Seppe Kuehn

Phylogenetic coherence in microbiome composition across environmental gradients

The paper investigates how environmental gradients shape microbial community composition by analyzing phylogenetic signals in response to environmental variables.

Bacterial vitamin sharing emerges from a balance between release and uptake

The paper quantifies vitamin B12 synthesis and uptake in bacterial isolates, revealing strategies that govern extracellular B12 availability through a balance between release and uptake.

The ecological context of enzymatic variation

This study links enzyme sequence variation to functional responses in microbial ecosystems using nitrate reductase as a model, showing predictable sequence-to-activity relationships.

Hierarchical control of bacterial growth efficiency by substrate and taxonomy

This study measures growth efficiency in 23 bacterial strains across two substrates, showing it is hierarchically controlled by substrate identity and taxonomy.

Natural Selection in the Wake of Catastrophe

This paper develops a data-validated theory of natural selection after catastrophe, showing mean fitness relaxes inversely with time and follows Levenberg-Marquardt optimization in E. coli.

Global epistasis in ecosystems arises from resource constraints

The paper explains global epistasis in ecosystems as arising from resource constraints, showing linear relationships in single- and multi-species systems.

Learning functional groups in complex microbiomes

This paper introduces a neural-network based method to identify functional groups in microbiomes, showing it can distill complex communities into few groups that explain community function across different environments.

Learning the mechanism of collective microbial function via random community-media pairing

This paper uses random community-media pairing with LASSO regression to uncover cross-feeding mechanisms in microbial communities.

Functional regimes define the response of the soil microbiome to environmental change

The paper uses microcosm experiments and modeling to identify three functional regimes governing soil microbiome responses to pH changes, revealing distinct metabolic dynamics and underlying mechanisms.

Inferring resource competition in microbial communities from time series

This study uses spectral methods to infer resource competition in microbial communities from time series data, showing they outperform simple correlations.

Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design

This study uses community-function landscapes to design synthetic microbial consortia for BPA degradation, showing that toxicity increases epistasis and enables predictable bioremediation.

Microbial functional guilds respond cohesively to rapidly fluctuating environments

The paper shows microbial functional guilds respond cohesively to rapid environmental fluctuations and competitively to slower ones, offering a framework for discovering guilds through nutrient perturbations.

Statistical design of a synthetic microbiome that suppresses diverse gut pathogens

The paper designs a synthetic microbiome that suppresses gut pathogens using a statistical approach, showing it effectively clears Kp-MH258 in multiple environments.