{"id":41,"date":"2023-10-19T12:31:07","date_gmt":"2023-10-19T12:31:07","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/?page_id=41"},"modified":"2025-02-11T10:27:41","modified_gmt":"2025-02-11T10:27:41","slug":"projects","status":"publish","type":"page","link":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/projects\/","title":{"rendered":"Projects"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-1\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-flagship-project\" data-vf-js-location-nearest-activation-target=\"\">Flagship project<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-microgrants\" data-vf-js-location-nearest-activation-target=\"\">Microgrants<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-embl-hzi-postdoctoral-programme\" data-vf-js-location-nearest-activation-target=\"\">EMBL-HZI Postdoctoral Programme<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-flagship-project\"><h2 class=\"vf-u-sr-only\">Flagship project<\/h2>\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">Establish new model species for the human gut microbiome<\/h2>\n\n\n\n<p>An important aspect of understanding microbiomes is increasing our knowledge of their composition \u2013 from viruses to bacteria to single-celled eukaryotes \u2013 and the functions they encode. For example, there are thousands of bacterial species that have been identified in the human gut microbiota from metagenomics datasets, yet <strong>most of these species are still <em>terra incognita<\/em> in terms of the functions they encode. <\/strong> Moreover, the available model organisms like <em>E. coli<\/em> are not suitable for studying the microbes that colonise the human gut because they are neither the most prevalent nor the most abundant bacteria in the gut microbiome.  The <strong>Flagship project <\/strong>aims to focus on two bacterial species that are abundant in the human gut but remain poorly characterised: <em><strong>Phocaeicola vulgatus<\/strong><\/em> and <strong><em>Bacteroides uniformis<\/em>. <\/strong> This aim is to use pioneering ways to molecularly characterise these species and to understand the underlying molecular mechanisms of microbiome\u2013host\u2013environment interactions.<\/p>\n\n\n\n<p>Among the participating teams of the flagship project:\u00a0<strong class=\"\"><a class=\"\" href=\"https:\/\/www.embl.org\/groups\/typas\/\">Typas group<\/a>\u00a0<\/strong>is pioneering tools for pooled and arrayed\u00a0<a class=\"\" href=\"https:\/\/europepmc.org\/article\/MED\/38142397\">transposon mutant libraries<\/a>\u00a0in these species to define gene essentiality and function &#8211; with a focus on functions these bacteria use to engraft in communties. The\u00a0<strong class=\"\"><a class=\"\" href=\"https:\/\/www.embl.org\/groups\/savitski\/\">Savitski group<\/a>\u00a0<\/strong>is employing a suite of proteomic methods, such as\u00a0<a class=\"\" href=\"https:\/\/www.embl.org\/news\/science\/heating-proteins-to-understand-how-genes-work\/\">multiplexed Thermal Proteome Profiling<\/a>, to construct a detailed protein-protein and protein-ligand interaction landscape in these organisms. The<strong class=\"\">\u00a0<a href=\"https:\/\/www.embl.org\/groups\/zimmermann-kogadeeva\/\">Zimmermann-Kogadeeva\u00a0group<\/a>\u00a0<\/strong>is integrating computational and experimental techniques to elucidate metabolic network architecture, and in collaboration with\u00a0<a class=\"\" href=\"https:\/\/www.helmholtz-hiri.de\/en\/about\/team\/detail\/person\/prof-alexander-westermann\/\"><strong class=\"\">Alex Westermann<\/strong><\/a>\u00a0from HIRI, aims to characterise transcriptional regulation in both species.\u00a0<a class=\"\" href=\"https:\/\/www.embl.org\/groups\/zimmermann\/\"><strong class=\"\">Michael Zimmermann\u2019s group<\/strong><\/a>, along with the groups of<strong class=\"\">\u00a0<\/strong><a class=\"\" href=\"https:\/\/www.embl.org\/groups\/typas\/\"><strong>Nassos Typas<\/strong><\/a><strong class=\"\">,\u00a0<a class=\"\" href=\"https:\/\/www.embl.org\/groups\/zeller\/\">Georg Zeller<\/a>,\u00a0<a class=\"\" href=\"https:\/\/www.embl.org\/groups\/bork\/\">Peer Bork<\/a>,\u00a0<a class=\"\" href=\"https:\/\/www.ebi.ac.uk\/research\/finn\/\">Rob Finn<\/a>\u00a0<\/strong>and\u00a0<a class=\"\" href=\"https:\/\/www.ebi.ac.uk\/research\/lees\/\"><strong class=\"\">John Lees<\/strong><\/a>, are functionally characterising the genetic and phenotypic intra-species diversity &#8211; specifically related to xeno-metabolism. Finally, the<strong class=\"\">\u00a0<a class=\"\" href=\"https:\/\/www.ebi.ac.uk\/research\/finn\/\">Finn group<\/a>\u00a0<\/strong>is developing a portable prokaryotic annotation pipeline to integrate data generated from the Flagship project.<\/p>\n\n\n\n<p>Together, this project will elucidate the functional roles of numerous unknown genes, proteins, and metabolites in two key species, ultimately enhancing our ability to <strong>understand, protect, and beneficially manipulate the gut microbiome.<\/strong><\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-large is-resized is-style-default\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"597\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/flagship-1-1024x597.jpg\" alt=\"\" class=\"wp-image-382\" style=\"width:1450px;height:auto\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/flagship-1-1024x597.jpg 1024w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/flagship-1-300x175.jpg 300w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/flagship-1-768x448.jpg 768w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/flagship-1-1536x896.jpg 1536w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/flagship-1.jpg 1540w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-microgrants\"><h2>Microgrants<\/h2><style>\n    <\/style>\n\n<section id=\"wp-block-1\">\n  <div class=\"vf-card-container vf-card-container__col-3 | vf-u-fullbleed  \n  | vf-u-background-color-ui--white \">\n        <div class=\"vf-card-container__inner\">\n            <div class=\"vf-section-header | vf-u-margin__bottom--600 | vf-u-sr-only\">\n        <h2 class=\"vf-section-header__heading\" >\n        Microgrants    <\/h2>\n              <\/div>\n      \n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"960\" height=\"480\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/METT_microgrant@3x.png\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/METT_microgrant@3x.png 960w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/METT_microgrant@3x-300x150.png 300w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/METT_microgrant@3x-768x384.png 768w\" sizes=\"auto, (max-width: 960px) 100vw, 960px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Elucidating the interplay between transcription and metabolism in Bacteroides uniformis    <\/h3>\n                <p class=\"vf-card__text\">This project aims to generate and integrate multi-omics data using genome-scale metabolic modeling and network analysis to elucidate the relationship between gene expression and metabolism in gut bacteria. The project will be conducted by <strong>Juan Miguel Escorcia-Rodriguez &#8211;<\/strong>Postdoctoral Fellow in the \u00a0<a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/zimmermann-kogadeeva\/\">Zimmermann-Kogadeeva\u2019s group<\/a>&#8211; in collaboration with the <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/zimmermann\/\">Zimmermann&#8217;s group<\/a> (both at EMBL Heidelberg) and the <a class=\"vf-card_link\" href=\"https:\/\/www.helmholtz-hiri.de\/en\/about\/team\/detail\/person\/prof-alexander-westermann\/\">Westermann&#8217;s group<\/a>\u00a0(Helmholtz, HIRI).<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"1024\" height=\"768\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/METT_MGA-1024x768.jpg\" class=\"vf-card__image\" alt=\"Picture of Argentinian Andes by Maria Garcia-Alai\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/METT_MGA-1024x768.jpg 1024w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/METT_MGA-300x225.jpg 300w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/METT_MGA-768x576.jpg 768w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/METT_MGA-1536x1152.jpg 1536w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/METT_MGA.jpg 2000w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      MicroAndes    <\/h3>\n                <p class=\"vf-card__text\">This project aims to understand the adaptations and interactions of polyextremophiles by co-culturing microbial communities isolated from high-altitude Andean lake ecosystems. This project is a collaborative effort between <strong><a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/garcia-alai\/\">Maria Garcia-Alai<\/a><\/strong> and <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/people\/person\/federico-vignale\/\">Federico Agustin Vignale<\/a> from the SPC Facility (EMBL Hamburg), the <a class=\"vf-card_link\" href=\"https:\/\/www.ebi.ac.uk\/research\/finn\/\">Finn group <\/a>(EMBL-EBI), and the <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/typas\/\">Typas group<\/a> (EMBL Heidelberg).<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"1000\" height=\"500\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/bacterial-defense-systems.png\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/bacterial-defense-systems.png 1000w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/bacterial-defense-systems-300x150.png 300w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/bacterial-defense-systems-768x384.png 768w\" sizes=\"auto, (max-width: 1000px) 100vw, 1000px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Investigating the role of convergent evolution in shaping phage anti-retron proteins    <\/h3>\n                <p class=\"vf-card__text\">This project aims to uncover the diverse strategies bacteriophages use to counteract bacterial defences, focusing on retrons, a specific type of bacterial defence system. This project is a collaboration between <strong><a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/people\/person\/federico-corona\/\">Federico Corona<\/a> &#8211;<\/strong>Postdoctoral Fellow in the <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/typas\/\">Typas&#8217; group<\/a> (EMBL Heidelberg)- with the <a class=\"vf-card_link\" href=\"https:\/\/www.ebi.ac.uk\/research\/finn\/\">\u00a0Finn&#8217;s group<\/a> (EMBL-EBI), \u00a0the <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/korbel\/\">\u00a0Korbel&#8217;s group<\/a> (EMBL Heidelberg) and the<a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/wilmanns\/\"> Wilmanns&#8217; group<\/a> (EMBL Hamburg).<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"578\" height=\"288\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/metalitbio-vusual.jpg\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/metalitbio-vusual.jpg 578w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/metalitbio-vusual-300x149.jpg 300w\" sizes=\"auto, (max-width: 578px) 100vw, 578px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      MetaLitBio: Advancing Microbiome Biology through Metagenomics Literature Integration    <\/h3>\n                <p class=\"vf-card__text\">This project aims to enrich the metagenomics literature by linking key concepts in scientific articles from Europe PMC to databases such as MGnify, SPIRE, and METALOG. This project is a collaboration between <strong><a class=\"vf-card_link\" href=\"https:\/\/www.ebi.ac.uk\/people\/person\/santosh-tirunagari\/\">Santosh Tirunagari<\/a><\/strong>, Senior Machine Learning Developer at the Literature Services team\/EMBL-EBI, <a class=\"vf-card_link\" href=\"https:\/\/www.ebi.ac.uk\/people\/person\/santiago-sanchez-fragoso\/\">Santiago Sanchez Fragoso <\/a>(Finn group, EMBL-EBI), <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/people\/person\/mkuhn\/\">Michael Kuhn<\/a> (Bork group, EMBL Heidelberg), and researchers from the Latvian Biomedical Research &amp; Study Centre.<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"1024\" height=\"799\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/20230214_201209_Mireia_plate-scaled-e1716997670424-1024x799.jpg\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/20230214_201209_Mireia_plate-scaled-e1716997670424-1024x799.jpg 1024w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/20230214_201209_Mireia_plate-scaled-e1716997670424-300x234.jpg 300w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/20230214_201209_Mireia_plate-scaled-e1716997670424-768x599.jpg 768w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/20230214_201209_Mireia_plate-scaled-e1716997670424-1536x1198.jpg 1536w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/20230214_201209_Mireia_plate-scaled-e1716997670424.jpg 1608w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Establishing a microfluidic platform for monitoring community dynamics in soil-like environments    <\/h3>\n                <p class=\"vf-card__text\">This project aims to develop a microfluidic platform to study predator-prey interactions between soil-dwelling bacteria and protists, starting with a well-established predator-prey model system around <em>Dictyostelium discoideum<\/em> with the goal of scaling up to natural soil communities. Work will be done\r\nby <strong><a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/people\/person\/vanessa-saskia-stuermer\/\">Vanessa Stuermer <\/a><\/strong>-predoctoral fellow in <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/van-gestel\/\">Van Gestel&#8217;s group <\/a>(EMBLHeidelberg)- \u00a0in collaboration with the <a class=\"vf-card_link\" href=\"https:\/\/www.biozentrum.unibas.ch\/research\/research-groups\/research-groups-a-z\/overview\/unit\/research-group-knut-drescher\">Drescher group <\/a>\u00a0(Biozentrum, Basel).\r\nImage credit: Mireia Garriga.<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"1024\" height=\"954\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/Asset-10-1024x954.png\" class=\"vf-card__image\" alt=\"Summary of the project, Federico Corona\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/Asset-10-1024x954.png 1024w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/Asset-10-300x279.png 300w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/Asset-10-768x715.png 768w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/Asset-10-1536x1430.png 1536w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/05\/Asset-10.png 1992w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Carbohydrate availability affects the microbiome-specific carrying capacity for antibiotic resistant mutants    <\/h3>\n                <p class=\"vf-card__text\">The project will investigate the effectiveness of artificial sweeteners in counter-selecting antibiotic-resistant pathogens in the human gut microbiome via carbohydrate competition. This project is a collaboration between <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/people\/person\/michael-knopp\/\"><strong>Michael Knopp <\/strong><\/a>\u00a0-Postdoctoral Fellow in the \u00a0<a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/typas\/\">Typas&#8217; group<\/a> (EMBL Heidelberg)- and the <a class=\"vf-card_link\" href=\"https:\/\/gulbenkian.pt\/ciencia\/research-groups\/kxavier\/\">Xavier&#8217;s group<\/a> (Instituto Gulbenkian de Ci\u00eancia, Portugal).<\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n<img decoding=\"async\" width=\"1024\" height=\"1024\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/Flora-1024x1024.png\" class=\"vf-card__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/Flora-1024x1024.png 1024w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/Flora-300x300.png 300w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/Flora-150x150.png 150w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/Flora-768x768.png 768w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/06\/Flora.png 1282w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/>  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      FISH-ME &#8211; FISHing the Unknown in Marine Microbial Ecosystems    <\/h3>\n                <p class=\"vf-card__text\">The FISH-ME project aims to develop a systematic bioinformatic workflow to design <em>in situ <\/em> hybridization probes for multiplexed detection of target species in diverse marine microbial communities. This project is led by <strong><a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/people\/person\/flora-vincent\/\">Flora Vincent <\/a><\/strong>(EMBL Heidelberg) in collaboration with EMBL Heidelberg based researchers: \u00a0<a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/people\/person\/gautam-dey\/\">Gautam Dey<\/a>, <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/people\/person\/sinem-saka\/\">Sinem Saka<\/a> and <a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/people\/person\/yannick-schwab\/\">Yannick Schwab.<\/a><\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<p><\/p>\n\n\n          <\/div>\n      <\/div>\n<\/section><\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-embl-hzi-postdoctoral-programme\"><h2>EMBL-HZI Postdoctoral Programme<\/h2>\n<p>The programme: <strong><em>\u201cThe human microbiome: From molecular understanding to exploiting microbial ecosystems for human health\u201d<\/em><\/strong> leverages the expertise of <strong>EMBL<\/strong> and those of <a href=\"https:\/\/www.helmholtz-hzi.de\/en\/\"><strong>Helmholtz Centre for Infection Research <\/strong><\/a>(<strong>HZI<\/strong>) in the field of human microbiota research. At the end of 2022, three postdoctoral fellowships were awarded and are currently ongoing.<\/p>\n\n\n\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">Understanding the factors underlying the predominance of <em>Prevotella <\/em>species in the gut microbiome of individuals consuming non-Western diets <\/h2>\n\n\n\n<p><strong>Caroline Tawk<\/strong> is a Postdoctoral fellow in the Microbial Immune Regulation group led by <strong><a href=\"https:\/\/www.helmholtz-hzi.de\/en\/research\/research-topics\/immune-response\/microbial-immune-regulation\/team\/\" data-type=\"link\" data-id=\"https:\/\/www.helmholtz-hzi.de\/en\/research\/research-topics\/immune-response\/microbial-immune-regulation\/team\/\">Till Strowig<\/a> <\/strong>(HZI). In collaboration with the<strong>  <a href=\"https:\/\/www.embl.org\/groups\/typas\/\" data-type=\"link\" data-id=\"https:\/\/www.embl.org\/groups\/typas\/\">Typas&#8217; group<\/a> <\/strong>(EMBL Heidelberg) &#8211; she aims to uncover what makes <em>Prevotellaceae<\/em> species so prevalent in the gut of non-westernised societies.<\/p>\n\n\n\n<p>The main goals of the project are: to establish if there is a direct competition between <em>Prevotellaceae<\/em> and <em>Bacteroidaceae<\/em> species in the gut; to find the causes underlying a <em>Prevotellaceae<\/em>-dominated microbiome in non-western societies and to determine if <em>Prevotellaceae <\/em>dominance is beneficial for health.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image size-full is-resized is-style-default\"><a href=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/prevotella.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"752\" height=\"524\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/prevotella.jpg\" alt=\"\" class=\"wp-image-532\" style=\"aspect-ratio:1.4351145038167938;width:535px;height:auto\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/prevotella.jpg 752w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/03\/prevotella-300x209.jpg 300w\" sizes=\"auto, (max-width: 752px) 100vw, 752px\" \/><\/a><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<p><\/p>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Exploring the&nbsp;<\/strong><em><strong>Bacteroidota<\/strong><\/em><strong>&nbsp;phylum for secondary metabolites with therapeutic potential<\/strong><\/h2>\n\n\n\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p><\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><strong><a href=\"https:\/\/www.embl.org\/internal-information\/people\/joachim-josef-hug\/\">Joachim Hug<\/a><\/strong> is a Postdoctoral fellow in <a href=\"https:\/\/www.embl.org\/groups\/typas\/\"><strong>Typas&#8217; group<\/strong><\/a> (EMBL Heidelberg), working in collaboration with<strong><strong> <\/strong><\/strong> the <a href=\"https:\/\/www.lumc.nl\/en\/afdelingen\/parasitologie\/gf-zeller\/\"><strong>Zeller&#8217;s group<\/strong><\/a><strong> <\/strong>(EMBL Heidelberg-LUMC) and <a href=\"https:\/\/www.helmholtz-hzi.de\/en\/research\/research-topics\/immune-response\/microbial-immune-regulation\/team\/\"><strong>Strowig&#8217;s group<\/strong><\/a> (HZI). His project combines state-of-the-art bioinformatic approaches, high-throughput genetics and phenotypical co-cultivation screening to characterise the metabolic and biosynthetic capability of the&nbsp;<em>Bacteroidota<\/em>&nbsp;phylum.&nbsp;<\/p>\n\n\n\n<p>The main goal of this project is to discover and characterise new groups of Bacteriocins and other secondary metabolites with a focus on  ribosomally synthesized and post-translationally modified peptides (RiPPs) with therapeutic potential.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"518\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/08\/fig-1024x518.jpg\" alt=\"\" class=\"wp-image-2043\" style=\"width:1450px;height:auto\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/08\/fig-1024x518.jpg 1024w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/08\/fig-300x152.jpg 300w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/08\/fig-768x389.jpg 768w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/08\/fig-1536x778.jpg 1536w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/08\/fig.jpg 1778w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Identification of microbiota-derived metabolites modulating tissue-resident regulatory T cells<\/strong><\/h2>\n\n\n\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p><strong><a href=\"https:\/\/www.embl.org\/people\/person\/shafaque-rahman\/\">Shafaque Rahman<\/a><\/strong> is a Postdoctoral fellow in<strong> <a href=\"https:\/\/www.helmholtz-hzi.de\/en\/nc\/research\/research-topics\/immune-response\/experimental-immunology\/team\/\">J. H\u00fchn&#8217;s group<\/a><\/strong> (HZI). In collaboration with the<strong> <a href=\"https:\/\/www.embl.org\/groups\/zimmermann\/\">Zimmermann&#8217;s grou<\/a><\/strong><a href=\"https:\/\/www.embl.org\/groups\/zimmermann\/\"><strong>p<\/strong><\/a> (EMBL Heidelberg), her project focuses on identifying the microbiota-derived metabolites that modulate the numbers and the functional properties of tissue-resident regulatory T cells. <\/p>\n\n\n\n<p>The main goal of this project is to find the molecular mechanisms underlying canonical and non-canonical microbiota-controlled functions of tissue-resident regulatory T cells in humans.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image size-full is-resized is-style-default\"><a href=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/04\/shafake.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"604\" height=\"574\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/04\/shafake.jpg\" alt=\"\" class=\"wp-image-647\" style=\"width:290px;height:auto\" srcset=\"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/04\/shafake.jpg 604w, https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-content\/uploads\/2024\/04\/shafake-300x285.jpg 300w\" sizes=\"auto, (max-width: 604px) 100vw, 604px\" \/><\/a><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n<\/section>\n<\/div><\/div>\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-41","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-json\/wp\/v2\/pages\/41","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-json\/wp\/v2\/comments?post=41"}],"version-history":[{"count":424,"href":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-json\/wp\/v2\/pages\/41\/revisions"}],"predecessor-version":[{"id":2072,"href":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-json\/wp\/v2\/pages\/41\/revisions\/2072"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-json\/wp\/v2\/media?parent=41"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/wp-json\/wp\/v2\/embl_taxonomy?post=41"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}