Navigation Links
Venter Institute-Led Team Recovers and Sequences Genome of Periodontal Pathogen from Biofilm in Hospital Sink using Single-Cell Genomics

LA JOLLA, Calif., April 5, 2013 /PRNewswire-USNewswire/ -- A team of researchers led by scientists from the J. Craig Venter Institute (JCVI) has published a study outlining the recovery and genomic analysis, using single-cell genomic techniques, of a periodontal pathogen, Porphyromonas gingivalis, from a hospital sink. This is the first time that a single-cell genome sequencing approach was used to isolate and analyze a single microbe from a biofilm in a healthcare setting. The team, led by JCVI's Jeffrey McLean published their study in the April 5 edition of the journal Genome Research.

Understanding the community of microbes living in biofilms, especially those in healthcare settings, has been limited partially because pathogens can be in very low numbers and many other bacterial types are not easily cultured.  A method for DNA sequencing from single cells developed by JCVI's Roger Lasken group, is now allowing researchers to sequence the vast numbers of uncultured microbes in the environment. With this approach this team hopes to sequence many hospital pathogens that have been otherwise inaccessible. 

In this study the team targeted bacterial cells in a biofilm sampled from a hospital bathroom sink. Using single-cell genomic sequencing combined with a new single-cell genome assembler, SPAdes, developed by Pavel Pevzner , University of California, San Diego, the team found 25 different types of bacteria within the biofilm. The bacteria represented environmental species, human commensals and human pathogens.

The team then reconstructed a near complete genome of one specific periodontal pathogen, P. gingivalis (designated as JCVI SC001) from a single cell. While this globally important pathogen is well known, only three other P. gingivalis genomes have been sequenced to date, and all of those were cultured from patients. This is the first strain sequenced from a single cell from the environment.  The team was able to compare the JCVI SC001 strain to the cultured strains, finding it to vary by 524 unique genes, some potentially altering its virulence. The team believes that the JCVI SC001 strain could potentially contain adaptations relevant to survival outside of the host and to transmission to humans.

The scientists conclude that using single cell sequencing and analysis will open up new avenues of research into environmental samples, including healthcare settings where biofilms are critical in harboring pathogens that contaminate water sources, medical instruments and catheters. This has important implications in better understanding infectious disease especially modes of transmission as well as the spread of antibiotic resistance. 

Researchers from the University of California, San Diego, Department of Medicine and Department of Mathematics; the University of Southern California; and St. Petersburg Academic University, Russian Academy of Sciences were key contributors to this study. Funding was provided by the Alfred P. Sloan Foundation, the National Institutes of Health, and the Government of the Russian Federation.

About JCVI

The JCVI is a not-for-profit research institute in Rockville, MD and San Diego, CA dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter , Ph.D., the JCVI is home to approximately 200 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy. The legacy organizations of the JCVI are: The Institute for Genomic Research (TIGR), The Center for the Advancement of Genomics (TCAG), the Institute for Biological Energy Alternatives (IBEA), the Joint Technology Center (JTC), and the J. Craig Venter Science Foundation. The JCVI is a 501 (c)(3) organization. For additional information, please visit

SOURCE J. Craig Venter Institute
Copyright©2012 PR Newswire.
All rights reserved

Related biology technology :

1. Human Genome Decoder and Artificial Life Creator, J. Craig Venter to Speak at "The Atlantic Meets the Pacific"
2. Richard H. Scheuermann, Ph.D. Joins J. Craig Venter Institute as Director of Informatics
3. Neural implant recovers ability to make decisions
4. Scientists Warn of Long Term Consequences of Budget Sequestration: BioInformatics LLC Report
5. Discovered Evolution of Genomic Sequences -- from Ocean Archaea to Brain Cancer -- Leads to New Synthetic Replikin Vaccines for Infectious Diseases and Cancer
6. Personal Genome Diagnostics Inc. Licenses Genome-Mapping Technology from Johns Hopkins University and Expands Its Cancer Genome Analysis Business
7. New York Genome Institute Selects Exemplar LIMS to Manage Next Gen Sequencing Labs
8. The Genome Analysis Center Selects Convey to Support Next-Generation Sequencing
9. Whole Genome Sequencing of Triple Negative Breast Cancer Reveals Previously Unreported Mutations
10. Pig genome offers insights into the feistiest of farm animals
11. Researchers unlock disease information hidden in genomes control circuitry
Post Your Comments:
(Date:11/25/2015)... , Nov. 25, 2015 /PRNewswire/ - Aeterna Zentaris Inc. ... its business and prospects remain fundamentally strong and ... (zoptarelin doxorubicin) recently received DSMB recommendation to continue ... following review of the final interim efficacy and ... Primary Endpoint in men with heavily pretreated castration- ...
(Date:11/24/2015)... 24, 2015  Asia-Pacific (APAC) holds the third-largest ... market. The trend of outsourcing to low-cost locations ... higher volume share for the region in the ... margins in the CRO industry will improve. ... ( ), finds that the market earned ...
(Date:11/24/2015)... ... November 24, 2015 , ... Copper is ... it is bound to proteins, copper is also toxic to cells. With a ... Polytechnic Institute (WPI) will conduct a systematic study of copper in the bacteria ...
(Date:11/24/2015)... ... November 24, 2015 , ... This fall, global software solutions leader SAP ... states to develop and pitch their BIG ideas to improve health and wellness in ... for votes to win the title of SAP's Teen Innovator, an all-expenses paid trip ...
Breaking Biology Technology:
(Date:11/20/2015)... Connecticut , November 20, 2015 ... authentication company focused on the growing mobile commerce market ... CEO, Gino Pereira , was recently interviewed on ... interview will air on this weekend on Bloomberg ... Latin America . --> NXTD ) ("NXT-ID" ...
(Date:11/17/2015)... Paris from 17 th until 19 ... from 17 th until 19 th November 2015. ... invented the first combined scanner in the world which scans ... now two different scanners were required: one for passports and ... the same surface. This innovation is an ideal solution for ...
(Date:11/12/2015)...  A golden retriever that stayed healthy despite having ... provided a new lead for treating this muscle-wasting disorder, ... of MIT and Harvard and the University of São ... Cell, pinpoints a protective gene that boosts ... The Boston Children,s lab of Lou Kunkel , ...
Breaking Biology News(10 mins):