Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables
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{"title"=>"Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables", "type"=>"journal", "authors"=>[{"first_name"=>"Jonathan W.", "last_name"=>"Leff", "scopus_author_id"=>"55498821100"}, {"first_name"=>"Noah", "last_name"=>"Fierer", "scopus_author_id"=>"8638392900"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84875430559", "doi"=>"10.1371/journal.pone.0059310", "pui"=>"368602321", "pmid"=>"23544058", "scopus"=>"2-s2.0-84875430559", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)"}, "id"=>"f76750b0-1fb4-328c-94d1-81d3b540f4d9", "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.", "link"=>"http://www.mendeley.com/research/bacterial-communities-associated-surfaces-fresh-fruits-vegetables-2", "reader_count"=>246, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>54, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>56, "Student > Postgraduate"=>8, "Student > Master"=>34, "Other"=>14, "Student > Bachelor"=>40, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>2, "Professor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>54, "Student > Doctoral Student"=>12, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1008390"], "description"=>"*<p>Bray-curtis dissimilarities were log transformed.</p>", "links"=>[], "tags"=>["plant biology", "microbiology", "Computational biology"], "article_id"=>669019, "categories"=>["Biological Sciences", "Microbiology", "Plant Biology"], "users"=>["Jonathan W. Leff", "Noah Fierer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059310.t002", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PERMANOVA_results_of_main_factors_/669019", "title"=>"PERMANOVA results of main factors.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-27 02:30:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008404"], "description"=>"a<p>Classifications determined using BLAST with the NCBI nucleotide database.</p>b<p>Values represent means.</p>", "links"=>[], "tags"=>["otus", "proportions", "bacterial"], "article_id"=>669032, "categories"=>["Biological Sciences", "Microbiology", "Plant Biology"], "users"=>["Jonathan W. Leff", "Noah Fierer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059310.t003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_OTUs_representing_large_proportions_gt_5_of_their_bacterial_community_on_a_given_produce_type_/669032", "title"=>"Bacterial OTUs representing large proportions (>5%) of their bacterial community on a given produce type.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-27 02:30:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008420"], "description"=>"<p>Produce varieties and sample numbers.</p>", "links"=>[], "tags"=>["varieties"], "article_id"=>669047, "categories"=>["Biological Sciences", "Microbiology", "Plant Biology"], "users"=>["Jonathan W. Leff", "Noah Fierer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059310.t001", "stats"=>{"downloads"=>4, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Produce_varieties_and_sample_numbers_/669047", "title"=>"Produce varieties and sample numbers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-27 02:30:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/999354"], "description"=>"<p>The dendrogram is based on mean Bray-Curtis dissimilarities and shows differences among produce types in the overall composition of the bacterial communities. The heatmap shows mean relative abundances (%) of bacterial families on produce types. Only families and unclassified groupings representing at least three percent on any produce type are represented.</p>", "links"=>[], "tags"=>["bacterial", "communities", "abundances"], "article_id"=>661332, "categories"=>["Biological Sciences", "Microbiology", "Plant Biology"], "users"=>["Jonathan W. Leff", "Noah Fierer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059310.g002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationships_between_bacterial_communities_on_each_produce_type_and_relative_abundances_of_bacterial_families_/661332", "title"=>"Relationships between bacterial communities on each produce type and relative abundances of bacterial families.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 09:02:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/999362"], "description"=>"<div><p>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.</p> </div>", "links"=>[], "tags"=>["communities", "surfaces", "fruits"], "article_id"=>661340, "categories"=>["Biological Sciences", "Microbiology", "Plant Biology"], "users"=>["Jonathan W. Leff", "Noah Fierer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059310", "stats"=>{"downloads"=>3, "page_views"=>44, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_Communities_Associated_with_the_Surfaces_of_Fresh_Fruits_and_Vegetables_/661340", "title"=>"Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 09:03:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008376"], "description"=>"*<p>Only families greater than or equal to 3% in one group and differed with a p-value less than 0.05 (t-test) are shown. No families met these criteria on the surfaces of strawberries.</p>", "links"=>[], "tags"=>["abundances", "organic-labeled", "equivalents"], "article_id"=>669002, "categories"=>["Biological Sciences", "Microbiology", "Plant Biology"], "users"=>["Jonathan W. Leff", "Noah Fierer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059310.t004", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_families_that_differ_in_their_relative_abundances_between_conventional_and_organic_labeled_equivalents_within_produce_types_/669002", "title"=>"Bacterial families that differ in their relative abundances between conventional and organic-labeled equivalents within produce types.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-27 02:30:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/999357"], "description"=>"<p>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. P-values were calculated using PERMANOVA.</p>", "links"=>[], "tags"=>["coordinates", "differences", "bacterial", "farming"], "article_id"=>661335, "categories"=>["Biological Sciences", "Microbiology", "Plant Biology"], "users"=>["Jonathan W. Leff", "Noah Fierer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059310.g004", "stats"=>{"downloads"=>1, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principal_coordinates_analysis_plots_showing_differences_in_bacterial_community_composition_between_farming_practices_/661335", "title"=>"Principal coordinates analysis plots showing differences in bacterial community composition between farming practices.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 09:02:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/999356"], "description"=>"<p>Each produce type and conventional and organic-labeled equivalents are shown. No organic-labeled equivalents were sampled for either type of sprouts.</p>", "links"=>[], "tags"=>["abundances", "belonging"], "article_id"=>661334, "categories"=>["Biological Sciences", "Microbiology", "Plant Biology"], "users"=>["Jonathan W. Leff", "Noah Fierer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059310.g003", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_relative_abundances_177_1_S_E_M_of_bacteria_belonging_to_the_family_Enterobacteriaceae_/661334", "title"=>"Mean relative abundances (±1 S.E.M) of bacteria belonging to the family Enterobacteriaceae.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 09:02:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/999352"], "description"=>"<p>Samples were rarefied at 200 sequences per sample. Circles represent outliers.</p>", "links"=>[], "tags"=>["taxon", "richness"], "article_id"=>661330, "categories"=>["Biological Sciences", "Microbiology", "Plant Biology"], "users"=>["Jonathan W. Leff", "Noah Fierer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0059310.g001", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Boxplot_of_taxon_richness_for_each_produce_type_and_conventional_C_and_organic_O_equivalents_/661330", "title"=>"Boxplot of taxon richness for each produce type and conventional (C) and organic (O) equivalents.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-28 09:01:54"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Agriculture", "average_usage"=>[241, 422, 551, 659, 765, 866, 954, 1043, 1142, 1235, 1311, 1397, 1462]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[281, 484, 611, 728, 835, 934, 1030, 1123, 1214, 1299, 1383, 1464]}, {"subject_area"=>"/Ecology and environmental sciences/Community ecology", "average_usage"=>[285, 478]}, {"subject_area"=>"/Ecology and environmental sciences/Ecology", "average_usage"=>[298, 487, 610, 722, 827, 929, 1029, 1125, 1217, 1306, 1388, 1464, 1535]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[264, 460, 584, 692, 794, 887, 978, 1067, 1154, 1241, 1328, 1408, 1474]}, {"subject_area"=>"/Medicine and health sciences/Pathology and laboratory medicine", "average_usage"=>[267, 466, 592, 709, 806, 901, 989, 1075, 1162, 1254, 1342, 1424, 1486]}]}
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