Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Untangling whole genomes of individual species from a microbial mix


New method opens window on invisible world

A new approach to studying microbes in the wild will allow scientists to sequence the genomes of individual species from complex mixtures. It marks a big advance for understanding the enormous diversity of microbial communities —including the human microbiome. The work is described in an article published May 22 in Early Online form in the journal G3: Genes|Genomes|Genetics, published by the Genetics Society of America.   

“This new method will allow us to discover many currently unknown microbial species that can’t be grown in the lab, while simultaneously assembling their genome sequences,” says co-author Maitreya Dunham, a biologist at the University of Washington’s Department of Genome Sciences. 

Microbial communities, whether sampled from the ocean floor or a human mouth, are made up of many different species living together. Standard methods for sequencing these communities combine the information from all the different types of microbes in the sample. The result is a hodgepodge of genes that is challenging to analyze, and unknown species in the sample are difficult to discover. 

“Our approach tells us which sequence fragments in a mixed sample came from the same genome, allowing us to construct whole genome sequences for individual species in the mix,” says co-author Jay Shendure, also of the University of Washington’s Department of Genome Sciences. 

The key advance was to combine standard approaches with a method that maps out which fragments of sequence were once near each other inside a cell. The cells in the sample are first treated with a chemical that links together DNA strands that are in close proximity.  Only strands that are inside the same cell will be close enough to link. The DNA is then chopped into bits, and the linked portions are isolated and sequenced. 

“This elegant method enables the study of microbes in the environment,” says Brenda Andrews, editor-in-chief of the journal G3: Genes|Genomes|Genetics. Andrews is alsoDirector of the Donnelly Centre and the Charles H. Best Chair of Medical Research at the University of Toronto. “It will open many windows into an otherwise invisible world.”

At a time when personal microbiome sequencing is becoming extremely popular, this method breaks important ground in helping researchers to build a complete picture of the genomic content of complex mixtures of microorganisms. This complete picture will be crucial for understanding the impact of varying microbiome populations and the relevance of particular microorganisms for individual health.

CITATION:  Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps Joshua N. Burton, Ivan Liachko, Maitreya J. Dunham, and Jay Shendure.  G3: Genes|Genomes|Genetics g3.114.011825; Early Online May 22, 2014, doi:10.1534/g3.114.011825; PMID 24855317.

FUNDING INFORMATION:  This work was supported by NIH/NHGRI grant T32HG000035 (J.N.B.), NIH/NHGRI grant HG006283 (J.S.), NIH/NIGMS grant P41 GM103533 (I.L. & M.J.D.), NSF grant 1243710 (I.L. & M.J.D.), DOE/-LBL-JGI grant 7074345/DE-AC02-05CH11231 (J.S.). M.J.D. is a Rita Allen Foundation Scholar and a Fellow in the Genetic Networks program at the Canadian Institute for Advanced Research.

* * *

About G3

G3: Genes|Genomes|Genetics publishes high-quality, valuable findings, regardless of perceived impact. G3 publishes research that generates useful genetic and genomic information such as genome maps, single gene studies, QTL studies, mutant screens and advances in methods and technology, novel mutant collections, genome-wide association studies (GWAS) including gene expression, SNP and CNV studies; exome sequences related to a specific disease, personal exome and genome sequencing case, disease and population reports, and more. Conceived by the Genetics Society of America, with its first issue published June 2011, G3 is fully open access. G3 uses a Creative Commons license that allows the most free use of the data, which anyone can download, analyze, mine and reuse, provided that the authors of the article receive credit. GSA believes that rapid dissemination of useful data is the necessary foundation for analysis that leads to mechanistic insights. It is our hope is that this strategy will spawn new discovery.

About the Genetics Society of America (GSA)

Founded in 1931, the Genetics Society of America (GSA) is the professional scientific society for genetics researchers and educators. The Society’s more than 5,000 members worldwide work to deepen our understanding of the living world by advancing the field of genetics, from the molecular to the population level. GSA promotes research and fosters communication through a number of GSA-sponsored conferences including regular meetings that focus on particular model organisms. GSA publishes two peer-reviewed, peer-edited scholarly journals: GENETICS, which has published high quality original research across the breadth of the field since 1916, and G3: Genes|Genomes|Genetics, an open-access journal launched in 2011 to disseminate high quality foundational research in genetics and genomics. The Society also has a deep commitment to education and fostering the next generation of scholars in the field. For more information about GSA, please visit

Raeka Aiyar | Eurek Alert!

Further reports about: GSA Genetics Genome Untangling analyze genomes microbes microbial sequences species

More articles from Life Sciences:

nachricht Tissue-engineered colon from human cells develop different types of neurons
02.10.2015 | Children's Hospital Los Angeles

nachricht Big eyes! – MDC Researchers Identify Cause of Inherited Form of Extreme Nearsightedness
02.10.2015 | Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: New Sinumerik features improve productivity and precision

EMO 2015, Hall 3, Booth E06/F03

  • Drive optimization called automatically by the part program boosts productivity
  • Automatically switching the dynamic values to rapid traverse and interpolation...

Im Focus: LZH presents additive manufacturing at the LABVOLUTION

The Laser Zentrum Hannover e.V. (LZH) will present how laser-based technologies can contribute to the laboratory of the future at the LABVOLUTION in Hannover in Hall 9, Stand E67/09, from October 6th to 8th, 2015. As a part of the model lab smartLAB, the LZH is showing how additive manufacturing, better known as 3-D printing, can make experimental setups more flexible.

Twelve partners from science and industry are presenting an intelligent and innovative model lab at the special display smartLAB. A part of this intelligent...

Im Focus: New polymer creates safer fuels

Before embarking on a transcontinental journey, jet airplanes fill up with tens of thousands of gallons of fuel. In the event of a crash, such large quantities of fuel increase the severity of an explosion upon impact.

Researchers at Caltech and JPL have discovered a polymeric fuel additive that can reduce the intensity of postimpact explosions that occur during accidents and...

Im Focus: 3-D printing techniques help surgeons carve new ears

When surgical residents need to practice a complicated procedure to fashion a new ear for children without one, they typically get a bar of soap, carrot or an apple.

To treat children with a missing or under-developed ear, experienced surgeons harvest pieces of rib cartilage from the child and carve them into the framework...

Im Focus: Walk the line

NASA studies physical performance after spaceflight

Walking an obstacle course on Earth is relatively easy. Walking an obstacle course on Earth after being in space for six months is not quite as simple. The...

All Focus news of the innovation-report >>>



Event News

EHFG 2015: Securing healthcare and sustainably strengthening healthcare systems

01.10.2015 | Event News

Conference in Brussels: Tracking and Tracing the Smallest Marine Life Forms

30.09.2015 | Event News

World Alzheimer`s Day – Professor Willnow: Clearer Insights into the Development of the Disease

17.09.2015 | Event News

Latest News

Infrared thermography can detect joint inflammation and help improving work ergonomics

02.10.2015 | Medical Engineering

Semiconductor nanoparticles show high luminescence in a polymer matrix

02.10.2015 | Materials Sciences

New Sinumerik features improve productivity and precision

02.10.2015 | Trade Fair News

More VideoLinks >>>