Recent microbiome study finds that Shoreline Biome products differentiate closely related gut bacteria in premature infants

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February 18, 2021

Recently published study describes novel, high-accuracy, high-throughput approach for neonatal gut microbiome bacterial strain tracking

FARMINGTON, Conn.— Products from Shoreline Biome demonstrated high-resolution tracking of specific bacterial strains in a recent microbiome study, the results of which are being applied to better understand how pathogens and commensals become established in premature infants in neonatal intensive care units (NICU), with the goal of improving outcomes for premature infants.

Shoreline Biome is a microbiome research company based in Farmington that develops tools for characterizing microbiome populations down to the strain level.

The research article, titled “High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon,” was published February 16, 2021 in mBio. The study describes how Shoreline Biome’s kits and software enable a novel, high-resolution ‘DNA fingerprint’ for bacteria that provides species- and strain-level resolution of the neonatal microbiome. The high-resolution taxonomy obtained from long amplicon sequencing enables the tracking of strains temporally and spatially as microbiomes are established in infants in the hospital environment.  “These highly vulnerable infants are at increased risk of developing life-threatening infections.” said Adam Matson, MD (Connecticut Children’s Medical Center and Assistant Professor of Pediatrics and Immunology at UConn Health) “This exciting new approach represents a major technical advancement in the classification of intestinal microbiota and will enable source-tracking of pathogenic and beneficial microbes in the NICU.” 

The researchers in the study used Shoreline Biome’s StrainID kits, SBanalyzer software, and Athena database (all recently patent-protected technology) to identify known and novel pathogens in the guts of infants, and follow how the microbial population responds to interventions designed to treat disease and improve health in this extremely vulnerable population. “Our study combines the Shoreline Biome StrainID kit and their custom Athena database with PacBio’s Sequel II, a highly-accurate system that allows us to sequence longer DNA molecules,” said Joerg Graf, Ph.D. (Professor of Molecular and Cell Biology at the University of Connecticut), lead author on the paper. “These advances provide a cost-effective method for us to track bacteria at the strain level and will help us better determine how pathogens and antibiotic resistant bacteria spread.”

“It’s no exaggeration to say this paper describes previously unattainable insights that have the potential to transform our understanding of early microbiome development. The ability to zero in on specific strains, including toxic Klebseilla that colonize early and damage the infant gut in the first few weeks of life, and follow them wherever they appear across patients and over time, is information that we feel confident our co-authors and collaborators in the clinic can use to save lives,” said Mark Driscoll, Ph.D., Shoreline Biome’s cofounder and Chief Science Officer. “In neonatal intensive care units (NICU), we are able to work with our collaborators Adam Matson, MD (Connecticut Children’s Medical Center and Assistant Professor of Pediatrics and Immunology at UConn Health) and Joerg Graf, Ph.D. (Professor of Molecular and Cell Biology at the University of Connecticut) to see that shortly after birth, ‘bad’ bacteria can become established in babies’ gut microbiomes, bacteria that are responsible for Necrotizing Enterocolitis (NEC) and other serious illnesses. Doctors currently have an incomplete understanding of where these pathogens come from and how they get around in the hospital. We’re honored that Shoreline Biome’s products are used in potentially life-saving research such as this.”

Three members of Shoreline Biome’s staff—Mark Driscoll, Ph.D., Cofounder and Chief Science Officer; Dawn Gratalo, Director of R&D; and Eric Jackson, R&D Scientist—are credited as co-authors in the study, alongside collaborators from the University of Connecticut, Pattern Genomics, and the Connecticut Children’s Medical Center.”

Characterizing the human microbiome and analyzing its role in human health and disease are high priority goals for researchers around the world. Shoreline Biome accelerates breakthroughs in microbiome research by developing transformative discovery tools that characterize microbiome populations down to the strain level. With Shoreline Biome products, all it takes is three easy steps: lyse, purify, and amplify. Shoreline Biome’s easy-to-use companion analysis software and comprehensive reference database enables straightforward strain-level identification and quantitation of all bacteria in the sample.

To learn more, visit shorelinebiome.com.

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