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Accueil > Pages Perso > Danis Abrouk

Plateforme iBio

Danis Abrouk

Activité

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

Publications

2016



  • Cavé L, et al. 2016. Efficiency and sensitivity of the digital droplet PCR for the quantification of antibiotic resistance genes in soils and organic residues. Applied Microbiology and Biotechnology. 1-12. doi: 10.1007/s00253-016-7950-5.
    Résumé : Droplet digital PCR (ddPCR) allows absolute quantification and tolerance to inhibitors and has been proposed as the method of choice to overcome limitations of qPCR. The aim of this study was to evaluate ddPCR and qPCR performances to detect low copy number and copy number variation of antibiotic resistance genes (sul1 and qnrB genes encoding for resistance to sulfonamides and quinolones, respectively) using bacterial genomic DNA (gDNA) and metagenomic DNA extracted from soil and organic residue samples. With gDNA, qPCR showed a better range of quantification but the lower limit of quantification was at 15 copies of qnrB target vs. 1.6 in ddPCR. In the presence of background DNA or inhibitors, we observed a high loss of sensitivity in qPCR and an overestimation of target sequences. When using high amount of environmental DNA templates (70 ng per reaction), ddPCR was still allowing accurate quantification without adding PCR facilitator (i.e., T4 Gene 32 protein). Sensitivity to detect copy number variation was tenfold higher in ddPCR than in qPCR. Finally, the advantages of using ddPCR in environmental studies were confirmed with the quantification of sul1 and qnrB in soils, manures, or urban wastes.
    Mots-clés : #8, #ibio.

2014



  • Sen A, et al. 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.

2011



  • Lassalle F, 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

Vulgarisation

Communications Orales

2015

  • Muller D. 2015. Compartimentalisation de la communauté bactérienne le long des racines dans la rhizosphère du maïs.
    Mots-clés : #colloque, #ibio.

Posters