Navigation Links
Exploring standards to advance microbial genomics

WALNUT CREEK, CA -- Microbes contribute to manifold human endeavors ranging from bioenergy to agriculture to medicine. Moreover, they make the Earth's biogeochemical cycles go round, a prerequisite for all life on the planet. Exceedingly numerous, they are also extremely diverse, encompassing most of Earth's total biodiversity. So it should come as no surprise to find that two-thirds of the nearly 5,000 genome projects reported in the Genomes OnLine Database ( involve microbes. But far more could be done with microbial genomics, according to DOE JGI Genome Biology head Nikos Kyrpides, if researchers would embrace the world of possibilities that lie beyond the present anthropocentric focus and would also institute shared standards for genomic data collection and analysis.

In a perspective piece published in the July issue of the journal Nature Biotechnology, Kyrpides reflects on the role of microbial studies in the genomics revolution of the past decade, and considers the factors that have hindered the advancement of the field. Although nearly 1,000 microbial genomes have been sequenced over the past 15 years, nearly a quarter of them by DOE JGI, he noted that the data obtained has been compromised by the lack of standards for so many critical procedures in the field, procedures ranging from simple data exchange to gene finding, function prediction, and metabolic pathway description. Echoing other researchers, most notably DOE JGI's Patrick Chain and Miriam Land during the recent "Sequencing, Finishing, Analysis in the Future" Conference, Kyrpides calls for the development of genome annotation standards and their adoption by sequencing centers around the world a necessity for meaningful genome comparisons.

Kyrpides offers numerous suggestions to meet these and other challenges that face genomics research in the decade ahead. For example, the list of microbial genomes for potential sequencing, limited to the approximately one percent of the organisms that can be cultured in the lab, has been further biased by a focus on a few groups of particular impact on human health or activities. Thus, vast realms of biodiversity remain unexplored. Kyrpides applauds the effort to coordinate balanced sampling of the Tree of Life recently launched through GEBA: the Genomic Encyclopedia of Bacteria and Archaea ( He also sees a way forward using single-cell genomics ⎯ a technique now being pursued in earnest by DOE JGI researcher Tanja Woyke and her colleagues ⎯ in partnership with environmental metagenomics to provide a more holistic understanding of microbial communities and their individual members.

Kyrpides also suggests several innovative approaches for easing the data processing bottleneck accompanying the exponential increase in genomic data. All-versus-all gene comparisons previously a common practice will become infeasible. To reduce the size of the datasets, he proposes a proxy approach in which one protein from each protein family or one species from each genus represents the group. Taking this one step farther, all the genes from all the sequenced strains in a species the pan-genome for that species would constitute the genome representing that species for gene comparisons.

Sharing his vision for the future of microbial genomics, Kyrpides observes: "The remarkable number of microbes⎯already estimated to be several orders of magnitude greater than the number of stars in the universe⎯urgently calls for a transition from random, anecdotal, and small scale surveys towards a systematic and comprehensive exploration of our planet." With new tools in hand and international initiatives for increased collaboration underway, the field of microbial genomics is poised for a decade of exciting advances.


Contact: David Gilbert
DOE/Joint Genome Institute

Related biology news :

1. Detecting dangerous chemicals with lasers, exploring the brains circuitry with light and more
2. UC Davis researchers exploring gene therapy to fight AIDS
3. Exploring the dynamic relationship between health and environment
4. Frost & Sullivan Looks at Biometrics Advancement in Civil Security: Exploring Opportunities for Today and Beyond
5. Minimum information standards -- all for 1 and 1 for all
6. CO2 emissions could violate EPA ocean-quality standards within decades
7. NIST, Army researchers pave the way for anthrax spore standards
8. UC Riverside to host conference on stricter air quality standards for Southern California
9. Standards in stem cell research
10. MSU biofilms research helps set standards for everyday products
11. Experts agree: Environmental standards needed for biofuels
Post Your Comments:
Related Image:
Exploring standards to advance microbial genomics
(Date:11/16/2015)... 2015  Synaptics Inc. (NASDAQ: SYNA ), ... announced expansion of its TDDI product portfolio with ... and display driver integration (TDDI) solutions designed to ... TDDI products add to the previously-announced TD4300 ... resolution), and TD4322 (FHD resolution) solutions. All four ...
(Date:11/10/2015)... 10, 2015  In this report, the ... of product, type, application, disease indication, and ... report are consumables, services, software. The type ... biomarkers, efficacy biomarkers, and validation biomarkers. The ... diagnostics development, drug discovery and development, personalized ...
(Date:11/2/2015)... Nov. 2, 2015  SRI International has been awarded ... preclinical development services to the National Cancer Institute (NCI) ... provide scientific expertise, modern testing and support facilities, and ... pharmacology and toxicology studies to evaluate potential cancer prevention ... The PREVENT Cancer Drug Development Program is an NCI-supported ...
Breaking Biology News(10 mins):
(Date:11/25/2015)... Studies reveal the differences in species of bacteria ... for more effective treatment for one of the most commonly ... --> --> Gum disease is one ... relatively little was understood about the bacteria associated with it ... researchers from the WALTHAM Centre for Pet Nutrition together with ...
(Date:11/25/2015)... , ... November 25, 2015 , ... ... the Organization of Black Aerospace Professionals (OPBAP) has been formalized with the signing ... AMA team leaders met with OPBAP leaders Capt. Karl Minter and Capt. Albert ...
(Date:11/24/2015)... Nov. 24, 2015  Asia-Pacific (APAC) holds the ... (CRO) market. The trend of outsourcing to low-cost ... but higher volume share for the region in ... however, margins in the CRO industry will improve. ... ( ), finds that the market ...
(Date:11/24/2015)... /CNW/ - iCo Therapeutics ("iCo" or "the Company") (TSX-V: ... the quarter ended September 30, 2015. Amounts, unless ... presented under International Financial Reporting Standards ("IFRS"). ... Andrew Rae , President & CEO of ... only value enriching for this clinical program, but ...
Breaking Biology Technology: