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Scott A. Beatson - One of the best experts on this subject based on the ideXlab platform.
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blast ring image generator brig simple Prokaryote genome comparisons
BMC Genomics, 2011Co-Authors: Nabil-fareed Alikhan, Nicola K. Petty, Nouri Ben L Zakour, Scott A. BeatsonAbstract:Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related Prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a Prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image.
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BLAST Ring Image Generator (BRIG): Simple Prokaryote genome comparisons
BMC Genomics, 2011Co-Authors: Nabil-fareed Alikhan, Nicola K. Petty, Nouri L. Ben Zakour, Scott A. BeatsonAbstract:BACKGROUND: Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related Prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a Prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. RESULTS: BLAST Ring Image Generator (BRIG) can generate images that show multiple Prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically. CONCLUSIONS: There is a clear need for a user-friendly program that can produce genome comparisons for a large number of Prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at http://sourceforge.net/projects/brig/.
Didier Raoult - One of the best experts on this subject based on the ideXlab platform.
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Halophilic & Halotolerant Prokaryotes in Humans
Future Microbiology, 2018Co-Authors: El Hadji Seck, Didier Raoult, Jean-charles Dufour, Jean-christophe LagierAbstract:: Halophilic Prokaryotes are described as microorganisms living in hypersaline environments. Here, we list the halotolerant and halophilic bacteria which have been isolated in humans. Of the 52 halophilic Prokaryotes, 32 (61.54%) were moderately halophilic, 17 (32.69%) were slightly halophilic and three (5.76%) were extremely halophilic Prokaryotes. At the phylum level, 29 (54.72%) belong to Firmicutes, 15 (28.84%) to Proteobacteria, four (7.69%) to Actinobacteria, three (5.78%) to Euryarchaeota and one (1.92%) belongs to Bacteroidetes. Halophilic Prokaryotes are rarely pathogenic: of these 52 halophilic Prokaryotes only two (3.92%) species were classified in Risk Group 2 (Vibrio cholerae, Vibrio parahaemolyticus) and one (1.96%), species in Risk Group 3 (Bacillus anthracis).
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the rebirth of culture in microbiology through the example of culturomics to study human gut microbiota
Clinical Microbiology Reviews, 2015Co-Authors: Jean-christophe Lagier, Perrine Hugon, Saber Khelaifia, Pierre-edouard Fournier, Bernard La Scola, Didier RaoultAbstract:SUMMARY Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a “dark matter” of Prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the “great plate count anomaly,” which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human Prokaryote repertoire.
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Molecular studies neglect apparently gram-negative populations in the human gut microbiota
Journal of Clinical Microbiology, 2013Co-Authors: Perrine Hugon, Jean-christophe Lagier, Catherine Robert, Catherine Lepolard, Laurent Papazian, Didier Musso, Bernard Vialettes, Didier RaoultAbstract:Studying the relationships between gut microbiota, human health, and diseases is a major challenge that generates contradictory results. Most studies draw conclusions about the gut repertoire using a single biased metagenomics approach. We analyzed 16 different stool samples collected from healthy subjects who were from different areas, had metabolic disorders, were immunocompromised, or were treated with antibiotics at the time of the stool collection. The analyses performed included Gram staining, flow cytometry, transmission electron microscopy (TEM), quantitative real-time PCR (qPCR) of the Bacteroidetes and Firmicutes phyla, and pyrosequencing of the 16S rRNA gene amplicons targeting the V6 region. We quantified 10(10) Prokaryotes per gram of feces, which is less than was previously described. The Mann-Whitney test revealed that Gram-negative proportions of the Prokaryotes obtained by Gram staining, TEM, and pyrosequencing differed according to the analysis used, with Gram-negative Prokaryotes yielding median percentages of 70.6%, 31.0%, and 16.4%, respectively. A comparison of TEM and pyrosequencing analyses highlighted a difference of 14.6% in the identification of Gram-negative Prokaryotes, and a Spearman test showed a tendency toward correlation, albeit not significant, in the Gram-negative/Gram-positive Prokaryote ratio (rho = 0.3282, P = 0.2146). In contrast, when comparing the qPCR and pyrosequencing results, a significant correlation was found for the Bacteroidetes/Firmicutes ratio (rho = 0.6057, P = 0.0130). Our study showed that the entire diversity of the human gut microbiota remains unknown because different techniques generate extremely different results. We found that to assess the overall composition of bacterial communities, multiple techniques must be combined. The biases that exist for each technique may be useful in exploring the major discrepancies in molecular studies.
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estimation of Prokaryote genomic dna g c content by sequencing universally conserved genes
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Pierre-edouard Fournier, Karsten Suhre, Ghislain Fournous, Didier RaoultAbstract:Determination of the DNA G+C content of prokaryotic genomes using traditional methods is time-consuming and results may vary from laboratory to laboratory, depending on the technique used. We explored the possibility of extrapolating the genomic DNA G+C content of Prokaryotes from gene sequences. For this, 127 universally conserved genes were studied from 50 prokaryotic genomes in the Clusters of Orthologous Groups database. Of these, 57 genes were present as a single copy in the genomes of 157 different Prokaryote species available in GenBank. There was a strong correlation [coefficient of determination (r 2) >95 %] between the DNA G+C contents of 20 genes and their corresponding genomes. For each of the 157 prokaryotic genomes studied, the DNA G+C content of the 20 genes was used to determine a ‘calculated’ genome DNA G+C content (CGC) and this value was compared with the ‘real’ genome DNA G+C content (RGC). In order to select the most suitable gene for the determination of CGC values, we compared the r 2 and median mol% difference between CGC and RGC as well as the sensitivity of each gene to provide CGC values for prokaryotic genomes that differ by less than 5 mol% from their RGC. The highly conserved ftsY gene (median size 1144 nucleotides), a vertically inherited member of the GTPase superfamily, showed the highest r 2 value of 0.98, the smallest median mol% difference between CGC and RGC of 1.06 and a sensitivity of 100 %. Using ftsY DNA G+C content values, the CGC values of 100 genomes not included in the calculation of r 2 differed by less than 5 mol% from their RGC values. These data suggest that the genomic DNA G+C content of Prokaryotes may be estimated easily and reliably from the ftsY gene sequence.
Nabil-fareed Alikhan - One of the best experts on this subject based on the ideXlab platform.
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blast ring image generator brig simple Prokaryote genome comparisons
BMC Genomics, 2011Co-Authors: Nabil-fareed Alikhan, Nicola K. Petty, Nouri Ben L Zakour, Scott A. BeatsonAbstract:Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related Prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a Prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image.
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BLAST Ring Image Generator (BRIG): Simple Prokaryote genome comparisons
BMC Genomics, 2011Co-Authors: Nabil-fareed Alikhan, Nicola K. Petty, Nouri L. Ben Zakour, Scott A. BeatsonAbstract:BACKGROUND: Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related Prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a Prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. RESULTS: BLAST Ring Image Generator (BRIG) can generate images that show multiple Prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically. CONCLUSIONS: There is a clear need for a user-friendly program that can produce genome comparisons for a large number of Prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at http://sourceforge.net/projects/brig/.
Richard R Stein - One of the best experts on this subject based on the ideXlab platform.
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On the need for widespread horizontal gene transfers under genome size constraint
Biology Direct, 2009Co-Authors: Hervé Isambert, Richard R SteinAbstract:Background While eukaryotes primarily evolve by duplication-divergence expansion (and reduction) of their own gene repertoire with only rare horizontal gene transfers, Prokaryotes appear to evolve under both gene duplications and widespread horizontal gene transfers over long evolutionary time scales. But, the evolutionary origin of this striking difference in the importance of horizontal gene transfers remains by and large a mystery. Hypothesis We propose that the abundance of horizontal gene transfers in free-living Prokaryotes is a simple but necessary consequence of two opposite effects: i) their apparent genome size constraint compared to typical eukaryote genomes and ii) their underlying genome expansion dynamics through gene duplication-divergence evolution, as demonstrated by the presence of many tandem and block repeated genes. In principle, this combination of genome size constraint and underlying duplication expansion should lead to a coalescent-like process with extensive turnover of functional genes. This would, however, imply the unlikely, systematic reinvention of functions from discarded genes within independent phylogenetic lineages. Instead, we propose that the long-term evolutionary adaptation of free-living Prokaryotes must have resulted in the emergence of efficient non-phylogenetic pathways to circumvent gene loss. Implications This need for widespread horizontal gene transfers due to genome size constraint implies, in particular, that Prokaryotes must remain under strong selection pressure in order to maintain the long-term evolutionary adaptation of their "mutualized" gene pool, beyond the inevitable turnover of individual Prokaryote species. By contrast, the absence of genome size constraint for typical eukaryotes has presumably relaxed their need for widespread horizontal gene transfers and strong selection pressure. Yet, the resulting loss of genetic functions, due to weak selection pressure and inefficient gene recovery mechanisms, must have ultimately favored the emergence of more complex life styles and ecological integration of many eukaryotes. Reviewers This article was reviewed by Pierre Pontarotti, Eugene V Koonin and Sergei Maslov.
Víctor M. Eguíluz - One of the best experts on this subject based on the ideXlab platform.
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Scaling of species distribution explains the vast potential marine Prokaryote diversity.
Scientific Reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, Juan Fernández-gracia, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Carlos M. DuarteAbstract:: Global ocean expeditions have provided minimum estimates of ocean's Prokaryote diversity, supported by apparent asymptotes in the number of Prokaryotes with sampling effort, of about 40,000 species, representing
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scaling of species distribution explains the vast potential marine Prokaryote diversity
Scientific Reports, 2019Co-Authors: Víctor M. Eguíluz, Guillem Salazar, John K. Pearman, Josep M. Gasol, Silvia G. Acinas, Shinichi Sunagawa, Xabier Irigoien, Juan Fernandezgracia, Carlos M. DuarteAbstract:: Global ocean expeditions have provided minimum estimates of ocean's Prokaryote diversity, supported by apparent asymptotes in the number of Prokaryotes with sampling effort, of about 40,000 species, representing <1% of the species cataloged in the Earth Microbiome Project, despite being the largest habitat in the biosphere. Here we demonstrate that the abundance of Prokaryote OTUs follows a scaling that can be represented by a power-law distribution, and as a consequence, we demonstrate, mathematically and through simulations, that the asymptote of rarefaction curves is an apparent one, which is only reached with sample sizes approaching the entire ecosystem. We experimentally confirm these findings using exhaustive repeated sampling of a Prokaryote community in the Red Sea and the exploration of global assessments of Prokaryote diversity in the ocean. Our findings indicate that, far from having achieved a thorough sampling of Prokaryote species abundance in the ocean, global expeditions provide just a start for this quest as the richness in the global ocean is much larger than estimated.
