Dataset Information

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities - a proof of concept under laboratory conditions.

ABSTRACT: High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using amplicon sequencing of a DNA barcode. Bulk RNA-seq (metatranscriptomics) has several advantages over DNA-based amplicon sequencing: it is less susceptible to amplification biases, it captures only living organisms, and it enables a larger set of genes to be used for taxonomic identification. Using a model mock community comprising 17 fungal isolates, we evaluated whether metatranscriptomics can accurately identify fungal species and subspecies in mixed communities. Overall, 72.9% of the RNA transcripts were classified, from which the vast majority (99.5%) were correctly identified at the species level. Of the 15 species sequenced, 13 were retrieved and identified correctly. We also detected strain-level variation within the Cryptococcus species complexes: 99.3% of transcripts assigned to Cryptococcus were classified as one of the four strains used in the mock community. Laboratory contaminants and/or misclassifications were diverse, but represented only 0.44% of the transcripts. Hence, these results show that it is possible to obtain accurate species- and strain-level fungal identification from metatranscriptome data as long as taxa identified at low abundance are discarded to avoid false-positives derived from contamination or misclassifications. This study highlights both the advantages and current challenges in the application of metatranscriptomics in clinical mycology and ecological studies.

SUBMITTER: Marcelino VR

PROVIDER: S-EPMC7184889 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities - a proof of concept under laboratory conditions.

Marcelino Vanesa R VR Irinyi Laszlo L Eden John-Sebastian JS Meyer Wieland W Holmes Edward C EC Sorrell Tania C TC

IMA fungus 20190808

High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using amplicon sequencing of a DNA barcode. Bulk RNA-seq (metatranscriptomics) has several advantages over DNA-based amplicon sequencing: it is less susceptible to amplification biases, it captures only living organisms, and it enables a larger set of genes to be us ...[more]

PMID: 32355612

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Project description:BackgroundDepression during the postnatal year is prevalent in mothers (17%) and fathers (9%), and suicide is the leading cause of maternal death in this period. Lifelong costs and consequences of untreated postnatal depression (PND) are high due to impacts on infants as well as parents. We aimed to improve access to PND treatment using digital screening. We developed a smartphone app (ClinTouch DAWN-P) that allows parents to monitor their mood daily with the Edinburgh Postnatal Depression Scale (EPDS), uploading responses in real-time to a secure server. We evaluated the app's feasibility, acceptability, validity and safety in a proof-of-concept study.MethodsPregnant women (≥ 36 weeks gestation) and partners were recruited from antenatal services and invited to complete daily EPDS assessments via the ClinTouch DAWN-P app until 6 weeks postpartum. Participants completed standard paper-based EPDS at two time points for validity comparisons. We examined app acceptability and usability at 6 weeks postpartum with qualitative interviews, examined using framework analysis, and the abridged Mobile App Rating Scale (convergent mixed methods design).ResultsMost (96%) eligible pregnant women approached were keen to try the app. Participating mothers (n = 15) and partners/fathers (n = 8) found the app easy to use, and 91% continued to use it for the full study period. Overall, 67% of daily app-based assessments were completed, with a history of depression predicting lower app usage. Participants suggested modifications to the app and its deployment to improve usability (e.g., extending the response window and including feedback and parenting advice). The validity of app-based responses was confirmed by high agreement with standard EPDS. App-based and paper-based ratings showed perfect agreement in identifying cases of likely PND. There were no serious adverse events relating to app use.ConclusionsDigital PND screening appears feasible, acceptable, valid and safe. It also benefits from being remotely delivered: we enrolled all participants remotely during the first COVID-19 lockdown. Use of digital screening could address known shortcomings of conventional health visitor-delivered screening such as limited staff time, parental unwillingness to disclose difficulties to a professional, lack of partner/father screening, and language barriers.Trial registrationThe study was prospectively registered (Clinicaltrials.gov: NCT04279093 ).

Project description:BackgroundMany workers performing manual handling tasks suffer from musculoskeletal disorders (MSD). Previous research has identified several loading aspects associated with manual handling, but it is still unknown if lifting on an unstable surface is associated with increased biomechanical loading of different body parts.AimThis proof-of-concept study aims to study what kinematic and kinetic movement parameters, such as movement time, joint angles, torque, and muscle activity are feasible and of importance when studying the effect of lifting on surfaces with varying degrees of stability in an experimental set-up.MethodsMeasurements were taken during three different surface conditions: stable, slightly unstable, and unstable. The participants were instructed to lift a box from the floor and place it on a table in front of them. The weight of the box varied from 0.5 to 15.5 kg. By using a motion capture system (VICON) with 28 reflective markers placed on the participants and one on the box, one Kistler force plate for measuring force levels and center of pressure movements (CoP), and four electromyographic transmitters (EMG), we analyzed the downward and upward phases of the lifting movement, using the Friedman's test for repeated measures.ResultsStatistically significant results with less joint movements in the lower and upper back were seen with increased instability during both the downward and upward phases. The decrease in trunk movements with increased instability resulted in a somewhat more flexed knee position during the movement, a lower torque in the lower back, and a decrease in CoP movements, but no differences in movement time or muscle activity in back and knee muscles.ConclusionLifting while standing on unstable surfaces resulted in an alteration of both kinematics and kinetics parameters; however, further studies regarding whether this is an additional risk factor for developing lower back pain are needed. Muscle activity levels were not altered due to instability and due to the complexity of the measurement, and we suggest not including EMG measures in future experiments of this type.

Dataset Information

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities - a proof of concept under laboratory conditions.

Publications

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities - a proof of concept under laboratory conditions.

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