Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

Abstract

Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries) tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms) which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Although potentially driven by factors other than farming practice, we also observed significant differences in community composition between conventional and organic analogs within produce types. These differences were often attributable to distinctions in the relative abundances of Enterobacteriaceae taxa, which were generally less abundant in organically-grown produce. Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically farmed varieties contributing to this variation.

Caenorhabditis elegans responses to bacteria from its natural habitats

“…Although likely an underestimate of the total diversity in these samples (Experimental Procedures), ∼2,400 observed OTUs represent four-to fivefold fewer than that observed in bulk soil samples and comparable to the levels that are observed in specialized niches like the rhizosphere (18,19). The specificity of the bacterial genera observed is supported by previous studies of analyses of fruit surfaces (20) (especially the apple phyllosphere) (21) and also microbiome studies of other fruit-associated animals like Drosophila (22,23). Particular bacterial phylotypes were identified from quite disparate habitats (e.g., a snail, a rotting apple, and a rotting orange), which could indicate their close association with C. elegans animals, but further studies of more habitats and C. elegans populations are needed to test this link.…”

Laboratory identification of anaerobic bacteria isolated on Clostridium difficile selective medium

“…Regarding fresh vegetables, they can harbor large and diverse populations of bacteria. A previous study [20] demonstrated significant differences in bacterial community structure dependent upon the type of vegetables involved, and also treatments undertaken in the course of production. In this context, several factors could play a role in the lower recovery of strains from raw food samples.…”

The science, development, and commercialization of postharvest biocontrol products

“…As a result, very little is known about the overall diversity and composition of microbial communities on harvested produce and how these communities vary across produce types. Based on recent studies on this topic (Rudi et al, 2002;Ponce et al, 2008;Ottesen et al, 2009;Rastogi et al, 2012;Leff and Fierer, 2013;), a few key patterns are emerging: (1) different produce types and cultivars can harbor different levels (abundances) of specific microbial groups (Critzer and Doyle, 2010), (2) farming and storage conditions can influence the composition and abundances of microbial communities found on produce, and (3) non-pathogenic microbes can interact with and inhibit microbial pathogens found on produce surfaces (Shi et al, 2009;Critzer and Doyle, 2010;Teplitski et al, 2011). Despite this recent body of work, we still have a limited understanding of the diversity of produce-associated microbial communities, their function, the factors that influence the composition of these communities after harvest and during storage, and the distribution of individual taxa (particularly those taxa that are difficult to culture) across different commodities.…”