{"id":45292,"date":"2021-12-15T17:00:00","date_gmt":"2021-12-15T16:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=45292"},"modified":"2024-09-30T22:38:53","modified_gmt":"2024-09-30T20:38:53","slug":"connecting-the-dots-between-bacterial-genes-around-the-world","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/connecting-the-dots-between-bacterial-genes-around-the-world\/","title":{"rendered":"Connecting the dots between bacterial genes around the world"},"content":{"rendered":"\n

Around the world, bacterial communities live in all kinds of habitats, from the human body to water and soil. Each community consists of a unique composition of species, called the microbiome. Each species harbours thousands of genes that encode both common functions and functions specific to the habitat. Scientists around the world have started to sequence microbiomes in individual habitats to understand the functional diversity of bacteria within them. However, little is known about where these habitat-specific genes and functionalities originate, whether they can cross environments, and how easily they can spread.<\/p>\n\n\n\n

To answer such questions and to enable more such research, the group of Peer Bork<\/a> in collaboration with Jaime Huerta-Cepas, formerly a scientist at EMBL Heidelberg and currently a group leader at the Centre for Plant Genomics and Biotechnology of Madrid (CBGP UPM-INIA\/CSIC<\/a>), has launched the Global Microbial Gene Catalog<\/a>. This database, created using publicly available data, contains more than 2 billion genes, 303 million of them dubbed unigenes. A unigene is a DNA sequence that scientists use during data analysis to represent a group of multiple almost-identical gene sequences that come from the same microbial species. These unigenes have been identified from 14 different environments, including human and animal bodies, as well as soil and water from different geographical locations. The resource aims to help the scientific community study various aspects of microbial planetary biology, such as similarities and differences between microbiomes found in distant locations or facing different environmental conditions.<\/p>\n\n\n\n

\u201cThis is a starting point for looking at the entire life of the planet and not only in specific habitats with their individual biases,\u201d said Professor Peer Bork.<\/p>\n\n\n\n

\u201cThanks to the methodological advances made in the Bork Group, we created a resource to analyse microbial metagenomes at the global scale,\u201d said Professor Luis Pedro Coelho<\/a>, who conducted this work as a postdoc in the Bork Group, and currently is a professor at the Fudan University in Shanghai.<\/p>\n\n\n\n

By having a closer look at the unigenes in the database, the scientists saw that only a few unigenes and microbial species could be found across habitats. Some of these exceptional unigenes are related to antibiotic resistance, and some are known to have the ability to move around the genome, or even cross from one species to another.<\/p>\n\n\n\n

Next, the scientists grouped the unigenes in the database based on their similarity and found that most of them belong to a relatively small number of families of related genes. This means that presumably most microbial genes on Earth evolved through the modification of a few existing genes rather than emerging from scratch.<\/p>\n\n\n\n

\u201cWe expected to see more genetic variety, resulting from adaptation to different habitats. However, with the data, we could show that this variety mostly appeared by pure chance without conferring a benefit to the organism,\u201d said Professor Coelho. \u201cThis implies that new genes emerge and existing ones disappear at a fast pace, with new strains being formed all the time. Hence, we might be able to sequence all microbial species on Earth, but not all their strains.\u201d<\/p>\n\n\n\n

This planetary approach represents a shift in how scientists think about microbiomes. Although microbiomes in individual environments have their own peculiarities, they might also exchange useful functions across habitats. \u201cInstead of looking at microbes in isolated spots, we should look at them globally, because they are all connected,\u201d said Professor Coelho. For example, antibiotic-resistant bacteria excreted by a cow might live in the soil and then hop onto the plants we eat. Understanding how bacteria and genes cross from one environment to another is therefore critical for human and planetary health.<\/p>\n\n\n\n

In the future, the scientists plan to expand the database and use it for studying the evolution and dispersal of genes and microbes at a much more fine-grained scale. For example, by analysing historical microbiome data collected over the last decade, they can investigate, for example, how different kinds of genes related to antimicrobial resistance spread geographically.<\/p>\n\n\n\n

\u201cThe overall collection of data will be useful for researchers in many ways. Our results illustrate the power of holistic approaches, including analysing samples from diverse environments to fully understand microbial diversity,\u201d said Professor Bork. \u201cFor example, finding the same antibiotic resistance genes in different habitats that are far, far apart implies a rapid spread of antimicrobial resistance, but could also provide means to help us understand this complex issue in new ways.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"

Bork Group at EMBL Heidelberg analysed a new global gene database to study how genes emerge and spread across various habitats on our planet. In the future, the group will expand the database and use it for studying microbial gene evolution and dispersal at a finer-grained scale.<\/p>\n","protected":false},"author":96,"featured_media":45310,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[87,365,782,1704,43,88,233,5736],"embl_taxonomy":[19179],"class_list":["post-45292","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-biodiversity","tag-bork","tag-database","tag-embl-programme","tag-heidelberg","tag-metagenomics","tag-microbiome","tag-planetary-biology","embl_taxonomy-bork-group"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"","article_intro":"

Understanding bacterial ecosystem connections made easier with new gene database<\/p>\n","related_links":[{"link_description":"Global Microbial Gene Catalog v1.0","link_url":"https:\/\/gmgc.embl.de\/"},{"link_description":"Bork Group ","link_url":"http:\/\/www.bork.embl.de\/"},{"link_description":"The impact of drugs on gut microbes is greater than we thought","link_url":"https:\/\/www.embl.org\/news\/science\/the-impact-of-drugs-on-gut-microbes-is-greater-than-we-thought\/"}],"source_article":[{"publication_title":"Towards the biogeography of prokaryotic genes.","publication_link":{"title":"","url":"https:\/\/www.nature.com\/articles\/s41586-021-04233-4","target":"_blank"},"publication_authors":"Coelho L.P. et al.","publication_source":"Nature","publication_date":"15 December 2021","publication_doi":"10.1038\/s41586-021-04233-4"}],"in_this_article":false,"press_contact":"None","vf_locked":false,"field_article_language":{"value":"english","label":"English"},"article_translations":false,"languages":""},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"bd910dd7-0cda-4618-8bfa-d37fbda8438e\";i:2;s:36:\"2ce7bcc2-0091-4187-b6cb-01c5b0f24f68\";}","parents":[],"name":["Bork Group"],"slug":"bork-group","description":"What > Molecular Systems Biology > Bork Group"}],"yoast_head":"\nConnecting the dots between bacterial genes around the world | EMBL<\/title>\n<meta name=\"description\" content=\"A gene database will enable scientists to study microbial gene evolution at a fine-grained scale.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" 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