Biology subjects

Schmitt, H.

Publications and source records attributed to Schmitt, H..

5 recordsLinked to original sources

bioRxiv2026

Calibrating for absolute microbiome abundances without spike-ins

Metagenomics is a widely used approach in microbiome research. However, a major limitation of metagenomic datasets is their compositional nature, which prevents direct quantification of absolute abundances and complicates cross-sample comparisons. Existing strategies for absolute quantification typically require additional experiments or spike-in controls. Here, we introduce the MetaGenome Calibrator (MGCalibrator), a new tool that enables spike-in free, absolute abundance estimation based on routine DNA concentration measurements. We validated the accuracy of absolute abundances obtained with MGCalibrator against qPCR for 5 targets. Our results show a strong correlation with qPCR data, indicating that MGCalibrator enables qPCR-like trend analyses. For Bacteroides dorei, the estimated abundances were highly similar between the two methods (r2 = 0.98, y = 1.00x). For other targets like crAssphage or the bacterial 16S rRNA gene, qPCR values were underrepresented by a factor of 7 or overrepresented by a factor of 4. Benchmarking with synthetic microbiome data demonstrated that our method accurately determines copy numbers in sequencing datasets, and application to whole-cell mock community samples produced expected values based on known extraction biases. In an extraction-bias-free experiment, MGCalibrator accurately quantified genome copy numbers within a twofold range in 98% of cases and determined 16S rRNA gene copies within 1.6-fold or less. Finally, we applied MGCalibrator to track temporal trends in antibiotic resistance genes (ARGs) in wastewater treatment plants in two Dutch provincial capitals. We observed an overall increase in ARGs--such as sul2 in Utrecht and qnrS5 in Houtrust--likely driven by rising bacterial loads. Our findings demonstrate that MGCalibrator provides robust calibration of metagenomic data, paving the way for metagenomics to play a central role in future surveillance by enabling trend analysis across thousands of genetic targets, similar to the capabilities of qPCR for individual genes. The source code and documentation for MGCalibrator are available at github.com/NimroddeWit/MGCalibrator.

microbiology↗

bioRxiv2024

Development of a highly-sensitive method to detect the carriage of carbapenem-resistant Pseudomonas aeruginosa in humans

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) causes severe and potentially life-threatening infections in hospitalized patients with mortality rates of more than 40%. To detect CRPA carriage in humans for surveillance purposes or to prevent spread and outbreaks in hospitals, a highly-sensitive culture method for CRPA carriage in humans is needed. We aimed to develop such a highly-sensitive method, that would be feasible in laboratories with limited resources. In this study, seven well-defined CRPA strains belonging to high-risk clones were used, including one CRPA without a carbapenemase gene and six carbapenem-resistant isolates with carbapenemase genes. We applied a stepwise approach wherein we included four enrichment broths and eight Pseudomonas aeruginosa-selective culture media. Spiking experiments were performed to further evaluate the combination of the most sensitive enrichment broths and selective agar plates in human samples. The two most sensitive enrichments broths were TSB-vancomycin and TSB-vancomycin with 2 mg/L imipenem and the most sensitive selective agar plates were Pseudomonas isolation agar Becton Dickinson, Pseudomonas isolation agar Sigma-Aldrich, and M-PA-C (Becton Dickinson). After the spiking experiment, the best method for detecting CRPA based on the sensitivity and the selectivity was the combination of TSB-vancomycin with 2 mg/L imipenem as an enrichment broth for overnight incubation, followed by subculturing the broth on M-PA-C agar plate. We have thus developed a highly-sensitive selective method to detect CRPA carriage in humans, which can also be applied in limited-resource laboratories. This may contribute to an overall effort to control CRPA.

microbiology↗

bioRxiv2020

Cycling in degradation of organic polymers and uptake of nutrients by a litter-degrading fungus

SummaryWood and litter degrading fungi are the main decomposers of lignocellulose and thus play a key role in carbon cycling in nature. Here we provide evidence for a novel lignocellulose degradation strategy employed by the litter degrading fungus Agaricus bisporus (known as the white button mushroom). Fusion of hyphae allows this fungus to synchronize the activity of its mycelium over large distances (50 cm). The synchronized activity has an 13-hour interval that increases to 20 h before becoming irregular and is associated with a 3.5-fold increase in respiration while compost temperature increases up to 2 °C. Transcriptomic analysis of this burst-like phenomenon supports a cyclic degradation of lignin, deconstruction of (hemi-) cellulose and microbial cell wall polymers, and uptake of degradation products during vegetative growth of A. bisporus. Cycling in expression of the ligninolytic system, enzymes involved in saccharification, and nutrient uptake is proposed to provide an efficient way for degradation of substrates such as litter.Competing Interest StatementThe authors have declared no competing interest.View Full Text

microbiology↗

bioRxiv2017

The microbiome and resistome of hospital sewage during passage through the community sewer system

Effluents from wastewater treatment plants (WWTPs) have been proposed to act as point sources of antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) in the environment. Hospital sewage may contribute to the spread of ARB and ARGs as it contains the feces and urine of hospitalized patients, who are more frequently colonized with multi-drug resistant bacteria than the general population. However, whether hospital sewage noticeably contributes to the quantity and diversity of ARGs in the general sewerage system has not yet been determined.\n\nHere, we employed culture-independent techniques, namely 16S rRNA and nanolitre-scale quantitative PCRs, to describe the role of hospital effluent as a point source of ARGs in the sewer system, through comparing microbiota composition and levels of ARGs in hospital sewage with WWTP influent, WWTP effluent and the surface water in which the effluent is released.\n\nCompared to other sample sites, hospital sewage was richest in human-associated bacteria and contained the highest relative levels of ARGs. Yet, the abundance of ARGs was comparable in WWTPs with and without hospital wastewater, suggesting that hospitals do not contribute to the spread of ARGs in countries with a functioning sewerage system.

microbiology↗

bioRxiv2017

Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries

EFFORT groupHaitske Graveland, Alieda van Essen, Bruno Gonzalez-Zorn, Gabriel Moyano, Pascal Sanders, Claire Chauvin, Julie David, Antonio Battisti, Andrea Caprioli, Jeroen Dewulf, Thomas Blaha, Katharina Wadepohl, Maximiliane Brandt, Dariusz Wasyl, Magdalena Skarzynska, Magdalena Zajac, Hristo Daskalov, Helmut W Saatkamp, Katharina D.C. Stark.\n\nAbstractAntimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. Use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (www.effort-against-amr.eu), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 gigabases of DNA sequence, using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and countries. We found that the total acquired AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. Novel, functionally-determined AMR genes were, however, not associated with total drug use.

microbiology↗