{"id":1526,"date":"2024-06-05T08:41:15","date_gmt":"2024-06-05T08:41:15","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/?page_id=1526"},"modified":"2025-02-12T10:01:08","modified_gmt":"2025-02-12T10:01:08","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.embl.org\/about\/info\/microbial-ecosystems\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n
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\n 2025 <\/h3>\n <\/div>\n<\/article>\n\n\n\n\n
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\n \n Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco). <\/a>\n <\/h3>\n

\n Potel CM, Burtscher ML, Garrido-Rodriguez M, Brauer-Nikonow A, Becher I, Le Sueur C, Typas A, Zimmermann M, Savitski MM <\/p>\n

\n Nature Structural & Molecular Biology 2025<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41594-025-01485-w <\/p>\n<\/article>\n\n\n\n

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\n \n Harnessing gut microbial communities to unravel microbiome functions <\/a>\n <\/h3>\n

\n Giri S, Shi H, Typas A, Huang KC <\/p>\n

\n Current Opinion in Microbiology 2025<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1016\/j.mib.2024.102578 <\/p>\n<\/article>\n\n\n\n

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\n 2024 <\/h3>\n <\/div>\n<\/article>\n\n\n\n\n
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\n \n Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses <\/a>\n <\/h3>\n

\n Bartolec T , Mitosch K , Potel C , Corona F , Yang ALJ , Burtscher ML , Koumoutsi A , Becher I , Bobonis J , Karcher N , Galardini M , Typas A, Savitski MM <\/p>\n

\n bioRxiv 2024<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1101\/2024.12.20.629319 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Emergence of community behaviors in the gut microbiota upon drug treatment <\/a>\n <\/h3>\n

\n Garcia-Santamarina S, Kuhn M, Devendran S, Maier L, Driessen M, Mateus A, Mastrorilli E, Brochado AR, Savitski MM, Patil KR, Zimmermann M, Bork P, Typas A <\/p>\n

\n Cell 2024<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1016\/j.cell.2024.08.037 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Principles of bacterial innate immunity against viruses <\/a>\n <\/h3>\n

\n Laub MT, Typas A <\/p>\n

\n Current Opinion in Immunology 2024<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/ 10.1016\/j.coi.2024.102445 <\/p>\n<\/article>\n\n\n\n

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\n \n Mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies <\/a>\n <\/h3>\n

\n Tatiana A. Gurbich, Martin Beracochea, Nishadi H. De Silva, Robert D. Finn <\/p>\n

\n BioRXiv 2024<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1101\/2024.07.11.603040 <\/p>\n<\/article>\n\n\n\n

\n

\n \n AllTheBacteria – all bacterial genomes assembled, available and searchable <\/a>\n <\/h3>\n

\n Hunt M , Lima L , Shen W , Lees J , Iqbal Z <\/p>\n

\n bioRxiv 2024<\/span>\n <\/p>\n\n

\n <\/p>\n<\/article>\n\n\n\n

\n

\n \n SPIRE: a Searchable, Planetary-scale mIcrobiome REsource <\/a>\n <\/h3>\n

\n Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P <\/p>\n

\n Nucleic Acids Research 2024<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1093\/nar\/gkad943 <\/p>\n<\/article>\n\n\n\n

\n

\n \n TAC-TIC, a high-throughput genetics method to identify triggers or blockers of bacterial toxin-antitoxin systems. <\/a>\n <\/h3>\n

\n Bobonis J, Yang ALJ, Voogdt CGP, Typas A <\/p>\n

\n Nature Protocols 2024<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41596-024-00988-y <\/p>\n<\/article>\n\n\n\n

\n

\n \n CELEBRIMBOR: Pangenomes from metagenomes <\/a>\n <\/h3>\n

\n Joel Hellewell, Samuel T Horsfield, Johanna von Wachsmann, Tatiana Gurbich, Robert D Finn, Zamin Iqbal, Leah W Roberts, John A Lees <\/p>\n

\n bioRxiv 2024<\/span>\n <\/p>\n\n

\n <\/p>\n<\/article>\n\n\n\n

\n

\n \n Exploring the microbial savanna: predator-prey interactions in the soil <\/a>\n <\/h3>\n

\n Sanchis Pla L, van Gestel J <\/p>\n

\n Molecular systems biology 2024<\/span>\n <\/p>\n\n

\n doi:10.1038\/s44320-024-00033-w <\/p>\n<\/article>\n\n\n\n

\n
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\n 2023 <\/h3>\n <\/div>\n<\/article>\n\n\n\n\n
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\n \n Decipher enzymes from human microbiota for drug discovery and development <\/a>\n <\/h3>\n

\n Beliaeva MA, Wilmanns M, Zimmermann M <\/p>\n

\n Current opinion in structural biology 2023<\/span>\n <\/p>\n\n

\n doi:10.1016\/j.sbi.2023.102567 <\/p>\n<\/article>\n\n\n\n

\n

\n \n MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues. <\/a>\n <\/h3>\n

\n Gurbich TA, Almeida A, Beracochea M, Burdett T, Burgin J, Cochrane G, Raj S, Richardson L, Rogers AB, Sakharova E, Salazar GA, Finn RD <\/p>\n

\n Journal of Molecular Biology 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1016\/j.jmb.2023.168016 <\/p>\n<\/article>\n\n\n\n

\n

\n \n MGnify: the microbiome sequence data analysis resource in 2023 <\/a>\n <\/h3>\n

\n Richardson L, Allen B, Baldi G, Beracochea M, Bileschi ML, Burdett T, Burgin J, Caballero-P\u00e9rez J, Cochrane G, Colwell LJ, Curtis T, Escobar-Zepeda A, Gurbich TA, Kale V, Korobeynikov A, Raj S, Rogers AB, Sakharova E, Sanchez S, Wilkinson DJ, Finn RD <\/p>\n

\n Nucleic Acids Research 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1093\/nar\/gkac1080 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Expansion of novel biosynthetic gene clusters from diverse environments using SanntiS <\/a>\n <\/h3>\n

\n Sanchez S, Rogers JD, Rogers AB, Nassar M, McEntyre J, Welch M, Hollfelder F, Finn RD <\/p>\n

\n bioRxiv 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1101\/2023.05.23.540769 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion <\/a>\n <\/h3>\n

\n van Gestel J, Wagner A, Ackermann M <\/p>\n

\n PLoS biology 2023<\/span>\n <\/p>\n\n

\n doi:10.1371\/journal.pbio.3002338 <\/p>\n<\/article>\n\n\n\n

\n

\n \n VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models. <\/a>\n <\/h3>\n

\n Rangel-Pineros G, Almeida A, Beracochea M, Sakharova E, Marz M, Reyes Mu\u00f1oz A, H\u00f6lzer M, Finn RD <\/p>\n

\n Plos Computational Biology 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1371\/journal.pcbi.1011422 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Consistency across multi-omics layers in a drug-perturbed gut microbial community <\/a>\n <\/h3>\n

\n Wuyts S, Alves R, Zimmermann-Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, M\u00fcller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P <\/p>\n

\n Molecular Systems Biology 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.15252\/msb.202311525 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Challenges and opportunities in sharing microbiome data and analyses <\/a>\n <\/h3>\n

\n Huttenhower C, Finn RD, McHardy AC <\/p>\n

\n Nature Microbiology 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41564-023-01484-x <\/p>\n<\/article>\n\n\n\n

\n

\n \n Unravelling metabolic cross-feeding in a yeast-bacteria community using 13 C-based proteomics. <\/a>\n <\/h3>\n

\n Gabrielli N, Maga-Nteve C, Kafkia E, Rettel M, Loeffler J, Kamrad S, Typas A, Patil KR <\/p>\n

\n Molecular Systems Biology 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.15252\/msb.202211501 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction <\/a>\n <\/h3>\n

\n Tripathi S, Voogdt CGP, Bassler SO, Anderson M, Huang PH, Sakenova N, Capraz T, Jain S, Koumoutsi A, Bravo AM, Trotter V, Zimmerman M, Sonnenburg JL, Buie C, Typas A, Deutschbauer AM, Shiver AL, Huang KC <\/p>\n

\n Cell Reports 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1016\/j.celrep.2023.113517 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics <\/a>\n <\/h3>\n

\n Voogdt CGP, Tripathi S, Bassler SO, McKeithen-Mead SA, Guiberson ER, Koumoutsi A, Bravo AM, Buie C, Zimmermann M, Sonnenburg JL, Typas A, Deutschbauer AM, Shiver AL, Huang KC <\/p>\n

\n Cell Reports 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1016\/j.celrep.2023.113519 <\/p>\n<\/article>\n\n\n\n

\n

\n \n High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities <\/a>\n <\/h3>\n

\n M\u00fcller P, de la Cuesta-Zuluaga J, Kuhn M, Baghai Arassi M, Treis T, Blasche S, Zimmermann M, Bork P, Patil KR, Typas A, Garcia-Santamarina S, Maier L <\/p>\n

\n Nature Protocols 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41596-023-00926-4 <\/p>\n<\/article>\n\n\n\n

\n

\n \n PyHMMER: a Python library binding to HMMER for efficient sequence analysis <\/a>\n <\/h3>\n

\n Larralde M, Zeller G <\/p>\n

\n Bioinformatics (Oxford, England) 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1093\/bioinformatics\/btad214 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Recent advances in data- and knowledge-driven approaches to explore primary microbial metabolism <\/a>\n <\/h3>\n

\n Bartmanski BJ , Rocha M, Zimmermann-Kogadeeva M <\/p>\n

\n Current Opinion in Chemical Biology 2023<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1016\/j.cbpa.2023.102324 <\/p>\n<\/article>\n\n\n\n

\n
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\n 2022 <\/h3>\n <\/div>\n<\/article>\n\n\n\n\n
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\n \n A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications. <\/a>\n <\/h3>\n

\n Nassar M, Rogers AB, Talo’ F, Sanchez S, Shafique Z, Finn RD , McEntyre J <\/p>\n

\n Gigascience 2022<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1093\/gigascience\/giac077 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs <\/a>\n <\/h3>\n

\n Periwal V, Bassler S, Andrejev S, Gabrielli N, Patil KR, Typas A, Patil KR <\/p>\n

\n Plos Computational Biology 2022<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1371\/journal.pcbi.1010029 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems <\/a>\n <\/h3>\n

\n Bobonis J, Mitosch K, Mateus A, Karcher N, Kritikos G, Selkrig J, Zietek M, Monzon V, Pfalz B, Garcia-Santamarina S, Galardini M, Sueki A, Kobayashi C, Stein F, Bateman A, Zeller G, Savitski MM, Elfenbein JR, Andrews-Polymenis HL, Typas A <\/p>\n

\n Nature 2022<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41586-022-05091-4 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial <\/a>\n <\/h3>\n

\n Sowah SA, Milanese A, Sch\u00fcbel R, Wirbel J, Kartal E, Johnson TS, Hirche F, Grafetst\u00e4tter M, Nonnenmacher T, Kirsten R, L\u00f3pez-Nogueroles M, Lahoz A, Schwarz KV, Okun JG, Ulrich CM, Nattenm\u00fcller J, von Eckardstein A, M\u00fcller D, Stangl GI, Kaaks R, K\u00fchn T, Zeller G <\/p>\n

\n Genome Medicine 2022<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1186\/s13073-022-01030-0 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments <\/a>\n <\/h3>\n

\n Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S <\/p>\n

\n Microbiome 2022<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1186\/s40168-022-01410-z <\/p>\n<\/article>\n\n\n\n

\n

\n \n Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota. <\/a>\n <\/h3>\n

\n Lindell AE, Zimmermann-Kogadeeva M , Patil KR <\/p>\n

\n ature reviews. Microbiology 2022<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41579-022-00681-5 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Systematic discovery of biomolecular condensate-specific protein phosphorylation <\/a>\n <\/h3>\n

\n Sridharan S, Hernandez-Armendariz A, Kurzawa N , Potel C , Memon D, Beltrao P , Bantscheff M , Huber W, Cuylen-Haering S , Savitski M <\/p>\n

\n Nat Chem Biol 2022<\/span>\n <\/p>\n\n

\n 10.1038\/s41589-022-01062-y <\/p>\n<\/article>\n\n\n\n

\n

\n \n Publisher Correction: A catalogue of 1,167 genomes from the human gut archaeome. <\/a>\n <\/h3>\n

\n Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, Brug\u00e8re JF, Gribaldo S, Finn RD, Schmitz RA, Moissl-Eichinger C <\/p>\n

\n Nature Microbiology 2022<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41564-022-01061-8 <\/p>\n<\/article>\n\n\n\n

\n
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\n 2021 <\/h3>\n <\/div>\n<\/article>\n\n\n\n\n
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\n \n Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. <\/a>\n <\/h3>\n

\n Saheb Kashaf S, Proctor DM, Deming C, Saary P, H\u00f6lzer M, NISC Comparative Sequencing Program, Taylor ME, Kong HH, Segre JA , Almeida A , Finn RD <\/p>\n

\n Nature Microbiology 2021<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41564-021-01011-w <\/p>\n<\/article>\n\n\n\n

\n

\n \n Unravelling the collateral damage of antibiotics on gut bacteria. <\/a>\n <\/h3>\n

\n Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, M\u00fcller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, L\u00f6ber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A <\/p>\n

\n Nature 2021<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/ <\/p>\n<\/article>\n\n\n\n

\n

\n \n Bioaccumulation of therapeutic drugs by human gut bacteria <\/a>\n <\/h3>\n

\n Kl\u00fcnemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, H\u00f6velmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, S\u00e9vin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR <\/p>\n

\n Nature 2021<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41586-021-03891-8 <\/p>\n<\/article>\n\n\n\n

\n

\n \n A unified catalog of 204,938 reference genomes from the human gut microbiome. <\/a>\n <\/h3>\n

\n Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P, Segata N , Kyrpides NC , Finn RD <\/p>\n

\n 2021<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41587-020-0603-3 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Global mapping of Salmonella enterica-host protein-protein interactions during infection <\/a>\n <\/h3>\n

\n Walch P, Selkrig J, Knodler LA, Rettel M, Stein F, Fernandez K, Vi\u00e9itez C, Potel CM, Scholzen K, Geyer M, Rottner K, Steele-Mortimer O, Savitski MM, Holden DW, Typas A <\/p>\n

\n Cell Host & Microbe 2021<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1016\/j.chom.2021.06.004 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Towards a mechanistic understanding of reciprocal drug\u2013microbiome interactions <\/a>\n <\/h3>\n

\n Zimmermann M, Patl KR, Typas A and Maier, L <\/p>\n

\n Mol Syst Biol 2021<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.15252\/msb.202010116 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Transcriptional and Post-Transcriptional Polar Effects in Bacterial Gene Deletion Libraries <\/a>\n <\/h3>\n

\n Mateus A , Shah M, Hevler J, Kurzawa N, Bobonis J, Typas A , Savitski M <\/p>\n

\n M systems 2021<\/span>\n <\/p>\n\n

\n 10.1128\/mSystems.00813-21 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Impact of phosphorylation on thermal stability of proteins. <\/a>\n <\/h3>\n

\n Potel CM , Kurzawa N, Becher I, Typas A, Mateus A, Savitski MM <\/p>\n

\n Nature Methods 2021<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41592-021-01177-5 <\/p>\n<\/article>\n\n\n\n

\n

\n \n Massive expansion of human gut bacteriophage diversity <\/a>\n <\/h3>\n

\n Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD <\/p>\n

\n Cell 2021<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1016\/j.cell.2021.01.029 <\/p>\n<\/article>\n\n\n\n

\n
\n

\n 2020 <\/h3>\n <\/div>\n<\/article>\n\n\n\n\n
\n

\n \n A unified catalog of 204,938 reference genomes from the human gut microbiome <\/a>\n <\/h3>\n

\n Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks D, Hugenholtz P, Segata N, Kyrpides NC, Finn RD <\/p>\n

\n Nature Biotechnology 2020<\/span>\n <\/p>\n\n

\n https:\/\/doi.org\/10.1038\/s41587-020-0603-3 <\/p>\n<\/article>\n\n\n\n

\n

\n \n The functional proteome landscape of Escherichia coli <\/a>\n <\/h3>\n

\n Mateus A, Hevler J, Bobonis J, Kurzawa N , Shah M , Mitosch K, Goemans C, Helm D , Stein F, Typas A, Savitski M <\/p>\n

\n Nature 2020<\/span>\n <\/p>\n\n

\n 10.1038\/s41586-020-3002-5 <\/p>\n<\/article>\n\n<\/div>\n<\/div>\n\n\n

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