Biology subjects

Aichinger, G.

Publications and source records attributed to Aichinger, G..

7 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↗

bioRxiv2026

Bidirectional interactions between gut microbiota and fluorochemical biotransformation and bioactivity

Fluorinated chemicals are increasingly prevalent in pharmaceuticals and agrochemicals, yet their influence on the human gut microbiome and the potential for microbial biotransformation to alter therapeutic and toxicological profiles remain poorly understood. Here, we investigated the bidirectional relationship between 15 structurally diverse fluorinated chemicals and the gut microbiota by using an ex vivo high-throughput fermentation system. Screening revealed that flutamide, fluazinam, and pretomanid were consistently biotransformed across the donor microbiomes, while other compounds showed substantial inter-individual variability in degradation. Furthermore, exposure to fluorinated chemicals induced compound-specific shifts in microbial diversity and community composition, demonstrating their capacity to alter gut microbial ecology. Using a computational workflow combining in silico biotransformation predictions with untargeted LC-MS/MS analysis, we identified nitroreduction as the primary gut microbial transformation across all three compounds. Single-strain experiments confirmed that the nitroreduction of flutamide to flu-6, previously attributed only to hepatic metabolism, is a widespread capacity among gut bacterial strains. Finally, in vitro cytotoxicity assays and in silico modelling further revealed flu-6 to be a less hepatotoxic derivative than the parent compound, suggesting a potential detoxifying role for the gut microbiota. Together, these findings establish an integrated ex vivo, in vitro, and in silico approach for assessing the bidirectional interactions between fluorinated chemicals and the gut microbiome.

pharmacology and toxicology↗

bioRxiv2026

Human internal exposures to alternariol and its monomethyl ether are predicted below thresholds of in vitro toxicity by physiologically based kinetic modeling

The foodborne mycotoxins alternariol (AOH) and alternariol monomethyl ether (AME) have been associated with several adverse effects, including cytotoxicity, genotoxicity, endocrine disruption, and immunomodulation. As these endpoints are typically observed in vitro at micromolar concentrations, the question arises whether such levels are attainable in exposed humans. To address this data gap in chemical risk assessment, a physiologically based kinetic (PBK) model was developed to predict internal exposure doses to AOH and AME in humans. As input parameters, kinetic constants for hepatic glucuronidation were obtained in vitro by incubating Sprague Dawley rat and human liver S9 fractions with 0.5-50 {micro}M AOH and 0.5-20 {micro}M AME, demonstrating rapid biotransformation in both species. Intestinal absorption of AME and physicochemical parameters were estimated using quantitative structure-activity relationship (QSAR) models. Sensitivity analysis identified parameters describing hepatic glucuronidation and gastrointestinal uptake as among the most influential, confirming the importance of their reliable estimation. The PBK model was evaluated against available rodent toxicokinetic data and subsequently extrapolated to humans. Ultimately, the currently available exposure estimates published by EFSA in 2016 were applied to predict target tissue concentrations, which were compared to points of departure (PoDs) for relevant toxicological endpoints. Even in the most susceptible group of male toddlers, predicted internal concentrations (10{square}{square} {micro}M range) were approximately four orders of magnitude below the respective PoDs. Consequently, under the applied exposure assumptions and considering the compounds as isolated chemicals, AOH and AME are not expected to reach systemic or tissue concentrations associated with the investigated effects.

pharmacology and toxicology↗

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↗

bioRxiv2025

Sulfoquinovose is differently degraded by the mouse and human gut microbiota and not metabolized by the host

BackgroundSulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for few human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism. Results13CO2 breath tests with germ-free C57BL/6 mice gavaged with 13C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the mouse gut. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain. ConclusionsOur findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.

microbiology↗

bioRxiv2024

Human internal exposures of bisphenol A and six data-poor analogues predicted by physiologically based kinetic models with multimodal parameterization

BackgroundBisphenols (BP) AF, B, E, F, M, and S have been introduced as substitutes for bisphenol A (BPA) and are increasingly used in consumer products. Despite widespread human exposure and potential adverse health outcomes related to BPF, BPB, BPS, and BPAF, their physiological disposition in humans is poorly characterized, which hinders assessment of associated risks. ObjectivesOur goal was to simulate the kinetic behavior of prevalent bisphenol analogs in organs of toxicological interest. To enable predictions of physiologically relevant internal concentrations of a family of structurally similar compounds with limited available human data, we aim to establish a reproducible framework using multimodal parameterization methods. MethodsHerein we developed physiologically based kinetic (PBK) models, following oral exposure. Their parametrization was primarily based on structural, physiological and experimental values, as well as quantitative structure-activity relationship (QSAR) predictions. Outputs were evaluated against available biomonitoring data for BPA and BPS. Critical parameters were identified by sensitivity analysis and iteratively re-sampled in Monte Carlo (MC) simulations to quantify uncertainties. ResultsAmong human models parametrized for males and females of different ages, we predicted that bisphenols reached the highest concentrations in 5-year-old males. Environmentally relevant exposure levels resulted in maximum concentrations in the blood and testes for BPS, and in the thyroid for BPM. After 96 hours, steady-state concentrations were not yet reached in the breasts for BPA, BPAF, BPB, BPE, BPF and BPM. ConclusionsThe data from this study suggest significant variability in internal concentrations for identical exposures to different bisphenols analogs that further depend on age, sex and organ. This diversity in toxicokinetic behavior should be considered for health risk assessment of these substitutes.

pharmacology and toxicology↗

bioRxiv2024

Predicting in vivo concentrations of dietary hop phytoestrogens by physiologically based kinetic modeling

Hop extracts containing prenylated polyphenols such as 8-prenylnaringenin (8-PN) and its precursor isoxanthohumol (iXN) are popular among women seeking natural alternatives to hormone therapy for postmenopausal symptoms. Due to structural similarities with estrogens, these compounds act as estrogen receptor agonists. Especially 8-PN, described as the most potent phytoestrogen known to date, poses a potential risk for endocrine disruption. Therefore, its use as a hormone replacement raises concerns for human health. However, a significant challenge in assessing the potential endocrine-disruptive effects of hop polyphenols is the lack of data on their toxicokinetics. Particularly, information on in vivo concentrations in target tissues is lacking. To address this gap, we developed a physiologically based kinetic (PBK) model tailored to female physiology. The model was used to predict the levels of hop polyphenols in human blood and target tissues under realistic exposure scenarios. The predictions suggest that iXN and 8-PN concentrations in target tissues reach the low nanomolar range after dietary supplementation. This study enhances our understanding of the safety profile of hop polyphenols and highlights the need for further research into their use as an alternative to hormone therapy in menopausal women.

pharmacology and toxicology↗