The rapid explosion in the throughput of DNA sequencing due to new technology platforms is fueling an increase in the number of sequenced microbial genomes and driving much greater availability of these data to the research community.
Traditionally, identifying the microorganisms selected for sequencing is often decided on the basis of a single universal marker gene. More recently, however, researchers have noticed that the identity of microbes for which whole-genome information has become available does not always match up with the identity determined by the approaches commonly used prior to the advent of next-generation high-throughput sequencing.
In a study published ahead online July 6, 2015 in Nucleic Acids Research (NAR), a team of researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility and their collaborators developed and evaluated a new method for classifying microbial species that could be supplemented – as needed – by traditional approaches relied on by microbiologists for decades. Study first author Neha Varghese of the DOE JGI says the Microbial Species Identifier (MiSI) method meets a “long standing need for a systematic, scalable, and objective microbial species assignment technique.”
“A fast, genome-sequence based method”
The standard whole-genome approach relies on the small subunit ribosomal RNA gene (16S rRNA); without sequencing, researchers used approaches such as DNA-DNA hybridization, phenotypic information – genotyping, phenotyping, or classifying by the chemical compounds that microbes share – to derive the needed information for microbial classification.
The MiSI method developed at the DOE JGI relies primarily on genome sequencing and is a combination of two metrics for determining how closely related two genomes are: genome-wide Average Nucleotide Identity (gANI) and alignment fraction (AF). Computational tool development is a critical element of the DOE JGI 10-Year Strategic Vision, essential to characterizing complex biological and environmental systems in support DOE’s research missions, as well as the Institute’s partnership with the National Energy Research Scientific Computing Center (NERSC).
“Scientists and practitioners of microbiology will much appreciate the robust, extensive, taxonomic organization of the microbial world provided by this fast, genome-sequence based method,” said Jim Tiedje, Director of the Center for Microbial Ecology at Michigan State University. “It provides a more accurate and clear-cut means to identify bacteria.” A DOE JGI collaborator on the Great Prairie Soil Metagenome Grand Challenge project, Tiedje and his former student Kostas Konstantinidis, one of the study’s co-authors, jointly developed the original genome-wide gANI metric modified by the DOE JGI team as a basis for the MiSI method.
The algorithm in the gANI method developed by Tiedje and Konstantinidis used segments sampled over the whole genome and the National Center for Biotechnology Information (NCBI) tool Basic Local Alignment Search Tool (BLAST) for sequence alignment. MiSI speeds up the computations dramatically—by about 10-fold—by using nucleotide sequences of genes and a modified BLAST-based similarity search.
The team implemented the MiSI method over a massive database of more than 13,000 bacterial and archaeal high quality genomes selected from the Integrated Microbial Genomes (IMG) database. These genomes were then classified into clusters represented by cliques or clique-groups where connectivity is determined by genomic similarity (a surrogate for evolutionary distance), and thus, for the first time, allowed researchers to diagram how genomes are related to each other across a large phylogenetic space.
The completely connected nature of these cliques helped the team identify highly conserved cores of species, while the semi-connect nature of clique groups helped identify species that could be revisited taxonomically. Further, since the clustering is based solely on genomic relatedness, the team was able to use this method to determine if an uncultured organism is either related to an existing species or is a novel candidate species.
“A universal method for species identification”
“The implications of using this method in transforming microbiology cannot be overstated,” said Kyrpides, head of the Prokaryote Super Program and co-corresponding author in this study. “We now have a universal method for species identification across all Archaea and Bacteria that relies on the entire genome rather than a single gene, or a small number of marker genes. When applied to all the sequenced genomes currently available, this method enabled us to observe species evolution in action, manifested through what we call clique groups. Perhaps one of the most dramatic observations we had was that more than half of all the species that had more than one sequenced genome, had at least one genome wrongly named.”
Kyrpides went on to say, “This method is also shedding light on the long debated issue of microbial species. The fact that over 86% of all the microbial species for which more than one genome has been sequenced are grouping into separate cliques, strongly supports the notion of a microbial species, as opposed to the idea of genetic continuum among microbial species, which however was observed for a small number of species, about 5%. It would be very interesting to see how these observations evolve as the numbers of microbial genomes sequenced explode.”
The DOE JGI sequencing pipeline is already using the MiSI method to determine the similarity of newly sequenced genomes to existing reference genomes. MiSI is available for use by the general research community through the IMG system and the data used by the DOE JGI team for this study are publicly available at https://ani.jgi-psf.org .
The U.S. Department of Energy Joint Genome Institute, User Facility of Lawrence Berkeley National Laboratory supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter.
DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.
Public Affairs Manager
U.S. Department of Energy Joint Genome Institute
David Gilbert | newswise
Symbiotic bacteria: from hitchhiker to beetle bodyguard
28.04.2017 | Johannes Gutenberg-Universität Mainz
Nose2Brain – Better Therapy for Multiple Sclerosis
28.04.2017 | Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB
More and more automobile companies are focusing on body parts made of carbon fiber reinforced plastics (CFRP). However, manufacturing and repair costs must be further reduced in order to make CFRP more economical in use. Together with the Volkswagen AG and five other partners in the project HolQueSt 3D, the Laser Zentrum Hannover e.V. (LZH) has developed laser processes for the automatic trimming, drilling and repair of three-dimensional components.
Automated manufacturing processes are the basis for ultimately establishing the series production of CFRP components. In the project HolQueSt 3D, the LZH has...
Reflecting the structure of composites found in nature and the ancient world, researchers at the University of Illinois at Urbana-Champaign have synthesized thin carbon nanotube (CNT) textiles that exhibit both high electrical conductivity and a level of toughness that is about fifty times higher than copper films, currently used in electronics.
"The structural robustness of thin metal films has significant importance for the reliable operation of smart skin and flexible electronics including...
The nearby, giant radio galaxy M87 hosts a supermassive black hole (BH) and is well-known for its bright jet dominating the spectrum over ten orders of magnitude in frequency. Due to its proximity, jet prominence, and the large black hole mass, M87 is the best laboratory for investigating the formation, acceleration, and collimation of relativistic jets. A research team led by Silke Britzen from the Max Planck Institute for Radio Astronomy in Bonn, Germany, has found strong indication for turbulent processes connecting the accretion disk and the jet of that galaxy providing insights into the longstanding problem of the origin of astrophysical jets.
Supermassive black holes form some of the most enigmatic phenomena in astrophysics. Their enormous energy output is supposed to be generated by the...
The probability to find a certain number of photons inside a laser pulse usually corresponds to a classical distribution of independent events, the so-called...
Microprocessors based on atomically thin materials hold the promise of the evolution of traditional processors as well as new applications in the field of flexible electronics. Now, a TU Wien research team led by Thomas Müller has made a breakthrough in this field as part of an ongoing research project.
Two-dimensional materials, or 2D materials for short, are extremely versatile, although – or often more precisely because – they are made up of just one or a...
28.04.2017 | Event News
20.04.2017 | Event News
18.04.2017 | Event News
28.04.2017 | Medical Engineering
28.04.2017 | Earth Sciences
28.04.2017 | Life Sciences