Dataset Information

Metagenomic datasets of air samples collected during episodes of severe smoke-haze in Malaysia.

ABSTRACT: Transboundary emissions of smoke-haze from land and forest fires have recurred annually during the dry period (June to October, over the past few decades) in South East Asia. Hazardous air quality has been recorded in Malaysia during these episodes. Agricultural practices such as slash-and-burn of biomass and peat fires particularly in Sumatera and Kalimantan, Indonesia, have been implicated as the major causes of the haze. Past findings have shown that a diversity of microbes can thrive in air including in smoke-haze polluted air. In this study, metagenomic data were generated to reveal the diversity of microorganisms in air during days with and without haze. Air samples were collected during non-haze (2013A01) and two haze (2013A04 and 2013A05) periods in the month of June 2013. DNA was extracted from the samples, subjected to Multiple Displacement Amplification and whole genome sequencing (Next Generation Sequencing) using the HiSeq 2000 Platform. Extensive bio-informatic analyses of the raw sequence data then followed. Raw reads from these six air samples were deposited in the NCBI SRA databases under Bioproject PRJNA662021 with accession numbers SRX9087478, SRX9087479 and SRX9087480.

SUBMITTER: James GL

PROVIDER: S-EPMC8166747 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Metagenomic datasets of air samples collected during episodes of severe smoke-haze in Malaysia.

James Grace Lymie GL Latif Mohd Talib MT Isa Mohd Noor Mat MNM Bakar Mohd Faizal Abu MFA Yusuf Nurul Yuziana Mohd NYM Broughton William W Murad Abdul Munir AM Abu Bakar Farah Diba FD

Data in brief 20210509

Transboundary emissions of smoke-haze from land and forest fires have recurred annually during the dry period (June to October, over the past few decades) in South East Asia. Hazardous air quality has been recorded in Malaysia during these episodes. Agricultural practices such as slash-and-burn of biomass and peat fires particularly in Sumatera and Kalimantan, Indonesia, have been implicated as the major causes of the haze. Past findings have shown that a diversity of microbes can thrive in air ...[more]

PMID: 34095374

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Project description:IntroductionMetagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories.MethodsMetagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed.ResultsOverall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection.ConclusionA wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.

Project description:This present work investigates several local and synoptic meteorological aspects associated with two wintertime haze episodes in Greater Bangkok using observational data, covering synoptic patterns evolution, day-to-day and diurnal variation, dynamic stability, temperature inversion, and back-trajectories. The episodes include an elevated haze event of 16 days (14-29 January 2015) for the first episode and 8 days (19-26 December 2017) for the second episode, together with some days before and after the haze event. Daily PM2.5 was found to be 50 µg m-3 or higher over most of the days during both haze events. These haze events commonly have cold surges as the background synoptic feature to initiate or trigger haze evolution. A cold surge reached the study area before the start of each haze event, causing temperature and relative humidity to drop abruptly initially but then gradually increased as the cold surge weakened or dissipated. Wind speed was relatively high when the cold surge was active. Global radiation was generally modulated by cloud cover, which turns relatively high during each haze event because cold surge induces less cloud. Daytime dynamic stability was generally unstable along the course of each haze event, except being stable at the ending of the second haze event due to a tropical depression. In each haze event, low-level temperature inversion existed, with multiple layers seen in the beginning, effectively suppressing atmospheric dilution. Large-scale subsidence inversion aloft was also persistently present. In both episodes, PM2.5 showed stronger diurnality during the time of elevated haze, as compared to the pre- and post-haze periods. During the first episode, an apparent contrast of PM2.5 diurnality was seen between the first and second parts of the haze event with relatively low afternoon PM2.5 over its first part, but relatively high afternoon PM2.5 over its second part, possibly due to the role of secondary aerosols. PM2.5/PM10 ratio was relatively lower in the first episode because of more impact of biomass burning, which was in general agreement with back-trajectories and active fire hotspots. The second haze event, with little biomass burning in the region, was likely to be caused mainly by local anthropogenic emissions. These findings suggest a need for haze-related policymaking with an integrated approach that accounts for all important emission sectors for both particulate and gaseous precursors of secondary aerosols. Given that cold surges induce an abrupt change in local meteorology, the time window to apply control measures for haze is limited, emphasizing the need for readiness in mitigation responses and early public warning.

Dataset Information

Metagenomic datasets of air samples collected during episodes of severe smoke-haze in Malaysia.

Publications

Metagenomic datasets of air samples collected during episodes of severe smoke-haze in Malaysia.

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