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Cornell Team Reports Low-Cost, High-Throughput Bacterial Genomics Workflow

A low-cost, high-throughput workflow for bacterial whole-genome sequencing is reported in Genome Biology this week, opening the door to affordable population genetic analyses of bacterial strains not currently possible with metagenomic data alone. Earth's environments harbor complex consortia of microbes, but understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. A team led by Cornell University scientists developed protocols, 3D-printed custom labware, and analysis pipelines to enable high-throughput whole-genome sequencing of the gut microbiome at a cost of approximately $10 per genome. They use their approach to assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos, quantifying intraspecific genomic diversity and revealing divergence of homologous plasmids between hosts. "The protocols presented here expand the accessibility of high-throughput microbial genomics, thereby increasing the diversity of environments from which microbial isolates and reference genomes can be obtained," the researchers write. "Given the interconnectedness of microbial genomic diversity in nature, expanding the breadth of such data will be of substantial benefit to researchers studying microbes from all sorts of environments."

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.