biochemical cycles, such as the carbon, nitrogen and iron cycles. The rhizosphere is also a changing environment where oxygen can be rapidly limited and anaerobic zones can be established. Microorganisms successfully colonize the rhizosphere when they possess specific traits referred to as rhizosphere competence. Anaerobic respiration flexibility contributes to the rhizosphere competence of microbes. Indeed, a wide range of compounds that are available in the rhizosphere can serve as alternative terminal electron acceptors during anaerobic respiration such as nitrates, iron, carbon compounds, sulfur, metalloids and radionuclides. In the presence of multiple terminal electron acceptors in a complex environment such as the rhizosphere and in the absence of O2, microorganisms will first use the most energetic option to sustain growth. Anaerobic respiration has been deeply studied, and the genes involved in anaerobic respiration have been identified. However, aqueous environment and paddy soils are the most studied environments for anaerobic respiration, even if we provide evidence in this review that anaerobic respiration also occurs in the plant rhizosphere. Indeed, we provide evidence by performing a BLAST analysis on metatranscriptomic data that genes involved in iron, sulfur, arsenate and selenate anaerobic respiration are expressed in the rhizosphere, underscoring that the rhizosphere environment is suitable for the establishment of anaerobic respiration. We thus focus this review on current research concerning the different types of anaerobic respiration that occur in the rhizosphere. We also discuss the flexibility of anaerobic respiration as a fundamental trait for the microbial colonization of roots, environmental and ecological adaptation, persistence and bioremediation in the rhizosphere. Anaerobic respiration appears to be a key process for the functioning of an ecosystem and interactions between plants and microbes.
    Mots-clés : #4, #ibio, adaptation, anaerobic respiration, Respiratory pathways, rhizobacteria, rhizosphere competence, root colonization, Terminal electron acceptors.

  • 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.


  • Sen, A., Daubin, V., Abrouk, D., Gifford, I., Berry, A. M., & Normand, P. (2014). The phylogeny of actinobacteria revisited in the light of complete genomes, the orders Frankiales and Micrococcales should be split into coherent entities. Proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. International Journal Of Systematic And Evolutionary Microbiology, ijs.0.063966-0. doi:10.1099/ijs.0.063966-0
    Résumé : The phylogeny of Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of Actinobacteria and evaluated eight different hypothesis for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S rDNA and 23S rDNA or their concatenation, and a tree based on the concatenate of MLSA genes (AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenate tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenate of 54 proteins. In that tree, the orders Bifidobacteriales, Coriobacteriales, Corynebacteriales, Micromonosporales, Propionibacteriales, Pseudonocardiales, Streptomycetales and Streptosporangiales were recovered while the Frankiales and Micrococcales were not. It is thus proposed that the invalidly published order Frankiales be split into Frankiales (Frankiaceae), Geodermatophilales (Geodermatophilaceae), Acidothermales (Acidothermaceae) and Nakamurellales (Nakamurellaceae). The order Micrococcales should also be split into Micrococcales (Kocuria, Rothia, Micrococcus, Arthrobacter, Tropheryma, Microbacterium, Leifsonia and Clavibacter), Cellulomonales (Beutenbergia, Cellulomonas, Xylanimonas, Jonesia and Sanguibacter) and Brachybacteriales (Brachybacterium) but this will have to wait until more genomes become available for a significant proportion of strains in this order.
    Mots-clés : #1, #ibio, Acidothermales, Frankiales, Genomes, Geodermatophilales, Nakamurellales.


  • Lassalle, F., Campillo, T., Vial, L., Baude, J., Costechareyre, D., Chapulliot, D., et al. (2011). Genomic Species Are Ecological Species as Revealed by Comparative Genomics in <i>Agrobacterium tumefaciens</i>. Genome Biology And Evolution, 3, 762-781. doi:10.1093/gbe/evr070
    Résumé : The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species.
    Mots-clés : #3, #4, #cesn, #ibio, Agrobacterium, bacterial evolution, bacterial species, ecological niche, linear chromosome.

Chapitres d’ouvrages


Communications Orales