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To assess differences in microbial community composition across the produce items beta diversity , we calculated both phylogenetic metrics weighted and unweighted UniFrac distances, [33] , [34] and a taxonomic metric Bray-curtis dissimilarities calculated from log-transformed OTU abundances. Differences in overall bacterial community composition among the produce types and between farming practice type organic versus conventional were assessed using a permutational multivariate ANOVA test PERMANOVA with produce type and farming practice as fixed factors and the grocery store brand as a random factor.

Significant differences in taxonomic richness were assessed across produce types using the nonparametric Kruskal-Wallis test and between conventional and organic labeled produce items using a t-test. Significant differences in the relative abundances of individual bacterial taxa across produce types or factor levels were determined using ANOVA and the false discovery rate FDR correction. T-tests were used when comparing the relative abundances of individual taxa between conventional and organic analogs.

Bacterial communities were highly diverse regardless of the produce type with between 17 and families being represented on the surfaces of each produce type. However, the majority of these families were rare; on average, only 3 to 13 families were represented by at least two sequences per produce type.

In some cases, OTUs assigned to a single bacterial family were dominant.

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Samples were rarefied at sequences per sample. Circles represent outliers. The dendrogram is based on mean Bray-Curtis dissimilarities and shows differences among produce types in the overall composition of the bacterial communities. Only families and unclassified groupings representing at least three percent on any produce type are represented. Across the produce types, bacterial communities also differed with respect to their taxonomic structure, and produce type had a far larger influence on the observed variation in bacterial community composition than farming practice or store brand Table 2.

Still, certain produce types shared more similar community structure than others. On average, tree fruits apples and peaches tended to share communities that were more similar in composition than they were to those on other produce types, and produce typically grown closer to the soil surface spinach, lettuce, tomatoes, and peppers shared communities relatively similar in composition. Surface bacterial communities on grapes and mushrooms were each strongly dissimilar from the other produce types studied Fig.

However, some families had high relative abundances on individual produce types Fig. Among these families, only 2 of 19 bacterial families did not significantly differ in relative abundances across the produce types Fig. As previously mentioned, Enterobacteriaceae is one major group responsible for the clustering patterns described above and in Fig.


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Apples and peaches tended to have greater relative abundances of Microbacteriaceae and Sphingomonadaceae than other produce types. Grape surface communities displayed relatively strong contributions from the families Bacillaceae and Acetobacteraceae, and mushrooms, which showed the strongest differences from other produce types, had large relative abundances of Micrococcaceae, Sphingobacteriaceae, and Pseudomonadaceae Fig. Patterns in community composition differences at the family level were also reflected by differences in the dominant genera across the produce types.

Pantoea sp. However, other produce types were generally characterized by dominant genera specific to that produce type Table 3. Each produce type and conventional and organic-labeled equivalents are shown.

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Microbiology of Fruits and Vegetables

No organic-labeled equivalents were sampled for either type of sprouts. Differences in taxonomic richness on the surfaces of conventional and organic-labeled analogs depended on the produce type Fig. Although the taxa driving the observed differences between conventional and organic-labeled produce were not consistent across the produce types Table 4 , conventional-labeled varieties had a greater relative abundance of Enterobacteriaceae taxa across several produce types, including spinach, lettuce, tomatoes, and peaches Table 4.

Differences among organic and conventional labeled individuals of other produce types were generally associated with families that were specific to that produce type Table 4. For example, the communities on grapes were distinguished by a greater relative abundance of Bacillaceae on the organic-labeled grapes Table 4. Plots are based on Bray-Curtis dissimilarities comparing surface bacterial communities of conventional-labeled filled circles and organic-labeled open circles produce items within each produce type.

Our results generally demonstrated high bacterial diversity across the eleven fruits and vegetables we analyzed. Six phylogenetically diverse phyla were well represented by the sequences in at least one produce type: Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and TM7 Fig.

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The bacterial taxa we observed were consistent with findings from other studies that have used culture-independent techniques to describe taxon abundances. We found the surface bacterial communities of spinach, lettuce, and tomatoes to be numerically dominated by Gammaproteobacteria, a pattern which has also been noted in previous studies [5] , [15] , [16] , [37] , [38]. Similarly, Ottesen et al. It is more difficult to directly compare our results with the large body of research on produce-associated bacteria that has been conducted using culture-based techniques as such techniques do not typically quantify proportions of bacteria belonging to specific taxonomic groups, rather binning them into operationally-defined groups determined by the culturing media used.

Furthermore, culture-based studies detect a different fraction of the bacterial community assessed using culture-independent techniques, and, in most cases, a small fraction of the total bacterial diversity [27]. We observed distinct bacterial communities and substantial variation in bacterial richness across the produce types we analyzed.

The family Enterobacteriaceae, which was relatively abundant in many of the samples, contributed strongly to this variation. Enterobacteriaceae taxa dominated the community composition in the majority of produce types, but several produce types apples, peaches, grapes, and mushrooms harbored a very low proportion of bacteria from this family Fig. This pattern also generally coincided with patterns in richness—produce types with greater proportions of taxa belonging to Enterobacteriaceae generally had a lower taxonomic richness Fig.

Other bacterial families rarely had high relative abundances on more than two produce types Fig. Nonetheless, one Enterobacteriaceae taxon, putatively classified as Pantoea sp. This taxon might play an important role in the ecology of their hosts as certain Pantoea spp. Overall, it is not surprising there were high relative abundances of Enterobacteriaceae across many of the produce types as members of this family are known to colonize certain fruits and vegetables [42] , [43].

What remains to be determined is why this family was dominant on certain produce types and relatively rare on others. Likewise, it is difficult to unequivocally determine the specific factors responsible for driving the divergence between the bacterial communities on different produce types, but it is likely that several factors contribute to the patterns observed.

Phyllosphere bacterial communities are known to strongly differ across plant species [23] likely due to variations in metabolites, physical characteristics, and symbiotic interactions with the host plant and other microbial inhabitants [37] , [44]. These characteristics may similarly select for specific microbial taxa on fruits and vegetables [13] , [37]. Additionally, the produce-growing medium could serve as a reservoir of bacteria that inoculate fruits and vegetables prior to harvest.

However, our data do not provide evidence that this is an important mechanism for driving the relative abundances of the dominant taxa. For example, bean sprouts and spinach harbored very similar communities but the sprouts were grown hydroponically while the spinach was grown in soil Fig. Differences in handling, transport, and storage could also play a role in structuring the microbial communities [15] , [16] , [25]. Only the lettuce and spinach samples, for example, were rinsed prior to packaging, and storage times likely differed among the produce items.


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  8. Furthermore, differences in storage temperatures among produce items due to refrigeration could influence the relative abundance of cold-tolerant bacteria [15] , [16]. Additional research needs to be conducted to disentangle the contribution of these factors in structuring produce-associated bacterial communities. In addition to variation among produce types, we also found a somewhat weaker, but significant effect, of organic versus conventional label on the produce-associated communities Fig.

    This effect could be attributable to a number of factors including: growing location, fertilizer use, pesticide use, other agricultural practices, and shipping and handling procedures.

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    Likewise, some of these differences could have been due to the direct application of bacterial agents used in organic pesticides e. Nevertheless, our results suggest that differences in farming practices could be influencing the relative abundance of specific taxa on the surfaces of fresh produce available at grocery stores. Overall, Enterobacteriaceae showed consistently greater relative abundances on conventional-labeled spinach, lettuce, tomatoes, and peaches when compared to organic-labeled varieties Table 4.

    Differences between the microbiota on conventional and organically farmed produce items have been reported in other studies [4] , [17] , [18] , [26] , but the differences in specific taxa may not always be consistent. For example, Oliveira et al.

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    Nonetheless, our data do suggest that shifts in community composition can persist for extended periods of time from the field to the grocery store and presumably, into the home of the consumer. This highlights the potential for differences in the microbiota between conventionally and organically farmed produce items to impact human health.

    However, as it was not our objective to differentiate between closely related taxa that may have pathogenic and non-pathogenic representatives, future research is required to assess whether the bacterial community changes associated with organic and conventional-labeled produce may impact human exposures to potential pathogens. Our results demonstrate differences among produce types in the diversity and composition of the produce-associated bacterial communities and the potential for farming practice to affect the types of bacteria that may be consumed. Moreover, they help to establish a basis on which to pose several further questions.


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    6. For example: Do the differences in communities among produce types and farming practices influence microbial degradation of produce? Do these differences infer variation in the abundance of human pathogens or human health? It will be important to initiate controlled experiments to determine which factors are driving the differences in bacterial communities among the different produce types and conventional and organic-labeled varieties.