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Monday, September 6, 2021

Revealing Mechanisms of Bacterial Virulence and Adaptation with PacBio SMRT Sequencing

In this talk, speakers will describe the importance of high accuracy and long read length for generating closed bacterial assemblies. Speakers will also share examples of how hard-to-assemble domains and plasmids impact important biological traits including, pathogen virulence and anti-microbial resistance. Finally, they will provide an overview of the advantages of highly accurate long-read sequencing for outbreak tracking.

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Monday, August 23, 2021

Identifying Key Players in Host-Microbiome Interactions with High Resolution 16S Sequencing

In this talk, speakers provide an understanding of how highly accurate long-read sequencing of extended 16S amplicons enables the identification of metagenome community members at higher taxonomic resolution than short-read methods. You’ll also hear examples of how metagenome functions that impact human health can be driven by specific species or strains within a community and learn how the gut microbiome can impact drug efficacy.

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Thursday, August 19, 2021

Case Study: Mining complex metagenomes for protein discovery with long-read sequencing

The bacteria living on and within us can impact health, disease, and even our behavior, but there is still much to learn about the breadth of their effects. The torrent of new discoveries unleashed by high-throughput sequencing has captured the imagination of scientists and the public alike. Scientists at Second Genome are hoping to apply these insights to improve human health, leveraging their bioinformatics expertise to mine bacterial communities for potential therapeutics. Recently they teamed up with scientists at PacBio to explore how long-read sequencing might supplement their short-read-based pipeline for gene discovery, using an environmental sample as a test…

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Thursday, August 19, 2021

Case Study: Diving Deep – Revealing the mysteries of marine life with SMRT Sequencing

Many scientists are using PacBio Single Molecule, Real-Time (SMRT) Sequencing to explore the genomes and transcriptomes of a wide variety of marine species and ecosystems. These studies are already adding to our understanding of how marine species adapt and evolve, contributing to conservation efforts, and informing how we can optimize food production through efficient aquaculture.

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Tuesday, July 27, 2021

Optimizing for Information: What Richer Data and Better Assemblies Reveal About Metagenome Structure and Function

In this talk, speakers provide an overview of PacBio-recommended tools for metagenome sequencing analysis, where to download example test data, the typical performance for HiFi metagenome sequencing of fecal samples, the impact of read accuracy on metagenome assembly of long-read data, and finally, how deep sequencing that combines HiFi reads and Hi-C data can enormously increase recovery of high-quality MAGs and connect plasmids and viruses to host strains.

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Tuesday, June 1, 2021

SMRT Sequencing and assembly of the human microbiome project Mock Community sample – a feasibility project.

While the utility of Single Molecule, Real-Time (SMRT) Sequencing for de novo assembly and finishing of bacterial isolates is well established, this technology has not yet been widely applied to shotgun sequencing of microbial communities. In order to demonstrate the feasibility of this approach, we sequenced genomic DNA from the Microbial Mock Community B of the Human Microbiome Project

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Tuesday, June 1, 2021

An interactive workflow for the analysis of contigs from the metagenomic shotgun assembly of SMRT Sequencing data.

The data throughput of next-generation sequencing allows whole microbial communities to be analyzed using a shotgun sequencing approach. Because a key task in taking advantage of these data is the ability to cluster reads that belong to the same member in a community, single-molecule long reads of up to 30 kb from SMRT Sequencing provide a unique capability in identifying those relationships and pave the way towards finished assemblies of community members. Long reads become even more valuable as samples get more complex with lower intra-species variation, a larger number of closely related species, or high intra-species variation. Here we…

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Tuesday, June 1, 2021

Developments in PacBio metagenome sequencing: Shotgun whole genomes and full-length 16S.

The assembly of metagenomes is dramatically improved by the long read lengths of SMRT Sequencing. This is demonstrated in an experimental design to sequence a mock community from the Human Microbiome Project, and assemble the data using the hierarchical genome assembly process (HGAP) at Pacific Biosciences. Results of this analysis are promising, and display much improved contiguity in the assembly of the mock community as compared to publicly available short-read data sets and assemblies. Additionally, the use of base modification information to make further associations between contigs provides additional data to improve assemblies, and to distinguish between members within a…

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Tuesday, June 1, 2021

A workflow for the analysis of contigs from the metagenomic shotgun assembly of SMRT Sequencing data

The throughput of SMRT Sequencing and long reads allows microbial communities to be analyzed using a shotgun sequencing approach. Key to leveraging this data is the ability to cluster sequences belonging to the same member of a community. Long reads of up to 40 kb provide a unique capability in identifying those relationships, and pave the way towards finished assemblies of community members. Long reads are highly valuable when samples are more complex and containing lower intra-species variation, such as a larger number of closely related species, or high intra-species variation. Here, we present a collection of tools tailored for…

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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

Low-input long-read sequencing for complete microbial genomes and metagenomic community analysis.

Microbial genome sequencing can be done quickly, easily, and efficiently with the PacBio sequencing instruments, resulting in complete de novo assemblies. Alternative protocols have been developed to reduce the amount of purified DNA required for SMRT Sequencing, to broaden applicability to lower-abundance samples. If 50-100 ng of microbial DNA is available, a 10-20 kb SMRTbell library can be made. A 2 kb SMRTbell library only requires a few ng of gDNA when carrier DNA is added to the library. The resulting libraries can be loaded onto multiple SMRT Cells, yielding more than enough data for complete assembly of microbial genomes…

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