Project description:MJ2.1 Metabolomics analysis of P70 and P91 stool samples - Data was acquired using a Bruker Daltonics maXis Impact and C18 RP-UHPLC. Positive polarity acquisition of LC-MS/MS.
Project description:Human and rat stool sample Data was acquired using a Bruker Daltonics maXis Impact and C18 RP-UHPLC. Positive polarity acquisition of LC-MS/MS.
Project description:IntroductionLow microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirate samples from premature infants, focusing on host DNA depletion and microbiome and resistome characterization.MethodsThree depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples.ResultsThe only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Host DNA content in non-depleted aliquots from pooled patient samples was 99%. Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). Other depletion protocols either retrieved too low total DNA yields, preventing further analysis, or failed to reduce host DNA content. By using Mol_MasterPure protocol on aliquots from pooled patient samples, we increased the number of bacterial reads by 7.6 to 1,725.8-fold compared to non-depleted reference samples. PCR results were indicative of achieved microbial enrichment. Individual patient samples processed with Mol_MasterPure protocol varied greatly in total DNA yield, host DNA content (from 40% to 98%), species and antibiotic resistance gene richness.DiscussionDespite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.
Project description:The presence of pharmaceutically active compounds (PhACs) in aquatic biota has been received much less attention than their presence in surface or waste water, and it was not until the mid-2000s, this gap started to be addressed. Here, we present SQUEEZe (Solid-liQuid Ultrasound Extraction with QuE Z-Sep/C18 as dispersive clean-up): a fast method for analysis of the trace 47 PhACs in fish muscle. Compared to our previously reported method [1], it offers alternatives with improvements in recoveries, number of analytes, sample volume and solvent used. The key aspects of this method are:• The ultrasound extraction was performed with acetonitrile/isopropanol 0.1% V/V formic acid. A clean-up step using QuE Z-Sep/C18 sorbents was employed to reduce lipid content of the extracts and further matrix effects in the detection of the analytes.• A HPLC separation with a Kinetex EVO C18 packed column in 11 min was optimized. MS and MS/MS data were collected using SWATH acquisition on the SCIEX X500R QTOF in (+)-ESI mode.• The method validated at 3 different concentrations levels: 5, 25 and 50 ng/g fish. It presented good intraday/interday reproducibility and absolute recoveries ? 60% for majority of analytes in composite homogenate muscle matrix of Squalius cephalus.• 10 out 47 compounds were detected in fish samples. Graphical abstract Image, graphical abstract
Project description:We developed a procedure for extracting maximal amounts of high-quality RNA from low-biomass producing (autotrophic) bacteria for experiments where sample volume is limited. Large amounts of high-quality RNA for downstream analyses cannot be obtained using larger quantities of culture volume. The performance of standard commercial silica-column based kit protocols and these procedures amended by ultrasonication or enzymatic lysis were assessed. The ammonium-oxidizing Nitrosomonas europaea and nitrite-oxidizing Nitrobacter winogradskyi were used as model organisms for optimization of the RNA isolation protocol. Enzymatic lysis through lysozyme digestion generated high-quality, high-yield RNA samples. Subsequent RNA-seq analysis resulted in qualitative data for both strains. The RNA extraction procedure is suitable for experiments with volume and/or biomass limitations, e.g., as encountered during space flight experiments. Furthermore, it will also result in higher RNA yields for whole transcriptome experiments where sample volume and/or biomass was increased to compensate the low-biomass characteristic of autotrophs.
Project description:MJ2.1 Metabolomics analysis of P70 and P91 stool samples - Data was acquired using a Bruker Daltonics maXis Impact and C18 RP-UHPLC. Negative polarity acquisition of LC-MS/MS.
Project description:Sulfatides (STs) are a group of glycosphingolipids that are highly expressed in brain. Due to their importance for normal brain function and their potential involvement in neurological diseases, development of accurate and sensitive methods for their determination is needed. Here we describe a high-throughput oriented and quantitative method for the determination of STs in cerebrospinal fluid (CSF). The STs were extracted using a fully automated liquid/liquid extraction method and quantified using ultra-performance liquid chromatography coupled to tandem mass spectrometry. With the high sensitivity of the developed method, quantification of 20 ST species from only 100 ?l of CSF was performed. Validation of the method showed that the STs were extracted with high recovery (90%) and could be determined with low inter- and intra-day variation. Our method was applied to a patient cohort of subjects with an Alzheimer's disease biomarker profile. Although the total ST levels were unaltered compared with an age-matched control group, we show that the ratio of hydroxylated/nonhydroxylated STs was increased in the patient cohort. In conclusion, we believe that the fast, sensitive, and accurate method described in this study is a powerful new tool for the determination of STs in clinical as well as preclinical settings.