Metagenomic Profile of the Bacterial Communities Associated with Ixodes ricinus Ticks
Publication Date
October 13, 2011
Journal
PLOS ONE
Authors
Giovanna Carpi, Francesca Cagnacci, Nicola E. Wittekindt, Fangqing Zhao, et al
Volume
6
Issue
10
Pages
e25604
DOI
https://dx.plos.org/10.1371/journal.pone.0025604
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0025604
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22022422
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192763
Europe PMC
http://europepmc.org/abstract/MED/22022422
Web of Science
000295978600024
Scopus
80054052509
Mendeley
http://www.mendeley.com/research/metagenomic-profile-bacterial-communities-associated-ixodes-ricinus-ticks
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Mendeley | Further Information

{"title"=>"Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks", "type"=>"journal", "authors"=>[{"first_name"=>"Giovanna", "last_name"=>"Carpi", "scopus_author_id"=>"24832623100"}, {"first_name"=>"Francesca", "last_name"=>"Cagnacci", "scopus_author_id"=>"24832983900"}, {"first_name"=>"Nicola E.", "last_name"=>"Wittekindt", "scopus_author_id"=>"6507062264"}, {"first_name"=>"Fangqing", "last_name"=>"Zhao", "scopus_author_id"=>"9246636300"}, {"first_name"=>"Ji", "last_name"=>"Qi", "scopus_author_id"=>"13608357200"}, {"first_name"=>"Lynn P.", "last_name"=>"Tomsho", "scopus_author_id"=>"6507296971"}, {"first_name"=>"Daniela I.", "last_name"=>"Drautz", "scopus_author_id"=>"22134157200"}, {"first_name"=>"Annapaola", "last_name"=>"Rizzoli", "scopus_author_id"=>"7005546158"}, {"first_name"=>"Stephan C.", "last_name"=>"Schuster", "scopus_author_id"=>"7202029217"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"362750911", "sgr"=>"80054052509", "issn"=>"19326203", "pmid"=>"22022422", "scopus"=>"2-s2.0-80054052509", "doi"=>"10.1371/journal.pone.0025604", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"8702bffd-bf54-3f15-b391-d6d48aec2218", "abstract"=>"Assessment of the microbial diversity residing in arthropod vectors of medical importance is crucial for monitoring endemic infections, for surveillance of newly emerging zoonotic pathogens, and for unraveling the associated bacteria within its host. The tick Ixodes ricinus is recognized as the primary European vector of disease-causing bacteria in humans. Despite I. ricinus being of great public health relevance, its microbial communities remain largely unexplored to date. Here we evaluate the pathogen-load and the microbiome in single adult I. ricinus by using 454- and Illumina-based metagenomic approaches. Genomic DNA-derived sequences were taxonomically profiled using a computational approach based on the BWA algorithm, allowing for the identification of known tick-borne pathogens at the strain level and the putative tick core microbiome. Additionally, we assessed and compared the bacterial taxonomic profile in nymphal and adult I. ricinus pools collected from two distinct geographic regions in Northern Italy by means of V6-16S rRNA amplicon pyrosequencing and community based ecological analysis. A total of 108 genera belonging to representatives of all bacterial phyla were detected and a rapid qualitative assessment for pathogenic bacteria, such as Borrelia, Rickettsia and Candidatus Neoehrlichia, and for other bacteria with mutualistic relationship or undetermined function, such as Wolbachia and Rickettsiella, was possible. Interestingly, the ecological analysis revealed that the bacterial community structure differed between the examined geographic regions and tick life stages. This finding suggests that the environmental context (abiotic and biotic factors) and host-selection behaviors affect their microbiome.Our data provide the most complete picture to date of the bacterial communities present within I. ricinus under natural conditions by using high-throughput sequencing technologies. This study further demonstrates a novel detection strategy for the microbiomes of arthropod vectors in the context of epidemiological and ecological studies.", "link"=>"http://www.mendeley.com/research/metagenomic-profile-bacterial-communities-associated-ixodes-ricinus-ticks", "reader_count"=>174, "reader_count_by_academic_status"=>{"Unspecified"=>6, "Professor > Associate Professor"=>7, "Researcher"=>44, "Student > Doctoral Student"=>15, "Student > Ph. D. Student"=>39, "Student > Postgraduate"=>8, "Other"=>4, "Student > Master"=>32, "Student > Bachelor"=>12, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>6, "Professor > Associate Professor"=>7, "Researcher"=>44, "Student > Doctoral Student"=>15, "Student > Ph. D. Student"=>39, "Student > Postgraduate"=>8, "Other"=>4, "Student > Master"=>32, "Student > Bachelor"=>12, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>12, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>14, "Agricultural and Biological Sciences"=>120, "Medicine and Dentistry"=>12, "Veterinary Science and Veterinary Medicine"=>2, "Business, Management and Accounting"=>1, "Social Sciences"=>3, "Immunology and Microbiology"=>5}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>12}, "Social Sciences"=>{"Social Sciences"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>120}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Unspecified"=>{"Unspecified"=>12}, "Environmental Science"=>{"Environmental Science"=>5}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>6, "United Kingdom"=>1, "Spain"=>2, "Russia"=>1, "New Zealand"=>1, "Netherlands"=>1, "Sweden"=>1, "Belgium"=>1, "Finland"=>1, "Brazil"=>2, "Mexico"=>1, "Italy"=>3, "France"=>3, "Germany"=>1}, "group_count"=>10}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/724430"], "description"=>"<p>The height of the bars corresponds to the number of hits for each genus. ‘Not assigned’ indicates sequences matching to sequences in the NCBI database that are not assigned to taxa. ‘No hits’ indicates reads for which no sequence match was found in the BLASTX analysis.</p>", "links"=>[], "tags"=>["bacterial", "taxonomic", "profiles", "genomic", "dna", "cdna-derived", "sequences", "tick", "ir"], "article_id"=>394765, "categories"=>["Microbiology", "Ecology", "Genetics", "Infectious Diseases"], "users"=>["Giovanna Carpi", "Francesca Cagnacci", "Nicola E. Wittekindt", "Fangqing Zhao", "Ji Qi", "Lynn P. Tomsho", "Daniela I. Drautz", "Annapaola Rizzoli", "Stephan C. Schuster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025604.g001", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MEGAN_comparison_of_the_bacterial_taxonomic_profiles_of_genomic_DNA_red_and_cDNA_derived_sequences_blue_from_tick_sample_Ir_1_4_/394765", "title"=>"MEGAN comparison of the bacterial taxonomic profiles of genomic DNA (red) and cDNA-derived sequences (blue) from tick sample Ir 1-4.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:19:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/366463", "https://ndownloader.figshare.com/files/366500", "https://ndownloader.figshare.com/files/366517", "https://ndownloader.figshare.com/files/366564", "https://ndownloader.figshare.com/files/366602", "https://ndownloader.figshare.com/files/366646"], "description"=>"<div><p>Assessment of the microbial diversity residing in arthropod vectors of medical importance is crucial for monitoring endemic infections, for surveillance of newly emerging zoonotic pathogens, and for unraveling the associated bacteria within its host. The tick <em>Ixodes ricinus</em> is recognized as the primary European vector of disease-causing bacteria in humans. Despite <em>I. ricinus</em> being of great public health relevance, its microbial communities remain largely unexplored to date. Here we evaluate the pathogen-load and the microbiome in single adult <em>I. ricinus</em> by using 454- and Illumina-based metagenomic approaches. Genomic DNA-derived sequences were taxonomically profiled using a computational approach based on the BWA algorithm, allowing for the identification of known tick-borne pathogens at the strain level and the putative tick core microbiome. Additionally, we assessed and compared the bacterial taxonomic profile in nymphal and adult <em>I. ricinus</em> pools collected from two distinct geographic regions in Northern Italy by means of V6-16S rRNA amplicon pyrosequencing and community based ecological analysis. A total of 108 genera belonging to representatives of all bacterial phyla were detected and a rapid qualitative assessment for pathogenic bacteria, such as <em>Borrelia, Rickettsia</em> and <em>Candidatus</em> Neoehrlichia, and for other bacteria with mutualistic relationship or undetermined function, such as <em>Wolbachia</em> and <em>Rickettsiella</em>, was possible. Interestingly, the ecological analysis revealed that the bacterial community structure differed between the examined geographic regions and tick life stages. This finding suggests that the environmental context (abiotic and biotic factors) and host-selection behaviors affect their microbiome.</p> <p>Our data provide the most complete picture to date of the bacterial communities present within <em>I. ricinus</em> under natural conditions by using high-throughput sequencing technologies. This study further demonstrates a novel detection strategy for the microbiomes of arthropod vectors in the context of epidemiological and ecological studies.</p> </div>", "links"=>[], "tags"=>["metagenomic", "bacterial", "communities", "ticks"], "article_id"=>132414, "categories"=>["Cancer", "Genetics", "Ecology", "Microbiology"], "users"=>["Giovanna Carpi", "Francesca Cagnacci", "Nicola E. Wittekindt", "Fangqing Zhao", "Ji Qi", "Lynn P. Tomsho", "Daniela I. Drautz", "Annapaola Rizzoli", "Stephan C. Schuster"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0025604.s001", "https://dx.doi.org/10.1371/journal.pone.0025604.s002", "https://dx.doi.org/10.1371/journal.pone.0025604.s003", "https://dx.doi.org/10.1371/journal.pone.0025604.s004", "https://dx.doi.org/10.1371/journal.pone.0025604.s005", "https://dx.doi.org/10.1371/journal.pone.0025604.s006"], "stats"=>{"downloads"=>7, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Metagenomic_Profile_of_the_Bacterial_Communities_Associated_with_Ixodes_ricinus_Ticks/132414", "title"=>"Metagenomic Profile of the Bacterial Communities Associated with <em>Ixodes ricinus</em> Ticks", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-10-13 00:40:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/725036"], "description"=>"a<p>TN region: Trento Province.</p>b<p>BL region: Belluno Province.</p>c<p>N tick stage: Nymphs.</p>d<p>AD tick stage: Adults.</p>", "links"=>[], "tags"=>["occurrence", "breadth", "bacterial", "ticks", "taxa", "overlap", "tick", "geographic", "indexes"], "article_id"=>395373, "categories"=>["Microbiology", "Ecology", "Genetics", "Infectious Diseases"], "users"=>["Giovanna Carpi", "Francesca Cagnacci", "Nicola E. Wittekindt", "Fangqing Zhao", "Ji Qi", "Lynn P. Tomsho", "Daniela I. Drautz", "Annapaola Rizzoli", "Stephan C. Schuster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025604.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Taxa_occurrence_breadth_in_bacterial_community_of_ticks_Levins_index_Bsta_and_taxa_occurrence_overlap_Pianka_index_O_between_tick_stages_and_geographic_regions_Indexes_vary_between_0_and_1_/395373", "title"=>"Taxa occurrence breadth in bacterial community of ticks (Levins index, Bsta) and taxa occurrence overlap (Pianka index, O) between tick stages, and geographic regions. Indexes vary between 0 and 1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-10-13 01:29:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/724838"], "description"=>"<p>Ordination of sites along the first two canonical axes and the environmental variables, represented by arrows are showed. AD: tick stage, TN: geographic region. Dots represent sites, i.e. 1: nymph ticks, TN region; 2: nymph ticks, BL region; 3: adult ticks, TN region; 4: adult ticks, BL region. Bacterial taxa were omitted for clarity.</p>", "links"=>[], "tags"=>["correspondence", "ordination"], "article_id"=>395189, "categories"=>["Microbiology", "Ecology", "Genetics", "Infectious Diseases"], "users"=>["Giovanna Carpi", "Francesca Cagnacci", "Nicola E. Wittekindt", "Fangqing Zhao", "Ji Qi", "Lynn P. Tomsho", "Daniela I. Drautz", "Annapaola Rizzoli", "Stephan C. Schuster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025604.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Canonical_correspondence_analysis_ordination_diagram_/395189", "title"=>"Canonical correspondence analysis ordination diagram.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:26:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/724745"], "description"=>"<p>The height of the bars corresponds to the number of hits for each genus. Highlighted in light yellow are bacteria genera recognized as tick-borne pathogens or tick endosymbionts.</p>", "links"=>[], "tags"=>["bacterial", "taxonomic", "profiles", "tick", "pools", "stages", "geographic", "v6", "amplicon", "16s", "rrna", "reads", "ribosomal"], "article_id"=>395075, "categories"=>["Microbiology", "Ecology", "Genetics", "Infectious Diseases"], "users"=>["Giovanna Carpi", "Francesca Cagnacci", "Nicola E. Wittekindt", "Fangqing Zhao", "Ji Qi", "Lynn P. Tomsho", "Daniela I. Drautz", "Annapaola Rizzoli", "Stephan C. Schuster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025604.g003", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MEGAN_comparison_of_bacterial_taxonomic_profiles_of_four_tick_pools_reflecting_different_life_stages_and_geographic_provenience_based_on_the_V6_amplicon_16S_rRNA_gene_sequence_reads_analyzed_against_the_Ribosomal_Database_/395075", "title"=>"MEGAN comparison of bacterial taxonomic profiles of four tick pools (reflecting different life stages and geographic provenience) based on the V6 amplicon 16S rRNA gene sequence reads analyzed against the Ribosomal Database.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:24:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/724974"], "description"=>"a<p>AD: adult tick life stage.</p>b<p>TN: TN region.</p><p>Goodness of fit of biplot is also shown.</p>", "links"=>[], "tags"=>["canonical", "correspondence", "eigenvalues", "ordination", "biplot"], "article_id"=>395325, "categories"=>["Microbiology", "Ecology", "Genetics", "Infectious Diseases"], "users"=>["Giovanna Carpi", "Francesca Cagnacci", "Nicola E. Wittekindt", "Fangqing Zhao", "Ji Qi", "Lynn P. Tomsho", "Daniela I. Drautz", "Annapaola Rizzoli", "Stephan C. Schuster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025604.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_Canonical_Correspondence_Analysis_Eigenvalues_of_first_two_ordination_axes_site_and_biplot_scores_/395325", "title"=>"Summary of Canonical Correspondence Analysis: Eigenvalues of first two ordination axes, site and biplot scores.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-10-13 01:28:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/724617"], "description"=>"<p>For the purpose of presentation the linear chromosomes of <i>Borrelia</i> spp. are circularized. The outer circle designed as ‘READS’ shows the coverage plot over the reference chromosome, while the inner circle displays the amount of estimated nucleotide mismatches. (A). Genomic DNA-derived sequences from Ir 13-4 mapped to the <i>B. garinii</i> PBi chromosome (NC_006156). (B) Genomic DNA-derived sequences from Ir 13-4 mapped to the four contigs of the <i>B. garinii</i> PBr chromosome (WGS ABJV00000000). (C) Genomic DNA-derived sequences from Ir 20-8 mapped to the <i>B. afzelii</i> PKo chromosome (NC_008277).</p>", "links"=>[], "tags"=>["genomic", "dna-derived", "sequences", "ticks", "paired-end", "chromosomes", "pathogenic"], "article_id"=>394958, "categories"=>["Microbiology", "Ecology", "Genetics", "Infectious Diseases"], "users"=>["Giovanna Carpi", "Francesca Cagnacci", "Nicola E. Wittekindt", "Fangqing Zhao", "Ji Qi", "Lynn P. Tomsho", "Daniela I. Drautz", "Annapaola Rizzoli", "Stephan C. Schuster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025604.g002", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_inGAP_mapping_of_genomic_DNA_derived_sequences_obtained_from_single_I_ricinus_ticks_Illumina_paired_end_reads_to_the_reference_chromosomes_of_pathogenic_Borrelia_species_/394958", "title"=>"inGAP mapping of genomic DNA-derived sequences obtained from single <i>I. ricinus</i> ticks (Illumina paired-end reads) to the reference chromosomes of pathogenic <i>Borrelia</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:22:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/724929"], "description"=>"a<p>Reads identified by the comparison against the NCBI non-redundant protein database using BLASTX and assigned to taxa by MEGAN. Bit score cutoff ≥40.</p>b<p>GenBank accession number of the four chromosome genomes used as reference genomes: <i>B. burgdorferi B31</i> NC_001318, <i>B. afzelii PKo</i> NC_008277, <i>B. garinii PBi</i> NC_006156 and <i>B. garinii PBr</i> WGS ABJV00000000.</p>c<p>Number of reads mapped to the reference genomes by BWA (mapping quality score ≥15).</p>d<p>Number of reads mapped to the reference genomes by inGAP.</p>e<p>Paired-end reads.</p>", "links"=>[], "tags"=>["gs", "flx", "illumina", "gaiix", "sequencing", "unfed", "ticks", "reads", "matching"], "article_id"=>395269, "categories"=>["Microbiology", "Ecology", "Genetics", "Infectious Diseases"], "users"=>["Giovanna Carpi", "Francesca Cagnacci", "Nicola E. Wittekindt", "Fangqing Zhao", "Ji Qi", "Lynn P. Tomsho", "Daniela I. Drautz", "Annapaola Rizzoli", "Stephan C. Schuster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025604.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_454_GS_FLX_and_Illumina_GAIIx_sequencing_statistics_of_three_single_unfed_adult_I_ricinus_ticks_and_number_of_sequence_reads_matching_to_reference_genomes_/395269", "title"=>"454 GS FLX and Illumina GAIIx sequencing statistics of three single unfed adult <i>I. ricinus</i> ticks and number of sequence reads matching to reference genomes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-10-13 01:27:49"}

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Relative Metric

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