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Wednesday, December 11, 2019

Long-Read Sequencing Could Improve the Sensitivity and Precision of 16S Studies Says Jackson Lab Study

It’s time to revisit the way scientists are using 16S rRNA gene sequencing to study microorganisms, according to a team of Jackson Laboratory researchers.  Popular targets for taxonomy and phylogeny studies because of their highly conserved nature, amplified sequences of the 16S ribosomal RNA genes can be compared with reference databases to determine the identity of the microorganisms that comprise a metagenomic sample. Sequences with a > 95% match are generally considered to represent the same genus, for example, while > 97% matches are considered the same species. However, these matches are often made by sequencing only part of the nine-region, ~1500 bp…

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Monday, April 8, 2019

Complete Genomes Within Reach: Multiplexing Enables Efficient Microbial Sequencing

Research interest in the human microbiome and the roles our bacterial, viral, and single-cell eukaryote co-inhabitants play in health, nutrition, immunity, and disease has exploded. Yet accurately measuring the composition of these microbial communities remains complex. Sequence-based approaches allow the genetic material from complete collections of microbes to be analyzed without the need to cultivate the microorganisms. But each step in the process of collecting, extracting, preparing, sequencing and analyzing the DNA and data introduces its own set of errors and biases. At the Innovation Lab of the University of Minnesota Genomics Center, research scientist Ben Auch and his colleagues…

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Wednesday, March 27, 2019

Collaborative Study with Second Genome: Mining Complex Metagenomes for Protein Discovery with Long-Read Sequencing

It seems like there is a new story every week in the mainstream press about the unexpected ways the bacteria living on and within us impact health, disease, and even our behavior. The torrent of new discoveries unleashed by high-throughput sequencing has captured the imagination of scientists and laypeople 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. Second Genome is a clinical stage pharmaceutical company with a mission to redefine disease in the context of microbiome medicine and create therapeutics that can…

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Thursday, April 12, 2018

SMRT Sequencing Enables Characterization of Cavities-Causing Bacteria in Children

We’re told to avoid sugar and refined carbohydrates if we want our teeth to remain strong and cavity-free. But what is the role of microbiota in our oral health? Cavities – or caries – actually occur as the result of bacterial infection that leads to sustained decalcification of tooth enamel and the layer beneath it, the dentin. Left unchecked, it can reach the tooth’s inner layer, with its soft pulp and sensitive nerve fibers, and, in some cases, can cause serious complications such as phylogenetic osteomyelitis and the life-threatening bacterial endocarditis. In addition to diet and host factors, the occurrence…

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Friday, March 9, 2018

Coral Microbiome Project Wins 2017 Microbial SMRT Grant

Rice coral (Montipora capitata) growing over Porites lobata. Credit: Dr. Dwayne Meadows, NOAA/NMFS/OPR Corals are critical to sustaining sea life in many parts of the world, contributing to an elaborate ecosystem that lives in and around their mineralized calcium carbonate skeletons. In addition to hosting photosynthetic endosymbionts in exchange for energy, corals harbor a diverse microbial community. What role does this microbial metagenome play in the health of the coral reef, especially during thermal challenges induced by climate change? Alexander Shumaker of Rutgers University will get a chance to investigate this question, thanks to long-read sequencing provided by PacBio and…

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Tuesday, December 12, 2017

Creating an Epigenetic Barcode to Accurately Characterize Microbial Communities

Unraveling the role of the microbiome in human health and environmental samples is an emerging priority in scientific study. But despite the best advances in sequencing technology, identifying the bacteria, fungi, and other organisms present in complex samples remains a huge challenge. Metagenomic shotgun sequencing can read chromosomes, plasmids, and bacteriophages, and comparison to reference genome sequences can be used to place them into putative taxa and species bins, but these methods fail to sufficiently distinguish between genomes that are very similar. A team of scientists from the Icahn School of Medicine at Mount Sinai, Sema4, and other institutions has…

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Thursday, December 8, 2016

ASM SMRT Grant Winner: Squirrel Microbiome!

We’re pleased to announce the winner of this year’s SMRT Grant, which launched during the American Society for Microbiology annual meeting this summer. The grant program, co-sponsored by PacBio and the Institute for Genome Sciences (IGS), was very competitive, with over 100 submitted proposals. From this broad range of entries, our judges faced quite a task choosing just one recipient for the grant. Congratulations to Jessica Sieber from the University of Minnesota Duluth, who impressed reviewers with her proposal, “Metagenomic analysis of the gut microbiota of the 13-lined ground squirrel, a model fat storing hibernator.” Ground squirrels have been models…

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Friday, February 19, 2016

AGBT Day 3: Human Genomes and Their Microbial Friends

We’ve been in the genomics world long enough to remember when it was a big deal to see a great single-gene assembly or microbial genome assembly reported in an AGBT talk. It’s really something to attend this year and see some beautifully assembled whole human genomes. Several of the Friday talks really captured our interest, but we can only cover a couple of them here. NCBI’s Valerie Schneider spoke about efforts through the Genome Reference Consortium to improve assembly of the human reference genome, noting that one challenge has been the shift from a clone-based approach during the Human Genome…

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