Biology subjects

Flörl, L.

Publications and source records attributed to Flörl, L..

4 recordsLinked to original sources

bioRxiv2026

Ecological inference and contaminant detection from fungal microbiome data with q2-fungal-traits

Fungi are key members of microbial communities, yet microbiome surveys often lack trait-based information required for ecologically meaningful interpretation of mycobiome data. To demonstrate the value of fungal trait-based phenotyping in microbiome research, we re-analyzed N=3,221 samples across four case studies spanning human, agricultural, and environmental systems. In human cancer and vineyard datasets, trait-based analysis detected fungi producing macroscopic fruiting bodies, likely introduced via airborne spore dispersal, indicating widespread contributions of transient or contaminant fungi that can confound interpretation of sequencing data from tumor biopsies and grape berries. In sourdough fermentations, filamentous fungi were highly abundant alongside traditionally-recognized yeast and occupied distinct ecological niches. In forest soils, increasing habitat disturbance was associated with increased prevalence and abundance of plant pathogens, and a marked decline in ectomycorrhizal and lichenized fungi. These changes were accompanied by a shift toward large-spored taxa in urban soils, consistent with enhanced stress tolerance. To facilitate broader adoption of fungal phenotyping in microbiome studies, we introduce q2-fungal-traits, a QIIME2 plugin for automated integration of fungal taxonomy derived from marker-gene or shotgun metagenome sequencing surveys with ecological and functional trait data. The plugin assigns lifestyle-related traits and spore size estimates through hierarchical taxonomic matching and integrates directly into standard microbiome workflows. Our case studies demonstrate that integrating trait-based ecology with mycobiota datasets can generate novel findings and testable hypotheses, enabling inference of the functional (ir)relevance of community constituents. Our work contributes to bridging the gap between descriptive community profiling and functional ecology in microbiome research.

microbiology↗

bioRxiv2025

A tale of two vineyards: parsing site-specific differences in bacterial and fungal communities of wine grapes from proximal vineyards, and their changes during processing in a single winery

Wine is a microbial product, naturally transformed through fermentation by a consortium of fungi and bacteria that originate from the vineyard and the cellar, in addition to any microorganisms that are intentionally inoculated. Previous work has shown that grapevine-associated microbiota follow distinct biogeographic patterns, associated with climate and soil properties, and that even neighboring vineyards can harbor distinct microbial communities, but it is unclear whether these differences persist when controlling for variations in farming practices, cultivar, and climate, and whether site-specific microbial profiles change during processing in the winery. Here we investigated the bacterial and fungal microbiota of fruit pre- and post-harvest from two nearby vineyards planted to a single variety, geographically close to one another, and farmed the same way, and then processed in a single winery. These communities subtly changed during processing yet retained distinct site-specific signatures, indicating a partial contribution of the winery environment to the microbiota of grape must and juice pre-fermentation. We also profiled the microbiota of key microbial sources in the winery environment, including fruit flies and processing equipment, demonstrating that the microbiota at these sites reflect contact with plant material, harbor communities distinct from fruit, and appear to partially contribute to the fermentation assemblage, especially via the contribution of fermentative yeasts that are rare or missing in the vineyard environment. These results bolster previous reports of site-specific microbial signatures in winegrowing and make a first estimation of the changes to the grape-associated microbiome during early processing. ImportanceNative wine fermentations are driven by microbes carried over from the vineyard or introduced in the winery. In this study, we tracked the microbiome dynamics of wine fermentations from two Chardonnay vineyards planted in close proximity to examine the relative contribution of vineyard- and winery-resident microbiota on microbial succession during wine fermentation. By tracking microbial changes from vineyard to winery, we show that the winery environment, including processing equipment and fruit flies, contributes to the fermentation microbiome but does not override vineyard-specific microbial differences. These findings support the concept of microbial terroir and highlight the importance of vineyard microbiomes in shaping wine fermentation. This work advances our understanding of how microbial diversity influences wine production and provides insight into the ecological dynamics of fermentation. By identifying key microbial sources and their contributions, this study lays the groundwork for future microbiome research in viticulture and wine making.

microbiology↗

bioRxiv2024

HighALPS: Ultra-High-Throughput Marker-Gene Amplicon Library Preparation and Sequencing on the Illumina NextSeq and NovaSeq Platforms

Microbiome research using amplicon sequencing of microbial marker genes has surged over the past decade, propelled by protocols for highly multiplexed sequencing with barcoded primer constructs. Newer Illumina platforms like the NovaSeq and NextSeq series significantly outperform older sequencers in terms of reads, output, and runtime. However these platforms are more prone to index-hopping, which limits the application of protocols designed for older platforms such as the Earth Microbiome Project (EMP) protocols, hence there is a need to adapt these established protocols. Here, we present an ultra-High-throughput Amplicon Library Preparation and Sequencing protocol (HighALPS) incorporating the capabilities of these newer sequencing platforms, designed for both 16S rRNA gene and fungal internal transcribed spacer (ITS) domain sequencing. Our results demonstrate good run performance across different sequencing platforms and flow cells, with successful sequencing of mock communities, validating the protocols effectiveness. The new HighALPS library preparation method offers a robust, cost effective, and ultra-high-throughput solution for microbiome research, compatible with the latest sequencing technologies. This protocol allows multiplexing thousands of samples in a single run at a read depth of tens of millions of sequences per sample.

microbiology↗

bioRxiv2022

Reproducible acquisition, management, and meta-analysis of nucleotide sequence (meta)data using q2-fondue

The volume of public nucleotide sequence data has blossomed over the past two decades, enabling novel discoveries via re-analysis, meta-analyses, and comparative studies for uncovering general biological trends. However, reproducible re-use and management of sequence datasets remains a challenge. We created the software plugin q2-fondue to enable user-friendly acquisition, re-use, and management of public nucleotide sequence (meta)data while adhering to open data principles. The software allows fully provenance-tracked programmatic access to and management of data from the Sequence Read Archive (SRA). Sequence data and accompanying metadata retrieved with q2-fondue follow a validated format, which is interoperable with the QIIME 2 ecosystem and its multiple user interfaces. To highlight the manifold capabilities of q2-fondue, we present several demonstration analyses using amplicon, whole genome, and shotgun metagenome datasets. These use cases demonstrate how q2-fondue increases analysis reproducibility and transparency from data download to final visualizations by including source details in the integrated provenance graph. We believe q2-fondue will lower existing barriers to comparative analyses of nucleotide sequence data, enabling more transparent, open, and reproducible conduct of meta-analyses. q2-fondue is a Python 3 package released under the BSD 3-clause license at https://github.com/bokulich-lab/q2-fondue.

bioinformatics↗