Biology subjects

Folz, J.

Publications and source records attributed to Folz, J..

6 recordsLinked to original sources

bioRxiv2026

Chemical probes reveal individualized gut microbiome biotransformation capacity and the impacts of ex vivo fermentation conditions

The gut microbiome transforms endogenous and exogenous chemicals, contributing to bioactivation or detoxification via the formation of metabolites with altered bioactivity. Most high content microbiome assays infer function from genetic composition rather than direct assessment of biotransformation activity, and it remains difficult to predict functional consequences of environmental factors and experimental variation. Therefore, we developed an anaerobic fecal fermentation workflow that couples targeted LC-MS/MS quantification of dynamic profiles of 20 chemical probes with untargeted metabolomics to profile human microbiome biotransformation capacity and used it to assess the impact of experimental conditions on biotransformation profiles. Across five donors and 240 fermentations, inoculum density and growth medium composition strongly influenced probe transformation rates, whereas the biotransformation capacities of fecal slurries frozen at -80{degrees}C did not differ from fresh fecal samples. Individual donors could be uniquely stratified on the basis of biotransformation profile data in a way that was not recapitulated by 16S rRNA taxonomic structure or predicted functional pathways. Finally, expected biotransformation products and metabolic trends could be confirmed with untargeted metabolomics characterization. This scalable platform directly profiles gut microbial biotransformation activity, supporting wider applications of standardized microbiome functional phenotyping in humans and quantitative models of microbiome-competent biokinetics assessment in pharmacology and toxicology.

microbiology↗

bioRxiv2025

Chemical activity profiling reveals how exposure to drugs or dietary compounds alters gut microbial biotransformation capacity

The gut microbiome catalyzes biotransformation reactions that influence intestinal absorption as a basis of microbiome-host interactions. A better understanding of microbiota biotransformation capacity, and its alteration in dysregulated states, would enable the prediction of individual responses to drugs and toxins and improve safety assessment. Here, we profiled chemical activities in rat gut microbiota ex vivo, and quantified biotransformation capacity changes induced by oral exposure to eight drugs and dietary compounds: tobramycin, colistin, acesulfame potassium, saccharin, bovine serum albumin (BSA), meropenem, doripenem, and daidzein. We implemented an approach involving inoculation with metabolic probes during microbiota fermentations and measured their degradation. In most exposure groups, we observed no alteration of microbiota biotransformation capacity, however, we detected significant alterations in biotransformation rates after exposure to meropenem, doripenem and tobramycin. Interestingly, common patterns of biotransformation capacity were observed in the gut microbiomes from rats exposed to carbapenems and partially shared in microbiomes exposed to tobramycin. These results aligned well with prior metagenomic and metabolomic findings. Further, correlations between microbial taxa and reaction rates were assessed to establish a link between specific bacteria and probe degradation. This functionally relevant strategy revealed alterations of microbiota biotransformation capacity, as induced by in vivo exposures.

microbiology↗

bioRxiv2024

Multi-state kinetics of the syringe-like injection mechanism of Tc toxins

Tc toxins are virulence factors of many insects and human pathogenic bacteria. They attach as soluble prepores to receptors on host cells and following acidification in the late endosome, perforate the cell membrane like a syringe to translocate toxic enzymes into the host cell through their pore-forming channel. Although this complex transformation has been structurally well studied, the functional aspects of this large-scale rearrangement, such as the reaction pathway with possible intermediate states and the resulting temporal evolution have remained elusive. Here, we used an integrated biophysical approach to monitor the prepore-to-pore transition and found that it takes [~]28 h when induced by high pH in the absence of other factors. In the presence of liposomes, an increasingly high pH or receptors, such as heparin or Vsg, the probability to transform prepores to pores increases by a factor of up to 4. This effect can also be mimicked by biotinylation or site-directed mutagenesis of the shell, demonstrating that shell destabilization is a crucial step in prepore-to-pore transition. We show that shell opening is a heterogeneous process with transition times ranging from 60 ms to 1.6 s and resolve three sequential intermediate states: an initial transient intermediate during shell destabilization, a first stable intermediate where the receptor-binding domains on the shell rearrange and a second stable intermediate with an open shell. In contrast, the ejection of the pore-forming channel from the open shell is highly cooperative with a transition time of < 60 ms. This detailed knowledge of the Tc toxin mechanism of action, even in the absence of receptors, is important for the future application of Tc toxins as biomedical devices or biopesticides.

biochemistry↗

bioRxiv2022

Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins

Single-molecule FRET (smFRET) has become an established tool to study biomolecular structure and dynamics in vitro and in live cells. We performed a worldwide blind study involving 19 labs to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems that undergo distinct conformational changes, we obtained an uncertainty of the FRET efficiency of less than {+/-} 0.06, corresponding to an interdye distance precision of [≤] 0.2 nm and accuracy of [≤] 0.5 nm. We further discuss the limits for detecting distance fluctuations with sensitivity down to [lsim] 10% of the Forster distance and provide guidelines on how to detect potential dye perturbations. The ability of smFRET experiments to simultaneously measure distances and avoid averaging of conformational dynamics slower than the fluorescence lifetime is unique for dynamic structural biology.

biophysics↗

bioRxiv2022

Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device

The spatiotemporal structure of the human microbiome and metabolome reflects and determines regional intestinal physiology and may have implications for disease. Yet, we know little about the distribution of microbes and their products in the gut because of reliance on stool samples and limited access only to some regions of the gut using endoscopy in fasting or sedated individuals. To address these deficiencies, we developed and evaluated a safe, ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. The collection of 240 intestinal samples from 15 healthy individuals using the device revealed significant differences between microbes and metabolites present in the intestines versus stool. Certain microbial taxa were differentially enriched, and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Overall, we identified heterogeneous intestinal profiles of bacterial taxa and metabolites indicating that non-invasive multi-regional sampling of the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.

microbiology↗

bioRxiv2021

Metabolite Damage and Damage-Control in a Minimal Genome

Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes with known metabolite damage repair or preemption functions were identified and experimentally validated, including 5-formyltetrahydrofolate cyclo-ligase, CoA disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage-control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal.

microbiology↗