SARS-CoV-2 infection and gut microbiome dysbiosis in mice

Description

To investigate the causal relationship between SARS-CoV-2 infection and gut microbiome dysbiosis, researchers inoculated K18-hACE2 male mice with one of four doses (10, 100, 1000, and 104 PFU) of SARS-CoV-2 or mock treatment diluted in phosphate-buffered saline (PBS). Fecal samples were collected from mice daily for microbiome analyses from day 0 (before infection) until sacrifice on days 5–7. Upon sacrifice, investigators collected a blood sample, whole lungs, and 1 cm of proximal duodenum, terminal ileum and proximal colon from each mouse. This dataset contains 219 16S rRNA sequences obtained from the four experiments, labeled as follows:

LB1: CTRL (mock infected), LD (10 PFU of SARS-CoV-2), HD (10000 PFU of SARS-CoV-2)
LB5: 0 (mock infected), 100 (100 PFU of SARS-CoV-2), 1000 (1000 PFU of SARS-CoV-2)
LB6: 0 (mock infected), 10000 (10000 PFU of SARS-CoV-2)
LB7: 0 (mock infected), 10000 (10000 PFU of SARS-CoV-2)

Subject of Study

Subject Domain

COVID-19

Genomics

Infectious Disease

Subject Sex

Male

Keywords

Gastrointestinal Microbiome

Access

Restrictions: Free to All
Instructions: Raw sequencing data are freely available from the Sequence Read Archive (SRA) through BioProject.; Access via BioProject
16s sequencing data
Accession #: PRJNA745367

Associated Publications

Bernard-Raichon L, Venzon M, Klein J, Axelrad JE, Zhang C, Sullivan AP, Hussey GA, Casanovas-Massana A, Noval MG, Valero-Jimenez AM, Gago J, Putzel G, Pironti A, Wilder E; Yale IMPACT Research Team, Thorpe LE, Littman DR, Dittmann M, Stapleford KA, Shopsin B, Torres VJ, Ko AI, Iwasaki A, Cadwell K, Schluter J. Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia. Nat Commun. 2022 Nov 1;13(1):5926.

Data Type

Genomic

Equipment Used

Agilent TapeStation System

Illumina MiSeq System

Illumina NovaSeq 6000

Invitrogen Qiant-iT Picogreen dsDNA Assay

LightCycler 480 Instrument II

MP Biomedicals FastPrep-24TM

QIAGEN RNAse-Free DNase Set

Zeiss Axiocam 503 mono

Zeiss AxioObserver Z1

Software Used

Bowtie2 v2.4.5

DADA2 v1.16

Kraken 2

lmerTest v3.1-3

MetaPhlAn2 v3

PyMC3 v3.11

QIIME v1.9.1

scikit-learn v1.0.2

Snippy

ZEN (blue edition)

Study Type

Interventional

Grant Support: P30 CA016087/NCI NIH

R01 AI121244/NIAID NIH

R01 HL123340/NHLBI NIH

R01 DK093668/NIDDK NIH

R01 AI130945/NIAID NIH

R01 AI140754/NIAID NIH

Jan Vilcek/David Goldfarb Fellowship/NYU Langone Health

Mathers Foundation/Mathers Foundation

T32 AI100853/NIAID NIH

HHMI Faculty Scholars/Howard Hughes Medical Institute

R01 DK124336/NIDDK NIH

R01 AI143639/NIAID NIH

R21 AI139374/NIAID NIH

Crohn’s & Colitis Foundation/Crohn’s & Colitis Foundation

Kenneth Rainin Foundation/Kenneth Rainin Foundation

Judith & Stewart Colton Center for Autoimmunity/NYU Langone Health

Antimicrobial-Resistant Pathogens Program/NYU Langone Health

S10 OD021747/OD NIH

DP2 AI164318/NIAID NIH

R01 CA269617/NCI NIH

OT2 HL161847/NHLBI NIH

19-A0-00-1003686/American Heart Association

Beatrice Kleinberg Neuwirth Fund/Beatrice Kleinberg Neuwirth Fund

Yale COVID-19 Research Resource Fund/Yale University

Bristol Meyers Squibb Foundation/Bristol Meyers Squibb Foundation
Other Resources: SILVA 138
Ribosomal RNA database

MiniKraken 2
Taxonomic classification system

NCBI RefSeq
Genome assemblies
Related Datasets: Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia

NYU Data Catalog

SARS-CoV-2 infection and gut microbiome dysbiosis in mice

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