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DGIMI - Diversity, Genomes and Insects-Microorganisms Interactions

DGIMI is a joint research unit supervised by INRAE and the University of Montpellier. It is located on the Triolet campus of the University of Montpellier, and houses staff from both INRAE and UM.

The research carried out by UMR DGIMI is devoted to the study of interaction mechanisms between insect crop pests, their pathogens and parasites, and their host plants. This research takes into account the diversity of the partners and is based on knowledge of their genomes.

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HAL : Dernières publications

  • [hal-05168860] The evaluation of shotgun sequencing and rpoB metabarcoding for taxonomic profiling of bacterial communities

    Abstract Background The importance of microbial community profiling has been increasingly recognized in biological and environmental research. While metabarcoding has been widely used for such analysis by targeting specific DNA sequences as markers, shotgun sequencing has been proposed as an alternative method because the analysis of whole genomes can potentially reduce biases introduced by targeted approaches. However, it is largely unknown whether shotgun sequencing may provide improved precision for qualitative taxonomic identification and quantitative abundance estimation compared with metabarcoding with housekeeping gene markers, such as the rpoB gene. Furthermore, the comparative performance of various bioinformatics pipelines for shotgun data analysis remains uncertain. In this study, we evaluated the performance of rpoB metabarcoding and shotgun sequencing coupled to various bioinformatic pipelines to describe the bacterial diversity of artificially generated mock bacterial communities, which included eukaryote gDNA intentional contamination or whole-genome amplification. For shotgun sequencing, the Assembly-Binning-Method and k-mer-based approaches were evaluated. Results For taxonomic profiling, the Assembly-Binning-Method and rpoB metabarcoding exhibited comparable sensitivity and precision, whereas k-mer approaches produced a notably high number of false negatives. In some cases, the Assembly-Binning-Method improved taxonomic resolution compared with rpoB metabarcoding by identifying taxa at the species level rather than the genus level. Regarding the quantification of microbial composition, the Assembly-Binning-Method consistently showed a higher correlation with expected values ​​and a lower dissimilarity index than rpoB metabarcoding. The use of three sets of reference genomes to calculate depth coverage did not systematically affect the precision of the Assembly-Binning-Method. Conclusions These results demonstrate that although shotgun sequencing and rpoB metabarcoding have nearly equivalent accuracy in taxonomic profiling, shotgun sequencing has better taxonomic resolution and outperforms rpoB metabarcoding in quantitative estimation of microbial community abundance using the Assembly-Binning approach.

    ano.nymous@ccsd.cnrs.fr.invalid (Karine Durand) 18 Jul 2025

    https://hal.inrae.fr/hal-05168860v1
  • [hal-05155756] Characterization of the genomic sequence of an iflavirus, a protoambidensovirus, and of three microviruses detected in mosquitoes (Aedes albopictus and Culex quinquefasciatus)

    We report the complete CDS of five viruses: XiangYun picorna-like virus 4 ( Iflaviridae ), Protoambidensovirus dipteran1 ( Parvoviridae ), and three microviruses ( Microviridae ), detected by viromics surveillance of Aedes albopictus and Culex quinquefasciatus from Réunion Island. The protoambidensovirus detected in A. albopictus belongs to a clade previously reported only in Culex pipiens.

    ano.nymous@ccsd.cnrs.fr.invalid (Sarah François) 10 Jul 2025

    https://hal.inrae.fr/hal-05155756v1
  • [hal-05162736] Will anomalies in the field of EPN associated-bacteria lead to a new paradigm?

    <div><p>According to the prevailing monoxenic paradigm, entomopathogenic nematodes (EPNs) form specific association with endosymbiotic bacteria. However, many anomalies have been observed over the last 60 years, with bacterial taxa other than the known endosymbiont isolated in culture-based approaches or detected by nextgeneration sequencing. We have reconsidered the role of this EPN-associated microbiotaknown as the second bacterial circlein the life-cycle of EPNs. In this review, we present arguments supporting a role for certain taxa in the death of the insect and propose hypotheses concerning other properties of the bacteria involved in their interactions with EPNs. Should these functional hypotheses be confirmed, then the bacterial "anomalies" would no longer be regarded as such. Instead, they would form the basis for the establishment of a new paradigm, the polyxenic paradigm.</p><p>☆ This article is part of a special issue entitled: 'EPN 100 years' published in Journal of Invertebrate Pathology.</p></div>

    ano.nymous@ccsd.cnrs.fr.invalid (Jean-Claude Ogier) 15 Jul 2025

    https://hal.inrae.fr/hal-05162736v1

News

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18 July 2025

By: A-N. Volkoff, N. Nègre , I. Seninet

A University of Montpellier's Associated Professor in microbiology position (sections 64-65) has been created in DGIMI

Applications must be submitted on Odyssée before 04/04/2025.
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A new scientific publication

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Invasive populations in Senegal show evidence of adaptive evolution on CYP450 genes that may explain their adaptation to maize

photo Peter Heeling

Website under restructuring

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Our website is currently being restructured.

Postdoctoral Position in CRISPR/Cas9 Gene Editing in Insects (University of Montpellier)

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Location: UMR-DGIMI, University of Montpellier, France / Duration: 18 months / Start Date: Preferably from April 2025