Annual Conference 2025 of the Association for General and Applied Microbiology - Jahrestagung 2025 der Vereinigung für Allgemeine und Angewandte Mikrobiologie

Prof.

Chair

Providing access to MGnify for microbiome data discovery and interpretation: challenges, successes, and future directions

FG Functional genomics / microbiome

The MGnify resource hosts one of the largest collections of publicly available assembled metagenomes, and an associated database containing billions of derived proteins. In recent years, MGnify has expanded its offerings to include biome-specific catalogues of metagenome-assembled genomes (MAGs), derived from these assemblies as well as community-contributed MAGs. These catalogues are providing valuable insights into microbial diversity across various environments and host-associated ecosystems, including those of humans. In this presentation, I will discuss the scientific considerations, technical advancements, and challenges encountered in making these data and services accessible to the research community. Particular focus will be placed on the efforts to ensure the provenance and transparency of our data products. Finally, I will explore the evolving landscape of microbiome research and the pivotal role MGnify will continue to play in advancing scientific discovery and collaboration.

Invited lecture

Discovering the hidden function of long non-coding RNAs of Aspergilli

Fungal pathogens of the Aspergillus genus pose significant threats to human health and food production. Despite progress in understanding pathogenicity mechanisms, a crucial knowledge gap remains regarding the role of long non-coding RNAs (lncRNAs) in the evolution of fungi into successful pathogens. LncRNAs represent a vital yet often overlooked aspect of fungal biology, particularly in how Aspergillus species withstand stress to endure and thrive under adverse conditions. For instance, in Candida auris, the lncRNA DINOR regulates fungal virulence by modulating stress responses and hyphal growth, suggesting that lncRNAs in Aspergillus may similarly influence pathogenic mechanisms.In our study, we aimed to unravel the role of lncRNAs in responding to changing conditions using a transcriptome analysis of >1000 samples A. flavus, A. fumigatus, A. nidulans, and A. niger available in public databases. Using two different machine learning algorithms we successfully predicted 4022, 1482, 3098, and 3129 potential lncRNAs for A. flavus, A. fumigatus, A. nidulans, and A. niger, respectively. Comparative analysis revealed that lncRNAs in these species share common characteristics, such as shorter length, lower expression levels, and reduced GC content compared to protein-coding genes. Notably, only A. fumigatus, the main pathogenic species, showed a lower proportion of lncRNAs relative to its genome size and a unique enrichment in subtelomeric regions. This finding suggests that the spatial organization of lncRNAs in A. fumigatus may play a critical role in regulating key processes, such as metabolism, contributing to its success as an opportunistic pathogen. We also identified lncRNAs that exhibited differential expression in response to stress and explored their potential functions by analyzing the nearby protein-coding genes. By employing this cis-regulation strategy, we identified diverse Gene Ontology (GO) terms and the biological functions impacted by lncRNAs across the four Aspergillus species.In conclusion, our approach to identifying lncRNAs in Aspergillus species offers new insights into fungal pathogenicity and potential strategies to combat infections.

Short lecture

Infection-induced glycosaminoglycan release promotes microbiota expansion in Drosophila gut

While the host genetics is known to affect the composition of intestinal microbial communities, whether the host genotype influences the abundance of intestinal commensals remains uninvestigated. To close this knowledge gap, we performed a genome-wide association study (GWAS) in the fruit fly Drosophila melanogaster to identify host genetic variants linked to the abundance of Lactiplantibacillus plantarum – a major gut commensal of fruit flies. Our GWA study uncovered a statistically significant association between polymorphisms in genes involved in heparan sulfate synthesis and L. plantarum load. RNAi-mediated knockdown of some of these genes resulted in reduced heparan sulfate synthesis and reduced abundance of L. plantarum. Thus, heparan sulfate mediates Drosophila gut colonization by L. plantarum. Mechanistically, heparan sulfate facilitates the adhesion of L. plantarum to host epithelium and promotes biofilm formation. We further showed that intestinal infection induces heparan sulfate synthesis by the host via activation of the Nf-kB immune signaling cascade. Increased availability of heparan sulfate during infection results in the expansion of L. plantarum population in the gut. Importantly, such commensal expansion is also beneficial for the host as L. plantarum protects the host from intestinal pathogens via colonization resistance. This work reports an intriguing case where commensal not only survives the inflammatory environment caused by the infection but also benefits from it by utilizing the additional resources made available during infection.

Uncovering synthetic steroid biotransformations in gut and environmental bacteria

Synthetic steroids are widely used in both pharmaceuticals and veterinary medicine. Designed for increased potency and resistance to metabolism, these compounds tend to persist in the environment, raising ecological concerns such as disruption of aquatic ecosystems and impacts on plant growth. While several environmental bacteria have shown the ability to degrade natural steroids, such as testosterone and estrone, the degradation of synthetic analogs remains poorly understood. In this study, we screened four environmental species and eight gut bacteria to investigate the biotransformation of 20 steroids and steroid prodrugs, including synthetic estrogens, progestogens, and corticosteroids. Through the development of a tandem mass spectrometry-based pipeline, we identified key steroid biotransformation intermediates and products, revealing distinct steroid metabolizing pathways for the different bacteria tested. These findings illustrate the specific roles in steroid metabolism that environmental and gut bacteria play and suggest that prior steroid exposure to gut microbiota may affect the fate of synthetic steroids in the environment. To uncover the enzymes and enzyme pathways involved, we employed genetic screens and homology searches. Our developed approach provides a robust platform to identify steroid metabolites and select enzymes of specific biocatalytic interest for further characterization, as well as allows for mapping the network of genes, proteins, and species capable of steroid biotransformations within specific ecosystems, such as the human gut and environmental habitats.

Prof. Dr.

From gut to data: An interactive platform for exploring human microbiome fingerprints via AutoML-Driven bioindicator discovery

Despite sequencing advances, characterized profiles of the human gut microbiome remain limited, hindering microbial community classification. Using dense deep clustering, we standardized 509,610 metagenome-assembled genomes (MAGs) to create comprehensive microbiome fingerprints. Our resulting interactive platform comes with AutoML-driven bioindicator detection, which can scan functional potential patterns across countries and disease conditions.We selected 14,082 metagenomic runs (>20MM depth) from HumanMetagenomeDB (https://web.app.ufz.de/hmgdb/) and recovered 302,781 MAGs using MuDoGeR. Following this, we included and harmonized 154,736 MAGs from Pasolli et al. (Cell, 2019) and 60,675 from Nayfach et al. (Nature, 2019) to create a unified, standardized dataset. After dereplication, we identified 6,794 species. All MAGs underwent gene annotation using the ISfinder, NCBI-RefSeq, UniProt, and HMM databases available via Prokka. Next, we created a presence/absence gene profile for each MAG in adult gut samples (>18 years), yielding 426,648 profiles with 40,424 non-redundant genes. Next, we implemented an autoencoder with dense layers and a rectified linear unit (ReLU) activation function, followed by DenMune clustering to capture metagenomic fingerprints. We analyzed MAG distribution across taxonomy, geography, and host medical conditions. Finally, we developed an interactive platform with AutoML-driven bioindicator detection to identify potential key microbiome elements from the embedded space using the HumanMetagenomeDB curated metadata.The embedded space revealed distinct microbiome profiles, showing significant differences between control and colorectal cancerous samples and separate libraries by country (PERMANOVA < 0.05). Additionally, the MAGs clusters based on functional potential identified taxonomical groups diverging from their majority cluster, which could signal relevant functional shifts in specific strains. Our AutoML bioindicator detection system uncovered geographical markers, with Lachnospira eligens, for instance, emerging as a promising bioindicator for differentiating Chinese and USA gut microbiomes. This study provided a standardized dataset, downloadable genome collection, and interactive webapp, expanding previously published resources for future microbiome research.

Prof

Can perennial wheat influence the root-rhizosphere axis to enhance rhizomicrobiome diversity?

The plant-associated microbiome plays a crucial role in enhancing agricultural productivity and ecosystem health. Thinopyrum intermedium, a perennial wheatgrass, offers potential ecosystem services but information about its microbiome. In the frame of the EU co-funded Biodiversa project NAPERDIV, we investigated the rhizomicrobiome of T. intermedium to assess biodiversity benefits compared to annual winter wheat. Using a metagenomic approach, rhizosphere soil samples were collected from T. intermedium and annual wheat fields across Sweden, Belgium, and France, spanning a North-South agro-climatic gradient over two years (2021–2022). Bacterial 16S rRNA genes were amplified, and bioinformatics analyses were conducted. We integrated our data with an agroecological database based on four indicators (rhizosphere, grassland, organic matter, no-tillage) to understand the generalizability of our findings. Also, we tested the potential of T. intermedium to ensure year-on-year stability of the rhizomicrobiome using Bray Curtis dissimilarity. Results indicated no significant differences in alpha diversity between the two crops, although T. intermedium hosted more amplicon sequence variants (ASVs). Beta diversity was more influenced by country, sampling depth, and sampling year than by crop type. Comparison with root endophytes showed that in both plants, the rhizomicrobiome was more diverse, affirming existing understanding that the endophytes are a subset of the rhizomicrobiome. Comaprison with the agroecological database revealed that the rhizomicrobiome of T. intermedium hosted more taxa associated with grasslands, organic matter, rhizosphere, and no-till practices. We confirmed that the rhizomicrobiome associated with T. intermedium was significantly stable compared to annual wheat based on year-on-year assessment.Overall, we found considerable similarities in the rhizomicrobiome of T. intermedium and annual wheat, suggesting minor influence of perenniality on the rhizomicrobiome. This study is the first to analyze the rhizomicrobiome of T. intermedium in a European context, providing additional insights into understanding the influence of perennialization on rhizomicrobiome.

SaxA-mediated degradation of ITC plant toxin functions as a public good in a bacterial community

Plant leaves host diverse microbial communities of beneficial commensals and opportunistic pathogens, whose balance is crucial for plant health. Brassicaceae plants like Arabidopsis thaliana defend against pathogens by producing glucosinolates (GLS), which are enzymatically converted into antimicrobial isothiocyanates (ITCs) upon tissue damage by bacteria. ITCs inhibit bacterial growth and are a key element of the plant defense. However, pathogenic Pseudomonas spp. can detoxify ITCs via the hydrolase SaxA, while commensals are typically unable to detoxify ITCs. Understanding the effects of ITC degradation dynamics on the leaf microbiome is essential for advancing knowledge of disease resistance in ecologically relevant plants.In this study, we test whether Pseudomonas viridiflava 3D9 (Ps 3D9)"s ability to degrade 4-methylsulfinylbutyl (4MSOB -ITC) can shield the entire bacterial leaf community from plant defenses, even when other commensals cannot. We explored this by constructing an artificial community of five commensals which were isolated along with Ps 3D9 from healthy wild A. thaliana leaves. We either added the wildtype Ps 3D9 or Ps 3D9ΔsaxA which does not degrade ITCs.We first examined the effects of 4MSOB-ITC on the growth rates of axenic cultures of Pseudomonas 3D9, its ΔsaxA mutant, and commensals. To assess the impact of detoxification, we further developed a mathematical model based on extended Lotka-Volterra equations, incorporating ITC toxicity and the ability of Pseudomonas to degrade it. We then extended the model to include interactions between ITC-degrading Pseudomonas and non-degrading commensals, predicting community composition at varying degrader concentrations. Our results identify the threshold where the degrader provides communal protection from ITC toxicity. Model predictions align well with experimental data, confirming the protective role of the degrader strain.Studying the GLS defense system in A. thaliana enhances our understanding of plant-microbe interactions and offers valuable insights for modeling microbial communities.

FG Functional genomics / Microbiome
Bioinformatics meets microbiomes

Appointment

Chair

Programme

FG Functional genomics / MicrobiomeBioinformatics meets microbiomes

Appointment

Chair

Programme

FG Functional genomics / Microbiome
Bioinformatics meets microbiomes