Vegetable microbiomes: is there a connection among opportunistic infections, human health and our 'gut feeling'?

Abstract

The highly diverse microbiomes of vegetables are reservoirs for opportunistic and emerging pathogens. In recent years, an increased consumption, larger scale production and more efficient distribution of vegetables together with an increased number of immunocompromised individuals resulted in an enhanced number of documented outbreaks of human infections associated with the consumption of vegetables. Here we discuss the occurrence of potential pathogens in vegetable microbiomes, the impact of farming and processing practices, and plant and human health issues. Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. Moreover, the potentially positive aspects of the vegetables microbiome for the gut microbiota and human health are presented.

Fig 1

Occurrence and taxonomic structure of opportunistic pathogens in the phyllosphere of Eruca sativa Mill. analyzed from a metagenomic data set. The relative abundance is based on the presented taxa and composed of 1.7% of the total bacterial fraction.

Fig 2

Functional diversity tree of the virulence, disease and defence cluster of Eruca sativa Mill. The data were compared with SEED using a maximum e-value of 1e-5, a minimum identity of 60 % and a minimum alignment length of 15 measured in aa for protein and bp for RNA databases. Colour shading indicates classification membership and investigated habitat (bar charts).

Fig 3

Escherichia coli cells on lettuce leaves and colonization of stomata visualized by Fluorescence in situ hybridization coupled with confocal laser scanning microscopy.A. Rendering of a confocal Z-stack volume.B and C. Isosurface models of A showing bacteria inside the stoma.