The Experts below are selected from a list of 4482 Experts worldwide ranked by ideXlab platform
Ian Joint - One of the best experts on this subject based on the ideXlab platform.
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Bias in assessments of marine microbial biodiversity in Fosmid libraries as evaluated by pyrosequencing
The ISME journal, 2009Co-Authors: Ben Temperton, Anna Oliver, Dawn Field, Bela Tiwari, Martin Muhling, Ian Joint, Jack A. GilbertAbstract:On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has an almost universal distribution, being detected as abundant sequences in all marine provinces. Yet, SAR11 sequences are rarely detected in Fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a Fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11–15% relative abundance of SAR11 within the community. In contrast, not a single SAR11 Fosmid was identified in a pooled shotgun sequence data set of 100 Fosmid clones. This underrepresentation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation and fragment recruitment. Analysis revealed a similar underrepresentation of low-GC Flavobacteriaceae. We speculate that a contributing factor towards the Fosmid bias may be DNA fragmentation during preparation because of the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that, although Fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic Fosmid libraries.
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Bias in culture-independent assessments of microbial biodiversity in the global ocean
Nature Precedings, 2009Co-Authors: Ben Temperton, Anna Oliver, Dawn Field, Bela Tiwari, Martin Muhling, Ian Joint, Jack GilbertAbstract:On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has almost universal distribution, being detected as abundant sequences in all marine provinces. Yet SAR11 sequences are rarely detected in Fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR 11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a Fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15% relative abundance of SAR11 within the community. In contrast not a single SAR11 Fosmid was identified in a pooled shotgun sequenced data set of 100 Fosmid clones. This under-representation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation; functional metabolic profiling and fragment recruitment. Analysis revealed a similar under-representation of low-GC Flavobacteriaceae. We speculate that the Fosmid bias may be due to DNA fragmentation during preparation due to the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that while Fosmid libraries can be extremely useful, caution must be used when directly inferring community composition from metagenomic Fosmid libraries.
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A rare SAR11 Fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome
The ISME Journal, 2008Co-Authors: Jack A. Gilbert, Martin Muhling, Ian JointAbstract:A sequence analysis is described of a Fosmid clone from a coastal marine metagenomic library that contains a 16S rRNA gene with high sequence similarity to that of the SAR11 bacterium ‘ Candidatus Pelagibacter ubique’ HTCC1062. The sequence of the Fosmid clone was 32 086 bp in length and contained 23 187 bp of the 48-kb hyper-variable region 2 (HVR2) present in the genome of ‘ Cand . P. ubique’. However, half of the sequences within the HVR2 region of the Fosmid clone show little sequence similarity to or have no representative homologues in the genome sequence of ‘ Cand. P. ubique’ HTCC1062. Given their putative functions, the acquisition of these genes suggests that SAR11 could harbour more diverse phenotypes than represented by the 16S rRNA taxonomy. Variation in SAR11 genomes from different locations might explain why SAR11 is abundant in so many diverse marine provinces.
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A rare SAR11 Fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome.
The ISME journal, 2008Co-Authors: Jack A. Gilbert, Martin Muhling, Ian JointAbstract:A rare SAR11 Fosmid clone confirming genetic variability in the ‘ Candidatus Pelagibacter ubique’ genome
Jack A. Gilbert - One of the best experts on this subject based on the ideXlab platform.
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Bias in assessments of marine microbial biodiversity in Fosmid libraries as evaluated by pyrosequencing
The ISME journal, 2009Co-Authors: Ben Temperton, Anna Oliver, Dawn Field, Bela Tiwari, Martin Muhling, Ian Joint, Jack A. GilbertAbstract:On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has an almost universal distribution, being detected as abundant sequences in all marine provinces. Yet, SAR11 sequences are rarely detected in Fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a Fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11–15% relative abundance of SAR11 within the community. In contrast, not a single SAR11 Fosmid was identified in a pooled shotgun sequence data set of 100 Fosmid clones. This underrepresentation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation and fragment recruitment. Analysis revealed a similar underrepresentation of low-GC Flavobacteriaceae. We speculate that a contributing factor towards the Fosmid bias may be DNA fragmentation during preparation because of the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that, although Fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic Fosmid libraries.
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A rare SAR11 Fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome
The ISME Journal, 2008Co-Authors: Jack A. Gilbert, Martin Muhling, Ian JointAbstract:A sequence analysis is described of a Fosmid clone from a coastal marine metagenomic library that contains a 16S rRNA gene with high sequence similarity to that of the SAR11 bacterium ‘ Candidatus Pelagibacter ubique’ HTCC1062. The sequence of the Fosmid clone was 32 086 bp in length and contained 23 187 bp of the 48-kb hyper-variable region 2 (HVR2) present in the genome of ‘ Cand . P. ubique’. However, half of the sequences within the HVR2 region of the Fosmid clone show little sequence similarity to or have no representative homologues in the genome sequence of ‘ Cand. P. ubique’ HTCC1062. Given their putative functions, the acquisition of these genes suggests that SAR11 could harbour more diverse phenotypes than represented by the 16S rRNA taxonomy. Variation in SAR11 genomes from different locations might explain why SAR11 is abundant in so many diverse marine provinces.
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A rare SAR11 Fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome.
The ISME journal, 2008Co-Authors: Jack A. Gilbert, Martin Muhling, Ian JointAbstract:A rare SAR11 Fosmid clone confirming genetic variability in the ‘ Candidatus Pelagibacter ubique’ genome
Sung-keun Rhee - One of the best experts on this subject based on the ideXlab platform.
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Metagenomic assessment of a sulfur-oxidizing enrichment culture derived from marine sediment
The Journal of Microbiology, 2010Co-Authors: Man-young Jung, Soo-je Park, Jong-chan Chae, Vinhhoa Pham, Sung-keun RheeAbstract:The biological oxidation of reduced sulfur compounds is a critically important process in global sulfur biogeochemistry. In this study, we enriched from marine sediments under denitrifying conditions, chemolithotrophic sulfur oxidizers that could oxidize a variety of reduced sulfur compounds: thiosulfate, tetrathionate, sulfide, and polysulfide. Two major phylotypes of 16S rRNA gene (>99% identity in each phylotype) were detected in this enrichment culture. In order to characterize sulfide oxidation, we sequenced and characterized one Fosmid clone (43.6 kb) containing the group I sulfide-quinone reductase ( sqr ) gene. Interestingly, four putative rhodanese genes were found in this clone. Furthermore, comparative alignment with the closest genome of Thiomicrospira crunogena XCL2 revealed that three homologous genes were located within the vicinity of the sqr gene. Fosmid clones harboring carbon fixation ( cbbL and cbbM ) and denitrification ( narG ) genes were screened, and the phylogeny of the functional genes was analyzed. Along with the comparison between the sqr -containing Fosmid clones and the relevant -proteobacteria, our phylogenetic study based on the 16S rRNA gene and carbon fixation genes suggest the prevalence of chemolithotrophic -proteobacteria in the denitrifying cultures. The findings of this study imply that a combination of cultivation and metagenomic approaches might provide us with a glimpse into the characteristics of sulfur oxidizers in marine sediments.
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Metagenome microarray for screening of Fosmid clones containing specific genes.
FEMS microbiology letters, 2008Co-Authors: Soo-je Park, Cheol-hee Kang, Jong-chan Chae, Sung-keun RheeAbstract:A critical step in the process of metagenome analysis is to screen for clones that contain specific genes among a large number of clones. To form one of the sequence-based screening tools of a metagenome library, we designed a format of microarray [metagenome microarray (MGA)] that is arrayed with Fosmid library clone DNA samples on a glass slide. We evaluated the MGA using random prime labeled fluorescent probes prepared from PCR products of the target gene and found that we could obtain specific hybridization signals only for the Fosmid clone that contained the target gene. We found that the detection limit of the MGA was c. 10 ng μL−1 of Fosmid clone DNA, and that the MGA-based hybridization was quantitative within a concentration range of 10–200 ng μL−1 of Fosmid clone DNA. We used the MGA successfully to identify two Fosmid clones that contained 16S rRNA genes from a Fosmid library from the sediment of the East Sea, Korea. In conclusion, we have demonstrated that the MGA can be used for screening for Fosmid clones containing specific genes in a metagenome library, and that this technology has potential application as a high-throughput metagenome screening tool.
Martin Muhling - One of the best experts on this subject based on the ideXlab platform.
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Bias in assessments of marine microbial biodiversity in Fosmid libraries as evaluated by pyrosequencing
The ISME journal, 2009Co-Authors: Ben Temperton, Anna Oliver, Dawn Field, Bela Tiwari, Martin Muhling, Ian Joint, Jack A. GilbertAbstract:On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has an almost universal distribution, being detected as abundant sequences in all marine provinces. Yet, SAR11 sequences are rarely detected in Fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a Fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11–15% relative abundance of SAR11 within the community. In contrast, not a single SAR11 Fosmid was identified in a pooled shotgun sequence data set of 100 Fosmid clones. This underrepresentation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation and fragment recruitment. Analysis revealed a similar underrepresentation of low-GC Flavobacteriaceae. We speculate that a contributing factor towards the Fosmid bias may be DNA fragmentation during preparation because of the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that, although Fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic Fosmid libraries.
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Bias in culture-independent assessments of microbial biodiversity in the global ocean
Nature Precedings, 2009Co-Authors: Ben Temperton, Anna Oliver, Dawn Field, Bela Tiwari, Martin Muhling, Ian Joint, Jack GilbertAbstract:On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has almost universal distribution, being detected as abundant sequences in all marine provinces. Yet SAR11 sequences are rarely detected in Fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR 11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a Fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15% relative abundance of SAR11 within the community. In contrast not a single SAR11 Fosmid was identified in a pooled shotgun sequenced data set of 100 Fosmid clones. This under-representation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation; functional metabolic profiling and fragment recruitment. Analysis revealed a similar under-representation of low-GC Flavobacteriaceae. We speculate that the Fosmid bias may be due to DNA fragmentation during preparation due to the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that while Fosmid libraries can be extremely useful, caution must be used when directly inferring community composition from metagenomic Fosmid libraries.
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A rare SAR11 Fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome
The ISME Journal, 2008Co-Authors: Jack A. Gilbert, Martin Muhling, Ian JointAbstract:A sequence analysis is described of a Fosmid clone from a coastal marine metagenomic library that contains a 16S rRNA gene with high sequence similarity to that of the SAR11 bacterium ‘ Candidatus Pelagibacter ubique’ HTCC1062. The sequence of the Fosmid clone was 32 086 bp in length and contained 23 187 bp of the 48-kb hyper-variable region 2 (HVR2) present in the genome of ‘ Cand . P. ubique’. However, half of the sequences within the HVR2 region of the Fosmid clone show little sequence similarity to or have no representative homologues in the genome sequence of ‘ Cand. P. ubique’ HTCC1062. Given their putative functions, the acquisition of these genes suggests that SAR11 could harbour more diverse phenotypes than represented by the 16S rRNA taxonomy. Variation in SAR11 genomes from different locations might explain why SAR11 is abundant in so many diverse marine provinces.
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A rare SAR11 Fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome.
The ISME journal, 2008Co-Authors: Jack A. Gilbert, Martin Muhling, Ian JointAbstract:A rare SAR11 Fosmid clone confirming genetic variability in the ‘ Candidatus Pelagibacter ubique’ genome
Heather Ebling - One of the best experts on this subject based on the ideXlab platform.
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Fosmid libraries for genomic structural variation detection
Current protocols in human genetics, 2007Co-Authors: William F. Donahue, Heather EblingAbstract:Fosmid libraries have demonstrated their utility for a number of applications. These include filling gaps between BACs and small insert libraries in sequence assemblies, performing hybridization/screening studies to isolate functional elements within the genome (Vergin et al., 1998), and detecting insertions, deletions, and rearrangements in structural variation studies (Tuzun et al., 2005). This unit covers the basic methodologies for the construction of Fosmid libraries with tight insert sizes suitable for these applications. Basic Protocol 1 covers the shearing, size selection, and recovery of DNA from a pulsed-field gel. Basic Protocol 2 covers the cloning of insert DNA into the Fosmid vector, packaging of DNA into infective phage particles, and the infection/transformation of bacteria. A commentary section is provided, which outlines many of the critical parameters involved in Fosmid library construction, along with some additional background information and a section discussing anticipated results. Curr. Protoc. Hum. Genet. 54:5.20.1-5.20.18. © 2007 by John Wiley & Sons, Inc. Keywords: Fosmid cloning; Fosmid library; Fosmid; Fosmid protocol; structural variation detection
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Current Protocols in Human Genetics - Fosmid Libraries for Genomic Structural Variation Detection
Current Protocols in Human Genetics, 2007Co-Authors: William F. Donahue, Heather EblingAbstract:Fosmid libraries have demonstrated their utility for a number of applications. These include filling gaps between BACs and small insert libraries in sequence assemblies, performing hybridization/screening studies to isolate functional elements within the genome (Vergin et al., 1998), and detecting insertions, deletions, and rearrangements in structural variation studies (Tuzun et al., 2005). This unit covers the basic methodologies for the construction of Fosmid libraries with tight insert sizes suitable for these applications. Basic Protocol 1 covers the shearing, size selection, and recovery of DNA from a pulsed-field gel. Basic Protocol 2 covers the cloning of insert DNA into the Fosmid vector, packaging of DNA into infective phage particles, and the infection/transformation of bacteria. A commentary section is provided, which outlines many of the critical parameters involved in Fosmid library construction, along with some additional background information and a section discussing anticipated results. Curr. Protoc. Hum. Genet. 54:5.20.1-5.20.18. © 2007 by John Wiley & Sons, Inc. Keywords: Fosmid cloning; Fosmid library; Fosmid; Fosmid protocol; structural variation detection
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Fosmid libraries for genomic structural variation detection.
Current protocols in human genetics, 2007Co-Authors: William F. Donahue, Heather EblingAbstract:Fosmid libraries have demonstrated their utility for a number of applications. These include filling gaps between BACs and small insert libraries in sequence assemblies, performing hybridization/screening studies to isolate functional elements within the genome (Vergin et al., 1998), and detecting insertions, deletions, and rearrangements in structural variation studies (Tuzun et al., 2005). This unit covers the basic methodologies for the construction of Fosmid libraries with tight insert sizes suitable for these applications. Basic Protocol 1 covers the shearing, size selection, and recovery of DNA from a pulsed-field gel. Basic Protocol 2 covers the cloning of insert DNA into the Fosmid vector, packaging of DNA into infective phage particles, and the infection/transformation of bacteria. A commentary section is provided, which outlines many of the critical parameters involved in Fosmid library construction, along with some additional background information and a section discussing anticipated results.