Use of a Four-Tiered Graph to Parse the Factors Leading to Phenotypic Clustering in Bacteria: A Case Study Based on Samples from the Aletsch Glacier
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{"title"=>"Use of a Four-Tiered Graph to Parse the Factors Leading to Phenotypic Clustering in Bacteria: A Case Study Based on Samples from the Aletsch Glacier", "type"=>"journal", "authors"=>[{"first_name"=>"Miroslav", "last_name"=>"Svercel", "scopus_author_id"=>"16643988200"}, {"first_name"=>"Manuela", "last_name"=>"Filippini", "scopus_author_id"=>"14041665300"}, {"first_name"=>"Nicolas", "last_name"=>"Perony", "scopus_author_id"=>"25223403100"}, {"first_name"=>"Valentina", "last_name"=>"Rossetti", "scopus_author_id"=>"35077295900"}, {"first_name"=>"Homayoun C.", "last_name"=>"Bagheri", "scopus_author_id"=>"16506461100"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84878609316", "sgr"=>"84878609316", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0065059", "pmid"=>"23741454", "pui"=>"369052196"}, "id"=>"9daf77ac-18c4-3f14-b5bc-b658ce6c0f87", "abstract"=>"An understanding of bacterial diversity and evolution in any environment requires knowledge of phenotypic diversity. In this study, the underlying factors leading to phenotypic clustering were analyzed and interpreted using a novel approach based on a four-tiered graph. Bacterial isolates were organized into equivalence classes based on their phenotypic profile. Likewise, phenotypes were organized in equivalence classes based on the bacteria that manifest them. The linking of these equivalence classes in a four-tiered graph allowed for a quick visual identification of the phenotypic measurements leading to the clustering patterns deduced from principal component analyses. For evaluation of the method, we investigated phenotypic variation in enzyme production and carbon assimilation of members of the genera Pseudomonas and Serratia, isolated from the Aletsch Glacier in Switzerland. The analysis indicates that the genera isolated produce at least six common enzymes and can exploit a wide range of carbon resources, though some specialist species within the pseudomonads were also observed. We further found that pairwise distances between enzyme profiles strongly correlate with distances based on carbon profiles. However, phenotypic distances weakly correlate with phylogenetic distances. The method developed in this study facilitates a more comprehensive understanding of phenotypic clustering than what would be deduced from principal component analysis alone.", "link"=>"http://www.mendeley.com/research/fourtiered-graph-parse-factors-leading-phenotypic-clustering-bacteria-case-study-based-samples-alets", "reader_count"=>11, "reader_count_by_academic_status"=>{"Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Other"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Other"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>4, "Physics and Astronomy"=>1, "Social Sciences"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Switzerland"=>1, "Spain"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1071570"], "description"=>"<p>(A) Principal component analysis based on Hamming distance of enzymatic profiles determined using API ZYM strips. The first two principal components explain 87% of the variance of the data. (B) Four-tiered graph linking bacteria and enzyme profiles. Links are to be followed from left to right. Bacteria showing similar enzymatic profiles (E1, E2, E3 E4, E5 and E6) group together. The number of enzymes produced by each equivalence class of bacteria and the number of bacteria classes that produce a certain enzyme are indicated at the right of the corresponding bacterial equivalence class and at the left of the corresponding enzyme equivalence class, respectively. The vertical positions of the bacterial classes correspond to their coefficient in the first principal component of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065059#pone-0065059-g001\" target=\"_blank\">Figure 1A</a>, though vertically-overlapping classes are separated from each other by a small distance to allow for an easy reading of the graph. Distances between the non-overlapping classes are preserved.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "microbiology", "bacteriology", "Bacterial taxonomy", "Bacterial evolution", "Bacterial physiology", "microbial ecology", "Microbial evolution", "Microbial metabolism"], "article_id"=>709641, "categories"=>["Biological Sciences"], "users"=>["Miroslav Svercel", "Manuela Filippini", "Nicolas Perony", "Valentina Rossetti", "Homayoun C. Bagheri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065059.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enzyme_profile_analysis_/709641", "title"=>"Enzyme profile analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-31 02:40:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/1071571"], "description"=>"<p>(A) Principal component analysis based on Hamming distance of carbon assimilation profiles measured with Biolog PM1. The first two principal components explain 84% of the variance of the data. (B) Four-tiered graph linking bacteria and carbon assimilation profiles. Bacteria showing similar carbon assimilation profiles group together (C1, C2, C3, C4, C5 and C6). This graph is constructed the same way as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065059#pone-0065059-g001\" target=\"_blank\">Figure 1B</a>. Here no two bacteria show identical profiles, hence they form single-member equivalence classes (each strain is linked to a unique node in the isolate equivalence class layer, second from the left). The vertical positions of the bacteria correspond to their coefficient in the first principal component of <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065059#pone-0065059-g002\" target=\"_blank\">Figure 2A</a>, though vertically-overlapping bacteria are separated from each other by a small distance. Distances between the non-overlapping classes are preserved.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "microbiology", "bacteriology", "Bacterial taxonomy", "Bacterial evolution", "Bacterial physiology", "microbial ecology", "Microbial evolution", "Microbial metabolism", "assimilation"], "article_id"=>709642, "categories"=>["Biological Sciences"], "users"=>["Miroslav Svercel", "Manuela Filippini", "Nicolas Perony", "Valentina Rossetti", "Homayoun C. Bagheri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065059.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Carbon_assimilation_profile_analysis_/709642", "title"=>"Carbon assimilation profile analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-31 02:40:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1071572"], "description"=>"<p>Profile of the strains presented in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065059#pone-0065059-g001\" target=\"_blank\">Figure 1</a> (four-tiered graph), listing the activity of the different enzymes (API ZYM strip) in each isolate or equivalent class of bacterial isolates. The ordering of the strains and the enzymes in the table was modified to match the graph in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065059#pone-0065059-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "microbiology", "bacteriology", "Bacterial taxonomy", "Bacterial evolution", "Bacterial physiology", "microbial ecology", "Microbial evolution", "Microbial metabolism", "enzymatic", "profiles"], "article_id"=>709643, "categories"=>["Biological Sciences"], "users"=>["Miroslav Svercel", "Manuela Filippini", "Nicolas Perony", "Valentina Rossetti", "Homayoun C. Bagheri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065059.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_enzymatic_profiles_for_all_strains_/709643", "title"=>"Overview of enzymatic profiles for all strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-31 02:40:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1071574"], "description"=>"<p>Profile of the strains presented in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065059#pone-0065059-g002\" target=\"_blank\">Figure 2</a> (four-tiered graph), listing the carbon substrates (BIOLOG 1) used by each isolate or equivalent class of bacterial isolates. The ordering of strains and the carbon substrates in the table was modified to match the graph in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065059#pone-0065059-g002\" target=\"_blank\">Figure 2</a>.</p>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "microbiology", "bacteriology", "Bacterial taxonomy", "Bacterial evolution", "Bacterial physiology", "microbial ecology", "Microbial evolution", "Microbial metabolism", "carbon", "assimilation", "profiles"], "article_id"=>709645, "categories"=>["Biological Sciences"], "users"=>["Miroslav Svercel", "Manuela Filippini", "Nicolas Perony", "Valentina Rossetti", "Homayoun C. Bagheri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065059.g004", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_carbon_assimilation_profiles_for_all_strains_/709645", "title"=>"Overview of carbon assimilation profiles for all strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-31 02:40:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1071575"], "description"=>"<div><p>An understanding of bacterial diversity and evolution in any environment requires knowledge of phenotypic diversity. In this study, the underlying factors leading to phenotypic clustering were analyzed and interpreted using a novel approach based on a four-tiered graph. Bacterial isolates were organized into equivalence classes based on their phenotypic profile. Likewise, phenotypes were organized in equivalence classes based on the bacteria that manifest them. The linking of these equivalence classes in a four-tiered graph allowed for a quick visual identification of the phenotypic measurements leading to the clustering patterns deduced from principal component analyses. For evaluation of the method, we investigated phenotypic variation in enzyme production and carbon assimilation of members of the genera <i>Pseudomonas</i> and <i>Serratia</i>, isolated from the Aletsch Glacier in Switzerland. The analysis indicates that the genera isolated produce at least six common enzymes and can exploit a wide range of carbon resources, though some specialist species within the pseudomonads were also observed. We further found that pairwise distances between enzyme profiles strongly correlate with distances based on carbon profiles. However, phenotypic distances weakly correlate with phylogenetic distances. The method developed in this study facilitates a more comprehensive understanding of phenotypic clustering than what would be deduced from principal component analysis alone.</p></div>", "links"=>[], "tags"=>["Evolutionary biology", "Evolutionary ecology", "microbiology", "bacteriology", "Bacterial taxonomy", "Bacterial evolution", "Bacterial physiology", "microbial ecology", "Microbial evolution", "Microbial metabolism", "four-tiered", "graph", "parse", "phenotypic", "clustering", "samples", "aletsch"], "article_id"=>709646, "categories"=>["Biological Sciences"], "users"=>["Miroslav Svercel", "Manuela Filippini", "Nicolas Perony", "Valentina Rossetti", "Homayoun C. Bagheri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065059", "stats"=>{"downloads"=>20, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Use_of_a_Four_Tiered_Graph_to_Parse_the_Factors_Leading_to_Phenotypic_Clustering_in_Bacteria_A_Case_Study_Based_on_Samples_from_the_Aletsch_Glacier_/709646", "title"=>"Use of a Four-Tiered Graph to Parse the Factors Leading to Phenotypic Clustering in Bacteria: A Case Study Based on Samples from the Aletsch Glacier", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-31 02:40:46"}

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Relative Metric

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