UMB Data Catalog

A project of the Health Sciences and Human Services Library
UMB Dataset

Dynamics of the Gut Microbiome in Shigella-Infected Children During the First Two Years of Life

UID: 183
Author(s): Esther Ndungo, Johanna B. Holm, Syze Gama, Andrea G. Buchwald, Sharon M. Tennant...
* Corresponding Author
Description
This dataset was used to overview the taxonomic composition of the gastrointestinal microbiomes during the first two years of life with the intent to better understand the effects of the invasive pathogen, Shigella. Data was collected through a two year longitudinal study of a mother-infant cohort in Malawi, using 16S rRNA amplicon sequencing to characterize the gastrointestinal microbiota. Rectal swab samples were collected every 6 six months during well-child visits or when an infant visiting the clinic presented diarrhea to diagnose Shigella infection. 16S rRNA gene amplicon libraries yielded an average of 23,720 reads per sample with a total of 8,729,027 reads and a total of 325 taxa were identified after quality filtering.
Timeframe
2016 - 2018
Geographic Coverage
Malawi
Subject of Study
Subject Domain
Gastrointestinal Microbiome
Genomics
Shigella
Population Age
Infant (1 to 23 months of age)
Infant, Newborn (first 28 days after birth)
Keywords
Sequence Analysis, RNA
Shannon diversity index

Access

Restrictions
Unrestricted access
Instructions
All of the raw sequencing data were deposited into NCBI SRA under BioProject ID PRJNA834726. Additional data supporting the article are present in the Supplementary Materials.
Access via NCBI SRA

Raw sequencing data
Accession #: PRJNA834726

Access via Supplemental Material

Datasets, figures, and tables

Associated Publications
Ndungo, E., Holm, J. B., Gama, S., Buchwald, A. G., Tennant, S. M., Laufer, M. K., Pasetti, M. F., & Rasko, D. A. (2022). Dynamics of the Gut Microbiome in Shigella-Infected Children during the First Two Years of Life. mSystems, 7(5), e0044222. https://doi.org/10.1128/msystems.00442-22
Data Type
Genomic
Equipment Used
DNA/RNA Shield

DNA and RNA stabilization solution for nucleic acids in any biological sample.

Hamilton StarPlus Automated Liquid Handler

Liquid handling robot with 8 channel pipetting arm, dual HEPA filter top, and 96 channel pipeting head with 1ml capacity. It can have tube racks, microplate racks, and 50mL temperature controlled tube rack.

QIAamp DNA Stool Extraction Kit

Used for the isolation of genomic, bacterial, viral, and parasite DNA

Qiagen Microbiome RNA/DNA isolation kit

Used for automated isolation of microbial RNA and DNA

Qiagen Tissue Lyser II

RNA and DNA purification analyzer

Software Used
DADA2 v1.5.2

Package for inferring amplicon sequence variants (ASVs)

QIIME

Performs microbiome analysis

Ribosomal Database Project (RDP) Classifier

Used to assign sequences derived from bacterial and archaeal 16S genes and fungal 28S gene to the corresponding taxonomy model

Silva v138

rRNA database

TagCleaner v0.16

Used to automatically detect and remove tag sequences from genomic and metagenomic sequence data

Study Type
Longitudinal
Dataset Format(s)
XLSX, FASTQ
Dataset Size
8082 Mb
Grant Support
U19AI110820/NIH
R01AI117734/NIH
R01AI125841/NIH
T32DK067872/NIH
3R01AI117734-04S1/NIH
1UL1TR003098/National Center for Advancing Translational Sciences (U.S.)