Biology subjects

Gregor, R.

Publications and source records attributed to Gregor, R..

5 recordsLinked to original sources

bioRxiv2025

A universal surface functionalization technique to chemically enhance live microbial cells

Microbial surface functionalization is a powerful strategy for endowing microbes with novel, non-genetic functions. However, existing methods are often species-specific, limited in scope, and compromise cell viability. Here, we present a universal and modular platform for high-density, reproducible surface functionalization across diverse microbial species--including Gram-positive, Gram-negative, aerobic, and anaerobic bacteria--using multiple molecular classes such as fluorophores, enzymes, and nucleic acids. Our method preserves cell viability, and achieves 50x higher functionalization efficiency than previous methods with a standardized protocol applicable to any azide-containing molecule. Applications of the method show reproducible and tunable phenotypic outcomes at the single-cell level: fluorophore labeling yielded adjustable fluorescence, {beta}-lactamase conferred scalable antibiotic resistance, and DNA coatings modulated adhesion and aggregation. This platform provides quantitative, non-genetic control over microbial phenotypes and complements genetic engineering approaches. It enables new possibilities for microbial design in biotechnology, medicine, and environmental applications where genetic modification is impractical or undesirable.

microbiology↗

bioRxiv2023

Widespread B-vitamin auxotrophy in marine particle-associated bacteria

Microbial community assembly is governed by trophic interactions that mediate the transfer of carbon sources and biomass building blocks between species. However, central metabolism corresponds to only a small fraction of the biosynthetic potential of microbes: metabolites such as antimicrobial compounds, signaling molecules, and co-factors are underexplored forces shaping microbial communities. Here, we focus on B vitamin exchange in coastal marine bacterial communities that degrade particulate organic matter and find that natural seawater communities are vitamin limited. While almost a third of bacterial isolates from these communities are B vitamin auxotrophs, the pioneering degraders that first arrive on particles are vitamin producers that likely support auxotrophs through cross-feeding. However, combining experiments and a resource-explicit model, we show that auxotroph growth is often not restored by coculture with vitamin producers, but rather requires lysis and subsequent vitamin recycling. Our results highlight the importance of vitamin auxotrophies and lysis-mediated cross-feeding as important factors controlling microbial community assembly and succession on marine particles.

microbiology↗

bioRxiv2022

Annotation-free discovery of functional groups in microbial communities

Recent studies have shown that microbial communities are composed of groups of functionally cohesive taxa, whose abundance is more stable and better associated with metabolic fluxes than that of any individual taxon. However, identifying these functional groups in a manner that is independent from error-prone functional gene annotations remains a major open problem. Here, we develop a novel approach that identifies functional groups of taxa in an unsupervised manner, solely based on the patterns of statistical variation in species abundance and environmental parameters. We demonstrate the power of this approach on three distinct data sets. On data of replicate microcosm with heterotrophic soil bacteria, our unsupervised algorithm recovered experimentally validated functional groups that divide metabolic labor and remain stable despite large variation in species composition. When leveraged against the ocean microbiome data, our approach discovered a functional group that combines aerobic and anaerobic ammonia oxidizers, whose summed abundance tracks closely with nitrate concentrations in the water column. Finally, we show that our framework can enable the detection of species groups that are likely responsible for the production or consumption of metabolites abundant in animal gut microbiomes, serving as a hypothesis generating tool for mechanistic studies. Overall, this work advances our understanding of structure-function relationships in complex microbiomes and provides a powerful approach to discover functional groups in an objective and systematic manner.

ecology↗

bioRxiv2021

GNPS Dashboard: Collaborative Analysis of Mass Spectrometry Data in the Web Browser

Access to web-based platforms has enabled scientists to perform research remotely. A critical aspect of mass spectrometry data analysis is the inspection, analysis, and visualization of the raw data to validate data quality and confirm statistical observations. We developed the GNPS Dashboard, a web-based data visualization tool, to facilitate synchronous collaborative inspection, visualization, and analysis of private and public mass spectrometry data remotely.

bioinformatics↗

bioRxiv2020

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS.

Gas chromatography-mass spectrometry (GC-MS) represents an analytical technique with significant practical societal impact. Spectral deconvolution is an essential step for interpreting GC-MS data. No public GC-MS repositories that also enable repository-scale analysis exist, in part because deconvolution requires significant user input. We therefore engineered a scalable machine learning workflow for the Global Natural Product Social Molecular Networking (GNPS) analysis platform to enable the mass spectrometry community to store, process, share, annotate, compare, and perform molecular networking of GC-MS data. The workflow performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization, using a Fast Fourier Transform-based strategy to overcome scalability limitations. We introduce a "balance score" that quantifies the reproducibility of fragmentation patterns across all samples. We demonstrate the utility of the platform with breathomics analysis applied to the early detection of oesophago-gastric cancer, and by creating the first molecular spatial map of the human volatilome.

bioinformatics↗