{"id":35540,"date":"2021-01-19T13:18:47","date_gmt":"2021-01-19T12:18:47","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=35540"},"modified":"2024-03-22T14:09:42","modified_gmt":"2024-03-22T13:09:42","slug":"puntseq-freshwater-bacteria","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/puntseq-freshwater-bacteria\/","title":{"rendered":"Monitoring dangerous bacteria in freshwater"},"content":{"rendered":"\n<p>Researchers from EMBL\u2019s European Bioinformatics Institute (EMBL-EBI) and the University of Cambridge have shown that portable DNA sequencing can easily monitor bacterial species in a river ecosystem. They used a smartphone-sized DNA sequencing device to monitor water samples taken from nine locations on the river Cam. Alongside many harmless bacteria, they also found several pathogenic species.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Harmful or not?<\/h2>\n\n\n\n<p>The researchers found that potentially harmful and wastewater-related bacteria strongly increased downstream of the most urbanised river sections. One example is <em>Pseudomonas aeruginosa<\/em>, a bacterium that can cause disease in plants and animals, including humans, varying from pneumonia to sepsis syndromes.<\/p>\n\n\n\n<p>The study, called PuntSeq, also identified the well-known <em>Leptospira<\/em> bacterium, which can cause the life-threatening disease leptospirosis. However, the <em>Leptospira<\/em> species found on this occasion were most likely not pathogenic. The full results of the research have been <a href=\"https:\/\/doi.org\/10.7554\/eLife.61504\">published in the journal <em>eLife<\/em><\/a>.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Quick and easy monitoring<\/h2>\n\n\n\n<p>\u201cWe set out with the aim of characterising the diversity of microbes in the river,\u201d explains Lara Urban, formerly a PhD student at EMBL-EBI and now a research fellow at the University of Otago, New Zealand. \u201cWe also wanted to see how viable it was to use portable DNA sequencers to monitor bacteria species in rivers. With the river Cam on our doorstep, it wasn\u2019t long before we were out collecting samples.\u201d<\/p>\n\n\n\n<p>Traditional microbial tests focus on the isolation of specific bacterial organisms in a laboratory, which is time consuming and reliant on specialised infrastructure and staff. By contrast, the method used in this study \u2013 called environmental metagenomics \u2013 can identify the DNA of the many bacteria present in a sample of river water. In recent years, devices for mobile DNA analysis have made environmental metagenomics more accessible, allowing real-time sequencing.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">A useful tool for public health<\/h2>\n\n\n\n<p>\u201cIn our study, we report a simple, cost-effective workflow to assess and monitor microbial freshwater ecosystems with targeted nanopore DNA sequencing,\u201d says Maximillian Stammnitz, formerly a PhD student in Cambridge, now a postdoc at the Centre for Genomic Regulation (CRG) in Barcelona. For this study, the researchers successfully quantified the proportions of hundreds of different bacteria at nine sites along the river. For most locations, the researchers collected several samples throughout the spring and summer months.<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2021\/01\/URBAN_Figure_1-1024x553.png\" alt=\"\" class=\"wp-image-35542\" width=\"780\" height=\"421\" srcset=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2021\/01\/URBAN_Figure_1-1024x553.png 1024w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2021\/01\/URBAN_Figure_1-300x162.png 300w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2021\/01\/URBAN_Figure_1-768x414.png 768w\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" \/><\/figure>\n\n\n\n<div style=\"height:27px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<p>&#8220;This study design has allowed us to provide real transparency on important local questions of public health, with a very exciting new technology,&#8221; says Andre Holzer, a PhD student at the University of Cambridge.<\/p>\n\n\n\n<p>\u201cWe believe this method could be useful for public health, local authorities, and researchers studying waterborne diseases around the world,\u201d Urban adds.&nbsp;<\/p>\n\n\n\n<p>This post was originally published on <a data-href=\"www.ebi.ac.uk\/about\/news\/announcements\/puntseq-freshwater-bacteria\" href=\"www.ebi.ac.uk\/about\/news\/announcements\/puntseq-freshwater-bacteria\" rel=\"canonical nofollow noopener noreferrer\" target=\"_blank\">EMBL-EBI News<\/a>.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\">Funding acknowledgements<\/h4>\n\n\n\n<p>Lara Urban\u2019s work on the Cam Water Sample Project was supported by the Fuchs Family Special Circumstances and Opportunities Fund at EMBL. One of the Fund\u2019s aims is to foster the professional development of EMBL PhD fellows by sponsoring special career-related opportunities like attendance at summer schools or courses. The Fund was established thanks to generous donations by Lilo and Dr. Manfred Fuchs.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Freshwater sports can cause waterborne infections, but real-time DNA sequencing could help.<\/p>\n","protected":false},"author":47,"featured_media":35544,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[580,1702,36,928,88,233,2032],"embl_taxonomy":[2906],"class_list":["post-35540","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-bacteria","tag-ecosystem","tag-embl-ebi","tag-infectious-disease","tag-metagenomics","tag-microbiome","tag-sequencing","embl_taxonomy-embl-ebi"],"acf":{"vf_locked":false,"featured":true,"show_featured_image":false,"color":"#007B53","link_color":"#fff","article_intro":"<p>The river Cam, which flows through the city of Cambridge, UK, is a hotspot for swimmers, rowers, and kayakers, many of whom develop waterborne infections caused by the bacteria found in the river.<\/p>\n","related_links":[{"link_description":"","link_url":""},{"link_description":"","link_url":""},{"link_description":"","link_url":""}],"article_sources":[{"source_description":"<p>Urban, <em>et al<\/em>.\u00a0<em>eLife<\/em>, (published online) 19 January 2021, DOI 10.7554\/eLife.61504<\/p>\n","source_link_url":"https:\/\/doi.org\/10.7554\/eLife.61504"}],"in_this_article":false,"youtube_url":"","mp4_url":"","video_caption":"","press_contact":"None","embl_taxonomy_term_who":false,"embl_taxonomy_term_what":false,"embl_taxonomy_term_where":false,"field_target_display":"embl","source_article":false},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"b14d3f13-5670-44fb-8970-e54dfd9c921a\";i:1;s:36:\"89e00fee-87f4-482e-a801-4c3548bb6a58\";i:2;s:36:\"a99d1a7c-ca83-4c00-ab61-d082d3e41ce3\";}","parents":[],"name":["EMBL-EBI"],"slug":"embl-ebi","description":"Where &gt; 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