{"350661":{"#nid":"350661","#data":{"type":"news","title":"Computational tools will help identify microbes in complex environmental samples","body":[{"value":"\u003Cp\u003EMicrobes of interest to clinicians and environmental scientists rarely exist in isolation. Organisms essential to breaking down pollutants or causing illness live in complex communities, and separating one microbe from hundreds of companion species can be challenging for researchers seeking to understand environmental issues or disease processes.\u0026nbsp;\u003C\/p\u003E\u003Cp\u003EA new National Science Foundation-supported project will provide computational tools designed to help identify and characterize the gene diversity of the residents of these microbial communities. The project, being done by researchers at the Georgia Institute of Technology and Michigan State University, will allow clinicians and scientists to compare the genomic information of organisms they encounter against the growing volumes of data provided by the world\u2019s scientific community.\u003C\/p\u003E\u003Cp\u003EThe tools will be hosted on a web server designed to be used by researchers who may not have training in the latest bioinformatics techniques. A prototype system containing a limited number of computational tools is already available at \u003Ca href=\u0022http:\/\/enve-omics.ce.gatech.edu\u0022\u003Ehttp:\/\/enve-omics.ce.gatech.edu\u003C\/a\u003E and is attracting more than 500 users each month.\u003C\/p\u003E\u003Cp\u003E\u201cAcross many areas of science, we are dealing with communities of microorganisms, and one challenge we\u2019ve had is to identify them because we haven\u2019t had good tools to tell apart individual microbes from the mixtures,\u201d said \u003Ca href=\u0022http:\/\/www.ce.gatech.edu\/people\/faculty\/711\/overview\u0022\u003EKostas Konstantinidis\u003C\/a\u003E, an associate professor in the \u003Ca href=\u0022http:\/\/www.ce.gatech.edu\/\u0022\u003ESchool of Civil and Environmental Engineering\u003C\/a\u003E at Georgia Tech and the project\u2019s principal investigator. \u201cOur tools will be designed to deal with the genomes of whole communities of organisms.\u201d\u003C\/p\u003E\u003Cp\u003ECurrent techniques identify individual microbes by examining their small subunit ribosomal RNA (SSU rRNA) genes, but the new tools will allow scientists to analyze entire genomes and meta-genomes.\u003C\/p\u003E\u003Cp\u003E\u201cWith the dawn of the genomic era, we can now get the whole genome of these organisms to see not only the ribosomal RNA, but also all the genes in the genome to get a better understanding of what the each organism\u2019s potential might be,\u201d said Konstantinidis. \u201cThere will be many advantages for looking at all the genes instead of just one, the SSU rRNA, such as to identify which organisms encode toxins or the enzymes for breaking down pollutants.\u201d\u003C\/p\u003E\u003Cp\u003ECollaborators on the three-year project include scientists who operate the Ribosomal Database Project at Michigan State University: Jim Tiedje, director of Michigan State University\u2019s Center for Microbial Ecology and James Cole, a Michigan State University research assistant professor and director of the Ribosomal Database Project.\u003C\/p\u003E\u003Cp\u003EThe ability to identify and enumerate the organisms in complex communities using culture-independent, genomic technologies and associated bioinformatics algorithms is becoming more important as scientists study organisms that can\u2019t be grown in the lab. The majority of the world\u2019s organisms resist traditional lab culture, meaning they have to be studied in the field and identified through genetic information.\u003C\/p\u003E\u003Cp\u003EKonstantinidis and his research group are studying such communities in the water of lakes in Chattahoochee River system in Georgia and elsewhere. They are examining how these communities respond to perturbations, such as oil or pesticide spills, and the role that different members of the community play in breaking down pollutants.\u003C\/p\u003E\u003Cp\u003E\u201cThese tools actually come from our research practice,\u201d said Konstantinidis. \u201cWe came to the point where we couldn\u2019t process the data to answer the questions we wanted to ask. That led us to this new project to develop the tools we and others need to interrogate the data and get the information we are looking for.\u201d\u003C\/p\u003E\u003Cp\u003EA single liter of lake water may contain as many as 500 different species, and together, their genomic information can total tens of billions of gene-coding letters. From Lake Lanier alone, the team has generated 200 gigabytes of genomic data.\u003C\/p\u003E\u003Cp\u003E\u201cWe want to figure out what organisms are there, and what genes they encode,\u201d Konstantinidis explained. \u201cThe tools we are developing will allow us to do this.\u201d\u003C\/p\u003E\u003Cp\u003EThe tools developed in the project will be useful to both clinical microbiologists and environmental researchers. \u201cThis will not be specific to any one discipline,\u201d he said. \u201cAs long as people are working with microbes, this will be helpful to them because some of the questions are universal.\u201d\u003C\/p\u003E\u003Cp\u003EThe system will also be built to provide user-friendly help to scientists who may not have training in the latest genomic and bioinformatics techniques. \u201cThere is a big need for big data analysis, and there are not many trained people right now,\u201d Konstantinidis said. \u201cThese tools will make the lives of researchers easier.\u201d\u003C\/p\u003E\u003Cp\u003EAmong the challenges ahead is building an infrastructure able to handle the growing amounts of genomic information produced worldwide.\u003C\/p\u003E\u003Cp\u003E\u201cWe will have to develop some computational solutions for the problems of keeping up with all the new data becoming available,\u201d said Konstantinidis. \u201cWe need to make tools that have high throughput to keep up with data volumes that are increasing geometrically.\u201d\u003C\/p\u003E\u003Cp\u003EThe system will initially operate on servers at Georgia Tech and Michigan State University, but if demand and data grow, additional resources may be sought, such as the National Science Foundation\u2019s XSEDE supercomputer.\u003C\/p\u003E\u003Cp\u003E\u003Cem\u003EThis research is supported by the National Science Foundation under award DBI-1356288. The opinions expressed in this article are those of the authors and do not necessarily reflect the official views of the National Science Foundation.\u003C\/em\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cem\u003EKostas Konstantinidis is the Carlton S. Wilder Junior Faculty Professor in the Georgia Tech School of Civil and Environmental Engineering.\u003C\/em\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EResearch News\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EGeorgia Institute of Technology\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003E177 North Avenue\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EAtlanta, Georgia\u0026nbsp; 30332-0181\u0026nbsp; USA\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EMedia Relations Contacts\u003C\/strong\u003E: John Toon (404-894-6986) (\u003Ca href=\u0022mailto:jtoon@gatech.edu\u0022\u003Ejtoon@gatech.edu\u003C\/a\u003E) or Brett Israel (404-385-1933) (\u003Ca href=\u0022mailto:brett.israel@comm.gatech.edu\u0022\u003Ebrett.israel@comm.gatech.edu\u003C\/a\u003E).\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EWrite\u003C\/strong\u003Er: John Toon\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EA new project will provide computational tools designed to help identify and characterize the gene diversity of the residents of microbial communities. The project, being done by researchers at the Georgia Institute of Technology and Michigan State University, will allow clinicians and scientists to compare the genomic information of organisms they encounter against the growing volumes of data provided by the world\u2019s scientific community.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"A new project will provide computational tools designed to help identify and characterize the gene diversity of the residents of microbial communities."}],"uid":"27303","created_gmt":"2014-12-01 11:48:43","changed_gmt":"2016-10-08 03:17:37","author":"John Toon","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2014-12-01T00:00:00-05:00","iso_date":"2014-12-01T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"350641":{"id":"350641","type":"image","title":"Microbial communities","body":null,"created":"1449245702","gmt_created":"2015-12-04 16:15:02","changed":"1475895078","gmt_changed":"2016-10-08 02:51:18","alt":"Microbial communities","file":{"fid":"201094","name":"microbial-genomics.jpg","image_path":"\/sites\/default\/files\/images\/microbial-genomics_0.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/microbial-genomics_0.jpg","mime":"image\/jpeg","size":1080014,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/microbial-genomics_0.jpg?itok=coyw3bZN"}},"350621":{"id":"350621","type":"image","title":"Water sampling","body":null,"created":"1449245702","gmt_created":"2015-12-04 16:15:02","changed":"1475894494","gmt_changed":"2016-10-08 02:41:34","alt":"Water sampling","file":{"fid":"201093","name":"water-sampling_0192.jpg","image_path":"\/sites\/default\/files\/images\/water-sampling_0192_0.jpg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/water-sampling_0192_0.jpg","mime":"image\/jpeg","size":285853,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/water-sampling_0192_0.jpg?itok=atNDCvyh"}}},"media_ids":["350641","350621"],"groups":[{"id":"1188","name":"Research Horizons"}],"categories":[{"id":"153","name":"Computer Science\/Information Technology and Security"},{"id":"154","name":"Environment"},{"id":"146","name":"Life Sciences and Biology"},{"id":"135","name":"Research"}],"keywords":[{"id":"807","name":"environment"},{"id":"12758","name":"Kostas Konstantinidis"},{"id":"7078","name":"microbe"},{"id":"111221","name":"microbial communities"},{"id":"51261","name":"microbial diversity"},{"id":"167864","name":"School of Civil and Environmental Engineering"}],"core_research_areas":[{"id":"39441","name":"Bioengineering and Bioscience"},{"id":"39431","name":"Data Engineering and Science"}],"news_room_topics":[{"id":"71911","name":"Earth and Environment"}],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003EJohn Toon\u003C\/p\u003E\u003Cp\u003EResearch News\u003C\/p\u003E\u003Cp\u003E(404) 894-6986\u003C\/p\u003E\u003Cp\u003E\u003Ca href=\u0022mailto:jtoon@gatech.edu\u0022\u003Ejtoon@gatech.edu\u003C\/a\u003E\u003C\/p\u003E","format":"limited_html"}],"email":["jtoon@gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}