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[PMID]:29296020
[Au] Autor:Swenson TL; Karaoz U; Swenson JM; Bowen BP; Northen TR
[Ad] Endereço:Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA.
[Ti] Título:Linking soil biology and chemistry in biological soil crust using isolate exometabolomics.
[So] Source:Nat Commun;9(1):19, 2018 01 02.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.
[Mh] Termos MeSH primário: Bactérias/metabolismo
Ecossistema
Metabolômica/métodos
Microbiologia do Solo
Solo/química
[Mh] Termos MeSH secundário: Bactérias/classificação
Proteínas de Bactérias/genética
Proteínas de Bactérias/metabolismo
Biomassa
Metagenoma/genética
Dinâmica Populacional
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Soil)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180104
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02356-9


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[PMID]:29371626
[Au] Autor:Carradec Q; Pelletier E; Da Silva C; Alberti A; Seeleuthner Y; Blanc-Mathieu R; Lima-Mendez G; Rocha F; Tirichine L; Labadie K; Kirilovsky A; Bertrand A; Engelen S; Madoui MA; Méheust R; Poulain J; Romac S; Richter DJ; Yoshikawa G; Dimier C; Kandels-Lewis S; Picheral M; Searson S; Jaillon O; Aury JM; Karsenti E; Sullivan MB; Sunagawa S; Bork P; Not F; Hingamp P; Raes J; Guidi L; Ogata H; de Vargas C; Iudicone D; Bowler C; Wincker P; Tara Oceans Coordinators
[Ad] Endereço:CEA - Institut de Biologie François Jacob, Genoscope, Evry, 91057, France.
[Ti] Título:A global ocean atlas of eukaryotic genes.
[So] Source:Nat Commun;9(1):373, 2018 01 25.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.
[Mh] Termos MeSH primário: Organismos Aquáticos
Eucariotos/genética
Células Eucarióticas/metabolismo
Metagenoma
Filogenia
Zooplâncton/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Atlas como Assunto
Bactérias/classificação
Bactérias/genética
Biodiversidade
Ecossistema
Eucariotos/classificação
Células Eucarióticas/citologia
Metagenômica/métodos
Oceanos e Mares
Fitoplâncton/classificação
Fitoplâncton/genética
Água do Mar
Vírus/classificação
Vírus/genética
Zooplâncton/classificação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180215
[Lr] Data última revisão:
180215
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180127
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02342-1


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[PMID]:27770744
[Au] Autor:Khan M; Kumar A
[Ad] Endereço:CSIR-Central Food Technological Research Institute, Resource Centre Lucknow, 226018 India. Electronic address: mahejibin@cftri.org.
[Ti] Título:Computational modelling and protein-ligand interaction studies of SMlipA lipase cloned from forest metagenome.
[So] Source:J Mol Graph Model;70:212-225, 2016 11.
[Is] ISSN:1873-4243
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The understanding of the 3-dimensional enzyme structure is important for the point of protein engineering and applications. Computer-based molecular modelling is a vital tool for theoretical predication of enzyme activities and finding their substrates and inhibitors. SMlipA lipase was cloned from forest soil metagenome and characterized as broad spectrum enzyme with high stability in various organic solvents. In the present study, to understand the mechanism of SMlipA lipase and to identify the key residues involved in enzyme-substrate interaction, three dimensional-computational model of SMlipA has been generated and validated for stereo-chemical and amino-acid environment quality using appropriate programs, and further validation of the active-site architecture was achieved by performing docking studies with different ligand. The three dimensional structure created here provide a new understanding of the ligand preferences and their interaction with protein.
[Mh] Termos MeSH primário: Florestas
Lipase/química
Metagenoma
Modelos Moleculares
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Domínio Catalítico
Internet
Ligantes
Estrutura Secundária de Proteína
Reprodutibilidade dos Testes
Alinhamento de Sequência
Homologia de Sequência de Aminoácidos
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Ligands); EC 3.1.1.3 (Lipase)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180216
[Lr] Data última revisão:
180216
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161023
[St] Status:MEDLINE


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[PMID]:28451970
[Au] Autor:Silva GGZ; Lopes FAC; Edwards RA
[Ad] Endereço:Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
[Ti] Título:An Agile Functional Analysis of Metagenomic Data Using SUPER-FOCUS.
[So] Source:Methods Mol Biol;1611:35-44, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:One of the main goals in metagenomics is to identify the functional profile of a microbial community from unannotated shotgun sequencing reads. Functional annotation is important in biological research because it enables researchers to identify the abundance of functional genes of the organisms present in the sample, answering the question, "What can the organisms in the sample do?" Most currently available approaches do not scale with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here, we present SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with real metagenomes, and the results show that it accurately predicts the subsystems present in the profiled microbial communities, is computationally efficient, and up to 1000 times faster than other tools. SUPER-FOCUS is freely available at http://edwards.sdsu.edu/SUPERFOCUS .
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Metagenoma/genética
Metagenômica/métodos
[Mh] Termos MeSH secundário: Bases de Dados Genéticas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-7015-5_4


  5 / 4880 MEDLINE  
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[PMID]:28451969
[Au] Autor:Sharifi F; Ye Y
[Ad] Endereço:School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave., Bloomington, IN, 47405, USA.
[Ti] Título:From Gene Annotation to Function Prediction for Metagenomics.
[So] Source:Methods Mol Biol;1611:27-34, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Microbes play important roles in almost every aspect of life, including human health and diseases. Facilitated by the rapid development of sequencing technologies, metagenomics research has accelerated the accumulation of genomic sequences of microbial species that had been inaccessible before. Analysis of the metagenomic sequencing data can reveal not only the species but also the functional composition of microbial communities. Here, we report a pipeline for functional annotation of metagenomic datasets. The pipeline is built from several programs that we have developed for metagenomic sequence analysis including a protein-coding gene predictor for short reads (or contigs) and a fast similarity search tool. Given a metagenomic dataset, the pipeline reports putative protein-coding genes (or gene fragments) and functional annotations of the genes in Gene Ontology (GO) terms and Enzyme Commission (EC) numbers, and potential metabolic pathways that are likely encoded by the metagenome. Fun4Me is available for download at https://sourceforge.net/projects/fun4me .
[Mh] Termos MeSH primário: Metagenômica/métodos
[Mh] Termos MeSH secundário: Algoritmos
Metagenoma/genética
Anotação de Sequência Molecular
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180212
[Lr] Data última revisão:
180212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-7015-5_3


  6 / 4880 MEDLINE  
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[PMID]:29304124
[Au] Autor:Krehenwinkel H; Fong M; Kennedy S; Huang EG; Noriyuki S; Cayetano L; Gillespie R
[Ad] Endereço:Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America.
[Ti] Título:The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota.
[So] Source:PLoS One;13(1):e0189188, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.
[Mh] Termos MeSH primário: Artrópodes/genética
Artrópodes/microbiologia
Código de Barras de DNA Taxonômico/métodos
DNA/análise
DNA/genética
Microbiota/genética
[Mh] Termos MeSH secundário: Animais
Artrópodes/classificação
Biodiversidade
Código de Barras de DNA Taxonômico/estatística & dados numéricos
Primers do DNA
Ecossistema
Hawaii
Metagenoma
Metagenômica/métodos
Metagenômica/estatística & dados numéricos
Reação em Cadeia da Polimerase/métodos
Viés de Seleção
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA Primers); 9007-49-2 (DNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180210
[Lr] Data última revisão:
180210
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180106
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0189188


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[PMID]:29324778
[Au] Autor:Tsuchiaka S; Naoi Y; Imai R; Masuda T; Ito M; Akagami M; Ouchi Y; Ishii K; Sakaguchi S; Omatsu T; Katayama Y; Oba M; Shirai J; Satani Y; Takashima Y; Taniguchi Y; Takasu M; Madarame H; Sunaga F; Aoki H; Makino S; Mizutani T; Nagai M
[Ad] Endereço:Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan.
[Ti] Título:Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population.
[So] Source:PLoS One;13(1):e0190819, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain). Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C-3A junction site. This paper presents the first report of the high prevalence of viruses carrying PL-CP in the EV-G population. Furthermore, possible inter- and intragenotype recombination events were found among EV-G strains, including G1-PL-CP strains. Our findings may advance the understanding of the molecular epidemiology and genetic evolution of EV-Gs.
[Mh] Termos MeSH primário: Infecções por Enterovirus/virologia
Enterovirus Suínos/genética
Variação Genética
Recombinação Genética
[Mh] Termos MeSH secundário: Animais
Proteínas do Capsídeo/genética
Cisteína Proteases/genética
Infecções por Enterovirus/epidemiologia
Enterovirus Suínos/enzimologia
Fezes/virologia
Japão
Metagenoma
Filogenia
Prevalência
Sus scrofa
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Capsid Proteins); EC 3.4.- (Cysteine Proteases)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180206
[Lr] Data última revisão:
180206
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180112
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190819


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[PMID]:28749495
[Au] Autor:Pedroso MM; Selleck C; Enculescu C; Harmer JR; Mitic N; Craig WR; Helweh W; Hugenholtz P; Tyson GW; Tierney DL; Larrabee JA; Schenk G
[Ad] Endereço:School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia. m.pedroso@uq.edu.au schenk@uq.edu.au.
[Ti] Título:Characterization of a highly efficient antibiotic-degrading metallo-ß-lactamase obtained from an uncultured member of a permafrost community.
[So] Source:Metallomics;9(8):1157-1168, 2017 Aug 16.
[Is] ISSN:1756-591X
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Antibiotic resistance is a major global health problem, one that threatens to derail the benefits garnered from arguably the greatest success of modern medicine, the discovery of antibiotics. Among the most potent agents contributing to antibiotic resistance are metallo-ß-lactamases (MBLs). The discovery of MBL-like enzymes in microorganisms that are not in contact with the human population is of particular concern as these proteins already have the in-built capacity to inactivate antibiotics, even though they may not need MBL activity for their survival. Here, we demonstrate that a microbiome from a remote and frozen environment in Alaska harbours at least one highly efficient MBL, LRA-8. LRA-8 is homologous to the B3 subgroup of MBLs and has a substrate profile and catalytic properties similar to well-known members of this enzyme family, which are expressed by major human pathogens. LRA-8 is predominantly a penicillinase, but is also active towards carbapenems, but not cephalosporins. Spectroscopic studies indicate that LRA-8 has an active site structure similar to that of other MBLs (in particular B3 subgroup representative AIM-1), and a combination of steady-state and pre-steady-state kinetic data demonstrate that the enzyme is likely to employ a metal ion-bridging hydroxide to initiate catalysis. The rate-limiting step is the decay of a chromophoric, tetrahedral intermediate, as is observed in various other MBLs. Thus, studying the properties of such "pristine" MBL-like proteins may provide insight into the structural plasticity of this family of enzymes that may facilitate functional promiscuity, while important insight into the evolution of MBLs may also be gained.
[Mh] Termos MeSH primário: Antibacterianos/metabolismo
Proteínas de Bactérias/metabolismo
Pergelissolo/microbiologia
beta-Lactamases/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Proteínas de Bactérias/química
Proteínas de Bactérias/genética
Catálise
Seres Humanos
Metagenoma
Metais/metabolismo
Modelos Moleculares
Fenótipo
Homologia de Sequência
Especificidade por Substrato
beta-Lactamases/química
beta-Lactamases/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Anti-Bacterial Agents); 0 (Bacterial Proteins); 0 (Metals); EC 3.5.2.6 (beta-Lactamases)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171229
[Lr] Data última revisão:
171229
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170728
[St] Status:MEDLINE
[do] DOI:10.1039/c7mt00195a


  9 / 4880 MEDLINE  
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[PMID]:28449715
[Au] Autor:Bedarf JR; Hildebrand F; Coelho LP; Sunagawa S; Bahram M; Goeser F; Bork P; Wüllner U
[Ad] Endereço:Department of Neurology, University of Bonn, Bonn, Germany.
[Ti] Título:Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.
[So] Source:Genome Med;9(1):39, 2017 04 28.
[Is] ISSN:1756-994X
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker. METHODS: We performed metagenomic shotgun analyses and compared the fecal microbiomes of 31 early stage, L-DOPA-naïve PD patients to 28 age-matched controls. RESULTS: We found increased Verrucomicrobiaceae (Akkermansia muciniphila) and unclassified Firmicutes, whereas Prevotellaceae (Prevotella copri) and Erysipelotrichaceae (Eubacterium biforme) were markedly lowered in PD samples. The observed differences could reliably separate PD from control with a ROC-AUC of 0.84. Functional analyses of the metagenomes revealed differences in microbiota metabolism in PD involving the ẞ-glucuronate and tryptophan metabolism. While the abundances of prophages and plasmids did not differ between PD and controls, total virus abundance was decreased in PD participants. Based on our analyses, the intake of either a MAO inhibitor, amantadine, or a dopamine agonist (which in summary relates to 90% of PD patients) had no overall influence on taxa abundance or microbial functions. CONCLUSIONS: Our data revealed differences of colonic microbiota and of microbiota metabolism between PD patients and controls at an unprecedented detail not achievable through 16S sequencing. The findings point to a yet unappreciated aspect of PD, possibly involving the intestinal barrier function and immune function in PD patients. The influence of the parkinsonian medication should be further investigated in the future in larger cohorts.
[Mh] Termos MeSH primário: Bactérias/genética
Microbioma Gastrointestinal/genética
Metagenoma
Doença de Parkinson/microbiologia
Vírus/genética
[Mh] Termos MeSH secundário: Idoso
Bactérias/isolamento & purificação
Seres Humanos
Levodopa
Masculino
Meia-Idade
Doença de Parkinson/virologia
Análise de Sequência de DNA
Vírus/isolamento & purificação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
46627O600J (Levodopa)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171212
[Lr] Data última revisão:
171212
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1186/s13073-017-0428-y


  10 / 4880 MEDLINE  
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[PMID]:29020009
[Au] Autor:Meyer KA; Davis TW; Watson SB; Denef VJ; Berry MA; Dick GJ
[Ad] Endereço:Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI, United States of America.
[Ti] Título:Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms.
[So] Source:PLoS One;12(10):e0183859, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M. wesenbergii LE013-01) and one from upstream Lake St. Clair (M. cf aeruginosa LSC13-02), and compared these data to the genomes of seventeen Microcystis spp. from across the globe as well as one metagenome and seven metatranscriptomes from a 2014 Lake Erie Microcystis bloom. For the publically available strains analyzed, the core genome is ~1900 genes, representing ~11% of total genes in the pan-genome and ~45% of each strain's genome. The flexible genome content was related to Microcystis subclades defined by phylogenetic analysis of both housekeeping genes and total core genes. To our knowledge this is the first evidence that the flexible genome is linked to the core genome of the Microcystis species complex. The majority of strain-specific genes were present and expressed in bloom communities in Lake Erie. Roughly 8% of these genes from the lower Great Lakes are involved in genome plasticity (rapid gain, loss, or rearrangement of genes) and resistance to foreign genetic elements (such as CRISPR-Cas systems). Intriguingly, strain-specific genes from Microcystis cultured from around the world were also present and expressed in the Lake Erie blooms, suggesting that the Microcystis pangenome is truly global. The presence and expression of flexible genes, including strain-specific genes, suggests that strain-level genomic diversity may be important in maintaining Microcystis abundance during bloom events.
[Mh] Termos MeSH primário: Eutrofização
Regulação Bacteriana da Expressão Gênica
Genes Bacterianos
Microcystis/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Sistemas CRISPR-Cas/genética
Great Lakes Region
Metagenoma
Microcystis/isolamento & purificação
Filogenia
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171031
[Lr] Data última revisão:
171031
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171012
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0183859



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