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• {"link"=>{"url"=>"http://www.citeulike.org/user/zwang/article/1616291"}, "post_time"=>"2007-09-03 15:16:47", "tag"=>["bacterial", "evolution", "genome"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pgen.0030138"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/17722982"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=17722982"}], "username"=>"zwang", "article_id"=>"1616291"}

Mendeley | Further Information

{"title"=>"Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria", "type"=>"journal", "authors"=>[{"first_name"=>"Stéphane", "last_name"=>"Audic", "scopus_author_id"=>"6602862007"}, {"first_name"=>"Catherine", "last_name"=>"Robert", "scopus_author_id"=>"7202855401"}, {"first_name"=>"Bernard", "last_name"=>"Campagna", "scopus_author_id"=>"20733711400"}, {"first_name"=>"Hugues", "last_name"=>"Parinello", "scopus_author_id"=>"12787548600"}, {"first_name"=>"Jean Michel", "last_name"=>"Claverie", "scopus_author_id"=>"7004518040"}, {"first_name"=>"Didier", "last_name"=>"Raoult", "scopus_author_id"=>"36040059800"}, {"first_name"=>"Michel", "last_name"=>"Drancourt", "scopus_author_id"=>"35232870100"}], "year"=>2007, "source"=>"PLoS Genetics", "identifiers"=>{"pmid"=>"17722982", "sgr"=>"34548415876", "pui"=>"47358083", "scopus"=>"2-s2.0-34548415876", "doi"=>"10.1371/journal.pgen.0030138", "issn"=>"15537390"}, "id"=>"e1a66d3f-0997-3623-87c0-b9a963b961c5", "abstract"=>"Filtration usually eliminates water-living bacteria. Here, we report on the complete genome sequence of Minibacterium massiliensis, a beta-proteobacteria that was recovered from 0.22-mum filtered water used for patients in the hospital. The unexpectedly large 4,110,251-nucleotide genome sequence of M. massiliensis was determined using the traditional shotgun sequencing approach. Bioinformatic analyses shows that the M. massiliensis genome sequence illustrates characteristic features of water-living bacteria, including overrepresentation of genes encoding transporters and transcription regulators. Phylogenomic analysis based on the gene content of available bacterial genome sequences displays a congruent evolution of water-living bacteria from various taxonomic origins, principally for genes involved in energy production and conversion, cell division, chromosome partitioning, and lipid metabolism. This phylogenomic clustering partially results from lateral gene transfer, which appears to be more frequent in water than in other environments. The M. massiliensis genome analyses strongly suggest that water-living bacteria are a common source for genes involved in heavy-metal resistance, antibiotics resistance, and virulence factors.", "link"=>"http://www.mendeley.com/research/genome-analysis-minibacterium-massiliensis-highlights-convergent-evolution-waterliving-bacteria", "reader_count"=>60, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>8, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>8, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>4, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>43, "Medicine and Dentistry"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>43}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>4, "Japan"=>1, "Brazil"=>1, "Mexico"=>2, "Italy"=>1, "United Kingdom"=>1, "Russia"=>1, "India"=>1}, "group_count"=>3}

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CrossRef

• http://doi.org/10.1073/pnas.0911354106
• http://doi.org/10.1111/j.1462-2920.2009.02010.x
• http://doi.org/10.1111/j.1469-185X.2010.00151.x
• http://doi.org/10.7202/1007627ar
• http://doi.org/10.1016/j.pep.2010.08.015
• http://doi.org/10.1111/j.1399-3054.2012.01670.x
• http://doi.org/10.3389/fmicb.2016.01668
• http://doi.org/10.1093/gbe/evq055
• http://doi.org/10.1093/gbe/evw111
• http://doi.org/10.1080/01490451.2010.515287
• http://doi.org/10.1016/j.ijmm.2009.05.004
• http://doi.org/10.1111/j.1574-6941.2008.00547.x
• http://doi.org/10.1089/ast.2011.0724
• http://doi.org/10.1371/journal.pone.0034754
• http://doi.org/10.1371/journal.pgen.1000185
• http://doi.org/10.1111/j.1574-6976.2009.00209.x
• http://doi.org/10.1128/AAC.06401-11
• http://doi.org/10.3389/fmicb.2016.02029
• http://doi.org/10.1038/nrmicro1858
• http://doi.org/10.1264/jsme2.ME10122
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• http://doi.org/10.1186/s40793-015-0103-0
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• http://doi.org/10.1111/j.1469-0691.2012.03781.x
• http://doi.org/10.1186/s40793-018-0313-3
• http://doi.org/10.1099/ijs.0.001685-0
• http://doi.org/10.1128/genomeA.00277-15
• http://doi.org/10.1007/s10482-009-9345-4
• http://doi.org/10.1128/genomeA.00689-15
• http://doi.org/10.1038/s41598-017-15164-4
• http://doi.org/10.1002/ece3.37
• http://doi.org/10.1371/journal.pone.0055045
• http://doi.org/10.2478/s11756-013-0274-3
• http://doi.org/10.7717/peerj.127
• http://doi.org/10.1038/s41598-018-33261-w
• http://doi.org/10.1016/j.micpath.2014.09.005
• http://doi.org/10.1073/pnas.0800981105
• http://doi.org/10.1111/j.1758-2229.2012.00336.x

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{"EMBL"=>1, "UNIPROT"=>3695}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/465700", "https://ndownloader.figshare.com/files/465754", "https://ndownloader.figshare.com/files/465889", "https://ndownloader.figshare.com/files/465940", "https://ndownloader.figshare.com/files/466079"], "description"=>"<div><p>Filtration usually eliminates water-living bacteria. Here, we report on the complete genome sequence of Minibacterium massiliensis, a β-proteobacteria that was recovered from 0.22-μm filtered water used for patients in the hospital. The unexpectedly large 4,110,251-nucleotide genome sequence of M. massiliensis was determined using the traditional shotgun sequencing approach. Bioinformatic analyses shows that the M. massiliensis genome sequence illustrates characteristic features of water-living bacteria, including overrepresentation of genes encoding transporters and transcription regulators. Phylogenomic analysis based on the gene content of available bacterial genome sequences displays a congruent evolution of water-living bacteria from various taxonomic origins, principally for genes involved in energy production and conversion, cell division, chromosome partitioning, and lipid metabolism. This phylogenomic clustering partially results from lateral gene transfer, which appears to be more frequent in water than in other environments. The M. massiliensis genome analyses strongly suggest that water-living bacteria are a common source for genes involved in heavy-metal resistance, antibiotics resistance, and virulence factors.</p></div>", "links"=>[], "tags"=>["genome", "highlights", "convergent", "water-living"], "article_id"=>151808, "categories"=>["Biological Sciences", "Ecology", "Genetics"], "users"=>["Stéphane Audic", "Catherine Robert", "Bernard Campagna", "Hugues Parinello", "Jean-Michel Claverie", "Didier Raoult", "Michel Drancourt"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.0030138.sg001", "https://dx.doi.org/10.1371/journal.pgen.0030138.sg002", "https://dx.doi.org/10.1371/journal.pgen.0030138.st001", "https://dx.doi.org/10.1371/journal.pgen.0030138.st002", "https://dx.doi.org/10.1371/journal.pgen.0030138.st003"], "stats"=>{"downloads"=>41, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Analysis_of_Minibacterium_massiliensis_Highlights_the_Convergent_Evolution_of_Water_Living_Bacteria/151808", "title"=>"Genome Analysis of Minibacterium massiliensis Highlights the Convergent Evolution of Water-Living Bacteria", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-08-24 00:30:08"}
• {"files"=>["https://ndownloader.figshare.com/files/946577"], "description"=>"<p>Phylogenetic trees for five consecutive genes in M. massiliensis illustrating lateral gene transfer with α-proteobacteria. Genes are labeled according to their names in the Kegg database, followed by the environmental category of the organism. The gene order is conserved among the three species, except for OppA, duplicated in <i>B. japonicum and R. palustris</i>. In this tree, gene names are colored according to the following code: <i>M. massiliensis,</i> blue; α-proteobacteria, yellow; β-proteobacteria, red; γ-proteobacteria, green; and others, black. The trees were built using a maximum likelihood substitution model and midpoint rooting.</p>", "links"=>[], "tags"=>["Computational biology", "ecology", "genetics and genomics"], "article_id"=>616930, "categories"=>["Biological Sciences", "Ecology", "Genetics"], "users"=>["Stéphane Audic", "Catherine Robert", "Bernard Campagna", "Hugues Parinello", "Jean-Michel Claverie", "Didier Raoult", "Michel Drancourt"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030138.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_En_Bloc_Gene_Transfer_/616930", "title"=>"En-Bloc Gene Transfer", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-24 01:55:30"}
• {"files"=>["https://ndownloader.figshare.com/files/946079"], "description"=>"<p>LCV measured 1,259 <u>+</u> 329 × 510 <u>+</u> 65 nm and SCV measured 615 <u>+</u> 185 × 185 <u>+</u> 52 nm. The distribution of length and diameter of organisms in the M. massiliensis cell population is also shown. (Bar = 500nm)</p>", "links"=>[], "tags"=>["electron", "microscopy", "featuring", "scv", "lcv"], "article_id"=>616437, "categories"=>["Biological Sciences", "Ecology", "Genetics"], "users"=>["Stéphane Audic", "Catherine Robert", "Bernard Campagna", "Hugues Parinello", "Jean-Michel Claverie", "Didier Raoult", "Michel Drancourt"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030138.g001", "stats"=>{"downloads"=>2, "page_views"=>39, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transmission_Electron_Microscopy_Featuring_SCV_and_LCV_of_M_massiliensis_/616437", "title"=>"Transmission Electron Microscopy Featuring SCV and LCV of M. massiliensis", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-24 01:47:17"}
• {"files"=>["https://ndownloader.figshare.com/files/946436"], "description"=>"<p>Organisms are colored according to taxonomy. The class membership of the organisms is also indicated: (1) obligate intracellular bacteria including endosymbionts, (2) pathogens and host-associated bacteria (3) waterborne free-living bacteria, (4) nonwaterborne, free-living bacteria, and (5) extremophiles. The position of M. massiliensis is indicated by a red triangle in the tree.</p>", "links"=>[], "tags"=>["cog", "phylogenomic"], "article_id"=>616790, "categories"=>["Biological Sciences", "Ecology", "Genetics"], "users"=>["Stéphane Audic", "Catherine Robert", "Bernard Campagna", "Hugues Parinello", "Jean-Michel Claverie", "Didier Raoult", "Michel Drancourt"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030138.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_All_COG_Phylogenomic_Representations_/616790", "title"=>"All COG Phylogenomic Representations", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-24 01:53:10"}
• {"files"=>["https://ndownloader.figshare.com/files/946776"], "description"=>"<p>Organisms are colored according to lifestyle, which are the same as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030138#pgen-0030138-g003\" target=\"_blank\">Figure 3</a>.</p>", "links"=>[], "tags"=>["putative"], "article_id"=>617129, "categories"=>["Biological Sciences", "Ecology", "Genetics"], "users"=>["Stéphane Audic", "Catherine Robert", "Bernard Campagna", "Hugues Parinello", "Jean-Michel Claverie", "Didier Raoult", "Michel Drancourt"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030138.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Putative_LGTs_/617129", "title"=>"Distribution of Putative LGTs", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-24 01:58:49"}
• {"files"=>["https://ndownloader.figshare.com/files/946700"], "description"=>"<p>Organisms are ranked according to the number of hits to the virulence factor database or the heavy-metal resistance database (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030138#s4\" target=\"_blank\">Materials and Methods</a>) they exhibited per unit length of genome size. For each rank, the fraction of organisms in this category with the same rank or below is plotted. The lifestyle categories are the same as those in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030138#pgen-0030138-g003\" target=\"_blank\">Figure 3</a>. In this representation, we show that the genomes of water-living organisms tend to rank higher, showing a higher density of virulence factors and heavy-metal resistance genes.</p>", "links"=>[], "tags"=>["virulence", "heavy-metal", "genes", "water-living"], "article_id"=>617048, "categories"=>["Biological Sciences", "Ecology", "Genetics"], "users"=>["Stéphane Audic", "Catherine Robert", "Bernard Campagna", "Hugues Parinello", "Jean-Michel Claverie", "Didier Raoult", "Michel Drancourt"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030138.g005", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prevalence_of_Virulence_Factors_and_Heavy_Metal_Resistance_Genes_in_Water_Living_Bacteria_/617048", "title"=>"Prevalence of Virulence Factors and Heavy-Metal Resistance Genes in Water-Living Bacteria", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-24 01:57:28"}
• {"files"=>["https://ndownloader.figshare.com/files/946226"], "description"=>"<p>The following features are displayed (from the outside in): position along the genome, protein-coding genes along both strands colored according to COG categories, tRNA genes as red arrows, rRNA genes as black arrows, the windowed difference of GC% with respect to the average, and the GC skew (G − C)/(G + C), with positive values in red and negative values in blue. Two regions of phage insertion are indicated by green boxes.</p>", "links"=>[], "tags"=>["Computational biology", "ecology", "genetics and genomics"], "article_id"=>616585, "categories"=>["Biological Sciences", "Ecology", "Genetics"], "users"=>["Stéphane Audic", "Catherine Robert", "Bernard Campagna", "Hugues Parinello", "Jean-Michel Claverie", "Didier Raoult", "Michel Drancourt"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030138.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_the_M_massiliensis_Chromosome_/616585", "title"=>"Map of the M. massiliensis Chromosome", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-24 01:49:45"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime