{"id":1005,"date":"2026-02-25T22:07:09","date_gmt":"2026-02-25T22:07:09","guid":{"rendered":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/?page_id=1005"},"modified":"2026-03-09T09:30:00","modified_gmt":"2026-03-09T09:30:00","slug":"services","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/services\/","title":{"rendered":"Services"},"content":{"rendered":"\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>The facility offers researchers access, support and training into cutting-edge instrumentation and unique knowhow related to automation for microbial work at scale. Our systems enable modular workflows and allow researchers to combine equipment according to their experimental needs.&nbsp;Our focus is on high-throughput cultivation, genetics and phenotyping of microbes and their communities.<\/p>\n\n\n\n<p>After an initial discussion with the user, MACCF staff advise on suitable instrumentation, program and test the automation according to individual needs, and provides hands-on support in experimental setup, execution and data analysis.&nbsp; Experienced users can book and use the different machines following SOPs we have established.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--striped vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n              <a class=\"vf-card__link\" href=\"https:\/\/ppms.embl.de\/start\/\">\n      PPMS online booking       <svg aria-hidden=\"true\" class=\"vf-card__heading__icon | vf-icon vf-icon-arrow--inline-end\" width=\"1em\" height=\"1em\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n          <path d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\" fill=\"currentColor\" fill-rule=\"nonzero\"><\/path>\n       <\/svg>\n        <\/a>\n          <\/h3>\n            <p class=\"vf-card__subheading\">Access for internal users only<\/p>\n            <p class=\"vf-card__text\">Find out how to book MACCF equipment and services.<\/p>\n      <\/div>\n<\/article>\n\n\n<\/div>\n<\/div>\n<\/div>\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<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-high-throughput-cultivation\" data-vf-js-location-nearest-activation-target=\"\">High-throughput cultivation<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-high-throughput-phenotyping\" data-vf-js-location-nearest-activation-target=\"\">High-throughput phenotyping<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-high-throughput-genetics\" data-vf-js-location-nearest-activation-target=\"\">High-throughput genetics<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-high-throughput-cultivation\"><h2 class=\"vf-u-sr-only\">High-throughput cultivation<\/h2>\n<p>The expertise of the staff combined with the automation enables high- throughput cultivation of different species, strain collections and communities. Our core experience lies on human-associated bacteria (and their viruses) and fungi, but we are open to work together with experienced researchers on microbes of other environments and other unicellular organisms \u2013 archaea, protists and algae.&nbsp;<\/p>\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"200\" src=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/variable-atmosphere-workstation-300x200.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/variable-atmosphere-workstation-300x200.jpg 300w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/variable-atmosphere-workstation-1024x683.jpg 1024w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/variable-atmosphere-workstation-768x512.jpg 768w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/variable-atmosphere-workstation.jpg 1200w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Growth of microbes &amp; their communities in controlled environments\n    <\/h3>\n\n  <p class=\"vf-summary__text\"><!-- wp:paragraph -->The facility houses 4 large environmental chambers, connected to customizable gas mixtures to provide precisely controlled atmospheres and temperatures, for the cultivation of a wide range of microbes, from strict anaerobes to microaerophiles, and from psychrophiles to thermophiles. These chambers are routinely used\u00a0for cultivation and phenotyping of human associated microbiomes.<\/p>\n<p class=\"vf-summary__text\"><!-- \/wp:paragraph --><!-- wp:paragraph -->The facility has 9 further incubators\/shakers, where different variables (temperature, light, atmosphere, shaking, humidity)\u00a0can be controlled to support cultivation of diverse microbes.<\/p>\n<p class=\"vf-summary__text\"><!-- \/wp:paragraph --><\/p>\n<\/article>\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"200\" src=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/libraries-1-1200x800-1-300x200.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/libraries-1-1200x800-1-300x200.jpg 300w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/libraries-1-1200x800-1-1024x683.jpg 1024w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/libraries-1-1200x800-1-768x512.jpg 768w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/libraries-1-1200x800-1.jpg 1200w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Handling of large number of microbial species and complex communities\n    <\/h3>\n\n  <p class=\"vf-summary__text\">With 3 automated and 5 semi-automated liquid handlers, the MACCF supports versatile liquid handling protocols on multi-well plates (96-, 384- formats) of different sizes\/volumes, for different purposes related to cultivation:<\/p>\n<ul>\n<li>propagation, (re)arraying of cryopreserved microbial libraries<\/li>\n<li>assembly of complex communities of different compositions<\/li>\n<li>handing of phages and large-scale infection assays<\/li>\n<li>automated PCR workflows (e.g. for 16S in communities)<\/li>\n<li>culturomics approaches \u2013using high-throughput plate assays in different media<\/li>\n<\/ul>\n<\/article>\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"250\" src=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/picker-2-1200x1000-1-300x250.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/picker-2-1200x1000-1-300x250.jpg 300w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/picker-2-1200x1000-1-1024x853.jpg 1024w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/picker-2-1200x1000-1-768x640.jpg 768w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/picker-2-1200x1000-1.jpg 1200w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    Microbial isolation\n    <\/h3>\n\n  <p class=\"vf-summary__text\">A main goal in microbial work is to isolate particular species\/strains from microbiomes of different complexity. With the colony picker and the single-cell dispenser, housed within controlled environments, the facility supports:<\/p>\n<ul>\n<li>HT picking and arraying of large number of colonies<\/li>\n<li>Assays to detect (NGS-based or phenotyping-based) targeted species\/strains<\/li>\n<li>microbial single cell dispensing<\/li>\n<\/ul>\n<\/article>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-high-throughput-phenotyping\"><h2 class=\"vf-u-sr-only\">High-throughput phenotyping<\/h2>\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"200\" src=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/biostack-microplate-stacker-300x200.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/biostack-microplate-stacker-300x200.jpg 300w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/biostack-microplate-stacker-1024x683.jpg 1024w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/biostack-microplate-stacker-768x512.jpg 768w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/biostack-microplate-stacker.jpg 1200w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    HT screens\n    <\/h3>\n\n  <p class=\"vf-summary__text\">We offer integrated platforms combining stackers\/ shakers housed within controlled chambers, and linked to multimode plate readers via robotic arms. We have also high-capacity for liquid handling to assemble assays\/screens, and multimodal plate readers that combine even microscopy and single-cell readouts. Within this setup we can support a variety of HTS, from compound screening to large-scale phenotyping of microbes and their interactions:<\/p>\n<ul>\n<li>HT compound screening \u2013 single compounds and combinations. The facility has 6 compound libraries relative to different aspects of microbial research, all commercially acquired, amounting to in total 7K compounds.<\/li>\n<li>quantitative phenotyping (from growth to single-cell readouts) with kinetics in multi-well plates<\/li>\n<li>microbial interaction screening \u2013 combinatorial (pairwise or higher-order) pooling with liquid handling and measuring compositions<\/li>\n<\/ul>\n<\/article>\n\n\n\n<article class=\"vf-summary vf-summary--has-image\">\n  <img decoding=\"async\" width=\"300\" height=\"200\" src=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/UTI-1-300x200.jpg\" class=\"vf-summary__image\" alt=\"\" style=\"width: 180px; height: auto; border: 1px solid #d0d0ce\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/UTI-1-300x200.jpg 300w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/UTI-1-1024x683.jpg 1024w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/UTI-1-768x512.jpg 768w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/02\/UTI-1.jpg 1200w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>  <h3 class=\"vf-summary__title\">\n    \n    High-throughput assays using high-density agar arrays\n    <\/h3>\n\n  <p class=\"vf-summary__text\">Arrayed libraries of microbes (mutants, species collections) can be pinned on high density format on agar (96, 384, 1536, 6144 colonies per plate) and assayed in 100\u2019s of conditions \u2013 from media requirements to different chemical stresses or drug libraries. The readouts can include growth (colony morphology), enzyme production (colorimetric), biofilm (colony morphology) or interactions. Plates can be grown on different environments and imaged with a versatile setup we have to allow for epi and trans illumination, fluorescence and luminescence detection. Colony phenotypes are analyzed by in-house software.<\/p>\n<\/article>\n\n\n\n<article class=\"vf-summary \">\n    <h3 class=\"vf-summary__title\">\n    \n    Imaging flow analysis\n    <\/h3>\n\n  <p class=\"vf-summary__text\">We offer high-throughput imaging flowcytometric analysis, which can be used to monitor live pathogenic cells, count cells and subpopulations within microbiomes, and for fitness competition assays in simple\/complex environments. Samples can be used past analysis for other assays, including for sorting.<\/p>\n<\/article>\n\n\n\n<article class=\"vf-summary \">\n    <h3 class=\"vf-summary__title\">\n    \n    Microscopy\n    <\/h3>\n\n  <p class=\"vf-summary__text\">We support automated live cell assays, from slide scanning to time-lapse combined with a multimode reader.\u00a0Our setting allows for\u00a0widefield fluorescence, brightfield and phase contrast microscopy under controlled environments (temperature,\u00a0CO<sub>2<\/sub>, O<sub>2<\/sub>-controlled) and for live S2 samples. Single cell parameters, including growth rates and fluorescence signal (reporters) can be quantified on 96\/384-well plates.<\/p>\n<\/article>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-high-throughput-genetics\"><h2 class=\"vf-u-sr-only\">High-throughput genetics<\/h2>\n<p>The facility has extensive knowhow on the generation and manipulation of genetic libraries (mutant, overexpression) in both model and gut bacteria. These libraries can be generated barcoded in pools, where barcode sequencing allows for large-scale fitness-dependent assays. They can also be arrayed so phenotypes can be assessed for each mutant separately (in high-density arrays), allowing for studying processes that are cell-autonomous (extracellular) or fitness-independent. The MACCF can train researchers in the design, construction and use of highly-saturated barcoded transposon mutant libraries in diverse microbes. This comes on top of the numerous available mutant and overexpression libraries available in the MACCF for use in experiments.<\/p>\n<\/section>\n<\/div><\/div>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      Service fees    <\/h3>\n                <p class=\"vf-card__text\"><p>We charge an\u00a0<strong>hourly\u00a0usage fee<\/strong>\u00a0as a contribution to our maintenance and consumables costs.<\/p>\r\n<ul>\r\n \t<li><a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/service-fees\/\">For external users<\/a><\/li>\r\n \t<li><a class=\"vf-card_link\" href=\"https:\/\/www.embl.org\/internal-information\/scientific-services-fees\/#microbial-automation-culturomics\">For internal users<\/a><\/li>\r\n<\/ul><\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"683\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/maccf-services-1024x683.jpg\" alt=\"\" class=\"wp-image-1237\" srcset=\"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/maccf-services-1024x683.jpg 1024w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/maccf-services-300x200.jpg 300w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/maccf-services-768x512.jpg 768w, https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-content\/uploads\/2026\/03\/maccf-services.jpg 1200w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<p><\/p>\n\n\n\n<div style=\"height:35px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":3,"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-1005","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-json\/wp\/v2\/pages\/1005","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-json\/wp\/v2\/comments?post=1005"}],"version-history":[{"count":14,"href":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-json\/wp\/v2\/pages\/1005\/revisions"}],"predecessor-version":[{"id":1403,"href":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-json\/wp\/v2\/pages\/1005\/revisions\/1403"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-json\/wp\/v2\/media?parent=1005"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/microbial-automation-culturomics\/wp-json\/wp\/v2\/embl_taxonomy?post=1005"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}