Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing
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{"title"=>"Bacterial community shift in treated periodontitis patients revealed by Ion Torrent 16S rRNA gene amplicon sequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Sebastian", "last_name"=>"Jünemann", "scopus_author_id"=>"26321076900"}, {"first_name"=>"Karola", "last_name"=>"Prior", "scopus_author_id"=>"7006321481"}, {"first_name"=>"Rafael", "last_name"=>"Szczepanowski", "scopus_author_id"=>"6603414650"}, {"first_name"=>"Inga", "last_name"=>"Harks", "scopus_author_id"=>"55330863600"}, {"first_name"=>"Benjamin", "last_name"=>"Ehmke", "scopus_author_id"=>"6602605240"}, {"first_name"=>"Alexander", "last_name"=>"Goesmann", "scopus_author_id"=>"6602252377"}, {"first_name"=>"Jens", "last_name"=>"Stoye", "scopus_author_id"=>"7006553911"}, {"first_name"=>"Dag", "last_name"=>"Harmsen", "scopus_author_id"=>"55648218700"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84864754044", "pui"=>"365367070", "doi"=>"10.1371/journal.pone.0041606", "isbn"=>"10.1371/journal.pone.0041606", "sgr"=>"84864754044", "pmid"=>"22870235"}, "id"=>"fea8c920-7e58-371c-bdcf-198c2abefe1d", "abstract"=>"Periodontitis, one of the most common diseases in the world, is caused by a mixture of pathogenic bacteria and inflammatory host responses and often treated by antimicrobials as an adjunct to scaling and root planing (SRP). Our study aims to elucidate explorative and descriptive temporal shifts in bacterial communities between patients treated by SRP alone versus SRP plus antibiotics. This is the first metagenomic study using an Ion Torrent Personal Genome Machine (PGM). Eight subgingival plaque samples from four patients with chronic periodontitis, taken before and two months after intervention were analyzed. Amplicons from the V6 hypervariable region of the 16S rRNA gene were generated and sequenced each on a 314 chip. Sequencing reads were clustered into operational taxonomic units (OTUs, 3% distance), described by community metrics, and taxonomically classified. Reads ranging from 599,933 to 650,416 per sample were clustered into 1,648 to 2,659 non-singleton OTUs, respectively. Increased diversity (Shannon and Simpson) in all samples after therapy was observed regardless of the treatment type whereas richness (ACE) showed no correlation. Taxonomic analysis revealed different microbial shifts between both therapy approaches at all taxonomic levels. Most remarkably, the genera Porphyromonas, Tannerella, Treponema, and Filifactor all harboring periodontal pathogenic species were removed almost only in the group treated with SPR and antibiotics. For the species T. forsythia and P. gingivalis results were corroborated by real-time PCR analysis. In the future, hypothesis free metagenomic analysis could be the key in understanding polymicrobial diseases and be used for therapy monitoring. Therefore, as read length continues to increase and cost to decrease, rapid benchtop sequencers like the PGM might finally be used in routine diagnostic.", "link"=>"http://www.mendeley.com/research/bacterial-community-shift-treated-periodontitis-patients-revealed-ion-torrent-16s-rrna-gene-amplicon", "reader_count"=>243, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>14, "Researcher"=>69, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>59, "Student > Postgraduate"=>21, "Student > Master"=>30, "Other"=>10, "Student > Bachelor"=>8, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>2, "Professor"=>13}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>14, "Researcher"=>69, "Student > Doctoral Student"=>12, "Student > Ph. D. Student"=>59, "Student > Postgraduate"=>21, "Student > Master"=>30, "Other"=>10, "Student > Bachelor"=>8, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>2, "Professor"=>13}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Agricultural and Biological Sciences"=>151, "Arts and Humanities"=>1, "Business, Management and Accounting"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>1, "Computer Science"=>3, "Earth and Planetary Sciences"=>1, "Engineering"=>3, "Environmental Science"=>12, "Biochemistry, Genetics and Molecular Biology"=>19, "Nursing and Health Professions"=>1, "Medicine and Dentistry"=>31, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Immunology and Microbiology"=>8}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>31}, "Unspecified"=>{"Unspecified"=>9}, "Environmental Science"=>{"Environmental Science"=>12}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>8}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>151}, "Computer Science"=>{"Computer Science"=>3}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>19}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"United States"=>12, "Uruguay"=>1, "United Kingdom"=>3, "Switzerland"=>1, "Portugal"=>1, "Spain"=>2, "Netherlands"=>1, "Sweden"=>1, "Belgium"=>2, "Luxembourg"=>1, "Macao"=>1, "Brazil"=>2, "South Africa"=>2, "Mexico"=>3, "Chile"=>4, "Australia"=>1, "Germany"=>2, "Estonia"=>1}, "group_count"=>10}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/598090"], "description"=>"*<p>OTU clusters were generated by complete linkage clustering at 97% identity threshold excluding singleton clusters; numbers in parentheses give OTU counts including singleton clusters.</p>", "links"=>[], "tags"=>["richness", "estimates", "subgingival", "plaque", "samples"], "article_id"=>268574, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Sebastian Jünemann", "Karola Prior", "Rafael Szczepanowski", "Inga Harks", "Benjamin Ehmke", "Alexander Goesmann", "Jens Stoye", "Dag Harmsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041606.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_OTU_counts_richness_and_diversity_estimates_for_the_bacteria_in_subgingival_plaque_samples_before_and_after_intervention_/268574", "title"=>"OTU counts, richness and diversity estimates for the bacteria in subgingival plaque samples before and after intervention.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-01 02:22:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/312584", "https://ndownloader.figshare.com/files/312602"], "description"=>"<div><p>Periodontitis, one of the most common diseases in the world, is caused by a mixture of pathogenic bacteria and inflammatory host responses and often treated by antimicrobials as an adjunct to scaling and root planing (SRP). Our study aims to elucidate explorative and descriptive temporal shifts in bacterial communities between patients treated by SRP alone versus SRP plus antibiotics. This is the first metagenomic study using an Ion Torrent Personal Genome Machine (PGM). Eight subgingival plaque samples from four patients with chronic periodontitis, taken before and two months after intervention were analyzed. Amplicons from the V6 hypervariable region of the 16S rRNA gene were generated and sequenced each on a 314 chip. Sequencing reads were clustered into operational taxonomic units (OTUs, 3% distance), described by community metrics, and taxonomically classified. Reads ranging from 599,933 to 650,416 per sample were clustered into 1,648 to 2,659 non-singleton OTUs, respectively. Increased diversity (Shannon and Simpson) in all samples after therapy was observed regardless of the treatment type whereas richness (ACE) showed no correlation. Taxonomic analysis revealed different microbial shifts between both therapy approaches at all taxonomic levels. Most remarkably, the genera <em>Porphyromonas</em>, <em>Tannerella</em>, <em>Treponema</em>, and <em>Filifactor</em> all harboring periodontal pathogenic species were removed almost only in the group treated with SPR and antibiotics. For the species <em>T. forsythia</em> and <em>P. gingivalis</em> results were corroborated by real-time PCR analysis. In the future, hypothesis free metagenomic analysis could be the key in understanding polymicrobial diseases and be used for therapy monitoring. Therefore, as read length continues to increase and cost to decrease, rapid benchtop sequencers like the PGM might finally be used in routine diagnostic.</p> </div>", "links"=>[], "tags"=>["bacterial", "treated", "periodontitis", "patients", "revealed", "ion", "torrent", "16s", "rrna", "amplicon", "sequencing"], "article_id"=>121658, "categories"=>["Cancer", "Genetics", "Microbiology"], "users"=>["Sebastian Jünemann", "Karola Prior", "Rafael Szczepanowski", "Inga Harks", "Benjamin Ehmke", "Alexander Goesmann", "Jens Stoye", "Dag Harmsen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041606.s001", "https://dx.doi.org/10.1371/journal.pone.0041606.s002"], "stats"=>{"downloads"=>5, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Bacterial_Community_Shift_in_Treated_Periodontitis_Patients_Revealed_by_Ion_Torrent_16S_rRNA_Gene_Amplicon_Sequencing/121658", "title"=>"Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-01 00:27:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/598022"], "description"=>"$<p>Sample abbreviations: Co, control group; Ex, experimental group; pre, before intervention; post, after intervention.</p>*<p>Number of remaining reads after applying quality criteria as described in the Methods section.</p>**<p>Unique high quality reads after de-noising the data by Single Linkage Preclustering at 2% edit distance.</p>", "links"=>[], "tags"=>["genetics and genomics", "Infectious diseases", "microbiology"], "article_id"=>268509, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Sebastian Jünemann", "Karola Prior", "Rafael Szczepanowski", "Inga Harks", "Benjamin Ehmke", "Alexander Goesmann", "Jens Stoye", "Dag Harmsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041606.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_sequence_processing_/268509", "title"=>"Summary of sequence processing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-01 02:21:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/597974"], "description"=>"*<p>not detected</p>", "links"=>[], "tags"=>["equivalents", "microliter", "Real-time"], "article_id"=>268463, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Sebastian Jünemann", "Karola Prior", "Rafael Szczepanowski", "Inga Harks", "Benjamin Ehmke", "Alexander Goesmann", "Jens Stoye", "Dag Harmsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041606.t004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_equivalents_per_microliter_of_P_gingivalis_and_T_forsythia_detected_by_real_time_PCR_/268463", "title"=>"Genomic equivalents per microliter of <i>P. gingivalis</i> and <i>T. forsythia</i> detected by real-time PCR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-01 02:21:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/598052"], "description"=>"$<p>Only phyla with a relative abundance of more than half a percent within at least a single sample are shown.</p>*<p>All remaining phyla with relative abundance lower than half a percent.</p>**<p>Reads where unambiguous taxonomic classification was not possible.</p>", "links"=>[], "tags"=>["abundance", "phyla", "subgingival", "plaque"], "article_id"=>268541, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Sebastian Jünemann", "Karola Prior", "Rafael Szczepanowski", "Inga Harks", "Benjamin Ehmke", "Alexander Goesmann", "Jens Stoye", "Dag Harmsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041606.t003", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundance_of_the_main_phyla_identified_in_subgingival_plaque_samples_/268541", "title"=>"Relative abundance of the main phyla identified in subgingival plaque samples.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-01 02:22:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/597891"], "description"=>"<p>Each bar displays the normalized relative abundance (individual relative abundance divided by the number of analyzed samples at the given time point) of the corresponding genera pre and post intervention. Each bar is further partitioned into four stacked parts for each of the four analyzed patients. The color indicates the type of intervention (blue for control, red for experimental group).</p>", "links"=>[], "tags"=>["abundance", "prevalent", "genera", "subgingival", "plaque", "samples"], "article_id"=>268374, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Sebastian Jünemann", "Karola Prior", "Rafael Szczepanowski", "Inga Harks", "Benjamin Ehmke", "Alexander Goesmann", "Jens Stoye", "Dag Harmsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041606.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundance_of_the_most_prevalent_genera_gt_8202_8202_1_relative_abundance_within_one_sample_in_subgingival_plaque_samples_before_and_after_intervention_/268374", "title"=>"Relative abundance of the most prevalent genera (> = 1% relative abundance within one sample) in subgingival plaque samples before and after intervention.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-01 02:19:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/597750"], "description"=>"<p>In total samples from four patients were analyzed two times, i.e., before (continuous lines) and two months after intervention (dashed lines). Two control group patients (Co) were treated by SRP alone whereas two experimental group patients (Ex) received SRP plus adjunctive antibiotics. Lines are colored according to the sample origin.</p>", "links"=>[], "tags"=>["clustering", "de-noised"], "article_id"=>268239, "categories"=>["Microbiology", "Genetics", "Infectious Diseases"], "users"=>["Sebastian Jünemann", "Karola Prior", "Rafael Szczepanowski", "Inga Harks", "Benjamin Ehmke", "Alexander Goesmann", "Jens Stoye", "Dag Harmsen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041606.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rarefaction_analysis_for_each_sample_based_on_clustering_of_high_quality_de_noised_reads_/268239", "title"=>"Rarefaction analysis for each sample based on clustering of high quality de-noised reads.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-01 02:17:19"}

PMC Usage Stats | Further Information

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Relative Metric

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