{"673300":{"#nid":"673300","#data":{"type":"news","title":"The Who\u0027s Who of Bacteria: A Reliable Way to Define Species and Strains","body":[{"value":"\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EWhat\u2019s in a name? A lot, actually. \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EFor the scientific community, names and labels help organize the world\u2019s organisms so they can be identified, studied, and regulated. But for bacteria, there has never been a reliable method to cohesively organize them into species and strains. It\u2019s a problem, because bacteria are one of the most prevalent life forms, making up roughly 75% of all living species on Earth.\u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EAn international research team sought to overcome this challenge, which has long plagued scientists who study bacteria. \u003Ca href=\u0022https:\/\/ce.gatech.edu\/directory\/person\/kostas-t-konstantinidis\u0022\u003EKostas Konstantinidis\u003C\/a\u003E, Richard C. Tucker Professor in the \u003Ca href=\u0022https:\/\/ce.gatech.edu\/\u0022\u003ESchool of Civil and Environmental Engineering\u003C\/a\u003E at the Georgia Institute of Technology, co-led a study to investigate natural divisions in bacteria with a goal of determining a scientifically viable method for organizing them into species and strains. To do this, the researchers let the data show them the way.\u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003ETheir research was \u003Ca href=\u0022https:\/\/www.nature.com\/articles\/s41467-023-44622-z\u0022\u003Epublished\u003C\/a\u003E in the journal \u003Cem\u003ENature Communications\u003C\/em\u003E. \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003E\u201cWhile there is a working definition for species and strains, this is far from widely accepted in the scientific community,\u201d Konstantinidis said. \u201cThis is because those classifications are based on humans\u2019 standards that do not necessarily translate well to the patterns we see in the natural environment.\u201d \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EFor instance, he said, \u201cIf we were to classify primates using the same standards that are used to classify \u003Cem\u003EE. coli\u003C\/em\u003E, then all primates \u2014 from lemurs to humans to chimpanzees \u2014 would belong to a single species.\u201d\u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EThere are many reasons why a comprehensive organizing system has been hard to devise, but it often comes down to who gets the most attention and why. More scientific attention generally leads to those bacteria becoming more narrowly defined. For example, bacteria species that contain toxic strains have been extensively studied because of their associations with disease and health. This has been out of the necessity to differentiate harmful strains from harmless ones. Recent discoveries have shown, however, that even defining types of bacteria by their toxicity is unreliable.\u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003E\u201cDespite the obvious, cornerstone importance of the concepts of species and strains for microbiology, these remain, nonetheless, ill-defined and confusing,\u201d Konstantinidis said. \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EThe research team collected bacteria from two salterns in Spain. Salterns are built structures in which seawater evaporates to form salt for consumption. They harbor diverse communities of microorganisms and are ideal locations to study bacteria in their natural environment. This is important for understanding diversity in populations because bacteria often undergo genetic changes when exposed in lab environments. \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EThe team recovered and sequenced 138 random isolates of \u003Cem\u003ESalinibacter ruber\u003C\/em\u003E bacteria from these salterns. To identify natural gaps in genetic diversity, the researchers then compared the isolates against themselves using a measurement known as average nucleotide identity (ANI) \u2014 a concept Konstantinidis developed early in his career. ANI is a robust measure of relatedness between any two genomes and is used to study relatedness among microorganisms and viruses, as well as animals. For instance, the ANI between humans and chimpanzees is about 98.7%. \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EThe analysis confirmed the team\u2019s previous observations that microbial species do exist and could be reliably described using ANI. They found that members of the same species of bacteria showed genetic relatedness typically ranging from 96 to 100% on the ANI scale, and generally less than 85% relatedness with members of other species. \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EThe data revealed a natural gap in ANI values around 99.5% ANI within the \u003Cem\u003ESalinibacter ruber\u003C\/em\u003E species that could be used to differentiate the species into its various strains. In a \u003Ca href=\u0022https:\/\/journals.asm.org\/doi\/10.1128\/mbio.02696-23\u0022\u003Ecompanion paper\u003C\/a\u003E published in \u003Cem\u003EmBio\u003C\/em\u003E, the flagship journal of the American Society for Microbiology, the team examined about 300 additional bacterial species based on 18,000 genomes that had been recently sequenced and become available in public databases. They observed similar diversity patterns in more than 95% of the species.\u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003E\u201cWe think this work expands the molecular toolbox for accurately describing important units of diversity at the species level and within species, and we believe it will benefit future microdiversity studies across clinical and environmental settings,\u201d Konstantinidis said. \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003EThe team expects their research will be of interest to any professional working with bacteria, including evolutionary biologists, taxonomists, ecologists, environmental engineers, clinicians, bioinformaticians, regulatory agencies, and others. It is available online through Konstantinidis\u2019 website and GitHub to facilitate access and use by scientific and regulatory communities.\u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003E\u201cWe hope that these communities will embrace the new results and methodologies for the more robust and reliable identification of species and strains they offer, compared to the current practice,\u201d Konstantinidis said. \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cstrong\u003ENote\u003C\/strong\u003E:\u0026nbsp;Tomeu Viver and Ramon Rossello-Mora from the Mediterranean Institutes for Advanced Studies also led the research. Additional researchers from the Georgia Institute of Technology, University of Innsbruck, University of Pretoria, University of Las Palmas de Gran Canaria, University of the Balearic Islands, and the Max Planck Institute also contributed.\u0026nbsp;\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cstrong\u003ECitation\u003C\/strong\u003E: Viver, T., Conrad, R.E., Rodriguez-R, L.M.\u0026nbsp;\u003Cem\u003Eet al.\u003C\/em\u003E\u0026nbsp;Towards estimating the number of strains that make up a natural bacterial population.\u0026nbsp;\u003Cem\u003ENat Commun\u003C\/em\u003E\u0026nbsp;\u003Cstrong\u003E15\u003C\/strong\u003E, 544 (2024). \u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cstrong\u003EDOI\u003C\/strong\u003E: \u003Ca href=\u0022https:\/\/doi.org\/10.1038\/s41467-023-44622-z\u0022\u003Ehttps:\/\/doi.org\/10.1038\/s41467-023-44622-z\u003C\/a\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cspan\u003E\u003Cstrong\u003EFunding\u003C\/strong\u003E: Spanish Ministry of Science, Innovation and Universities, European Regional Development Fund, U.S. National Science Foundation.\u003C\/span\u003E\u003C\/span\u003E\u003C\/span\u003E\u003C\/p\u003E\r\n","summary":"","format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EThe researchers used data to investigate natural divisions in bacteria with a goal of determining a viable method for organizing them into species and strains.\u003C\/p\u003E\r\n","format":"limited_html"}],"field_summary_sentence":[{"value":"The researchers used data to investigate natural divisions in bacteria with a goal of determining a viable method for organizing them into species and strains."}],"uid":"36123","created_gmt":"2024-03-04 14:58:04","changed_gmt":"2024-03-07 20:53:22","author":"Catherine Barzler","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2024-03-04T00:00:00-05:00","iso_date":"2024-03-04T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"673283":{"id":"673283","type":"image","title":"saltern Ponds_1.jpeg","body":"\u003Cp\u003EA photo of the saltern site in Spain where a significant portion of the research was done. A saltern is used to produce salt for human consumption and is a natural environment for\u003Cem\u003E Salinibacter ruber \u003C\/em\u003Ebacterium\u003Cem\u003E.\u003C\/em\u003E\u003C\/p\u003E\r\n","created":"1709564152","gmt_created":"2024-03-04 14:55:52","changed":"1709564848","gmt_changed":"2024-03-04 15:07:28","alt":"A photo of a saltern site with structured ponds in the foreground and large mounds of salt in the background. ","file":{"fid":"256652","name":"Ponds_1.jpeg","image_path":"\/sites\/default\/files\/2024\/03\/04\/Ponds_1.jpeg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/2024\/03\/04\/Ponds_1.jpeg","mime":"image\/jpeg","size":134383,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/2024\/03\/04\/Ponds_1.jpeg?itok=luOcug4U"}},"673282":{"id":"673282","type":"image","title":"bacteria Konstantinidis.jpeg","body":"\u003Cp\u003EA microscopy photo of\u0026nbsp;\u003Cem\u003ESalinibacter ruber,\u003C\/em\u003E\u0026nbsp;a bacterium that thrives in salterns.\u003C\/p\u003E\r\n","created":"1709564015","gmt_created":"2024-03-04 14:53:35","changed":"1709563837","gmt_changed":"2024-03-04 14:50:37","alt":"A microscopy image of bacteria highlighted in green, pink, and indigo colors.","file":{"fid":"256651","name":"All_FISH.jpeg","image_path":"\/sites\/default\/files\/2024\/03\/04\/All_FISH.jpeg","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/2024\/03\/04\/All_FISH.jpeg","mime":"image\/jpeg","size":65231,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/2024\/03\/04\/All_FISH.jpeg?itok=s_Ame7nm"}},"673284":{"id":"673284","type":"image","title":"small Screenshot 2024-03-04 at 9.45.47\u202fAM.png","body":"\u003Cp\u003EA screenshot from a team meeting. The study\u0027s international team has researchers based in the U.S., Spain, Germany, Austria, and South Africa.\u003C\/p\u003E\r\n","created":"1709564709","gmt_created":"2024-03-04 15:05:09","changed":"1709564505","gmt_changed":"2024-03-04 15:01:45","alt":"A screenshot of a video conference with 12 people","file":{"fid":"256653","name":"small Screenshot 2024-03-04 at 9.45.47\u202fAM.png","image_path":"\/sites\/default\/files\/2024\/03\/04\/small%20Screenshot%202024-03-04%20at%209.45.47%E2%80%AFAM.png","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/2024\/03\/04\/small%20Screenshot%202024-03-04%20at%209.45.47%E2%80%AFAM.png","mime":"image\/png","size":770873,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/2024\/03\/04\/small%20Screenshot%202024-03-04%20at%209.45.47%E2%80%AFAM.png?itok=6wOHSa9O"}}},"media_ids":["673283","673282","673284"],"groups":[{"id":"1214","name":"News Room"},{"id":"1188","name":"Research Horizons"},{"id":"1278","name":"College of Sciences"},{"id":"1275","name":"School of Biological Sciences"}],"categories":[],"keywords":[{"id":"187915","name":"go-researchnews"},{"id":"193266","name":"cos-research"},{"id":"192250","name":"cos-microbial"}],"core_research_areas":[],"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\u003ECatherine Barzler, Senior Research Writer\/Editor\u003C\/p\u003E\r\n\r\n\u003Cp\u003E\u003Ca href=\u0022mailto:catherine.barzler@gatech.edu\u0022\u003Ecatherine.barzler@gatech.edu\u003C\/a\u003E\u003C\/p\u003E\r\n","format":"limited_html"}],"email":["catherine.barzler@gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}