•Antimicrobial pharmacokinetics is an emerging area of gut microbiome research.•Omadacyline is a tetracycline-class antibiotic with potent activity against Clostridioides difficile and a low ...propensity to cause C. difficile infection.•This study developed and validated a LC-MS/MS method to quantify omadacycline and its epimerization in stool.•A remarkable epimerization of omadacycline was observed in stool samples.
This study developed and validated a new liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to quantify omadacycline and its epimerization in stool to facilitate microbiome studies. Omadacycline was extracted in a methanol-water-ethylenediaminetetraacetic acid (ETDA) solvent containing deuterated omadacycline as internal standard, followed by dilution. In an optimal gradient elution mode, omadacycline and its C4 epimer were separated within 5 min on reversed-phase C18 column. The method showed a broad working range of 0.1–200 ng/ml with a limitation of detection (LOD) of 0.03 ng/ml, little fecal matrix effect, good intra-day and inter-day accuracy (90–101 %), precision (2–15 %), and recovery rate (99–105 %). The method was sufficiently sensitive to quantify omadacycline in human fecal samples (n = 82) collected during a 10-day therapy course and at follow-up (day 13 and day 30) that ranged from 1 to 4785 µg/g. Further analysis revealed that ∼9 % of omadacycline was epimerized in fecal matrix control while, on average, 37.4 % was epimerized in human fecal samples. This study developed and validated a novel, simple, sensitive, and accurate method utilizing LC-MS/MS to quantify omadacycline its epimerization in the human gut. This has important implications for future studies of omadacycline and other tetracycline-class antibiotics as part of gut microbiome studies.
A novel chemiluminescent immunoassay method based on gold nanoparticles was developed for the detection of microcystins (MCs). The immunoassay included three main steps: indirect competitive ...immunoreaction, oxidative dissolution of gold nanoparticles, and indirect determination for MCs with Au
3+
-catalysed luminol chemiluminesent system. The method has a wide working range (0.05-10 µg L
−1
, r
2
= 0.9914), the limit of detection was determined to be 0.024 µg L
−1
, which is much lower than the World Health Organization's proposed guidelines (1 µg L
−1
) for drinking-water. The proposed method was applied to MC analysis in natural water and fish tissue samples, and most results in the proposed method were in agreement with the conventional indirect competitive enzyme-linked immunosorbent assay method, which indicated that the new chemiluminescent immunoassay was sensitive, reliable, and suitable for MC analysis in natural water and fish tissue samples.
Clostridioide difficile is the leading cause of diarrhea disease worldwide and is a CDC-designated urgent threat level pathogen. Mammalian models are commonly utilized as gold standard to study the ...pathogenesis of C. difficile infection (CDI); however, alternatives are needed due to cost, higher throughput ability, and mammalian animal ethics. Nonmammalian models such as great wax worm, nematode, fruit fly, and zebrafish have been used as CDI models. This review provides a comprehensive summary of nonmammalian models used to study CDI. Multiple studies were identified using these models to study C. difficile infection, pathogenicity, colonization, host immunity, and therapy. Translational outcomes and strength and weakness of each nonmammalian model are discussed.
•Mammalian models are used to study the pathogenesis of C. difficile.•Alternatives experimental models are needed.•Great wax worm, nematode, fruit fly, and zebrafish are non-mammalian CDI models.•This review summarized these CDI infection models.
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•Fecal bile acid (BA) analysis is an emerging area of gut microbiome research.•Sample preparation procedures for fecal BA analysis are not standardized.•After correcting for water ...loss fecal BA analysis from original and lyophilized results were comparable.•A single aliquot or original or lyophilized sample can be used for fecal BA analysis.
Fecal bile acid (BA) analysis is an emerging area of gut microbiome research. However, sample preparation procedures for fecal BA analysis are not standardized. Current fecal BA analysis often utilizes either original or lyophilized aliquot, and fecal BA result difference between these two processing steps remains not systematically investigated. Moreover, the distribution pattern of fecal BA in the collected stool sample also remains unclear but affects interpretation of fecal BA for downstream experiments. To address these two questions regarding effect of lyophilization on fecal BA and fecal heterogeneity, fourteen separate BAs were quantified from 60 aliquots obtained from 10 clinical fecal samples using liquid chromatography-tandem mass spectrometry (LC-MS/MS). BA concentrations in the lyophilized sample were typically 2–4 folds higher than those in the original sample, but were almost identical using a water-adjusted lyophilized BA concentration. The fecal BA compositional profile and four BA ratios were similar utilizing either the original or lyophilized samples. BA concentrations were similar among different aliquots of differing starting mass except for the relatively trace-level BA. Therefore, it is suggested that fecal BA concentrations should be presented as the original sample concentration or water-adjusted lyophilization concentration to allow comparisons between studies. A single aliquot (20–100 mg) of stool can be used to reflect the concentrations in the entire sample. These results help to standardize analyses in this emerging field.
In recent years, extensive exploration has contributed to significant advancements in the geological formations of the Kuqa Depression. In particular, the Paleogene Kumugeliemu Formation exhibits the ...development of expansive bedded evaporites. The combination of red sandstone, red mudstone, and gypsum-salt layers holds immense potential as a reservoir and cap association, thereby offering promising prospects for oil and gas exploration. However, our understanding of the sedimentary system and model governing this formation remains limited, impeding progress in the field of oil and gas exploration. To address this gap, this study delved into a detailed examination of the stratigraphy, depositional system, and model of the Kumugeliemu Formation through the application of core samples, logging data, and seismic analyses. The primary objective of this study was to establish a comprehensive theoretical foundation for future oil and gas exploration efforts targeting the Kumugeliemu Formation. The findings revealed a distinct division of the Kumugeliemu Formation into two 3rd order sequences, each characterized by a lowstand systems tract, transgressive systems tract, and highstand systems tract. Moreover, all systems tracts were further subdivided into 14 parasequence sets. During the depositional period of the Kumugeliemu Formation, alluvial fan, delta, and salt lake deposition systems developed from the periphery to the central region of the Kuqa Depression. The alluvial fan mainly exhibited braided channel sedimentary microfacies, whereas the delta region indicated plain distributary channels, submerged distributary channels, and interdistributary sedimentary microfacies. The salt lake area is characterized by shore-shallow lacustrine mud, beach-bar, salt mud flat, and salt flat sedimentary microfacies. Throughout the deposition of the Kumugeliemu Formation, the climate of the Kuqa Depression oscillated between arid and humid. During arid periods, the depression experienced diminished water body extent, heightened salinity levels, and extensive distribution of salt and salt mud flats within the basin, with alluvial fans and delta deposits primarily confined to the basin margins. Conversely, during the humid period, the depression experienced an expansion in the extent of the water bodies, leading to a decrease in salinity levels. The distribution of salt flat and salt mud flat deposits within the basin diminished, whereas alluvial fan and delta deposits advanced extensively across the basin. The establishment and spatial arrangement of the sedimentary system within the Kumugeliemu Formation were governed by a complex interplay of certain factors, such as the semi-closed paleotectonic pattern, paleoclimatic conditions of both dry and wet alternation, and the salt source supply brought by the transgression of the Paleo-Tethys Ocean. The findings of this study offer not only a valuable reference framework for the prospective exploration of hydrocarbon resources within the Kumugeliemu Formation of the Kuqa Depression but also potential insights into the evolution of similar depressions in other basins.
This study examines the development trajectory and current trends of three-dimensional (3D) geological modelling. In recent years, due to the rising global energy demand and the increasing frequency ...of regional geological disasters, significant progress has been made in this field. The purpose of this study is to clarify the potential complexity of 3D geological modelling, identify persistent challenges, and propose potential avenues for improvement. The main objectives include simplifying the modelling process, improving model accuracy, integrating different data sources, and quantitatively evaluating model parameters. This study integrates global research in this field, focusing on the latest breakthroughs and applications in mineral exploration, engineering geology, geological disaster assessment, and military geosciences. For example, unmanned aerial vehicle (UAV) tilt photography technology, multisource data fusion, 3D geological modelling method based on machine learning, etc. By identifying areas for improvement and making recommendations, this work aims to provide valuable insights to guide the future development of geological modelling toward a more comprehensive and accurate “Transparent Earth”. This review underscores the global applications of 3D geological modelling, highlighting its crucial role across various sectors such as mineral exploration, the oil and gas industry, urban planning, geological hazard assessment, and geoscientific research. The review emphasizes the sector-specific importance of this technology in enhancing modelling accuracy and efficiency, optimizing resource management, driving technological innovation, and improving disaster response capabilities. These insights provide a comprehensive understanding of how 3D geological modelling can significantly impact and benefit multiple industries worldwide.
Reduction of Clostridioides difficile infection (CDI) recurrence is an essential endpoint for CDI-directed antibiotic development that is often not evaluated until Phase III trials. The purpose of ...this project was to use a functional and metagenomic approach to predict the potential anti-CDI recurrence effect of ibezapolstat, a DNA polymerase IIIC inhibitor, in clinical development for CDI. As part of the Phase I ibezapolstat clinical study, stool samples were collected from 22 healthy volunteers, who were given either ibezapolstat or vancomycin. Stool samples were evaluated for microbiome changes and bile acid concentrations. Ibezapolstat 450 mg and vancomycin, but not ibezapolstat 300 mg, showed statistically significant changes in alpha diversity over time compared to that of a placebo. Beta diversity changes confirmed that microbiota were significantly different between study groups. Vancomycin had a more wide-ranging effect on the microbiome, characterized by an increased proportion of Gammaproteobacteria. Ibezapolstat demonstrated an increased proportion of Actinobacteria, including the Bifidobacteriaceae family. Using a linear regression analysis, vancomycin was associated with significant increases in primary bile acids as well as primary:secondary bile acid ratios. An overabundance of Enterobacteriaceae was most highly correlated with primary bile acid concentrations (r = 0.63; P < 0.0001). Using Phase I healthy volunteer samples, beneficial changes suggestive of a lower risk of CDI recurrence were associated with ibezapolstat compared to vancomycin. This novel omics approach may allow for better and earlier prediction of anti-CDI recurrence effects for antibiotics in the clinical development pipeline.
Abstract
Background
This study was the first human validation of the gram-positive bacterial DNA polymerase IIIC target in patients with Clostridioides difficile infection. The primary objectives ...were to assess clinical cure rates and adverse events (AEs). Secondary objectives were to evaluate plasma/fecal pharmacokinetics, microbiologic eradication, microbiome and bile acid effects, and sustained clinical cure (SCC) with ibezapolstat.
Methods
This single-arm, open-label, phase 2a study enrolled adults with C. difficile infection at 4 US centers. Patients received ibezapolstat 450 mg orally every 12 hours for 10 days and followed for an additional 28 days to assess study objectives.
Results
Ten patients with a mean (standard deviation SD) age of 49 15 years were enrolled. Seven AEs were reported classified as mild-moderate. Plasma levels of ibezapolstat ranged from 233 to 578 ng/mL while mean (SD) fecal levels were 416 (494) µg/g stool by treatment day 3 and >1000 µg/g stool by days 8–10. A rapid increase in alpha diversity in the fecal microbiome was noted after starting ibezapolstat therapy, which was maintained after completion of therapy. A proportional decrease in Bacteroidetes phylum was observed (mean change SD, −10.0% 4.8%; P = .04) with a concomitantly increased proportion of Firmicutes phylum (+14.7% 5.4%; P = .009). Compared with baseline, total primary bile acids decreased by a mean (SD) of 40.1 (9.6) ng/mg stool during therapy (P < .001) and 40.5 (14.1) ng/mg stool after completion of therapy (P = .007). Rates of both initial clinical cure and SCC at 28 days were 100% (10 of 10 patients).
Conclusions
In this phase 2a study, 10 of 10 patients achieved SCC, demonstrated favorable pharmacokinetics, minimal AEs, and beneficial microbiome and bile acids results. These results support continued clinical development.
This single-arm, phase 2a study was the first validation of ibezapolstat in adult patients with Clostridioides difficileinfection. Ten of 10 patients achieved sustained clinical cure and demonstrated favorable pharmacokinetics, minimal adverse events, and beneficial microbiome and bile acids results.
Abstract
Background
Clostridioides difficile infection (CDI) is a common healthcare-associated infection with limited treatment options. Omadacycline, an aminomethylcycline tetracycline, has potent ...in vitro activity against C difficile and a low propensity to cause CDI in clinical trials. We aimed to assess fecal pharmacokinetics and gut microbiome effects of oral omadacycline compared to oral vancomycin in healthy adults.
Methods
This was a phase 1, nonblinded, randomized clinical trial conducted in healthy volunteers aged 18–40 years. Subjects received a 10-day course of omadacycline or vancomycin. Stool samples were collected at baseline, daily during therapy, and at follow-up visits. Omadacycline and vancomycin stool concentrations were assessed, and microbiome changes were compared.
Results
Sixteen healthy volunteers with a mean age of 26 (standard deviation SD, 5) years were enrolled; 62.5% were male, and participants’ mean body mass index was 23.5 (SD, 4.0) kg/m2. Omadacycline was well tolerated with no safety signal differences between the 2 antibiotics. A rapid initial increase in fecal concentrations of omadacycline was observed compared to vancomycin, with maximum concentrations achieved within 48 hours. A significant difference in alpha diversity was observed following therapy in both the omadacycline and vancomycin groups (P < .05). Bacterial abundance and beta diversity analysis showed differing microbiome changes in subjects who received omadacycline versus vancomycin.
Conclusions
Subjects given omadacycline had high fecal concentrations with a distinct microbiome profile compared to vancomycin.
Clinical Trials Registration
NCT06030219.
Omadacycline, an aminomethylcycline tetracycline, was demonstrated to have a distinct and protective gut microbiome profile and similarly achieve high fecal concentrations compared to vancomycin.
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