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Publications in peer reviewed journals

2 Publications found
  • A Bioinformatics Guide to Plant Microbiome Analysis.

    Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T
    2019 - Front Plant Sci, 1313


    Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.

  • Man-made microbial resistances in built environments.

    Mahnert A, Moissl-Eichinger C, Zojer M, Bogumil D, Mizrahi I, Rattei T, Martinez JL, Berg G
    2019 - Nat Commun, 1: 968


    Antimicrobial resistance is a serious threat to global public health, but little is known about the effects of microbial control on the microbiota and its associated resistome. Here we compare the microbiota present on surfaces of clinical settings with other built environments. Using state-of-the-art metagenomics approaches and genome and plasmid reconstruction, we show that increased confinement and cleaning is associated with a loss of microbial diversity and a shift from Gram-positive bacteria, such as Actinobacteria and Firmicutes, to Gram-negative such as Proteobacteria. Moreover, the microbiome of highly maintained built environments has a different resistome when compared to other built environments, as well as a higher diversity in resistance genes. Our results highlight that the loss of microbial diversity correlates with an increase in resistance, and the need for implementing strategies to restore bacterial diversity in certain built environments.

Book chapters and other publications

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