Publications – Microbial Ecosystems

Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco).

Potel CM, Burtscher ML, Garrido-Rodriguez M, Brauer-Nikonow A, Becher I, Le Sueur C, Typas A, Zimmermann M, Savitski MM

Nature Structural & Molecular Biology 2025

https://doi.org/10.1038/s41594-025-01485-w

Harnessing gut microbial communities to unravel microbiome functions

Giri S, Shi H, Typas A, Huang KC

Current Opinion in Microbiology 2025

https://doi.org/10.1016/j.mib.2024.102578

Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses

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

bioRxiv 2024

https://doi.org/10.1101/2024.12.20.629319

Emergence of community behaviors in the gut microbiota upon drug treatment

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

Cell 2024

https://doi.org/10.1016/j.cell.2024.08.037

Principles of bacterial innate immunity against viruses

Laub MT, Typas A

Current Opinion in Immunology 2024

https://doi.org/ 10.1016/j.coi.2024.102445

Mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies

Tatiana A. Gurbich, Martin Beracochea, Nishadi H. De Silva, Robert D. Finn

BioRXiv 2024

https://doi.org/10.1101/2024.07.11.603040

AllTheBacteria – all bacterial genomes assembled, available and searchable

Hunt M , Lima L , Shen W , Lees J , Iqbal Z

bioRxiv 2024

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

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

Nucleic Acids Research 2024

https://doi.org/10.1093/nar/gkad943

TAC-TIC, a high-throughput genetics method to identify triggers or blockers of bacterial toxin-antitoxin systems.

Bobonis J, Yang ALJ, Voogdt CGP, Typas A

Nature Protocols 2024

https://doi.org/10.1038/s41596-024-00988-y

CELEBRIMBOR: Pangenomes from metagenomes

Joel Hellewell, Samuel T Horsfield, Johanna von Wachsmann, Tatiana Gurbich, Robert D Finn, Zamin Iqbal, Leah W Roberts, John A Lees

bioRxiv 2024

Exploring the microbial savanna: predator-prey interactions in the soil

Sanchis Pla L, van Gestel J

Molecular systems biology 2024

doi:10.1038/s44320-024-00033-w

Decipher enzymes from human microbiota for drug discovery and development

Beliaeva MA, Wilmanns M, Zimmermann M

Current opinion in structural biology 2023

doi:10.1016/j.sbi.2023.102567

MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues.

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

Journal of Molecular Biology 2023

https://doi.org/10.1016/j.jmb.2023.168016

MGnify: the microbiome sequence data analysis resource in 2023

Richardson L, Allen B, Baldi G, Beracochea M, Bileschi ML, Burdett T, Burgin J, Caballero-Pérez 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

Nucleic Acids Research 2023

https://doi.org/10.1093/nar/gkac1080

Expansion of novel biosynthetic gene clusters from diverse environments using SanntiS

Sanchez S, Rogers JD, Rogers AB, Nassar M, McEntyre J, Welch M, Hollfelder F, Finn RD

bioRxiv 2023

https://doi.org/10.1101/2023.05.23.540769

Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion

van Gestel J, Wagner A, Ackermann M

PLoS biology 2023

doi:10.1371/journal.pbio.3002338

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.

Rangel-Pineros G, Almeida A, Beracochea M, Sakharova E, Marz M, Reyes Muñoz A, Hölzer M, Finn RD

Plos Computational Biology 2023

https://doi.org/10.1371/journal.pcbi.1011422

Consistency across multi-omics layers in a drug-perturbed gut microbial community

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

Molecular Systems Biology 2023

https://doi.org/10.15252/msb.202311525

Challenges and opportunities in sharing microbiome data and analyses

Huttenhower C, Finn RD, McHardy AC

Nature Microbiology 2023

https://doi.org/10.1038/s41564-023-01484-x

Unravelling metabolic cross-feeding in a yeast-bacteria community using 13 C-based proteomics.

Gabrielli N, Maga-Nteve C, Kafkia E, Rettel M, Loeffler J, Kamrad S, Typas A, Patil KR

Molecular Systems Biology 2023

https://doi.org/10.15252/msb.202211501

Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction

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

Cell Reports 2023

https://doi.org/10.1016/j.celrep.2023.113517

Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics

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

Cell Reports 2023

https://doi.org/10.1016/j.celrep.2023.113519

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities

Müller 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

Nature Protocols 2023

https://doi.org/10.1038/s41596-023-00926-4

PyHMMER: a Python library binding to HMMER for efficient sequence analysis

Larralde M, Zeller G

Bioinformatics (Oxford, England) 2023

https://doi.org/10.1093/bioinformatics/btad214

Recent advances in data- and knowledge-driven approaches to explore primary microbial metabolism

Bartmanski BJ , Rocha M, Zimmermann-Kogadeeva M

Current Opinion in Chemical Biology 2023

https://doi.org/10.1016/j.cbpa.2023.102324

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications.

Nassar M, Rogers AB, Talo’ F, Sanchez S, Shafique Z, Finn RD , McEntyre J

Gigascience 2022

https://doi.org/10.1093/gigascience/giac077

Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs

Periwal V, Bassler S, Andrejev S, Gabrielli N, Patil KR, Typas A, Patil KR

Plos Computational Biology 2022

https://doi.org/10.1371/journal.pcbi.1010029

Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems

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

Nature 2022

https://doi.org/10.1038/s41586-022-05091-4

Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial

Sowah SA, Milanese A, Schübel R, Wirbel J, Kartal E, Johnson TS, Hirche F, Grafetstätter M, Nonnenmacher T, Kirsten R, López-Nogueroles M, Lahoz A, Schwarz KV, Okun JG, Ulrich CM, Nattenmüller J, von Eckardstein A, Müller D, Stangl GI, Kaaks R, Kühn T, Zeller G

Genome Medicine 2022

https://doi.org/10.1186/s13073-022-01030-0

Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments

Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S

Microbiome 2022

https://doi.org/10.1186/s40168-022-01410-z

Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota.

Lindell AE, Zimmermann-Kogadeeva M , Patil KR

ature reviews. Microbiology 2022

https://doi.org/10.1038/s41579-022-00681-5

Systematic discovery of biomolecular condensate-specific protein phosphorylation

Sridharan S, Hernandez-Armendariz A, Kurzawa N , Potel C , Memon D, Beltrao P , Bantscheff M , Huber W, Cuylen-Haering S , Savitski M

Nat Chem Biol 2022

10.1038/s41589-022-01062-y

Publisher Correction: A catalogue of 1,167 genomes from the human gut archaeome.

Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, Brugère JF, Gribaldo S, Finn RD, Schmitz RA, Moissl-Eichinger C

Nature Microbiology 2022

https://doi.org/10.1038/s41564-022-01061-8

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions.

Saheb Kashaf S, Proctor DM, Deming C, Saary P, Hölzer M, NISC Comparative Sequencing Program, Taylor ME, Kong HH, Segre JA , Almeida A , Finn RD

Nature Microbiology 2021

https://doi.org/10.1038/s41564-021-01011-w

Unravelling the collateral damage of antibiotics on gut bacteria.

Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A

Nature 2021

https://doi.org/

Bioaccumulation of therapeutic drugs by human gut bacteria

Klünemann 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, Hövelmann 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, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR

Nature 2021

https://doi.org/10.1038/s41586-021-03891-8

A unified catalog of 204,938 reference genomes from the human gut microbiome.

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

2021

https://doi.org/10.1038/s41587-020-0603-3

Global mapping of Salmonella enterica-host protein-protein interactions during infection

Walch P, Selkrig J, Knodler LA, Rettel M, Stein F, Fernandez K, Viéitez C, Potel CM, Scholzen K, Geyer M, Rottner K, Steele-Mortimer O, Savitski MM, Holden DW, Typas A

Cell Host & Microbe 2021

https://doi.org/10.1016/j.chom.2021.06.004