Independent Studies Using Deep Sequencing Resolve the Same Set of Core Bacterial Species Dominating Gut Communities of Honey Bees
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{"title"=>"Independent studies using deep sequencing resolve the same set of core bacterial species dominating gut communities of honey bees", "type"=>"journal", "authors"=>[{"first_name"=>"Zakee L.", "last_name"=>"Sabree", "scopus_author_id"=>"7801694891"}, {"first_name"=>"Allison K.", "last_name"=>"Hansen", "scopus_author_id"=>"23473162900"}, {"first_name"=>"Nancy A.", "last_name"=>"Moran", "scopus_author_id"=>"7103226925"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"365285019", "sgr"=>"84864058226", "issn"=>"19326203", "pmid"=>"22829932", "scopus"=>"2-s2.0-84864058226", "doi"=>"10.1371/journal.pone.0041250", "isbn"=>"1932-6203"}, "id"=>"a352ec27-5c63-36f1-abb8-6cc54d789cf4", "abstract"=>"Starting in 2003, numerous studies using culture-independent methodologies to characterize the gut microbiota of honey bees have retrieved a consistent and distinctive set of eight bacterial species, based on near identity of the 16S rRNA gene sequences. A recent study [Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton ILG (2012) Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PLoS ONE 7(3): e32962], using pyrosequencing of the V1-V2 hypervariable region of the 16S rRNA gene, reported finding entirely novel bacterial species in honey bee guts, and used taxonomic assignments from these reads to predict metabolic activities based on known metabolisms of cultivable species. To better understand this discrepancy, we analyzed the Mattila et al. pyrotag dataset. In contrast to the conclusions of Mattila et al., we found that the large majority of pyrotag sequences belonged to clusters for which representative sequences were identical to sequences from previously identified core species of the bee microbiota. On average, they represent 95% of the bacteria in each worker bee in the Mattila et al. dataset, a slightly lower value than that found in other studies. Some colonies contain small proportions of other bacteria, mostly species of Enterobacteriaceae. Reanalysis of the Mattila et al. dataset also did not support a relationship between abundances of Bifidobacterium and of putative pathogens or a significant difference in gut communities between colonies from queens that were singly or multiply mated. Additionally, consistent with previous studies, the dataset supports the occurrence of considerable strain variation within core species, even within single colonies. The roles of these bacteria within bees, or the implications of the strain variation, are not yet clear.", "link"=>"http://www.mendeley.com/research/independent-studies-using-deep-sequencing-resolve-same-set-core-bacterial-species-dominating-gut-com", "reader_count"=>126, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>6, "Researcher"=>29, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>5, "Other"=>3, "Student > Master"=>19, "Student > Bachelor"=>12, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>6, "Researcher"=>29, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>5, "Other"=>3, "Student > Master"=>19, "Student > Bachelor"=>12, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>8, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>14, "Agricultural and Biological Sciences"=>91, "Medicine and Dentistry"=>2, "Physics and Astronomy"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>4, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>91}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Unspecified"=>{"Unspecified"=>8}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"New Zealand"=>1, "Canada"=>1, "Colombia"=>1, "Czech Republic"=>1, "United States"=>6, "United Kingdom"=>2, "France"=>1, "Germany"=>2}, "group_count"=>11}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/607044"], "description"=>"<p>“Other” includes the CFB-1 species group, which was uncommon in all samples.</p>", "links"=>[], "tags"=>["abundances", "bee-associated", "bacterial", "mattila", "et"], "article_id"=>277531, "categories"=>["Ecology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Zakee L. Sabree", "Allison K. Hansen", "Nancy A. Moran"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041250.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundances_of_the_typical_bee_associated_bacterial_species_in_the_Mattila_et_al_2012_dataset_/277531", "title"=>"Relative abundances of the typical bee-associated bacterial species in the Mattila et al. (2012) dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-19 02:05:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/607405"], "description"=>"<p>Honey bee species group designations after Babendreier et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041250#pone.0041250-Babendreier1\" target=\"_blank\">[8]</a>.</p>#<p>-For studies using T-RFLP or similar method, presence is shown as “+.” Number of unique associated sequences are indicated in parentheses. For studies with random sequencing, percent representation is given.</p>*<p>-Several other distant lineages retrieved but frequencies cannot be estimated due to the methods used in these studies.</p>̂<p>-Sequences were mostly from cultured isolates and thus may not represent all bacteria in the gut.</p>$<p>-Reads that clustered within the Alpha-2 species group did not pass our initial filtering criteria. These reads were identified after selecting for those between 310–350 bp long. The average abundance of Alpha-2 reads in our analysis of the Mattila et al. (2012) dataset was 1.22%, SD = 0.80%.</p>&<p>-Includes the CFB-1 bee species group.</p>", "links"=>[], "tags"=>["bacterial", "groups", "ubiquitous"], "article_id"=>277900, "categories"=>["Ecology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Zakee L. Sabree", "Allison K. Hansen", "Nancy A. Moran"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041250.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Common_honey_bee_gut_bacterial_species_groups_are_ubiquitous_and_detected_by_multiple_approaches_/277900", "title"=>"Common honey bee gut bacterial species groups are ubiquitous and detected by multiple approaches.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-19 02:11:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/607219"], "description"=>"<p>Putative pathogens include <i>Enterobacteriaceae</i> and a known larval pathogen, <i>Melissococcus plutonius</i>.</p>", "links"=>[], "tags"=>["putative", "pathogens", "mattila", "et"], "article_id"=>277713, "categories"=>["Ecology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Zakee L. Sabree", "Allison K. Hansen", "Nancy A. Moran"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041250.g003", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_Bifidobacterium_and_putative_pathogens_in_the_Mattila_et_al_2012_dataset_/277713", "title"=>"Relationship between <i>Bifidobacterium</i> and putative pathogens in the Mattila et al. (2012) dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-19 02:08:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/607138"], "description"=>"<p>(A) NMS ordination plot showing the two axes representing most of the variation among honey bee gut communities (N = 20). Samples S5 and S7 were omitted as outliers. (B) Species accumulation curves for the two treatments. Dotted lines indicate confidence intervals (±2 SD) for species and distance curves.</p>", "links"=>[], "tags"=>["comparing", "microbiota", "colonies", "singly", "mated", "multiply"], "article_id"=>277634, "categories"=>["Ecology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Zakee L. Sabree", "Allison K. Hansen", "Nancy A. Moran"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041250.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analyses_comparing_microbiota_between_colonies_with_singly_mated_and_multiply_mated_queens_/277634", "title"=>"Analyses comparing microbiota between colonies with singly mated and multiply mated queens.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-19 02:07:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/607367"], "description"=>"*<p>-Species tags for known bee-associated species are the same as those in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041250#pone.0041250-CoxFoster1\" target=\"_blank\">[7]</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041250#pone.0041250-Martinson2\" target=\"_blank\">[10]</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041250#pone.0041250-Moran1\" target=\"_blank\">[14]</a>.</p>", "links"=>[], "tags"=>["taxa", "mattila", "et"], "article_id"=>277861, "categories"=>["Ecology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Zakee L. Sabree", "Allison K. Hansen", "Nancy A. Moran"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041250.t003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Many_of_the_most_active_taxa_from_the_Mattila_et_al_15_study_are_identical_to_known_bee_species_groups_/277861", "title"=>"Many of the most active taxa from the Mattila et al. [15] study are identical to known bee species groups.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-19 02:11:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/607334"], "description"=>"%<p>-Downloaded on March 25, 2012 from the Sequence Read Archive (SRA accession number DRA000526).</p>̂<p>-Raw sequence reads were trimmed to remove low quality (<27 Phred score) base calls and reads that had a) 1 or more errors in the barcode or primer regions, b) a <27 Phred score in >10% of the sequence, or c) were <350 or >400 bp long were omitted.</p>&<p>-OTUs not represented by at least two sequence reads in at least two samples were omitted from final OTUs that were used in our analysis. Proportion of total, high-quality reads after frequency-filtering shown in parentheses.</p>", "links"=>[], "tags"=>["et", "dataset", "pyrotag"], "article_id"=>277829, "categories"=>["Ecology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Zakee L. Sabree", "Allison K. Hansen", "Nancy A. Moran"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041250.t002", "stats"=>{"downloads"=>2, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mattila_et_al_2012_dataset_pyrotag_processing_summary_/277829", "title"=>"Mattila et al. (2012) dataset pyrotag processing summary.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-19 02:10:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/316748", "https://ndownloader.figshare.com/files/316808", "https://ndownloader.figshare.com/files/316913"], "description"=>"<div><p>Starting in 2003, numerous studies using culture-independent methodologies to characterize the gut microbiota of honey bees have retrieved a consistent and distinctive set of eight bacterial species, based on near identity of the 16S rRNA gene sequences. A recent study [<em>Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton ILG (2012) Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PLoS ONE 7(3): e32962</em>], using pyrosequencing of the V1–V2 hypervariable region of the 16S rRNA gene, reported finding entirely novel bacterial species in honey bee guts, and used taxonomic assignments from these reads to predict metabolic activities based on known metabolisms of cultivable species. To better understand this discrepancy, we analyzed the Mattila et al. pyrotag dataset. In contrast to the conclusions of Mattila et al., we found that the large majority of pyrotag sequences belonged to clusters for which representative sequences were identical to sequences from previously identified core species of the bee microbiota. On average, they represent 95% of the bacteria in each worker bee in the Mattila et al. dataset, a slightly lower value than that found in other studies. Some colonies contain small proportions of other bacteria, mostly species of Enterobacteriaceae. Reanalysis of the Mattila et al. dataset also did not support a relationship between abundances of <em>Bifidobacterium</em> and of putative pathogens or a significant difference in gut communities between colonies from queens that were singly or multiply mated. Additionally, consistent with previous studies, the dataset supports the occurrence of considerable strain variation within core species, even within single colonies. The roles of these bacteria within bees, or the implications of the strain variation, are not yet clear.</p> </div>", "links"=>[], "tags"=>["studies", "sequencing", "bacterial", "dominating", "communities", "bees"], "article_id"=>122515, "categories"=>["Ecology", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Zakee L. Sabree", "Allison K. Hansen", "Nancy A. Moran"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041250.s001", "https://dx.doi.org/10.1371/journal.pone.0041250.s002", "https://dx.doi.org/10.1371/journal.pone.0041250.s003"], "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Independent_Studies_Using_Deep_Sequencing_Resolve_the_Same_Set_of_Core_Bacterial_Species_Dominating_Gut_Communities_of_Honey_Bees/122515", "title"=>"Independent Studies Using Deep Sequencing Resolve the Same Set of Core Bacterial Species Dominating Gut Communities of Honey Bees", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-07-19 00:41:55"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[319, 556, 679, 785, 881, 970, 1062, 1149, 1236, 1323, 1402, 1474, 1545, 1617, 1681, 1754, 1822, 1892, 1963, 2031, 2099, 2165, 2233, 2299, 2359]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[331, 557, 677, 777, 868, 960, 1050, 1136, 1223, 1307, 1390, 1466, 1536, 1603, 1673, 1741, 1814, 1889, 1954, 2028, 2096, 2164, 2233, 2305, 2362]}]}
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