Contact Information
Available for logged-in reporters only
Newswise BETHESDA, MD May 23, 2014 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 cant be grown in the lab, while simultaneously assembling their genome sequences, says co-author Maitreya Dunham, a biologist at the University of Washingtons 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 Washingtons 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 also Director 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.
Originally posted here:
Untangling Whole Genomes of Individual Species From a Microbial Mix
- June 11th At Westport, CT: Federal Red Flags, HIPAA Security Rules and Fraud Prevention - November 7th, 2009 [November 7th, 2009]
- Do not learn Dvorak! - November 7th, 2009 [November 7th, 2009]
- You Can’t Solve Problems By Making It Illegal To Have The Problem - November 7th, 2009 [November 7th, 2009]
- A Force Fix for Healthcare - November 7th, 2009 [November 7th, 2009]
- Yahble, HIT, Bubblecon, BIZDEV!, Solid State - November 7th, 2009 [November 7th, 2009]
- 15 things that suck about the Palm Pre - November 7th, 2009 [November 7th, 2009]
- What an Indie Genomics Lab Looks Like - November 7th, 2009 [November 7th, 2009]
- Practice Fusion: Class D Felony? - February 26th, 2010 [February 26th, 2010]
- Practice Fusion Responds - March 7th, 2010 [March 7th, 2010]
- Practice Fusion: Do the math: $44,000 is a LIE - March 10th, 2010 [March 10th, 2010]
- How Much Until Doctors Approve of 23andMe? - March 10th, 2010 [March 10th, 2010]
- Biochemicals as Media, Not Methods - March 10th, 2010 [March 10th, 2010]
- More Practice Fusion Reality Distortion - March 10th, 2010 [March 10th, 2010]
- Same Test Results: 23andMe is Myriad is BRCA is Medicine - March 12th, 2010 [March 12th, 2010]
- BRCA is 23andMe is Myriad is Medicine - March 13th, 2010 [March 13th, 2010]
- Getting Serious About Genomics as Common Medical Practice - March 15th, 2010 [March 15th, 2010]
- The New John Mackey of Genetics: Linda Avey? - March 15th, 2010 [March 15th, 2010]
- Keep the Medical, Well, Medical - March 16th, 2010 [March 16th, 2010]
- If 23andMe shuts down, it won’t be for some mundane reason like the bills weren’t paid - March 16th, 2010 [March 16th, 2010]
- If I Run A Medical Practice, How Do I Use A 23andMe? - March 17th, 2010 [March 17th, 2010]
- 23andMe Contract in Bad Faith - March 19th, 2010 [March 19th, 2010]
- Doctors CANNOT Use 23andMe Due To 23andMe’s Bad Faith Contract - March 20th, 2010 [March 20th, 2010]
- Pathway Compared to 23andMe and Navigenics - March 22nd, 2010 [March 22nd, 2010]
- There’s a Word for “Views Differ” When One View Is The State - March 24th, 2010 [March 24th, 2010]
- Association for Molecular Pathology, et al. v. USPTO, et al. – Opinion - March 29th, 2010 [March 29th, 2010]
- Birth of a Super Villain - April 3rd, 2010 [April 3rd, 2010]
- “Medical Products” like 23andMe must not become the new “Financial Products” - April 4th, 2010 [April 4th, 2010]
- How I Would Apply Genomic Technology In Clinical Use Today - April 5th, 2010 [April 5th, 2010]
- Gmail Enterprise: World’s Best EMR - April 6th, 2010 [April 6th, 2010]
- Brief Primer on Health Law Compliance - April 9th, 2010 [April 9th, 2010]
- Spoiler: You ARE the “Valids” - April 9th, 2010 [April 9th, 2010]
- Rachel Lehmann-Haupt Line by Line Take Down - April 9th, 2010 [April 9th, 2010]
- Is Medicare Bankrupt? What the Hell Is Going On? - April 17th, 2010 [April 17th, 2010]
- The Big Shuffle: Medicare Cuts Rates by 21.3% (but not “technically”) - April 17th, 2010 [April 17th, 2010]
- “Tech Hiring Binge” == “Fear for Your Job, Nerds” - April 18th, 2010 [April 18th, 2010]
- How Bad is Bad? $.20 on the Private Medical Insurance Dollar - April 20th, 2010 [April 20th, 2010]
- Update: How Bad is Bad? It Used to Be $.45 on the Medical Insurance Dollar - April 20th, 2010 [April 20th, 2010]
- World’s Best “EMR” for $1000: Google Spreadsheets + iPad - April 21st, 2010 [April 21st, 2010]
- Don’t Insult Me with your “AOL Keyword” Strategy, Google Health - April 21st, 2010 [April 21st, 2010]
- How to Play LAWGAMES - April 23rd, 2010 [April 23rd, 2010]
- Top 4 Predatory Schemes Encroaching on American Medicine: Part 1 - April 25th, 2010 [April 25th, 2010]
- What’s the Big Deal About iPads? - April 27th, 2010 [April 27th, 2010]
- Got Google Android for Google I/O - April 27th, 2010 [April 27th, 2010]
- Google Enterprise meets HIPAA and HITECH Compliant Laws - April 29th, 2010 [April 29th, 2010]
- Pixels of Accuracy CHALENGE: Diagnostic Medical Imaging - April 29th, 2010 [April 29th, 2010]
- 23andMe Launder AlioGenetics Doesn’t Even Bother to Remove 23andMe Logo - April 30th, 2010 [April 30th, 2010]
- Anthem of CT Denies $600 Until “Subscriber Responds to our Coordination of Benefits Questionnaire” - May 1st, 2010 [May 1st, 2010]
- Apple And Google Team Up To Launch Revolutionary Mobile Health System - May 1st, 2010 [May 1st, 2010]
- Funny Pictures from This Year Building the Medical Practice - May 6th, 2010 [May 6th, 2010]
- Remote Medical Video Monitoring on iPad and iPhone - May 7th, 2010 [May 7th, 2010]
- Google Calendar Overhead Waiting Room Display - May 7th, 2010 [May 7th, 2010]
- Various Whiteboards on Solid State Medical Operations - May 7th, 2010 [May 7th, 2010]
- The Raw Facts about Counsyl - May 7th, 2010 [May 7th, 2010]
- Brawndo: Still Mutilating Thirst, Still Not Yet Sold at the Stop-n-Shop Pharmacy - May 9th, 2010 [May 9th, 2010]
- Video: Google Enterprise to Outsource Medical Administration - May 9th, 2010 [May 9th, 2010]
- Gattaca: “The Matrix” of Genomics - May 11th, 2010 [May 11th, 2010]
- 23andMe Now Diagnoses Fatal Tay-Sachs Disease - May 12th, 2010 [May 12th, 2010]
- Why Was Pathway Targeted for FDA Enforcement and Not 23andMe? - May 15th, 2010 [May 15th, 2010]
- John Dolan on Aging and the Horrifying Conclusion of GWAS - May 16th, 2010 [May 16th, 2010]
- Sam R. Riley Wants To Tell You About Practice Fusion - May 17th, 2010 [May 17th, 2010]
- Response to “Genomic Medicine: Lost” - May 19th, 2010 [May 19th, 2010]
- Death And Taxes: CMS to IRS - May 19th, 2010 [May 19th, 2010]
- Please Stop Antagonizing the AMA - May 26th, 2010 [May 26th, 2010]
- Dan Vorhaus, Attorney At Law, Legally Advises Medical Doctors Can Use 23andMe To Provide Medical Advice - May 28th, 2010 [May 28th, 2010]
- Singularity Summit 2010 in San Francisco to Explore Intelligence Augmentation - June 7th, 2010 [June 7th, 2010]
- OpenPCR: DNA amplification for anyone - June 10th, 2010 [June 10th, 2010]
- FDA sends letters to 5 genetic testing companies - June 11th, 2010 [June 11th, 2010]
- Amazon And The NIH Team Up To Put Human Genome In The Cloud - March 31st, 2012 [March 31st, 2012]
- ReproSource Comments on New Study Linking Infertility to Genetics - April 25th, 2012 [April 25th, 2012]
- Genetics 101 Part 1: What are genes? - Video - April 30th, 2012 [April 30th, 2012]
- Red Ice Radio - David Icke - Hour 1 - The Manipulation of Humanity - Video - April 30th, 2012 [April 30th, 2012]
- Genetics Part 5: Human Genetic Disorders - Video - April 30th, 2012 [April 30th, 2012]
- C2CAM - The Nephilim, Genetic Manipulation - April 30th, 2012 [April 30th, 2012]
- Human Nature talk with Robert Sapolsky, Gabor Mate, James Gilligan, Richard Wilkinson - Video - April 30th, 2012 [April 30th, 2012]
- Human Genetic Diseases - Video - April 30th, 2012 [April 30th, 2012]
- Alien Scientist on Genetics, Implants - April 30th, 2012 [April 30th, 2012]
- Research and Markets: Genetics, 6th Edition International Student Version Continues To Educate Today's Students for ... - May 4th, 2012 [May 4th, 2012]
- Myriad Genetics to Present at the Bank of America Merrill Lynch 2012 Health Care Conference - May 4th, 2012 [May 4th, 2012]
- Genetics may explain some people's dislike of meat - May 4th, 2012 [May 4th, 2012]
- 'Blond Genes' May Vary Around the World - May 4th, 2012 [May 4th, 2012]