Comparing Bacterial Community Composition between Healthy and White Plague-Like Disease States in Orbicella annularis Using PhyloChip™ G3 Microarrays
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{"title"=>"Comparing bacterial community composition between healthy and white plague-like disease states in Orbicella annularis using PhyloChip™ G3 microarrays", "type"=>"journal", "authors"=>[{"first_name"=>"Christina A.", "last_name"=>"Kellogg", "scopus_author_id"=>"7006039925"}, {"first_name"=>"Yvette M.", "last_name"=>"Piceno", "scopus_author_id"=>"6603297197"}, {"first_name"=>"Lauren M.", "last_name"=>"Tom", "scopus_author_id"=>"36629380400"}, {"first_name"=>"Todd Z.", "last_name"=>"DeSantis", "scopus_author_id"=>"6602743913"}, {"first_name"=>"Michael A.", "last_name"=>"Gray", "scopus_author_id"=>"7401584667"}, {"first_name"=>"David G.", "last_name"=>"Zawada", "scopus_author_id"=>"6506437885"}, {"first_name"=>"Gary L.", "last_name"=>"Andersen", "scopus_author_id"=>"7202552651"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"372435554", "sgr"=>"84893409175", "doi"=>"10.1371/journal.pone.0079801", "scopus"=>"2-s2.0-84893409175", "pmid"=>"24278181"}, "id"=>"fddf9b3c-122f-3b6d-b66c-c8778dc0abeb", "abstract"=>"<p>Coral disease is a global problem. Diseases are typically named or described based on macroscopic changes, but broad signs of coral distress such as tissue loss or discoloration are unlikely to be specific to a particular pathogen. For example, there appear to be multiple diseases that manifest the rapid tissue loss that characterizes ‘white plague.’ PhyloChip™ G3 microarrays were used to compare the bacterial community composition of both healthy and white plague-like diseased corals. Samples of lobed star coral (<italic>Orbicella annularis</italic>, formerly of the genus <italic>Montastraea</italic> <xref ref-type=\"bibr\" rid=\"pone.0079801-Budd1\">[1]</xref>) were collected from two geographically distinct areas, Dry Tortugas National Park and Virgin Islands National Park, to determine if there were biogeographic differences between the diseases. In fact, all diseased samples clustered together, however there was no consistent link to <italic>Aurantimonas coralicida</italic>, which has been described as the causative agent of white plague type II. The microarrays revealed a large amount of bacterial heterogeneity within the healthy corals and less diversity in the diseased corals. Gram-positive bacterial groups (Actinobacteria, Firmicutes) comprised a greater proportion of the operational taxonomic units (OTUs) unique to healthy samples. Diseased samples were enriched in OTUs from the families Corynebacteriaceae, Lachnospiraceae, Rhodobacteraceae, and Streptococcaceae. Much previous coral disease work has used clone libraries, which seem to be methodologically biased toward recovery of Gram-negative bacterial sequences and may therefore have missed the importance of Gram-positive groups. The PhyloChip™data presented here provide a broader characterization of the bacterial community changes that occur within <italic>Orbicella annularis</italic> during the shift from a healthy to diseased state.</p>", "link"=>"http://www.mendeley.com/research/comparing-bacterial-community-composition-between-healthy-white-plaguelike-disease-states-orbicella", "reader_count"=>35, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>2, "Researcher"=>5, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Other"=>3, "Student > Master"=>9, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>2, "Researcher"=>5, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Other"=>3, "Student > Master"=>9, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>6}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Hong Kong"=>1, "Belgium"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1290005"], "description"=>"<p>The 12 families shown were those representing greater than 5% of at least one sample. The remaining families are collectively represented by the ‘other’ category. The size of each color block (assigned to families in the key below) represents the number of OTUs detected in the family relative to the total number of OTUs detected in that sample. Individual samples are presented on the left and cumulative healthy and diseased profiles on the right.</p>", "links"=>[], "tags"=>["bacterial", "plague-like", "diseased"], "article_id"=>858285, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "David G. Zawada", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079801.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_diversity_within_bacterial_families_associated_with_healthy_and_white_plague_like_diseased_corals_/858285", "title"=>"Relative diversity within bacterial families associated with healthy and white plague-like diseased corals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-20 03:31:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1290001"], "description"=>"<p>Panel A is based on total OTUs (13,441). Panel B is based on the subset of OTUs that include at least one coral-associated sequence (313).</p>", "links"=>[], "tags"=>["multidimensional", "scaling", "bray-curtis", "otu"], "article_id"=>858281, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "David G. Zawada", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079801.g001", "stats"=>{"downloads"=>1, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Non_metric_multidimensional_scaling_NMDS_plot_of_samples_based_on_Bray_Curtis_similarity_of_presence_absence_OTU_data_/858281", "title"=>"Non-metric multidimensional scaling (NMDS) plot of samples, based on Bray-Curtis similarity of presence/absence OTU data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-20 03:31:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1290009"], "description"=>"<p>Operational taxonomic units (OTUs) unique to diseased samples and present in ≥50% (five or more) diseased replicates.</p>", "links"=>[], "tags"=>["taxonomic", "units", "diseased", "samples"], "article_id"=>858289, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "David G. Zawada", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079801.t004", "stats"=>{"downloads"=>17, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Operational_taxonomic_units_OTUs_unique_to_diseased_samples_and_present_in_8805_50_five_or_more_diseased_replicates_/858289", "title"=>"Operational taxonomic units (OTUs) unique to diseased samples and present in ≥50% (five or more) diseased replicates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-20 03:31:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1290007"], "description"=>"<p>Top panel includes all OTUs. Bottom panel excludes singletons (defined as OTUs present only in a single sample).</p>", "links"=>[], "tags"=>["taxonomic", "members", "replicate", "diseased", "coral", "samples", "sunagawa", "et"], "article_id"=>858287, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "David G. Zawada", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079801.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enumeration_of_taxonomic_rank_members_detected_across_replicate_PhyloChips_8482_from_healthy_and_diseased_coral_samples_after_Sunagawa_et_al_2009_/858287", "title"=>"Enumeration of taxonomic rank members detected across replicate PhyloChips™ from healthy and diseased coral samples (after Sunagawa et al, 2009).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-20 03:31:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1290008"], "description"=>"<p>A healthy sample designated VIISMAH08 was collected but no 16S rRNA gene PCR product was obtained, so it was not included in this table since it does not appear in any subsequent figures.</p><p>Note that in spite of extensive searching, the three samples of white plague-like disease collected in DRTO were the only ones encountered.</p>", "links"=>[], "tags"=>["samples", "microarray"], "article_id"=>858288, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "David G. Zawada", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079801.t001", "stats"=>{"downloads"=>3, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Orbicella_annularis_samples_collected_for_microarray_analysis_/858288", "title"=>"<i>Orbicella annularis</i> samples collected for microarray analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-20 03:31:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1290006"], "description"=>"<p>Operational taxonomic units (OTUs) unique to healthy samples and present in greater than 50% (five or more) healthy replicates.</p>", "links"=>[], "tags"=>["taxonomic", "units", "samples"], "article_id"=>858286, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "David G. Zawada", "Gary L. Andersen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0079801.t003", "stats"=>{"downloads"=>9, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Operational_taxonomic_units_OTUs_unique_to_healthy_samples_and_present_in_greater_than_50_five_or_more_healthy_replicates_/858286", "title"=>"Operational taxonomic units (OTUs) unique to healthy samples and present in greater than 50% (five or more) healthy replicates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-20 03:31:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1290011", "https://ndownloader.figshare.com/files/1290012", "https://ndownloader.figshare.com/files/1290013", "https://ndownloader.figshare.com/files/1290014"], "description"=>"<div><p>Coral disease is a global problem. Diseases are typically named or described based on macroscopic changes, but broad signs of coral distress such as tissue loss or discoloration are unlikely to be specific to a particular pathogen. For example, there appear to be multiple diseases that manifest the rapid tissue loss that characterizes ‘white plague.’ PhyloChip™ G3 microarrays were used to compare the bacterial community composition of both healthy and white plague-like diseased corals. Samples of lobed star coral (<i>Orbicella annularis</i>, formerly of the genus <i>Montastraea</i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079801#pone.0079801-Budd1\" target=\"_blank\">[1]</a>) were collected from two geographically distinct areas, Dry Tortugas National Park and Virgin Islands National Park, to determine if there were biogeographic differences between the diseases. In fact, all diseased samples clustered together, however there was no consistent link to <i>Aurantimonas coralicida</i>, which has been described as the causative agent of white plague type II. The microarrays revealed a large amount of bacterial heterogeneity within the healthy corals and less diversity in the diseased corals. Gram-positive bacterial groups (Actinobacteria, Firmicutes) comprised a greater proportion of the operational taxonomic units (OTUs) unique to healthy samples. Diseased samples were enriched in OTUs from the families Corynebacteriaceae, Lachnospiraceae, Rhodobacteraceae, and Streptococcaceae. Much previous coral disease work has used clone libraries, which seem to be methodologically biased toward recovery of Gram-negative bacterial sequences and may therefore have missed the importance of Gram-positive groups. The PhyloChip™data presented here provide a broader characterization of the bacterial community changes that occur within <i>Orbicella annularis</i> during the shift from a healthy to diseased state.</p></div>", "links"=>[], "tags"=>["comparing", "bacterial", "plague-like", "states", "g3", "microarrays"], "article_id"=>858291, "categories"=>["Biological Sciences", "Earth and Environmental Sciences"], "users"=>["Christina A. Kellogg", "Yvette M. Piceno", "Lauren M. Tom", "Todd Z. DeSantis", "Michael A. Gray", "David G. Zawada", "Gary L. Andersen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0079801.s001", "https://dx.doi.org/10.1371/journal.pone.0079801.s002", "https://dx.doi.org/10.1371/journal.pone.0079801.s003", "https://dx.doi.org/10.1371/journal.pone.0079801.s004"], "stats"=>{"downloads"=>7, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparing_Bacterial_Community_Composition_between_Healthy_and_White_Plague_Like_Disease_States_in_Orbicella_annularis_Using_PhyloChip_G3_Microarrays/858291", "title"=>"Comparing Bacterial Community Composition between Healthy and White Plague-Like Disease States in <i>Orbicella annularis</i> Using PhyloChip™ G3 Microarrays", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-11-20 03:31:41"}

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/Marine biology", "average_usage"=>[379, 624, 751, 898, 1019, 1162, 1280, 1377, 1482, 1611, 1750, 1853, 1936, 1987]}, {"subject_area"=>"/Biology and life sciences/Microbiology", "average_usage"=>[293, 503, 638, 755, 861, 960, 1056, 1146, 1239, 1323, 1403, 1491, 1568]}, {"subject_area"=>"/Earth sciences/Marine and aquatic sciences", "average_usage"=>[299, 492, 619, 718, 826, 932, 1037, 1143, 1246, 1333, 1414, 1517, 1575]}, {"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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