NYU Data Catalog

NYU Dataset

Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia

Part of: RAMEN Labs | RAtional Microbiome ENgineering Labs
UID: 10596
Author(s): Lucie Bernard-Raichon, Mericien Venzon, Jon Klein, Jordan E. Axelrad, Chenzhen Zhang...
* Corresponding Author
Description

To investigate the relationship between gut microbiome dysbiosis and translocation of bacteria into the blood during SARS-CoV-2 infection in humans, researchers obtained blood culture and stool samples from positive COVID-19 patients who were seen at NYU Langone Health and Yale New Haven Hospital. 67 stool samples were obtained from 60 patients at NYU Langone Health and 63 samples were obtained from 36 patients at Yale New Haven Hospital for a total of 130 stool samples from 96 patients. Clinical characteristics of these patients are described in Supplemental Table 1 in the associated publication. 26 patients had positive blood cultures for bloodstream infection.

Timeframe
2020
Geographic Coverage
Connecticut - New Haven
New York (State) - New York City
Subject of Study
Vero E6 cells
C57BL/6J mice
K18-hACE2 mice
WA1/2020
Subject Domain
COVID-19
Genomics
Infectious Disease
Risk Factors
Keywords
Bacteria
Comorbidities
Coronavirus
COVID-19
Dysbiosis
Feces
Gastrointestinal Microbiome
Genomics
Infectious Diseases
Metagenome
Microbiota
Risk Factors
Sepsis

Access

Restrictions
Free to All
Instructions
Bacterial 16S rRNA sequencing data extracted from human stool samples are freely available from the Sequence Read Archive (SRA) through BioProject.
Access via BioProject

Raw sequence reads
Accession #: PRJNA746322

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

Automated electrophoresis system

Illumina MiSeq System

Next generation sequencing platform

Illumina NovaSeq 6000

Whole-genome sequencer

LightCycler­ 480 Instrument II

Real-time PCR amplification and detection instrument

MP Biomedicals FastPrep-24TM

High-speed benchtop homogenizer

QIAGEN QIAcube HT

Automated nucleic acid purification

Software Used
Bowtie2 v2.4.5

Sequence reads alignment tool

DADA2 v1.16

Fast and accurate sample inference

Kraken 2

Taxonomic classification system

lmerTest v3.1-3

Tests in linear mixed effects models

MetaPhlAn2 v3

Metagenomic phylogenetic analysis

PyMC3 v3.11

Python package for probabilistic programming

QIIME v1.9.1

Performs microbiome analysis

scikit-learn v1.0.2

Python package for predictive data analysis

Study Type
Observational
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

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