Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome
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SciScore for 10.1101/2021.02.23.21252221: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Anti-Spike SARS-CoV-2 antibody profiling in BAL: BAL samples were heat-treated at 56°C for one hour, and centrifuged at 14000g for 5 min. Anti-Spike SARS-CoV-2suggested: NoneAfter washing the beads, bound antibodies were labeled with anti IgG-DyLight488, anti IgA-PE and anti IgM-PECy7, and the fluorescence intensities were measured in Intellicyt IQue3 (Sartorius). anti IgG-DyLight488suggested: Noneanti IgA-PEsuggested: (Santa Cruz Biotechnology Cat# sc-3695, RRID:AB_648816)anti IgM-PECy7suggested: NoneThe acquired data [median fluorescence intensity (MFI)] were normalized using the MFI values of the … SciScore for 10.1101/2021.02.23.21252221: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Anti-Spike SARS-CoV-2 antibody profiling in BAL: BAL samples were heat-treated at 56°C for one hour, and centrifuged at 14000g for 5 min. Anti-Spike SARS-CoV-2suggested: NoneAfter washing the beads, bound antibodies were labeled with anti IgG-DyLight488, anti IgA-PE and anti IgM-PECy7, and the fluorescence intensities were measured in Intellicyt IQue3 (Sartorius). anti IgG-DyLight488suggested: Noneanti IgA-PEsuggested: (Santa Cruz Biotechnology Cat# sc-3695, RRID:AB_648816)anti IgM-PECy7suggested: NoneThe acquired data [median fluorescence intensity (MFI)] were normalized using the MFI values of the CR3022 antibodies to compensate for variations across plates. CR3022suggested: NoneExperimental Models: Cell Lines Sentences Resources SARS-CoV-2 preparation and neutralization assay: icSARS-CoV-2-mNG (isolate USA/WA/1/2020, obtained from the UTMB World Reference Center for Emerging Viruses and Arboviruses) was amplified once in Vero E6 cells (P1 from the original stock). Vero E6suggested: RRID:CVCL_XD71)Software and Algorithms Sentences Resources DNA was then used for whole genome shotgun (WGS) sequencing using it as input into the NexteraXT library preparation kit following the manufacturer’s protocol. WGSsuggested: NoneMicrobial community characterization using whole genome shotgun sequencing (WGS) and RNA metatranscriptome: For all metagenomic and metatranscriptomic reads, Trimmomatic v0.3682, with leading and trailing values set to 3 and minimum length set to 36, was used to remove adaptor sequences. Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)All rRNA reads were then removed from the metatranscriptomic reads using SortMeRNA v4.2.083 with default settings. SortMeRNAsuggested: (SortMeRNA, RRID:SCR_014402)Metagenomic and filtered metatranscriptomic reads were mapped to the human genome using Bowtie2 v2.3.4.184 with default settings and all mapping reads were excluded from subsequent microbiome, mycobiome, and virome metagenomic and metatranscriptomic analysis. Bowtie2suggested: (Bowtie 2, RRID:SCR_016368)Taxonomic profiles for all metagenomic and metatranscriptomic samples were generated using Kraken v2.0.785 and Bracken v2.5 [https://doi.org/10.7717/peerj-cs.104] run with default settings. Krakensuggested: (Kraken, RRID:SCR_005484)The database used for quantifying taxonomic profiles was generated using a combined database containing human, bacterial, fungal, archaeal, and viral genomes downloaded from NCBI RefSeq on January 8, 2021. RefSeqsuggested: (RefSeq, RRID:SCR_003496)Differentially abundant bacterial and viral taxa were identified for the BAL and UA samples groups individually using DESeq2 v1.28.186 with the three group clinical outcome meta-data readouts set as the sample groupings. DESeq2suggested: (DESeq, RRID:SCR_000154)For functional microbial profiling, processed sequencing reads were further depleted of human-mapping reads by removing all reads classified as human by Kraken v2.0.785 using KrakenTools v0.1-alpha (https://github.com/jenniferlu717/KrakenTools). KrakenToolssuggested: NoneAntibiotic resistance genes were quantified in all metagenome and metatranscriptome samples using Salmon v1.3.091 run with --keepDuplicates for indexing and --libtype A -- allowDovetail --meta for quantification. Salmonsuggested: (Salmon, RRID:SCR_017036)Transcriptome of BAL cells: RNA-Seq was performed on bronchial epithelial cells obtained by airway brushing, as described92–94, using the Hi-seq/Illumina platform at the NYU Langone Genomic Technology Center (data available at Sequence Read Archive: # PRJNA592149). Sequence Read Archivesuggested: (DDBJ Sequence Read Archive, RRID:SCR_001370)Pathway analysis using differentially regulated genes (FDR<0.25) was done using Ingenuity Pathway Analysis, RRID:SCR_0-at least 1 count per million in at least two samples were retained. Ingenuity Pathway Analysissuggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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