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Lab-led publications, made clear.

A guided archive of recent papers, preprints, reviews and commentaries led by Hildebrand Lab researchers.

21 lab-led publications7 years of research1 open lab record

Fast profiling from species to strains

2026 bioRxiv · Bioinformatics preprint

Protal: Ultra-fast metagenomic profiling and strain-resolved analysis

Joachim Fritscher, Anthony Duncan & Falk Hildebrand

Introduces a fast alignment-based method that profiles microbial species and reconstructs strain relationships in the same workflow.

Enriching low-abundance gut microeukaryotes

2026 bioRxiv · Methods preprint

Enriching the Human Stool Microeukaryotes for Shotgun Sequencing

Ezgi Özkurt, David Schneider, Steve A. James et al. · Falk Hildebrand

Develops and benchmarks a bacterial-cell depletion protocol that increases the representation and taxonomic diversity of low-abundance microeukaryotes in stool metagenomes.

From complex data to stable signatures

2025 Nucleic Acids Research · Methods

Detecting signatures underlying the composition of biological data

Anthony Duncan, Wing Koon, Katarzyna Sidorczuk, Christopher Quince, Clémence Frioux & Falk Hildebrand

Introduces cvaNMF, which selects stable, reproducible patterns in complex biological data, from gut microbiomes to cell populations.

Reproducible analysis of 16S amplicons

2025 Springer Protocols · Methods chapter

Bioinformatics Processing of 16S Datasets

Alise J. Ponsero, Anthony Duncan, Judit Tálas, Katarzyna Sidorczuk, Wing Koon, Falk Hildebrand & Andrea Telatin

Sets out practical quality-control, feature-inference, taxonomy and phylogeny steps for 16S rRNA amplicon data, including reproducible workflows in QIIME 2, nf-core/ampliseq and LotuS2.

Complementary routes through shotgun data

2025 Springer Protocols · Methods chapter

Bioinformatics Processing of Whole Metagenome Shotgun Datasets

Anthony Duncan, Wing Koon, Katarzyna Sidorczuk, Alise J. Ponsero, Sumeet K. Tiwari, Falk Hildebrand & Andrea Telatin

Explains how read-based taxonomic and functional profiling complements assembly and recovery of metagenome-assembled genomes, with guidance on method choice and computational requirements.

Diet reshapes microbial and host metabolism

2025 medRxiv · Preprint

Dietary bioactives increase gut microbiome diversity and alter host and microbial metabolite profiles

Anthony Duncan, Federico Bernuzzi et al. · Falk Hildebrand & Maria H. Traka

Reports a randomised crossover study of 20 adults in which diets matched for fibre and macronutrients produced modest microbial-diversity differences and larger metabolite differences.

Preserving long DNA for complete genomes

2025 bioRxiv · Preprint

Optimizing storage, high-molecular weight DNA extraction and genome reconstructions from human faecal samples

Klara Cerk, Anthony Duncan, Nabina Shrestha et al. · Falk Hildebrand

Compares 32 storage, extraction and lysis combinations for long-read faecal metagenomics, showing how both choices affect community profiles and genome reconstruction.

Metabolic recovery despite persistent dysbiosis

2025 npj Parkinson's Disease · Pilot intervention

A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's disease

Janis Rebecca Bedarf, Stefano Romano, Silke Sophie Heinzmann et al. · Falk Hildebrand

In 11 patient and spouse pairs, a four-week high-fibre diet with lactulose increased faecal short-chain fatty acids and reduced gastrointestinal symptoms, while established compositional differences persisted.

Mapping the bacterial adhesiome

2024 BMC Genomics · Software

adhesiomeR: a tool for Escherichia coli adhesin classification and analysis

Katarzyna Sidorczuk, Michał Burdukiewicz, Klara Cerk, Joachim Fritscher et al. · Falk Hildebrand

Presents an open tool and database for classifying E. coli adhesins, the genes that help bacteria attach to surfaces and hosts, across thousands of genomes.

Connecting genomes into community models

2024 Microbial Biotechnology · Review

Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing

Klara Cerk et al. · Falk Hildebrand & Clémence Frioux

Reviews how genome-resolved metagenomics and metabolic models can be combined to understand the functions and exchanges that shape a microbial community.

Five recurring gut-community guilds

2023 Cell Host & Microbe · Research article

Enterosignatures define common bacterial guilds in the human gut microbiome

Clémence Frioux, Rebecca Ansorge, Ezgi Özkurt et al. · Falk Hildebrand

Uses non-negative matrix factorisation on 5,230 metagenomes to describe gut communities as continuous mixtures of five recurrent bacterial guilds rather than discrete sample classes.

Turning raw reads into reliable profiles

2022 Microbiome · Software

LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo et al. · Falk Hildebrand

Integrates demultiplexing, filtering, OTU or ASV inference, taxonomy and standard outputs in a configurable amplicon-analysis workflow.

From species to the rarest genetic variants

2021 mSystems · Commentary

Ultra-resolution metagenomics: when enough is not enough

Falk Hildebrand

Defines the data and computational requirements for resolving rare within-population variants and observing microbial evolution over ecological timescales.

How strains persist and disperse

2021 Cell Host & Microbe · Research article

Dispersal strategies shape persistence and evolution of human gut bacteria

Falk Hildebrand, Toni I. Gossmann, Clémence Frioux, Ezgi Özkurt et al.

Analyses 5,278 metagenomes to distinguish bacterial populations that persist within individuals from those more frequently transmitted within families or distributed across regions.

Charting the chicken gut microbiome

2021 PeerJ · Genome resource

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Rachel Gilroy, Anuradha Ravi, Maria Getino et al. · Falk Hildebrand & Mark J. Pallen

Builds a large gene-and-genome catalogue that reveals hundreds of previously unknown chicken gut microbial species.

Separating microbial signal from artefact

2021 Microbiome · Methods

Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson's disease individuals

Janis R. Bedarf, Naiara Beraza, Hassan Khazneh et al. · Falk Hildebrand

Demonstrates how off-target amplification can create false bacterial signals in low-biomass brain samples.

Microbial trajectories across the lifespan

2021 Nature Aging · News & Views

Lifelong sex-dependent trajectories of the human gut microbiota

Ezgi Özkurt & Falk Hildebrand

Explains emerging evidence that gut microbial communities follow sex-dependent trajectories across human life, linking host biology and microbial persistence.

Bacteria and fungi across global habitats

2021 Environmental Microbiology · Research article

Metagenomic assessment of the global diversity and distribution of bacteria and fungi

Mohammad Bahram, Tarquin Netherway, Clémence Frioux et al. · Peer Bork & Falk Hildebrand

Compares bacterial and fungal diversity and relative abundance in 13,483 metagenomes from 29 environments, finding distinct habitat associations for the two groups.

Finding metabolic complementarity

2020 eLife · Software and methods

Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand & Anne Siegel

Introduces a workflow that reconstructs metabolic networks from genomes, tests community-scale metabolic complementarity and identifies minimal sets of organisms able to provide specified functions.

Moving from gene lists to connected genomes

2020 Computational and Structural Biotechnology Journal · Review

From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes

Clémence Frioux, Dipali Singh, Tamás Korcsmáros & Falk Hildebrand

Explains why connecting functions back to individual genomes gives a clearer picture of what a microbial community can do and how its members interact.

Naming newly discovered microbial taxa

2020 Gut · Letter

Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology

Falk Hildebrand, Mark J. Pallen & Peer Bork

Proposes a systematic way to give stable, informative names to the many prokaryotic taxa discovered through sequencing.

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