QIAGEN Joins Consortium to Map Microbial Genomes
News Jul 02, 2016
QIAGEN N.V. has announced a collaboration with Weill Cornell Medicine in a global study seeking insights on the prevalence of pathogens, including antimicrobial resistance, in urban environments. Starting, researchers will simultaneously collect DNA and RNA samples from high-traffic areas in subway systems, buses and parks in 54 cities around the world – expanding on a metagenomic portrait of microbes in the New York City subways published in 2015. The project will use QIAGEN sample technologies and library preparation workflows to extract and prepare genomic materials for analysis.
“Mapping the unseen genomes and epigenomes of cities across six continents is an exciting effort that illustrates the potential for metagenomics to create new insights into interactions among humans, our environment and the microbes that have an impact on our health,” said Colin Baron, Senior Director and Head of QIAGEN’s Product Management NGS Life Sciences. “QIAGEN is pleased that the scientific leaders in this international collaboration have selected our MO BIO PowerSoil® sample technology kits for sample extraction and QIAseq FX DNA library preparation kits to enable reliable next-generation sequencing.”
Dr. Christopher E. Mason, Associate Professor of Physiology and Biophysics and of Computational Genomics in Computational Biomedicine in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine at Weill Cornell Medicine, is principal investigator on the study, in collaboration with colleagues at other institutions and the MetaSUB Consortium, which consists of 54 member cities.
“Just as our PathoMap study created a profile of New York City’s metagenome based on mass-transit areas, the MetaSUB researchers and laboratories will work to establish a worldwide ‘DNA map’ of microbes in subways and other transit systems,” Dr. Mason said. “This five-year commitment will yield insights on antimicrobial resistance in urban areas and lead to discovery of new biosynthetic gene clusters revealing interactions of microbes and the environment. Sample preparation and library preparation powered by QIAGEN are key steps in this analysis, and we expect significant findings to emerge that can benefit both scientific understanding and the public health.”
The MetaSUB team’s collection of samples from subways and other urban sites is synchronized with Global Ocean Sampling Day to provide a “genetic snapshot” of the world’s cities and oceans at the same time. In some cities such as New York, Boston and Montevideo, metagenomic data also will be generated from sewer systems and beaches and compared to findings from the other environments. The data, methods, techniques and results will all be made open to the public and free for all to use.
A related project will look at metagenomic impacts of the Olympics in Rio de Janeiro in August 2016, which MetaSub calls a “natural experiment” illustrating a global human migration event. An estimated 500,000 people from around the world will attend the Olympics in August. Sampling of RNA and DNA before, during and after the Olympics will include a search for RNA viruses such as influenza and Zika. The MetaSUB study is a Grand Challenges Explorations winner, an initiative of the Bill & Melinda Gates Foundation that seeks to foster innovation to solve key global health and development problems.
A number of public funding agencies, other foundations and companies also are supporting or partnering in the effort. Advancing the understanding of microbiomes – complex microbial content, such as in the human gut or the environment – is currently aim of many life sciences funding initiatives in which QIAGEN technologies are being used, including the National Microbiome Initiative (NMI) announced by the White House earlier this month.
Cities in 32 countries are currently taking part in the MetaSUB Consortium: Argentina (Buenos Aires), Australia (Sydney), Austria (Vienna), Brazil (Ribeirão Preto, Rio Da Janeiro, and São Paulo) Chile (Santiago), China (Beijing, Guangzhou, Hong Kong, Shanghai), Colombia (Bogota), Croatia (Zagreb), Egypt (Cairo), France (Marseille and Paris), Germany (Berlin), India (Hyderabad and New Delhi), Iran (Tehran), Italy (Rome), Japan (Sendai and Tokyo), Mexico (Mexico City), New Zealand (Auckland City), Nigeria (Ilorin and Lagos), Norway (Oslo), Portugal (Lisbon and Porto), Qatar (Doha), Russia (Moscow), Singapore (Singapore), South Africa (Johannesburg), South Korea (Seoul), Spain (Barcelona), Sweden (Stockholm), Switzerland (Zurich), Turkey (Izmir), United Kingdom (Sheffield and London), Uruguay (Montevideo), United States (Baltimore, Boston, Chicago, Denver, Fairbanks, New York City, Sacramento, San Francisco, Seattle, and Washington, DC).
Computer scientists at Carnegie Mellon University say neural networks and supervised machine learning techniques can efficiently characterize cells that have been studied using single cell RNA-sequencing (scRNA-seq). This finding could help researchers identify new cell subtypes and differentiate between healthy and diseased cells.