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Friday, June 18, 2021

Application Note: Microbial multiplexing workflow on the Sequel System

Obtaining microbial genomes with the highest accuracy and contiguity is extremely important when exploring the functional impact of genetic and epigenetic variants on a genome-wide scale. A comprehensive view of the bacterial genome, including genes, regulatory regions, IS elements, phage integration sites, and base modifications is vital to understanding key traits such as antibiotic resistance, virulence, and metabolism. SMRT Sequencing provides complete genomes, often assembled into a single contig. Our streamlined microbial multiplexing procedure for the Sequel System, from library preparation to genome assembly, can be completed with less than 8 hours bench time. Starting with high-quality genomic DNA (gDNA),…

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Tuesday, June 1, 2021

Harnessing kinetic information in Single-Molecule, Real-Time Sequencing.

Single-Molecule Real-Time (SMRT) DNA sequencing is unique in that nucleotide incorporation events are monitored in real time, leading to a wealth of kinetic information in addition to the extraction of the primary DNA sequence. The dynamics of the DNA polymerase that is observed adds an additional dimension of sequence-dependent information, and can be used to learn more about the molecule under study. First, the primary sequence itself can be determined more accurately. The kinetic data can be used to corroborate or overturn consensus calls and even enable calling bases in problematic sequence contexts. Second, using the kinetic information, we can…

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Tuesday, June 1, 2021

New discoveries from closing Salmonella genomes using Pacific Biosciences continuous long reads.

The newer hierarchical genome assembly process (HGAP) performs de novo assembly using data from a single PacBio long insert library. To assess the benefits of this method, DNA from several Salmonella enterica serovars was isolated from a pure culture. Genome sequencing was performed using Pacific Biosciences RS sequencing technology. The HGAP process enabled us to close sixteen Salmonella subsp. enterica genomes and their associated mobile elements: The ten serotypes include: Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) S. Bareilly, S. Heidelberg, S. Cubana, S. Javiana and S. Typhimurium, S. Newport, S. Montevideo, S. Agona, and S. Tennessee. In addition,…

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Tuesday, June 1, 2021

Metagenomes of native and electrode-enriched microbial communities from the Soudan Iron Mine.

Despite apparent carbon limitation, anoxic deep subsurface brines at the Soudan Underground Iron Mine harbor active microbial communities. To characterize these assemblages, we performed shotgun metagenomics of native and enriched samples. Following enrichment on poised electrodes and long read sequencing, we recovered from the metagenome the closed, circular genome of a novel Desulfuromonas sp. with remarkable genomic features that were not fully resolved by short read assembly alone. This organism was essentially absent in unenriched Soudan communities, indicating that electrodes are highly selective for putative metal reducers. Native community metagenomes suggest that carbon cycling is driven by methyl-C1 metabolism, in…

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Tuesday, June 1, 2021

Comparative metagenome-assembled genome analysis of “Candidatus Lachnocurva vaginae”, formerly known as Bacterial Vaginosis Associated bacterium – 1 (BVAB1)

Bacterial Vaginosis Associated bacterium 1 (BVAB1) is an as-yet uncultured bacterial species found in the human vagina that belongs to the family Lachnospiraceae within the order Clostridiales. As its name suggests, this bacterium is often associated with bacterial vaginosis (BV), a common vaginal disorder that has been shown to increase a woman’s risk for HIV, Chlamydia trachomatis, and Neisseria gonorrhoeae infections as well as preterm birth. Further, BVAB1 is associated with the persistence of BV following metronidazole treatment, increased vaginal inflammation, and adverse obstetrics outcomes. There is no available complete genome sequence of BVAB1, which has made it di?cult to…

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Friday, February 5, 2021

User Group Meeting: New genotype to phenotype associations in viral metagenomes enabled by SMRT Sequencing

In this PacBio User Group Meeting lightning talk, Shawn Polson of the University of Delaware speaks about viral metagenomes, which are more challenging to distinguish than their bacterial counterparts because viruses have no 16S equivalent. By using SMRT Sequencing, his team generated higher-resolution data about viral genomes and aims to use this information as a guide to how these genomes function.

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Friday, February 5, 2021

Webinar: Bioinformatics lunch & learn – Better assemblies of bacterial genomes and plasmids with the new microbial assembly pipeline in SMRT Link v8.0

Microbial Assembly is our latest pipeline, specifically designed to assemble bacterial genomes (between 2 and 10 Mb) and plasmids. This pipeline includes the implementation of a new, circular-aware read alignment tool (Raptor), among other algorithmic improvements, which will be covered in this webinar. The topics covered include, staged assembly of bacterial chromosomes and plasmids, implementation of Raptor, a circular-aware read aligner, himeric read detection, origin of replication orientation, troubleshooting and more.

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Tuesday, April 21, 2020

Tracking short-term changes in the genetic diversity and antimicrobial resistance of OXA-232-producing Klebsiella pneumoniae ST14 in clinical settings.

To track stepwise changes in genetic diversity and antimicrobial resistance in rapidly evolving OXA-232-producing Klebsiella pneumoniae ST14, an emerging carbapenem-resistant high-risk clone, in clinical settings.Twenty-six K. pneumoniae ST14 isolates were collected by the Korean Nationwide Surveillance of Antimicrobial Resistance system over the course of 1 year. Isolates were subjected to whole-genome sequencing and MIC determinations using 33 antibiotics from 14 classes.Single-nucleotide polymorphism (SNP) typing identified 72 unique SNP sites spanning the chromosomes of the isolates, dividing them into three clusters (I, II and III). The initial isolate possessed two plasmids with 18 antibiotic-resistance genes, including blaOXA-232, and exhibited resistance to 11 antibiotic…

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Tuesday, April 21, 2020

Evolution of a 72-kb cointegrant, conjugative multiresistance plasmid from early community-associated methicillin-resistant Staphylococcus aureus isolates.

Horizontal transfer of plasmids encoding antimicrobial-resistance and virulence determinants has been instrumental in Staphylococcus aureus evolution, including the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA). In the early 1990s the first CA-MRSA isolated in Western Australia (WA), WA-5, encoded cadmium, tetracycline and penicillin-resistance genes on plasmid pWBG753 (~30 kb). WA-5 and pWBG753 appeared only briefly in WA, however, fusidic-acid-resistance plasmids related to pWBG753 were also present in the first European CA-MRSA at the time. Here we characterized a 72-kb conjugative plasmid pWBG731 present in multiresistant WA-5-like clones from the same period. pWBG731 was a cointegrant formed from pWBG753 and a…

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Tuesday, April 21, 2020

Transcriptional initiation of a small RNA, not R-loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae.

Neisseria gonorrhoeae, the sole causative agent of gonorrhea, constitutively undergoes diversification of the Type IV pilus. Gene conversion occurs between one of the several donor silent copies located in distinct loci and the recipient pilE gene, encoding the major pilin subunit of the pilus. A guanine quadruplex (G4) DNA structure and a cis-acting sRNA (G4-sRNA) are located upstream of the pilE gene and both are required for pilin antigenic variation (Av). We show that the reduced sRNA transcription lowers pilin Av frequencies. Extended transcriptional elongation is not required for Av, since limiting the transcript to 32 nt allows for normal…

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Tuesday, April 21, 2020

Efficacy of Newly Isolated and Highly Potent Bacteriophages in a Mouse Model of XDRAB Bacteremia.

Bacteremia can be caused by Acinetobacter baumannii with clinical manifestations ranging from transient bacteremia to septic shock. Extensively drug-resistant A. baumannii (XDRAB) strains producing the New Delhi metallo-ß-lactamase, which confers resistance to all ß-lactams including carbapenems, have emerged and infected patients suffer increased mortality, morbidity and length of hospitalization. The lack of new antimicrobials led to a renewed interest into phage therapy, the so-called forgotten cure. Accordingly, we tested new lytic bacteriophages in a Galleria mellonella and a mouse model of XDRAB-induced bacteremia.Galleria mellonella were challenged with 5.105 CFU of the XDRAB strain FER. Phages vB_AbaM_3054 and vB_AbaM_3090 were administrated…

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Tuesday, April 21, 2020

Complete genome of Pseudomonas sp. DMSP-1 isolated from the Arctic seawater of Kongsfjorden, Svalbard

The genus Pseudomonas is highly metabolically diverse and has colonized a wide range of ecological niches. The strain Pseudomonas sp. DMSP-1 was isolated from Arctic seawater (Kongsfjorden, Svalbard) using dimethylsulfoniopropionate (DMSP) as the sole carbon source. To better understand its role in the Arctic coastal ecosystem, the genome of Pseudomonas sp. strain DMSP-1 was completely sequenced. The genome contained a circular chromosome of 6,282,445?bp with an average GC content of 60.01?mol%. A total of 5510 protein coding genes, 70 tRNA genes and 19 rRNA genes were obtained. However, no genes encoding known enzymes associated with DMSP catabolism were identified in…

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Tuesday, April 21, 2020

Complete genome sequence of Pseudoalteromonas sp. MEBiC 03485, isolated from deep-sea sediment

Pseudoalteromonas strains are widely distributed in the marine environment and most have attracted considerable interest owing to their ability to synthesize biologically active metabolites. In this study, we report and describe the genome sequence of Pseudoalteromonas sp. MEBiC 03485, isolated from the deep-sea sediment of Pacific Ocean at a depth of 2000?m. The complete genome consisted of three contigs with a total genome size of 4,167,407?bp and a GC content of 40.76?l%, and was predicted to contain 4194 protein-coding genes and 131 non-coding RNA genes. The strain MEBiC 03485 genome was also shown to contain genes for diverse metabolic pathways.…

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Tuesday, April 21, 2020

The genomic architecture of introgression among sibling species of bacteria

Gene transfer between bacterial species is an important mechanism for adaptation. For example, sets of genes that confer the ability to form nitrogen-fixing root nodules on host plants have frequently moved between Rhizobium species. It is not clear, though, whether such transfer is exceptional, or if frequent inter-species introgression is typical. To address this, we sequenced the genomes of 196 isolates of the Rhizobium leguminosarum species complex obtained from root nodules of white clover (Trifolium repens). Core gene phylogeny placed the isolates into five distinct genospecies that show high intra-genospecies recombination rates and remarkably different demographic histories. Most gene phylogenies…

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