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 heterozygous 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. The biospecimen samples were examined for evidence of bacterial translocation and inflammatory response to infection through immunofluorescence imaging, microbiome profiling, and cell quantification. 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

Genomics

Infectious Disease

Subject Sex

Male

Keywords

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

LightCycler 480 Instrument II

MP Biomedicals FastPrep-24TM

Zeiss Axio Observer 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)

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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